TF	TypeRegulated	Regulated	Effect	PMID	NumSentence	TypeSentence	Sentence	OriginalIdSentence	OriginalSentence	SectionNum	SectionName	Organisms	OrganismScore	OrganismCertain Level	Hedge	Knowledge type	Negation	Source	Confirmation Level
InvF	gene	invF	regulator	28335027	1	ver/dev	Transcription of the sic/sip operon is activated directly by the SPI-1 encoded transcription factor InvF could therefore be mediated through direct regulation of invF .	361	Transcription of the sic/sip operon is activated directly by the SPI-1 encoded transcription factor InvF and the effect of tnpA on sicAsipBC could therefore be mediated through direct regulation of invF .	17	REPRESSION OF SPI-1 ENCODED GENES BY TNPA	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	ndk	repressor	15256548	12	ver/dev	Fis repressed transcription of ndk .	650	Fis repressed transcription of ndk , the gene that encodes nucleoside diphosphate kinase ( Table 4 ) .	14	GENES INVOLVED IN METABOLISM AND TRANSPORT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	siiA	regulator	24021902	5	ver/dev	effector protein _ regulated by SlyA siiA STM4257 SPI-4 genes effector protein	127	pipB2 STM2780 Type III secretion system effector protein , regulated by SlyA siiA STM4257 SPI-4 genes that encode an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein , regulated by SlyA c srcA STM2138 SPI-2 effector chaperone required for systemic infection in c mice sseK2 STM2137 Type III secretion system effector protein c sseL STM2287 Type III secretion system effector protein , functions as a c deubiquitinase in vivo , regulated by SlyA steB STM1629 Type III secretion system effector protein c steC STM1698 Type III secretion system effector protein c STM2239 SPI-12-encoded genes regulated by SsrB , enhance fitness in c vivo , STM2239 encodes a transcriptional regulator STM2340 STM3117 SPI-13-encoded genes with suggested function in c biosynthesis of the cell wall peptidoglycan layer STM3118 c STM3119	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	activator	11755422	0	att	Transcription of the mgtA and mgtCB loci occurs in a PhoP-dependent manner and is repressed by Mg2 + and Ca2 + [ 30 , 31 ] .	95	Transcription of the mgtA and mgtCB loci occurs in a PhoP-dependent manner and is repressed by Mg2 + and Ca2 + [ 30 , 31 ] .	6	5. THE SALMONELLA PHOP/PHOQ REGULON PROMOTES VIRULENCE AND RESISTANCE TO INNATE IMMUNITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	mgtA	activator	12519186	21	att	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	62	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB medium was determined for strains harbouring lac transcriptional fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	12519186	28	att	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	93	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	activator	12618457	2	att	To examine the effects of the PhoQ-T48X mutations on the entire PhoP/PhoQ signaling pathway in-vivo , we measured the expression of mgtA ( a PhoP-activated gene that encodes a Mg2 transporter ) by measuring the - ga-lactosidase activity of the mgtA : : lacZ-transcriptional-fusion ( 18 ) .	125	To examine the effects of the PhoQ-T48X mutations on the entire PhoP/PhoQ signaling pathway in vivo , we measured the expression of mgtA ( a PhoP-activated gene that encodes a Mg2 transporter ) by measuring the - ga-lactosidase activity of the mgtA : : lacZ transcriptional fusion ( 18 ) .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	12618457	2	att	To examine the effects of the PhoQ-T48X mutations on the entire PhoP/PhoQ signaling pathway in-vivo , we measured the expression of mgtA ( a PhoP-activated gene that encodes a Mg2 transporter ) by measuring the - ga-lactosidase activity of the mgtA : : lacZ-transcriptional-fusion ( 18 ) .	125	To examine the effects of the PhoQ-T48X mutations on the entire PhoP/PhoQ signaling pathway in vivo , we measured the expression of mgtA ( a PhoP-activated gene that encodes a Mg2 transporter ) by measuring the - ga-lactosidase activity of the mgtA : : lacZ transcriptional fusion ( 18 ) .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	14563863	3	att	Strains EG9523 ( mgtA : : MudJ phoP : : Tn10 ) , EG9313 ( slyB : : MudJ phoP : : Tn10 ) , EG9529 ( mgtC : : MudJ phoP : : Tn10 ) , EG9280 ( pmrC : : MudJ phoP : : Tn10 ) , and EG9332 ( pcgL : : MudJ phoP : : Tn10 ) ( 10 , 42 , 43 ) were transformed with plasmid pEG9014 or with the pUHE21-2lacIq vector ( 41 ) and were used for PhoP-dependent pag expression analysis .	52	Strains EG9523 ( mgtA : : MudJ phoP : : Tn10 ) , EG9313 ( slyB : : MudJ phoP : : Tn10 ) , EG9529 ( mgtC : : MudJ phoP : : Tn10 ) , EG9280 ( pmrC : : MudJ phoP : : Tn10 ) , and EG9332 ( pcgL : : MudJ phoP : : Tn10 ) ( 10 , 42 , 43 ) were transformed with plasmid pEG9014 or with the pUHE21-2lacIq vector ( 41 ) and were used for PhoP-dependent pag expression analysis .	3	MATERIALS AND METHODS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	15703297	0	att	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5-7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8-10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in-vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	12	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5–7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8–10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Shigella flexneri;Yersinia pestis;Pectobacterium carotovorum;Neisseria meningitidis;Photorhabdus luminescens;Escherichia coli;Escherichia coli	0.5	L3	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	mgtA	activator	15910283	1	att	Transcription of the mgtA gene ( a PhoP-activated gene ) from the E. coli MG1607 strain carrying plasmids pPRO ( control plasmid ) , pPRO-Q ( PhoQ ) or pPRO-QHis ( PhoQHis ) .	113	Transcription of the mgtA gene ( a PhoP-activated gene ) from the E. coli MG1607 strain carrying plasmids pPRO ( control plasmid ) , pPRO-Q ( PhoQ ) or pPRO-QHis ( PhoQHis ) .	11	IN VITRO GLOBAL ACTIVITY ASSAYS	Escherichia coli;unidentified plasmid	0.5	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	activator	15910283	2	att	We first examined the effect of the C-terminal His tag on PhoQ activity in-vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ-transcriptional-fusion [ 15 ] .	133	We first examined the effect of the C-terminal His tag on PhoQ activity in vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ transcriptional fusion [ 15 ] .	14	RESULTS INFLUENCE OF THE C-TERMINAL HIS TAG ON PHOQ ACTIVITY	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	15910283	2	att	We first examined the effect of the C-terminal His tag on PhoQ activity in-vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ-transcriptional-fusion [ 15 ] .	133	We first examined the effect of the C-terminal His tag on PhoQ activity in vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ transcriptional fusion [ 15 ] .	14	RESULTS INFLUENCE OF THE C-TERMINAL HIS TAG ON PHOQ ACTIVITY	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtA	activator	16339942	12	att	A BIAcore biosensor was used to examine , in real-time , the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .	303	A BIAcore biosensor was used to examine , in real-time , the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .	10	DNA BINDING OF PHOP PROTEINS BY SPR	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	mgtA	activator	18248433	0	att	To characterize the physiological role of the Mg ribos-21 witch present in mgtA , the expression of both mgtA and mgtC was determined in the presence of increasing Mg 21 concentrations in the culture medium and compared them with that obtained for other PhoP-activated genes .	169	To characterize the physiological role of the Mg ribos-21 witch present in mgtA , the expression of both mgtA and mgtC was determined in the presence of increasing Mg 21 concentrations in the culture medium and compared them with that obtained for other PhoP-activated genes .	10	RESULTS	Glyptocephalus cynoglossus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	18248433	2	att	PhoP overexpression from the pPB1019 plasmid results in a Mg - and PhoQ-indepen-21 dent expression of the PhoP-activated genes ( Lejona et al. , 2004 ) , with the notable exception of mgtA and mgtC , whose expression was still modulated by Mg ( Fig. 1c ) .	309	PhoP overexpression from the pPB1019 plasmid results in a Mg - and PhoQ-indepen-21 dent expression of the PhoP-activated genes ( Lejona et al. , 2004 ) , with the notable exception of mgtA and mgtC , whose expression was still modulated by Mg ( Fig. 1c ) .	10	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	18248433	3	att	Here , it was shown that the expression of mgtA and mgtCB , both harbouring long 50UTR regions , is highly diminished in the presence of submillimolar Mg 21 concentrations in the culture medium , a condition in which the rest of the PhoP-activated genes are actively expressed ( Fig. 1 ) .	328	Here , it was shown that the expression of mgtA and mgtCB , both harbouring long 50UTR regions , is highly diminished in the presence of submillimolar Mg 21 concentrations in the culture medium , a condition in which the rest of the PhoP-activated genes are actively expressed ( Fig. 1 ) .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	18792679	2	att	coli .52 It isnot surprising that the phoPQand mgtApromoters , which display the best matches to the PhoP box consensus , exhibit the highest affinity for the E. coli PhoP protein in-vitro .44 This scenario may also play in other enteric bacterial species given the widespread distribution ofthe mgtAgene and that the phoPQoperon is positively autoregulated in Salmonella and E. coli .5 o. 51,53 Like mgtA , the genes listed above , which harbor a `` prototypical '' PhoP-activated promoter , are found in several organisms in addition to Salmonella .	115	coli .52 It isnot surprising that the phoPQand mgtApromoters , which display the best matches to the PhoP box consensus , exhibit the highest affinity for the E. coli PhoP protein in vitro .44 This scenario may also play in other enteric bacterial species given the widespread distribution ofthe mgtAgene and that the phoPQoperon is positively autoregulated in Salmonella and E. coli .5 o. 51,53 Like mgtA , the genes listed above , which harbor a `` prototypical '' PhoP-activated promoter , are found in several organisms in addition to Salmonella .	5	DIRECT TRANSCRIPTIONAL CONTROL BYTHE PHOP PROTEIN	Escherichia coli;Salmonella;Escherichia coli;Salmonella	0.5	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtA	activator	19805196	0	att	Recently , it has been shown that high-level expression of the Rob protein , which is a transcriptional activator of genes involved in resistance to antibiotics , heavy metals , superoxide , and organic solvents , results in the induction of the mgtA gene from a PhoP-independent promoter that is 43 nt downstream of the major PhoP-dependent promoter .	53	Recently , it has been shown that high-level expression of the Rob protein , which is a transcriptional activator of genes involved in resistance to antibiotics , heavy metals , superoxide , and organic solvents , results in the induction of the mgtA gene from a PhoP-independent promoter that is 43 nt downstream of the major PhoP-dependent promoter .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	19805196	1	att	It is possible that the PhoP-dependent transcription initiation at the mgtA promoter might not be very sensitive to the Mg2 concentration , and most of the transcriptional control of the mgtA gene is provided by the riboswitch .	114	It is possible that the PhoP-dependent transcription initiation at the mgtA promoter might not be very sensitive to the Mg2 concentration , and most of the transcriptional control of the mgtA gene is provided by the riboswitch .	5	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtA	activator	22431636	3	att	( C ) β-Galactosidase activity expressed by isogenic Salmonella strains carrying a chromosomal lac transcriptional-fusion at position 2190 ( EG9170 ) or position 6 ( EG9220 ) with respect to the PhoP-dependent mgtA transcription start site .	66	( C ) β-Galactosidase activity expressed by isogenic Salmonella strains carrying a chromosomal lac transcriptional fusion at position 2190 ( EG9170 ) or position 6 ( EG9220 ) with respect to the PhoP-dependent mgtA transcription start site .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	activator	23504014	16	att	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	277	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	23782700	2	att	A , - galactosidase activity from lacZ-transcriptional-fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	168	A , - galactosidase activity from lacZ transcriptional fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	activator	25182488	12	att	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	250	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	25624475	0	att	The PhoP-activated mgtA gene specifies a Mg2 + transporter that enhances PhoP-P levels by transporting Mg2 + away from the periplasm , where it acts as an inhibitory signal for PhoQ ( 16 ) .	8	The PhoP-activated mgtA gene specifies a Mg2 + transporter that enhances PhoP-P levels by transporting Mg2 + away from the periplasm , where it acts as an inhibitory signal for PhoQ ( 16 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	25624475	1	att	This regulatory architecture defines a two-tier structure among PhoP-activated genes based on whether they require mgtA for maximal expression ( 16 ) .	10	This regulatory architecture defines a two-tier structure among PhoP-activated genes based on whether they require mgtA for maximal expression ( 16 ) .	2	ABSTRACT	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtA	activator	25624475	2	att	The PhoP-activated genes most dependent on the MgtA protein specify proteins of unknown function and , like the mgtA gene , are not required for virulence in an animal ( 19 -- 21 ) .	12	The PhoP-activated genes most dependent on the MgtA protein specify proteins of unknown function and , like the mgtA gene , are not required for virulence in an animal ( 19 -- 21 ) .	3	ABSTRACT	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	mgtA	activator	25624475	4	att	This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 's own F1Fo ATPase , and a small protein of unknown function , respectively .	20	This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 's own F1Fo ATPase , and a small protein of unknown function , respectively .	4	MAIN	Salmonella;unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	mgtA	activator	25624475	8	att	The PhoP-activated mgtA , mgtC , and pagM genes are required for motility on 0.3 % agarose low Mg2 + media .	116	The PhoP-activated mgtA , mgtC , and pagM genes are required for motility on 0.3 % agarose low Mg2 + media .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	27849575	1	ver/dev	Transcription of mgtA is regulated at activation of the promoter by PhoP .	62	Transcription of mgtA is regulated at two steps : activation of the promoter by PhoP , which is phosphorylated by PhoQ in response to low [ Mg2 + ] and other periplasmic signals ( inset 1 ) ( 4 ) , and translation of mgtL ( encoded by nucleotides 71 -- 124 ) ( 12 ) , which governs folding of the 5 ′ LR mRNA and Rho-dependent termination .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	29739882	15	att	Because transcription elongation into the mgtA coding regions is triggered in low cytoplasmic Mg2 + ( 39 ) , expression of a subset of PhoP-activated genes takes place only when the bacterium experiences the signals promoting mgtA expression .	187	Because transcription elongation into the mgtA coding regions is triggered in low cytoplasmic Mg2 + ( 39 ) , expression of a subset of PhoP-activated genes takes place only when the bacterium experiences the signals promoting mgtA expression .	6	DISCUSSION	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	29739882	15	att	Because transcription elongation into the mgtA coding regions is triggered in low cytoplasmic Mg2 + ( 39 ) , expression of a subset of PhoP-activated genes takes place only when the bacterium experiences the signals promoting mgtA expression .	187	Because transcription elongation into the mgtA coding regions is triggered in low cytoplasmic Mg2 + ( 39 ) , expression of a subset of PhoP-activated genes takes place only when the bacterium experiences the signals promoting mgtA expression .	6	DISCUSSION	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	activator	30967459	9	att	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	144	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	3	RESULTS	Salmonella;unidentified plasmid;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	mgtA	activator	33045730	50	att	Control experiments showed that the SsrB binding site mutant retained normal H-NS binding to the STM14 3310 DNA ( Figure 3F ) , one of the genes most tightly bound by H-NS ( 50 ) , and no detectable binding to the DNA region upstream of mgtA ( Figure 3F ) , a PhoP-activated gene not bound by H-NS ( 50 ) .	249	Control experiments showed that the SsrB binding site mutant retained normal H-NS binding to the STM14 3310 DNA ( Figure 3F ) , one of the genes most tightly bound by H-NS ( 50 ) , and no detectable binding to the DNA region upstream of mgtA ( Figure 3F ) , a PhoP-activated gene not bound by H-NS ( 50 ) .	27	SSRB ANTAGONIZES THE GENE SILENCER H-NS IN THE UGTL PRO- MOTER REGION	nan	1	L2	OTHER	Other	NEG	New	Level 1
RtsA	gene	dsbA	activator	16045614	7	ver/dev	RtsA in particular , also activate , independent of dsbA , encoding the periplasmic disulphide bond isomerase .	44	The three regulators , RtsA in particular , also activate , independent of HilA and InvF , the effector gene slrP ( Ellermeier and Slauch , 2003 ) and dsbA , encoding the periplasmic disulphide bond isomerase required for the function of SPI1 and other TTSSs ( Ellermeier and Slauch , 2004 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	dsbA	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by RtsA independently of InvF .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	dsbA	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by RtsA independently of both HilA .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcnR	gene	rcnA	regulator	21722794	9	ver/dev	RcnR binds directly to the rcnA promoter to repress transcription	703	RcnR binds directly to the rcnA promoter to repress transcription and this interaction is inhibited by nickel and cobalt .	24	6.2. TRANSCRIPTIONAL REGULATION BY RCNR AND RCNA METAL EXPORT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	bapA	regulator	16313619	8	ver/dev	Altogether , these results show that bapA , like csgAB , is regulated by CsgD , which plays a central role in biofilm formation in Salmonella strains .	249	Altogether , these results show that bapA , like adrA and csgAB , is regulated by CsgD and is therefore a new member of the CsgD regulon , which plays a central role in biofilm formation in Salmonella strains .	10	TRANSCRIPTIONAL REGULATION OF BAPA	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	bapA	regulator	20545866	17	ver/dev	Interestingly , the gene bapA , which are regulated by CsgD in S. enterica serovar Enteritidis strains -LRB- Latasa et al. , 2005 ;	109	Interestingly , the gene bapA and genes of the capsule operons , which are regulated by CsgD in S. enterica serovar Enteritidis strains ( Latasa et al. , 2005 ;	6	DETECTION OF THE CSGD BINDING SITES	Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
ArcA	gene	arcA	regulator	30038032	0	att	To obtain a global view of ArcA-controlled biological processes , we classified proteins with altered expression levels in S. Typhimurium arcA cells into Clusters of Orthologous Groups ( COGs ) ( Table I ) .	166	To obtain a global view of ArcA-controlled biological processes , we classified proteins with altered expression levels in S. Typhimurium arcA cells into Clusters of Orthologous Groups ( COGs ) ( Table I ) .	6	COMPARATIVE PROTEOMICS ANALYSIS OF S. TYPHIMURIUM AND ITS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	ftnB	repressor	30682134	33	ver/dev	Thus , repression of ftnB by CsrA may be more closely related to repression of the oxidative-stress response than to iron storage .	272	Thus , repression of ftnB and dps by CsrA may be more closely related to repression of the oxidative stress response than to iron storage .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	ftnB	repressor	30682134	33	ver/dev	Thus , repression of ftnB by CsrA may be more closely related to repression of the oxidative-stress response than to iron storage .	272	Thus , repression of ftnB and dps by CsrA may be more closely related to repression of the oxidative stress response than to iron storage .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	cdd	regulator	21148209	33	ver/dev	This mechanism has been described for the tandem regulation of the cdd promoters in E. coli ; in both cases , a second sequence located upstream are relevant for CRP transcriptional activation .	270	This mechanism has been described for the tandem regulation of the cdd and melR promoters in E. coli ; in both cases , a sequence close to the 235 and a second sequence located upstream are relevant for CRP transcriptional activation ( Busby et al. , 1994 ; Savery et al. , 1996 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	cdd	regulator	21148209	33	ver/dev	This mechanism has been described for the tandem regulation of the cdd promoters in E. coli ; in both cases , a sequence close to the 235 are relevant for CRP transcriptional activation .	270	This mechanism has been described for the tandem regulation of the cdd and melR promoters in E. coli ; in both cases , a sequence close to the 235 and a second sequence located upstream are relevant for CRP transcriptional activation ( Busby et al. , 1994 ; Savery et al. , 1996 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ydhI	regulator	29857034	15	ver/dev	For genes , we found two genes , ydhI are negatively regulated by SlyA .	312	For genes involved in multidrug resistance , we found two genes , ydhJ and ydhI ( STM14_1740 ; STM14_1741 ) , which are transcribe divergent to slyA and are negatively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YdiV	gene	fliZ	repressor	25161191	2	ver/dev	YdiV indirectly represses fliZ transcription through FlhD4C2	37	FliZ directly represses ydiV transcription , and YdiV indirectly represses fliZ transcription through FlhD4C2 ( Fig. 1 ) ( 10 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	ompR	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Sigma70	gene	fliC	activator	9765212	5	att	Reaction mixtures contained 30 nM His-core RNAP ( E ) and 3 nM template DNA [ either the s28-dependent fliC promoter ( s ) , or the s70-dependent tac promoter ( d ) ] .	77	Reaction mixtures contained 30 nM His-core RNAP ( E ) and 3 nM template DNA [ either the s28-dependent fliC promoter ( s ) , or the s70-dependent tac promoter ( d ) ] .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	pilT	repressor	27601577	4	ver/dev	Under microaerobic conditions , the absence of FNR resulted in a downregulation of pilT transcription , demonstrating the integration of the pilus gene expression with the global metabolic regulatory setup of Salmonella .	224	Under microaerobic conditions , the absence of FNR resulted in a downregulation of pilV , pilS , and pilT transcription and lower pESI conjugation , demonstrating the integration of the pilus gene expression with the global metabolic regulatory setup of Salmonella .	5	DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
ChbR	gene	chiP	regulator	24450479	12	ver/dev	ChbR bound to the region upstream of the chiP gene in Salmonella at the sequence .	82	ChbR bound to the region upstream of the chiP gene in Salmonella at the sequence resembling the previously identified ChbR consensus ( Plumbridge and Pellegrini , 2004 ; Kachroo et al. , 2007 ) ( Fig. 2A and B ) at a concentration ( 50 nM ) comparable to its affinity at chbB in E. coli measured under similar conditions ( Plumbridge and Pellegrini , 2004 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
ChbR	gene	chiP	regulator	24450479	13	ver/dev	no binding of ChbR to the chiP upstream region of E. coli was detected ( D )	83	However , no binding of ChbR to the chiP upstream region of E. coli was detected ( Fig. 2C and D ) and the sequence protected in Salmonella , unlike the NagC site , is not conserved in E. coli ( Fig. 1C ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
ChbR	gene	chiP	regulator	24450479	13	ver/dev	no binding of ChbR to the chiP upstream region of E. coli was detected ( Fig. 2C )	83	However , no binding of ChbR to the chiP upstream region of E. coli was detected ( Fig. 2C and D ) and the sequence protected in Salmonella , unlike the NagC site , is not conserved in E. coli ( Fig. 1C ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	10913067	0	ver/dev	We chose to start with examination of the rpoS gene since , among gram-negative bacteria , many genes are regulated by RpoS .	9	We chose to start with examination of the rpoS gene since , among gram-negative bacteria , many genes needed for survival are regulated by RpoS , the stationary-phase sigma factor .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	11260470	3	ver/dev	Consistent with a role for RpoS in the regulation of the KatN protein was not produced in the Salmonella rpoS Fig. 2A .	170	Consistent with a role for RpoS in the regulation of katN , the KatN protein was not produced in the Salmonella rpoS mutant SL1344K ( Fig. 2A ) .	8	TRANSCRIPTION OF KATN IS RPOS AND GROWTH PHASE DEPENDENT	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	11260470	3	ver/dev	Consistent with a role for RpoS in the regulation of the KatN protein was not produced in the Salmonella rpoS mutant SL1344K .	170	Consistent with a role for RpoS in the regulation of katN , the KatN protein was not produced in the Salmonella rpoS mutant SL1344K ( Fig. 2A ) .	8	TRANSCRIPTION OF KATN IS RPOS AND GROWTH PHASE DEPENDENT	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	12127492	0	att	The increased sensitivity of the rpoS minus mutant suggests a role for RpoS-controlled gene expression for the higher resistance of stationary-phase cells to UV-C .	108	The increased sensitivity of the rpoS minus mutant suggests a role for RpoS-controlled gene expression for the higher resistance of stationary phase cells to UV-C .	12	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	rpoS	regulator	15632439	4	att	They suggested that the difference in the CFA synthase level may be the result of different rpoS alleles , since the expression of another RpoS-regulated gene , poxB , was lower in FT1 than ZK126 ( Wang & Cronan , 1994 ) .	430	They suggested that the difference in the CFA synthase level may be the result of different rpoS alleles , since the expression of another RpoS-regulated gene , poxB , was lower in FT1 than ZK126 ( Wang & Cronan , 1994 ) .	11	DISCUSSION	Cell fusing agent virus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	regulator	16023758	5	att	Nickerson and Curtiss found that RpoS-regulated genes are essential for colonisation of gut-associated lymphoid tissue despite the fact that the rpoS mutant colonised the gut as eficiently as did the wild-type strain [ 38 ] .	115	Nickerson and Curtiss found that RpoS-regulated genes are essential for colonisation of gut-associated lymphoid tissue despite the fact that the rpoS mutant colonised the gut as eficiently as did the wild-type strain [ 38 ] .	8	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	16023758	2	ver/dev	Total rpoS expression is controlled at all levels starting from regulation of RpoS proteolysis .	98	Total rpoS expression is controlled at all levels starting from transcription [ 24 -- 26 ] , regulation of mRNA stability , translational eficiency , and regulation of RpoS proteolysis .	8	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	16023758	2	ver/dev	Total rpoS expression is controlled at all levels starting from regulation of RpoS proteolysis .	98	Total rpoS expression is controlled at all levels starting from transcription [ 24 -- 26 ] , regulation of mRNA stability , translational eficiency , and regulation of RpoS proteolysis .	8	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	17012381	3	ver/dev	An isogenic rpoS mutant strain of rpoS and a pACYC/rpoS-complemented strain ( rpoS ) were included as controls for RpoS activity .	356	An isogenic rpoS mutant strain of ATCC 14028 ( rpoS ) and a pACYC/rpoS-complemented strain ( rpoS ) were included as controls for RpoS activity .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	17012381	3	ver/dev	An isogenic rpoS mutant strain of ATCC 14028 and a pACYC/rpoS-complemented strain ( rpoS ) were included as controls for RpoS activity .	356	An isogenic rpoS mutant strain of ATCC 14028 ( rpoS ) and a pACYC/rpoS-complemented strain ( rpoS ) were included as controls for RpoS activity .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	17178790	20	att	In accord with this , rpoS mutants of serotype Typhimurium , with or without the virulence plasmid that possesses RpoS-regulated genes that play no role in the colonization of the gut-associated lymphoid tissue ( 19 , 52 ) , exhibit diminished immunogenicities ( 5 , 7 ) .	394	In accord with this , rpoS mutants of serotype Typhimurium , with or without the virulence plasmid that possesses RpoS-regulated genes that play no role in the colonization of the gut-associated lymphoid tissue ( 19 , 52 ) , exhibit diminished immunogenicities ( 5 , 7 ) .	7	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	17293430	24	ver/dev	Negative control by RpoS appears to result in the selection of rpoS mutants in bacterial populations .	367	Negative control by RpoS appears to be as significant as the positive control ( 17 , 27 ) and appears to result in a growth advantage of rpoS mutants and thus the selection of rpoS mutants in bacterial populations ( 25 ) .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
RpoS	gene	rpoS	regulator	17293430	24	ver/dev	Negative control by RpoS appears to result in a growth advantage of rpoS mutants in bacterial populations .	367	Negative control by RpoS appears to be as significant as the positive control ( 17 , 27 ) and appears to result in a growth advantage of rpoS mutants and thus the selection of rpoS mutants in bacterial populations ( 25 ) .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
RpoS	gene	rpoS	regulator	17725620	1	att	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	247	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	20	LF1036 4.49 LF1037 7.58	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	regulator	17725620	1	att	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	247	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	20	LF1036 4.49 LF1037 7.58	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	regulator	17784910	33	ver/dev	Presumably , the posttranscriptional mechanisms responsible for regulation of RpoS protein expression were sufficiently robust to withstand our attempts at overwhelming them through ectopic transcriptional upregulation of the rpoS gene .	548	Presumably , the posttranscriptional mechanisms responsible for regulation of RpoS protein expression were sufficiently robust to withstand our attempts at overwhelming them through ectopic transcriptional upregulation of the rpoS gene .	14	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	regulator	23385142	10	ver/dev	To verify the role of RpoS in the regulation of entry of KLX2 into the VBNC state , the rpoS gene was deleted in KLX2 DrpoS , KLX6 strain .	182	To verify the role of RpoS in the regulation of entry of KLX2 into the VBNC state , the rpoS gene was deleted in KLX2 ( KLX2 DrpoS , KLX6 strain ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	23385142	10	ver/dev	To verify the role of RpoS in the regulation of entry of KLX2 into the VBNC state , the rpoS gene was deleted in KLX2 .	182	To verify the role of RpoS in the regulation of entry of KLX2 into the VBNC state , the rpoS gene was deleted in KLX2 ( KLX2 DrpoS , KLX6 strain ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	24885225	31	ver/dev	Since rpoS is regulated at multiple levels , we determined whether the changes in the rpoS transcription also lead to changes in RpoS accumulation .	114	Since rpoS is regulated at multiple levels [ 26 ] , we determined whether the changes in the rpoS transcription also lead to changes in RpoS accumulation .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by RhlR ,61 while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by RhlR ,61 while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by LasR while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by LasR while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by QS regulators while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by QS regulators while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by RhlR ,61 while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by RhlR ,61 while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by RhlR ,61 while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by RhlR ,61 while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by LasR while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by LasR while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by LasR while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by LasR while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by QS regulators while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by QS regulators while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by QS regulators while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	26387845	1	ver/dev	A study showed the expression of rpoS by QS regulators while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .	249	A study showed the expression of rpoS by QS regulators , LasR and RhlR ,61 while Whiteley and coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa as well as in E. coli and S. enterica .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	regulator	30524381	31	ver/dev	In Salmonella , YciF was reported to be under positive control of RpoS , yet our previous study showed that OmpR repressed rpoS during osmotic-stress .	319	In Salmonella , YciF was reported to be under positive control of RpoS ( Ibanez-Ruiz et al. , 2000 ) , yet our previous study showed that OmpR repressed rpoS during osmotic stress ( Chakraborty et al. , 2017 ) , which would decrease yciF transcription .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	8045891	13	ver/dev	Since stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	8045891	13	ver/dev	Since stiB are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	rpoS	regulator	8045891	13	ver/dev	Since the stiA are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
FNR	gene	sodC	regulator	18362154	0	ver/dev	the E. coli sodC gene in which the iron-sulfur-cluster-containing protein FNR , an oxygen-sensitive transcriptional regulator , has been suggested to be the primary regulator of anaerobic sodC repression	243	Anaerobic repression has been reported for the E. coli sodC gene ( 6 , 53 ) , in which the iron-sulfur cluster-containing protein FNR , an oxygen-sensitive transcriptional regulator , has been suggested to be the primary regulator of anaerobic sodC repression ( 6 ) .	3	RESULTS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
YgaE	gene	ompF	repressor	24592164	5	ver/dev	The repression of YgaE to ompF means less pathways for antibiotics .	227	The repression of YgaE to ompC and ompF means less pathways for nutrition and antibiotics .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YgaE	gene	ompF	repressor	24592164	5	ver/dev	The repression of YgaE to ompF means less pathways for nutrition .	227	The repression of YgaE to ompC and ompF means less pathways for nutrition and antibiotics .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YgaE	gene	ompF	repressor	24592164	7	ver/dev	One explanation for these phenomena is the repression of YgaE to ompF occurs only in the very early stage of hyperosmotic-stress as an emergency approach to protect the bacteria .	233	One explanation for these phenomena is the repression of YgaE to ompC and ompF occurs only in the very early stage of hyperosmotic stress as an emergency approach to protect the bacteria .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YgaE	gene	ompF	repressor	24592164	8	ver/dev	As time goes by , other mechanisms are involved in the process of handling the hyperosmotic-stress , the repression of YgaE to ompF relieves .	234	As time goes by , other mechanisms are involved in the process of handling the hyperosmotic stress , the repression of YgaE to ompC and ompF relieves .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YgaE	gene	ompF	repressor	24592164	9	ver/dev	the expressions of ompF were obviously repressed by YgaE at the early stage	249	Oppositely , the expressions of ompC and ompF were obviously repressed by YgaE at the early stage and no apparent regulation of OmpC and OmpF by YgaE was observed in the 2-DE results at the late stage of hyperosmotic stress .	10	3.4. YGAE REPRESSES THE EXPRESSION OF OMPA AT THE LATE STAGE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	sopB	regulator	33119619	21	ver/dev	In agreement with our results , we previously demonstrated that purified H-NS does not bind to the sopB regulatory region .	275	In agreement with our results indicating that InvF does not act as an anti-H-NS factor on sopB , we previously demonstrated that purified H-NS does not bind to the sopB regulatory region [ 16,51 ] .	24	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	gene	sopB	regulator	33119619	22	ver/dev	ChIP-on-chip experiments by Lucchini et al. did not show a significant signal for binding of H-NS to the sopB promoter	276	Moreover , ChIP-on-chip experiments by Lucchini et al. [ 12 ] and Navarre et al. [ 13 ] did not show a significant signal for binding of H-NS to the sopB promoter nor they showed overexpression of sopB in the absence of H-NS .	24	DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
HNS	gene	sopB	regulator	33119619	23	ver/dev	These findings strongly suggest that H-NS is not directly involved in the regulation of sopB .	277	These findings strongly suggest that H-NS is not directly involved in the regulation of sopB .	24	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	sdiA	activator	22149171	50	att	RpoS-dependent sdiA expression in stationary-phase	355	RpoS-dependent sdiA expression in stationary phase	19	RPOS-DEPENDENT SDIA EXPRESSION IN STATIONARY PHASE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	sdiA	activator	22149171	53	ver/dev	RpoS may control the expression of a stationary-phase activator of sdiA .	359	RpoS may control the expression of a stationary-phase activator of sdiA .	19	RPOS-DEPENDENT SDIA EXPRESSION IN STATIONARY PHASE	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
sigma-28	gene	hha	repressor	17600486	2	ver/dev	Of hha sigma-28 , pagD , hha encodes a noted global repressor of virulence genes .	559	Of the 5 virulence-related genes ( hha sigma 28 ( fliA ) , ychP , bigA , hype , and pagD ) that were induced , hha encodes a noted global repressor of virulence genes .	17	VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
sigma-28	gene	hha	repressor	17600486	2	ver/dev	Of hha sigma-28 , hype , hha encodes a noted global repressor of virulence genes .	559	Of the 5 virulence-related genes ( hha sigma 28 ( fliA ) , ychP , bigA , hype , and pagD ) that were induced , hha encodes a noted global repressor of virulence genes .	17	VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
sigma-28	gene	hha	repressor	17600486	2	ver/dev	Of hha sigma-28 , bigA , hha encodes a noted global repressor of virulence genes .	559	Of the 5 virulence-related genes ( hha sigma 28 ( fliA ) , ychP , bigA , hype , and pagD ) that were induced , hha encodes a noted global repressor of virulence genes .	17	VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
sigma-28	gene	hha	repressor	17600486	2	ver/dev	Of hha sigma-28 , ychP , hha encodes a noted global repressor of virulence genes .	559	Of the 5 virulence-related genes ( hha sigma 28 ( fliA ) , ychP , bigA , hype , and pagD ) that were induced , hha encodes a noted global repressor of virulence genes .	17	VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	hisJ	regulator	19074398	4	att	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	25	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	2	MAIN	Salmonella;unidentified plasmid;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	regulator	10844688	7	ver/dev	Recent studies indicate that HilA binds to specific sequences in the prgH promoters .	270	Recent studies indicate that HilA binds to specific sequences in the prgH and invF promoters that are necessary for expression of these SPI1 genes , suggesting that HilA directly activates these promoters ( Lostroh et al. , 2000 ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	prgH	regulator	28439039	9	ver/dev	It is known that prgH is under the regulation of HilA .	327	It is known that prgH is under the regulation of many global regulators , such as HilA , InvF , PhoP , and SirA .	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilA	gene	prgH	regulator	28575106	5	att	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	167	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	8	THE GENE LOIA IS THE VIRULENCE DETERMINANT IN SPI-14	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	prgH	regulator	32316180	4	ver/dev	HilA binds to the prgH promoters , triggering the activation of T3SE genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	regulator	32316180	4	ver/dev	HilA binds to the prgH promoters , triggering the activation of T3SS genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	proP	regulator	11123690	24	att	However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential-growth and a decrease in expression during stationary-phase ( Xu and Johnson , 1995 ) .	176	However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential growth and a decrease in expression during stationary phase ( Xu and Johnson , 1995 ) .	9	DISCUSSION	Escherichia coli	0	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	TU	otsBA	regulator	21311887	1	ver/dev	Among the 38 genes , otsBA were previously reported to be regulated by RpoS .	120	Among the 38 genes , four ( osmC , osmY , osmB , and otsBA ) were previously reported to be regulated by RpoS [ 4 , 7 , 10 , 12 , 16 , 37 ] .	9	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	surA	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	surA	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	surA	regulator	12438352	23	att	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	331	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	5	DISCUSSION	nan	1	L1	SPEC	Fact	NEG	Other	Level 1
CpxR	gene	csgA	repressor	14643403	15	ver/dev	In line with this hypothesis , in a cpxR mutant csgA transcription was only slightly enhanced , indicating that under those environmental conditions repression by CpxR plays a minor role .	178	In line with this hypothesis , in a cpxR mutant csgA transcription was only slightly enhanced , indicating that under those environmental conditions repression by CpxR plays a minor role [ 12 ] .	19	6.4. CPXR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	csgA	repressor	25153529	7	ver/dev	As a consequence , CpxR would start inhibiting expression of csgA .	377	As a consequence , CpxR would become phosphorylated and start inhibiting expression of csgD as well as csgA .	10	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pcgL	regulator	14563863	10	att	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	125	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pcgL	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FabR	gene	yqfA	repressor	27004424	6	ver/dev	Combining it with a transcriptomics approach reduces its inherent noise This provided the first evidence for the direct repression of yqfA expression by FabR in S. Typhimurium .	52	Combining it with a transcriptomics approach allows the discrimination between direct and indirect target genes and reduces its inherent noise [ 33 -- 36 ] This provided the first evidence for the direct repression of fabA , fabB and yqfA expression by FabR in S. Typhimurium , confirming current knowledge generated in E. coli .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FabR	gene	yqfA	repressor	27004424	6	ver/dev	its inherent noise This provided the first evidence for the direct repression of yqfA expression by FabR in S. Typhimurium _ confirming current knowledge	52	Combining it with a transcriptomics approach allows the discrimination between direct and indirect target genes and reduces its inherent noise [ 33 -- 36 ] This provided the first evidence for the direct repression of fabA , fabB and yqfA expression by FabR in S. Typhimurium , confirming current knowledge generated in E. coli .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SoxS	gene	zwf	regulator	19460824	15	ver/dev	Examination of the sequence revealed that SoxS binds with high affinity in a manner characteristic of class I promoters in the zwf promoters of E. coli .	190	Examination of the sequence associated with the PQ-inducible ompW promoter revealed that SoxS binds with high affinity in a manner characteristic of class I promoters in the forward orientation , such as the zwf and sodA promoters of E. coli .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	crp	repressor	19843227	24	ver/dev	Indeed , a StpA-dependent decrease of crp expression was observed in 1.6-fold .	141	Indeed , a StpA-dependent decrease of crp expression was observed in our experiment ( 1.6-fold ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	crp	repressor	19843227	24	ver/dev	Indeed , a StpA-dependent decrease of crp expression was observed in our experiment .	141	Indeed , a StpA-dependent decrease of crp expression was observed in our experiment ( 1.6-fold ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	mdtABC	activator	33751923	12	ver/dev	Two of mdtABC , are induced by the BaeR RR .	472	Two of these efflux pumps , arcD and mdtABC , are induced by the BaeR RR ( Nishino et al. 2007 ) .	13	BAESR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssrA	activator	12753201	8	ver/dev	SsrB also appears to activate ssrA , although the mechanism of regulation remains to be determined	75	Thus , OmpR appears to function as an activator of ssrA , as reported previously ( Lee et al. , 2000 ) , and SsrB also appears to activate ssrA , although the mechanism of regulation remains to be determined .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssrA	activator	12753201	11	ver/dev	L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	93	1134 X. Feng , R. Oropeza and L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	ssrA	activator	12753201	11	ver/dev	R. Oropeza suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	93	1134 X. Feng , R. Oropeza and L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	ssrA	activator	12753201	11	ver/dev	1134 X. Feng suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	93	1134 X. Feng , R. Oropeza and L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	ssrA	activator	15491370	4	ver/dev	The response regulator SsrB , in turn , is autoregulated , activating ssrA	37	The response regulator SsrB , in turn , is autoregulated , activating ssrB , ssrA and spiC ( Feng et al. , 2003 ) , as well as other genes located both inside and outside of	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssrA	activator	15491370	9	ver/dev	SsrB , in turn , activates ssrA .	88	SsrB , in turn , activates ssrB , ssrA and spiC ( ssaB ) as well as additional genes , including srfH .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssrA	activator	17630976	25	ver/dev	SsrB activates transcription in the absence of ssrA Previous work from our laboratory demonstrated that transcription of ssrB genes occurs from separate promoters .	218	SsrB activates transcription in the absence of ssrA Previous work from our laboratory demonstrated that transcription of the adjacent ssrA and ssrB genes occurs from separate promoters ( Feng et al. , 2003 ) .	8	ACTIVATION OF SPI-2 GENES IN VITRO REQUIRES SSRB AND ACIDIC PH	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	ssrA	activator	17630976	25	ver/dev	SsrB activates transcription in the absence of ssrA Previous work from our laboratory demonstrated that transcription of the adjacent ssrA occurs from separate promoters .	218	SsrB activates transcription in the absence of ssrA Previous work from our laboratory demonstrated that transcription of the adjacent ssrA and ssrB genes occurs from separate promoters ( Feng et al. , 2003 ) .	8	ACTIVATION OF SPI-2 GENES IN VITRO REQUIRES SSRB AND ACIDIC PH	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	ssrA	activator	29930310	17	ver/dev	ssrA genes led to enhanced expression of SsrB protein	160	Salmonella expressing ssrADsc overexpressed ssrA and ssrB genes , which led to enhanced expression of SsrB protein and the downstream ssaG gene .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	rpsL	regulator	30941426	3	ver/dev	To further test whether a HilD deficiency causes down-regulation of rpsL * strains , we overexpressed HilD on a plasmid under the control of a lac promoter .	240	To further test whether a HilD deficiency causes down-regulation of SPI-1 genes in the rpsD * and rpsL * strains , we overexpressed HilD on a plasmid under the control of a lac promoter .	24	NON-OPTIMAL TRANSLATIONAL FIDELITY IMPAIRS HOST-CELL INTERAC- TIONS AND ANIMAL INFECTION	unidentified plasmid	1	L3	SPEC	Other	OTHER	New	Level 1
OxyR	gene	agn43	repressor	17905993	0	ver/dev	the OxyR repressor for hemi-methylated GATC sites has been shown to regulate phase variation in the E. coli agn43 gene .	40	Competition between SeqA and the OxyR repressor for hemi-methylated GATC sites has been shown to regulate phase variation in the E. coli agn43 gene ( 9 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	wzz	regulator	21719537	0	ver/dev	Our results indicate that only the PmrA regulator binds to the wzz promoter , inducing fepE gene expression .	35	Our results indicate that only the PmrA regulator binds to the wzz promoter , inducing fepE gene expression , which increases the amount of VL O-Ag .	3	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	rprA	activator	32392214	3	att	To test this hypothesis , we examined the fluorescence of isogenic Salmonella strains with mutations in various rcs genes and harboring a medium copy number plasmid with a transcriptional-fusion between the RcsB-activated rprA promoter and a promoterless gfp gene .	91	To test this hypothesis , we examined the fluorescence of isogenic Salmonella strains with mutations in various rcs genes and harboring a medium copy number plasmid with a transcriptional fusion between the RcsB-activated rprA promoter and a promoterless gfp gene .	9	A CONDITION THAT ACTIVATES THE REGULATOR RCSB INDEPENDENTLY OF THE RCSC, RCSD, AND RCSF PROTEINS	Salmonella;unidentified plasmid	1	L2	OTHER	Investigation	OTHER	Other	Level 1
RcsB	gene	rprA	activator	32392214	6	att	These results indicate that the RcsB-dependent rprA gene is still expressed in the absence of either RcsC or RcsD [ 15 , 16 ] .	100	These results indicate that the RcsB-dependent rprA gene is still expressed in the absence of either RcsC or RcsD [ 15 , 16 ] .	9	A CONDITION THAT ACTIVATES THE REGULATOR RCSB INDEPENDENTLY OF THE RCSC, RCSD, AND RCSF PROTEINS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rprA	activator	32392214	8	att	To identify the gene ( s ) responsible for the RcsB-dependent RcsC - and RcsD-independent activation of the rprA promoter , we screened ~ 9,000 transposon Tn10dTc-generated mutants of the rcsC rcsD strain carrying the rprA-gfp fusion for decreased fluorescence on LB agar plates .	110	To identify the gene ( s ) responsible for the RcsB-dependent RcsC - and RcsD-independent activation of the rprA promoter , we screened ~ 9,000 transposon Tn10dTc-generated mutants of the rcsC rcsD strain carrying the rprA-gfp fusion for decreased fluorescence on LB agar plates .	10	RCSB ACTIVATION BY THE PHOSPHORELAY SENSOR BARA	Transposon Tn10	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	rprA	activator	33638994	1	ver/dev	In this context , phosphorylated RcsB activates expression of cps operon ; rprA ; osmB , two genes also regulated by RpoS ; and , the cell division gene ftsZ , among others .	43	In this context , phosphorylated RcsB activates expression of the capsule ( cps ) operon ( 10 ) ; rprA , which encodes the small RNA RprA ( 11 ) ; osmC and osmB , two genes also regulated by RpoS ( 12 ) ; and , the cell division gene ftsZ ( 13 ) , among others .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rprA	activator	33638994	1	ver/dev	In this context , phosphorylated RcsB activates expression of cps operon ; rprA ; osmC , two genes also regulated by RpoS ; and , the cell division gene ftsZ , among others .	43	In this context , phosphorylated RcsB activates expression of the capsule ( cps ) operon ( 10 ) ; rprA , which encodes the small RNA RprA ( 11 ) ; osmC and osmB , two genes also regulated by RpoS ( 12 ) ; and , the cell division gene ftsZ ( 13 ) , among others .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rprA	activator	33751923	21	ver/dev	When phosphorylated , RcsB binds RcsA to activate expression of rprA .	645	When phosphorylated , RcsB binds RcsA to activate expression of several genes , such as osmB , osmC , bdm , ftsZ , rprA , wza , and rcsA .	25	RCSBCD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	fliZ	regulator	29018419	0	ver/dev	fliC Flagellar biosynthesis ; flagellin , filament structural protein fliZ Putative regulator of FliA	104	fliC Flagellar biosynthesis ; flagellin , filament structural protein fliZ Putative regulator of FliA	5	MOTILITY, CHEMOTAXIS, AND ADHERENCE	nan	1	L2	SPEC	Other	OTHER	New	Level 1
FlhDC	gene	fliZ	activator	24992093	4	ver/dev	FlhDC , activates transcription of fliZ .	124	FlhDC , the master regulator of flagellar gene expression , activates transcription of class II flagellar genes , such as fliA and fliZ [ 45,46 ] .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	fliZ	activator	31262841	15	att	Given the effect on flagellar gene expression , we then hypothesized that PinT could also control hilA by affecting expression of the FlhDC-activated flagellar gene fliZ , encoding a major regulator of HilD protein activity ( 72 , 73 , 77 ) .	192	Given the effect on flagellar gene expression , we then hypothesized that PinT could also control hilA by affecting expression of the FlhDC-activated flagellar gene fliZ , encoding a major regulator of HilD protein activity ( 72 , 73 , 77 ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	srfN	activator	21711513	1	att	We also verified SsrB - and PhoP-dependent transcription of srfN measuring mRNA levels during-growth in AMM1 medium ( Additional file 12 , Figure S8 ) .	171	We also verified SsrB - and PhoP-dependent transcription of srfN measuring mRNA levels during growth in AMM1 medium ( Additional file 12 , Figure S8 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	slrP	regulator	27601571	35	ver/dev	A particularly intriguing antisense RNA is positively regulated by RtsA from a binding site within slrP .	311	A particularly intriguing antisense RNA initiates within slrP and is positively regulated by RtsA from a binding site within slrP ( Fig. 5B ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	regulator	27601571	37	ver/dev	slrP is bound by RtsA	314	Regulation of slrP by RtsA has been described previously ( 10 ) , but the reporter gene fusion used in that study lacked the region within slrP that is bound by RtsA .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	regulator	27601571	38	ver/dev	that an additional level of regulation by RtsA occurs via the antisense RNA within the slrP gene	315	We propose that the previously observed regulation of slrP by RtsA ( 10 ) occurs indirectly , via SprB ( Fig. 2 ) , and that an additional level of regulation by RtsA occurs via the antisense RNA within the slrP gene .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	regulator	27601571	38	ver/dev	that the previously observed regulation of slrP by RtsA occurs indirectly , via SprB	315	We propose that the previously observed regulation of slrP by RtsA ( 10 ) occurs indirectly , via SprB ( Fig. 2 ) , and that an additional level of regulation by RtsA occurs via the antisense RNA within the slrP gene .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	fimZ	regulator	18776023	0	ver/dev	Lrp is a positive regulator of the expression of type 1 fimbriae in Salmonella through direct interaction with the fimZ promoter region .	291	Lrp is a positive regulator of the expression of type 1 fimbriae in Salmonella through direct interaction with the fimZ promoter region .	7	UNKNOWN FUNCTIONS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	fimZ	regulator	19074398	4	att	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	25	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	2	MAIN	Salmonella;unidentified plasmid;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	regulator	23938383	1	ver/dev	The Lrp directly binds the fimZ promoter	118	The Lrp directly binds the fimZ promoter and assists fimZ expression , and consequently fimA is activated ( McFarland et al. 2008 ) .	13	3.4 LRP GENE EXPRESSION IN RAW264.7 MACROPHAGES AND IN STATIC BROTH CULTURE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	regulator	27909434	6	ver/dev	EMSA was used to test the binding of Lrp at indicated concentrations to 6 ′ - FAM-labeled fimZ promoter .	267	EMSA was used to test the binding of Lrp at indicated concentrations to 6 ′ - FAM-labeled fimZ promoter .	24	SITE-SPECIFIC ACETYLATION AT K36 SHOWS DEFICIENCY IN DNA-BINDING ABILITY OF LRP	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	narK	activator	29857034	19	ver/dev	narK -LRB- are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfJ	repressor	29270156	1	ver/dev	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by the repressor of the myo-inositol utilization genes in S. Typhimurium .	60	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR ( Cordero-Alba et al. , 2012 ) , the repressor of the myo-inositol ( MI ) utilization genes in S. Typhimurium ( Kröger and Fuchs , 2009 ) .	4	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilA	regulator	11123690	24	att	However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential-growth and a decrease in expression during stationary-phase ( Xu and Johnson , 1995 ) .	176	However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential growth and a decrease in expression during stationary phase ( Xu and Johnson , 1995 ) .	9	DISCUSSION	Escherichia coli	0	L2	SPEC	Other	OTHER	Other	Level 1
Fis	gene	hilA	regulator	11123690	23	ver/dev	In our model , we propose that Fis acts as a positive regulator of hilA .	175	In our model , we propose that Fis acts as a positive regulator of hilA , a conclusion that might seem at odds with the opposite expression profiles of the two proteins .	9	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	hilA	regulator	11123690	24	ver/dev	However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth .	176	However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential growth and a decrease in expression during stationary phase ( Xu and Johnson , 1995 ) .	9	DISCUSSION	Escherichia coli	0	L2	SPEC	Other	OTHER	Other	Level 1
Fis	gene	hilA	regulator	14553938	0	ver/dev	Positive regulation of SPI-1 genes by Fis was expected considering the fact that hilA , is upregulated by Fis .	142	Positive regulation of SPI-1 genes by Fis was expected considering the fact that hilA , a transcriptional regulator of SPI-1 , is upregulated by Fis [ 16 ] .	12	3.3. FIS IS INVOLVED IN SPI EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilA	regulator	16949866	7	ver/dev	The hilA promoter is directly controlled by Fis .	53	The hilA promoter is a target site for numerous evolutionarily conserved `` housekeeping '' regulators , and is directly controlled by BarA/SirA , Hha , RtsAB , and Fis ( Baxter et al. , 2003 ; Fahlen et al. , 2001 ; Olekhnovich and Kadner , 2006 ; Teplitski et al. , 2003 ) .	5	CORRESPONDING AUTHOR. TEL.: +1 352 392 1951X254; FAX: +1 352 392 3902.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NarL	gene	nirB	regulator	29186528	3	ver/dev	Supplementary Table S2 dimerize similarly as the NarL DBD domains bound to its own promoters , nirB and narG	136	Dimerization of RcsBBeF is not only produced through the REC domain but also through the DBD domains ( Supplementary Table S2 ) , which dimerize similarly as the NarL DBD domains bound to its own promoters , nirB and narG ( 37,38 ) .	15	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NarL	gene	nirB	regulator	29186528	3	ver/dev	the DBD domains dimerize similarly as the NarL DBD domains bound to its own promoters , nirB and narG	136	Dimerization of RcsBBeF is not only produced through the REC domain but also through the DBD domains ( Supplementary Table S2 ) , which dimerize similarly as the NarL DBD domains bound to its own promoters , nirB and narG ( 37,38 ) .	15	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NarL	gene	nirB	regulator	29186528	15	ver/dev	In this , the DBD acquires an organization competent to bind promoters in a tail-to-tail arrangement , as we have confirmed in-vitro by checking the binding of different mutants to P1flhDC , similar to NarL with its nirB promoter .	410	In this phosphorylated asymmetric conformation , the DBD acquires an organization competent to bind promoters in a tail-to-tail arrangement , as we have confirmed in vitro by checking the binding of different mutants to P1flhDC and the rcsA promoters , similar to the organization observed in the complex structure of DBD -- NarL with its nirB promoter ( 38 ) .	20	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	csgD	activator	14643403	11	ver/dev	Binding of H-NS to the intergenic region caused moderate activation of the regulated csgD promoter .	170	Binding of H-NS to the intergenic region caused moderate activation of the regulated csgD promoter .	18	6.3. HISTONE-LIKE NUCLEOID STRUCTURING PROTEIN (H-NS)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	STM3611	regulator	25437188	48	ver/dev	STM3611 , as a class III flagellar gene , is indirectly regulated by STM1697 via FliA .	556	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC , STM1344 and STM1697 via FliA ( Figure 2 ) .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	STM3611	regulator	25437188	48	ver/dev	STM3611 , as a class III flagellar gene , is indirectly regulated by STM1344 via FliA .	556	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC , STM1344 and STM1697 via FliA ( Figure 2 ) .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	STM3611	regulator	25437188	48	ver/dev	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC via FliA .	556	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC , STM1344 and STM1697 via FliA ( Figure 2 ) .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	ssrA	repressor	19074398	14	ver/dev	Transcription of ssrA genes is repressed by Lrp .	276	Transcription of the hilA , invF , and ssrA genes is repressed by Lrp .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hlyE	repressor	24885225	17	ver/dev	Fis participates in the repression of hlyE at transcriptional level CRP is a regulator .	58	Fis participates in the repression of hlyE at transcriptional level CRP is a regulator that acts as a cAMP receptor .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hlyE	repressor	24885225	24	ver/dev	Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .	103	CRP and Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay using purified CRP activated with cAMP and the DNA corresponding to the taiA -- hlyE promoter region .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
OxyR	gene	agn43	regulator	17905993	0	ver/dev	the OxyR repressor for hemi-methylated GATC sites has been shown to regulate phase variation in the E. coli agn43 gene .	40	Competition between SeqA and the OxyR repressor for hemi-methylated GATC sites has been shown to regulate phase variation in the E. coli agn43 gene ( 9 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
OxyR	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of OxyR while switching of pap is controlled by PapI .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of OxyR while switching of pap is controlled by PapI .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of OxyR while switching of pap is controlled by two main regulators .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of OxyR while switching of pap is controlled by two main regulators .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma54	gene	dctA	activator	12125817	10	att	Rhizobium meliloti and Rhizobium leguminosarum dctD gene products bind to tandem sites in an activation sequence located upstream of s54-dependent dctA promoters .	409	Rhizobium meliloti and Rhizobium leguminosarum dctD gene products bind to tandem sites in an activation sequence located upstream of s54-dependent dctA promoters .	28	REFERENCES	Sinorhizobium meliloti;Rhizobium leguminosarum	0	L3	OTHER	Other	OTHER	New	Level 2
Sigma54	gene	dctA	activator	12581721	10	att	Rhizobium meliloti and Rhizobium leguminosarum dctD gene products bind to tandem sites in an activation sequence located upstream of s54-dependent dctA promoters .	409	Rhizobium meliloti and Rhizobium leguminosarum dctD gene products bind to tandem sites in an activation sequence located upstream of s54-dependent dctA promoters .	28	REFERENCES	Sinorhizobium meliloti;Rhizobium leguminosarum	0	L3	OTHER	Other	OTHER	New	Level 2
DnaA	gene	dnaA	repressor	23637809	0	ver/dev	a specific site _ termed the repression of dnaA transcription immediately after replication by the activity of SeqA , the regulatory inactivation of DnaA ( RIDA ) system	41	These include the titration of DnaA to a specific site termed datA locus , the repression of dnaA transcription immediately after replication by the activity of SeqA , the regulatory inactivation of DnaA ( RIDA ) system which promotes ATP hydrolysis in a replication-coupled manner to yield initiation-inactive ADP -- DnaA , and the transcriptional autoregulation through the binding of DnaA to DnaA boxes in the promoter region , which prevents an over-abundance of DnaA and additional initiation events [ 18,22 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DnaA	gene	dnaA	repressor	23637809	0	ver/dev	a specific site _ termed the repression of dnaA transcription immediately after replication by the activity of SeqA , the regulatory inactivation of DnaA ( RIDA ) system	41	These include the titration of DnaA to a specific site termed datA locus , the repression of dnaA transcription immediately after replication by the activity of SeqA , the regulatory inactivation of DnaA ( RIDA ) system which promotes ATP hydrolysis in a replication-coupled manner to yield initiation-inactive ADP -- DnaA , and the transcriptional autoregulation through the binding of DnaA to DnaA boxes in the promoter region , which prevents an over-abundance of DnaA and additional initiation events [ 18,22 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	spvABCD	repressor	19074398	5	ver/dev	In addition , Lrp represses expression of the spvABCD operon .	32	In addition , Lrp represses expression of the spvABCD operon ( 64 ) , which is required for the establishment of a systemic infection by Salmonella in mice ( 41 , 42 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	activator	12753201	9	ver/dev	OmpR activates the expression of ssrB	79	OmpR activates the expression of ssrB , and ssrB is autoregulated .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	activator	12753201	10	ver/dev	As we observed with OmpR activation of ssrA , activation of ssrB by OmpR also depends upon the kinase EnvZ .	80	As we observed with OmpR activation of ssrA , activation of ssrB by OmpR also depends upon the kinase EnvZ .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrB	activator	12753201	44	ver/dev	How does OmpR activate expression of ssrB ?	240	How does OmpR activate expression of ssrA and ssrB ?	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	activator	15491370	13	ver/dev	Elimination of ompR on the srfH -- lacZ activity was comparable with elimination of ssrB , perhaps the apparent OmpR stimulation of srfH is via its effect on expression of SsrB .	219	Elimination of ompR on the srfH -- lacZ activity was comparable with elimination of ssrB ( Fig. 3 ) , perhaps the apparent OmpR stimulation of srfH is via its effect on expression of SsrB ( see Discussion ) .	8	PRIMER EXTENSION OF SRFH	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
OmpR	gene	ssrB	activator	15491370	17	ver/dev	Our previous characterization of OmpR activation of an ssrB -- lacZ fusion indicated that EnvZ was also required , i.e. the form was OmpR-P .	316	Our previous characterization of OmpR activation of an ssrB -- lacZ fusion indicated that EnvZ was also required , i.e. the form required for activation was OmpR-P ( Feng et al. , 2003 ) .	9	SSRA IS EXPRESSED IN VARIOUS BACKGROUNDS UNDER SPI-2 ACTIVATING CONDITIONS AT PH 5.7	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	activator	15491370	17	ver/dev	OmpR activation of an ssrB -- lacZ fusion indicated that EnvZ was also required , i.e. the form _ required for activation	316	Our previous characterization of OmpR activation of an ssrB -- lacZ fusion indicated that EnvZ was also required , i.e. the form required for activation was OmpR-P ( Feng et al. , 2003 ) .	9	SSRA IS EXPRESSED IN VARIOUS BACKGROUNDS UNDER SPI-2 ACTIVATING CONDITIONS AT PH 5.7	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	activator	21388802	3	ver/dev	OmpR activates ssrB expression .	160	OmpR activates slyA , phoP and ssrB expression and represses rpoS .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	activator	26880544	1	ver/dev	Under low osmolality , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrB	activator	26880544	1	ver/dev	Under acidic pH , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrB	activator	34202800	20	ver/dev	As a result , OmpR activate transcription of ssrB genes .	390	As a result , OmpR and PhoP activate transcription of ssrA and ssrB genes , leading to the formation of SsrA and SsrB .	11	3.3.4. THE ENVZ/OMPR SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SgrR	gene	lacZ	activator	26324451	2	ver/dev	The effects of SgrR variants on expression of lacZ from pDM1402 with and without induction by - MG were measured in nutrient medium .	210	The effects of SgrR variants on expression of lacZ from pDM1402 with and without induction by - MG were measured in nutrient medium .	6	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RamA	TU	acrAB	regulator	18577510	16	ver/dev	To understand the regulation of acrAB by RamA , EMSA with the RamA protein were performed .	188	To understand the regulation of acrAB by RamA , electrophoretic mobility shift assays ( EMSA ) with the RamA protein were performed .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	18577510	16	ver/dev	To understand the regulation of acrAB by RamA , electrophoretic-mobility-shift assays with the RamA protein were performed .	188	To understand the regulation of acrAB by RamA , electrophoretic mobility shift assays ( EMSA ) with the RamA protein were performed .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	18577510	27	ver/dev	Bile RamA directly controls the expression of acrAB .	236	Bile RamA directly controls the expression of acrAB and tolC .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	regulator	18984645	8	ver/dev	bile-mediated 52 regulation of AcrAB in Salmonella is also that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium	315	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	17	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	regulator	19018673	1	ver/dev	These authors describe that acrAB is 1 12 actually regulated by RamA in Salmonella Typhimurium .	194	These authors describe that acrAB is 1 12 actually regulated by RamA in Salmonella Typhimurium .	13	DISCUSSION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	19230852	13	ver/dev	These results suggest that RamA is the major regulator of Salmonella may mask the contributions of any other acrAB regulators .	363	These results suggest that RamA is the major regulator of Salmonella acrAB and may mask the contributions of any other acrAB regulators .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	regulator	19230852	13	ver/dev	These results suggest that RamA is the major regulator of Salmonella acrAB .	363	These results suggest that RamA is the major regulator of Salmonella acrAB and may mask the contributions of any other acrAB regulators .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	regulator	19230852	18	ver/dev	RamA controls the expression of acrAB in response to environmental signals	394	Salmonella has a specific regulator , RamA , which controls the expression of acrAB in response to environmental signals .	10	7. ROLE OF DRUG EFFLUX PUMPS IN VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	regulator	19230852	19	ver/dev	that RamA is a master regulator of acrAB	395	We suggest that RamA is a master regulator of acrAB and that the AcrAB induction pathway in Salmonella is different from that in E. coli .	10	7. ROLE OF DRUG EFFLUX PUMPS IN VIRULENCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	21081542	0	ver/dev	A recent study suggests that RamA is 27 a master regulator of Salmonella acrAB .	39	A recent study suggests that RamA is 27 a master regulator of Salmonella acrAB .	3	INTRODUCTION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	regulator	21148208	22	ver/dev	According to analysis of the relationship between Salmonella AcrAB regulators , RamA is the most effective regulator of Salmonella acrAB .	264	According to analysis of the relationship between tigecycline resistance and Salmonella AcrAB regulators , RamA is the most effective regulator of Salmonella acrAB ( Horiyama et al. , 2011 ) .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	21148208	22	ver/dev	According to analysis of the relationship between tigecycline resistance , RamA is the most effective regulator of Salmonella acrAB .	264	According to analysis of the relationship between tigecycline resistance and Salmonella AcrAB regulators , RamA is the most effective regulator of Salmonella acrAB ( Horiyama et al. , 2011 ) .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	21858134	2	ver/dev	It has been confirmed that RamA can bind to the upstream promoter region of acrAB .	48	It has been confirmed that RamA can bind to the upstream promoter region of acrAB and tolC and increase the expression level of the efflux [ 16 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	regulator	23230062	0	ver/dev	Activation of the acrAB operon is achieved through the direct binding of RamA , to the operator regions of these genes .	27	Activation of the acrAB operon and tolC gene transcription is achieved through the direct binding of RamA , a positive regulator of the AraC/XylS family , to the operator regions of these genes [ 13 , 14 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	23503095	1	ver/dev	In the expression of acrAB is regulated by RamA et al. , Abouzeed et al. ,	28	In particular , the expression of acrAB is regulated by the global regulators , RamA , SoxS , MarA , and Rob ( Rosenberg et al. , 2003 ; Abouzeed et al. ,	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	23503095	1	ver/dev	In the expression of acrAB is regulated by RamA et al. , 2003 ,	28	In particular , the expression of acrAB is regulated by the global regulators , RamA , SoxS , MarA , and Rob ( Rosenberg et al. , 2003 ; Abouzeed et al. ,	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	23503095	3	ver/dev	In S. Haardt , RamA mainly regulates the expression of acrAB .	31	In S. Typhimurium and S. Haardt , RamA mainly regulates the expression of acrAB ( Figure 1 ; Nikaido et al. , 2008 ; Zheng et al. , 2009 ; Kim and Woo , 2011 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	regulator	23503095	3	ver/dev	In S. Typhimurium , RamA mainly regulates the expression of acrAB .	31	In S. Typhimurium and S. Haardt , RamA mainly regulates the expression of acrAB ( Figure 1 ; Nikaido et al. , 2008 ; Zheng et al. , 2009 ; Kim and Woo , 2011 ) .	2	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	regulator	28631419	1	ver/dev	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor by the AraC/XylS-like regulators RamA , MarA , SoxS and	25	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor encoded nearby , and by the AraC/XylS-like regulators RamA , MarA , SoxS and	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	29042652	0	ver/dev	the acrAB gene is regulated by the activator RamA	12	In Salmonella enterica , the RND pump is translated from the acrAB gene , which is regulated by the activator RamA .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	regulator	34202800	10	ver/dev	Nikaido et al. showed that induction of the acrAB via indole is regulated by the RamA .	283	Nikaido et al. [ 89 ] showed that induction of the acrAB via indole is regulated by the RamA .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	sdiA	regulator	12562806	13	att	Both hypotheses need to be tested , but we already know that expression of sdiA from a plasmid increases the expression of SdiA-regulated genes in the absence of signal ( 1 , 22 ) .	377	Both hypotheses need to be tested , but we already know that expression of sdiA from a plasmid increases the expression of SdiA-regulated genes in the absence of signal ( 1 , 22 ) .	5	DISCUSSION	unidentified plasmid	1	L2	SPEC	Fact	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	15130116	12	ver/dev	Given that the Salmo-nella promoters are confirmed to respond to chromosomal sdiA and AHL , whereas the ftsQP2 promoter is not , we suspect that the binding of SdiA to the ftsQP2 promoter may not be physiologically relevant .	257	Given that the Salmo-nella promoters are confirmed to respond to chromosomal sdiA and AHL , whereas the ftsQP2 promoter is not , we suspect that the binding of SdiA to the ftsQP2 promoter may not be physiologically relevant .	5	THE SALMONELLA SDIA SYSTEM	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L1	SPEC	Analysis	NEG	New	Level 1
SdiA	gene	sdiA	regulator	18665275	1	ver/dev	Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in cow models of infection .	80	Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in mouse , chicken , or cow models of infection [ 1 ] .	7	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Bos taurus	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
SdiA	gene	sdiA	regulator	18665275	1	ver/dev	Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in chicken .	80	Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in mouse , chicken , or cow models of infection [ 1 ] .	7	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Gallus gallus	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
SdiA	gene	sdiA	regulator	18665275	1	ver/dev	Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in mouse .	80	Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in mouse , chicken , or cow models of infection [ 1 ] .	7	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus musculus	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
SdiA	gene	sdiA	regulator	20121449	1	ver/dev	Despite the regulation of putative virulence genes by SdiA , a sdiA mutant of S. enterica sv .	54	Despite the regulation of putative virulence genes by SdiA , a sdiA mutant of S. enterica sv .	2	J. T. NOEL,1 J. JOY,2 J. N. SMITH,3 M. FATICA,2 K. R. SCHNEIDER,2 B. M. M. AHMER,3 AND M. TEPLITSKI1 1SOIL AND WATER SCIENCE DEPARTMENT AND 2DEPARTMENT OF FOOD SCIENCE AND HUMAN NUTRITION, UNIVERSITY OF FLORIDA-IFAS, GAINESVILLE 32610, U.S.A.; 3DEPARTMENT OF MICROBIOLOGY, OHIO STATE UNIVERSITY, COLUMBUS 43210, U.S.A.	Salmonella;Salmonella	1	L2	SPEC	Other	OTHER	New	Level 1
SdiA	gene	sdiA	regulator	20121449	6	ver/dev	Therefore , binding of plant compounds to SdiA can not explain the lack of sdiA expression in planta .	259	Therefore , binding of plant compounds to SdiA can not explain the lack of sdiA expression in planta .	8	CONCLUSIONS.	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
SdiA	gene	sdiA	regulator	22149171	5	att	AHL-dependent expression of the SdiA-regulated gene rck correlated to the observed sdiA transcriptional changes in regulator mutants .	13	AHL-dependent expression of the SdiA-regulated gene rck correlated to the observed sdiA transcriptional changes in regulator mutants .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	sdiA	regulator	22149171	56	att	To test whether observed differences in sdiA expression among mutants and media conditions resulted in actual differences in SdiA levels , SdiA-regulated rck expression was measured .	365	To test whether observed differences in sdiA expression among mutants and media conditions resulted in actual differences in SdiA levels , SdiA-regulated rck expression was measured .	20	REGULATORY INPUT AT THE SDIA PROMOTER AFFECTS SDIA OUTPUT	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	22610437	1	ver/dev	To chromosomal fusion in E. coli K-12 strain BW25113 to test the more thoroughly investigate SdiA activity in the presence of in - regulation of sdiA by indole .	150	To chromosomal fusion in E. coli K-12 strain BW25113 to test the more thoroughly investigate SdiA activity in the presence of in - regulation of sdiA by indole .	13	6 22	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	sdiA	regulator	25080967	5	ver/dev	It seems that SdiA needs the binding of AHLs for proper protein folding before interacting with DNA although some studies suggested that the overexpression of sdiA could be sufficient to activate it -LRB- without AHLs -RRB- .	67	It seems that SdiA needs the binding of AHLs for proper protein folding before interacting with DNA ( Yao et al. , 2006 ; Gnanendra et al. , 2012 ) although some studies suggested that the overexpression of sdiA could be sufficient to activate it ( without AHLs ) ( Michael et al. , 2001 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	27920756	2	ver/dev	In mice , infection with a sdiA mutant resulted in increased bacterial loads in the livers of infected mice indicating that SdiA may be a negative regulator of virulence .	162	In mice , infection with a sdiA mutant lacking AHL signaling resulted in increased fecal shedding and bacterial loads in the livers of infected mice ( Volf et al. , 2002 ) indicating that SdiA may be a negative regulator of virulence .	7	INTERSPECIES AND INTERKINGDOM COMMUNICATION	Mus sp.;Mus sp.	0	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	27920756	2	ver/dev	In mice , infection with a sdiA mutant resulted in increased fecal shedding in the livers of infected mice indicating that SdiA may be a negative regulator of virulence .	162	In mice , infection with a sdiA mutant lacking AHL signaling resulted in increased fecal shedding and bacterial loads in the livers of infected mice ( Volf et al. , 2002 ) indicating that SdiA may be a negative regulator of virulence .	7	INTERSPECIES AND INTERKINGDOM COMMUNICATION	Mus sp.;Mus sp.	0	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	33133465	2	ver/dev	Typhimurium is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence-factors ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes	147	Typhimurium including pefI/srgC operon , srgE and sirA genes is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence factors which in turn will decrease the flagella formation ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes derived from genes located on the pathogenic islands 1 and 4.18,28-31	8	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	33133465	2	ver/dev	pefI/srgC operon is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence-factors ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes	147	Typhimurium including pefI/srgC operon , srgE and sirA genes is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence factors which in turn will decrease the flagella formation ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes derived from genes located on the pathogenic islands 1 and 4.18,28-31	8	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SdiA	gene	sdiA	regulator	33257526	2	ver/dev	FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes , highlighting a regulatory link between intercellular communication .	16	FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes , highlighting a regulatory link between flagellar motility and intercellular communication .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	sdiA	regulator	33257526	2	ver/dev	FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes , highlighting a regulatory link between flagellar motility .	16	FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes , highlighting a regulatory link between flagellar motility and intercellular communication .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	sdiA	regulator	9495757	1	ver/dev	To test this hypothesis , we determined that S. typhimurium encodes SdiA regulated by sdiA .	44	To test this hypothesis , we determined that S. typhimurium encodes a LuxR homolog ( SdiA ) and then performed a screen for genes regulated by sdiA .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
DksA	gene	maeB	activator	20851888	5	att	Genes encoding glucose-6-phosphate dehydrogenase ( zwf ) , isocitrate dehydrogenase ( icdA ) , and malic enzyme ( maeB ) responsible for the generation of NADPH , and the sucAB-encoded subunits of - oxaloacetate dehydrogenase associated with generation of NADH all showed DksA-dependent regulation ( Fig. 3A , bold red font ) .	178	Genes encoding glucose-6-phosphate dehydrogenase ( zwf ) , isocitrate dehydrogenase ( icdA ) , and malic enzyme ( maeB ) responsible for the generation of NADPH , and the sucAB-encoded subunits of - oxaloacetate dehydrogenase associated with generation of NADH all showed DksA-dependent regulation ( Fig. 3A , bold red font ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FliA	gene	flgM	activator	1655712	1	att	Upstream of this region lies a sequence , 5 ' - TAAA-N15-GCCGATGA-3 ' , which is a close match to the published consensus for FliA-dependent promoter sequences ( 5 ' - TAAA-N15-GCCGATAA-3 ' [ 14 , 25 , 29 ] ) and may be the promoter for the putative flgM gene .	176	Upstream of this region lies a sequence , 5 ' - TAAA-N15-GCCGATGA-3 ' , which is a close match to the published consensus for FliA-dependent promoter sequences ( 5 ' - TAAA-N15-GCCGATAA-3 ' [ 14 , 25 , 29 ] ) and may be the promoter for the putative flgM gene .	5	RESULTS	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
FliA	gene	flgM	activator	1655712	2	att	If the presumed FliA-dependent promoter sequence described above were responsible for promoting transcription of the putative flgM gene , then transcripts beginning from that region would extend into a TnlOOO insert located downstream .	178	If the presumed FliA-dependent promoter sequence described above were responsible for promoting transcription of the putative flgM gene , then transcripts beginning from that region would extend into a TnlOOO insert located downstream .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	ssrB	regulator	26300871	18	ver/dev	Taken together , these results show that CpxR represses the autoregulation of ssrB located in SPI-2 .	390	Taken together , these results show that CpxR represses the autoregulation of HilD , which in turn affects the expression of hilA and thus the SPI-1 genes , as well as of other virulence genes regulated by HilD , such as ssrB and sseB located in SPI-2 .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	ssrB	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of ssrB we performed EMSA with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged Fig 3B .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	ssrB	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of ssrB we performed EMSA with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	ssrB	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of ssrB we performed electrophoretic-mobility-shift assays with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged Fig 3B .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	ssrB	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of ssrB we performed electrophoretic-mobility-shift assays with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	ssrB	regulator	30716090	32	ver/dev	We checked the coding strand of ssrB for binding of CpxR ~ P .	379	We checked the coding strand of ssrB for binding of CpxR ~ P but did not observe significant binding ( S3 Fig ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	cas1	activator	30760616	1	att	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	148	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	phoH	regulator	27886269	3	ver/dev	InvF , regulates the expression of phoH .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	10874730	8	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .	626	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .	49	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11260470	9	ver/dev	Norel , F. Relationships between H-NS S phase in the control of spvR , the regulatory gene of operon .	482	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , s , SpvR and growth S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11260470	9	ver/dev	Norel , F. Relationships between H-NS S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	482	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , s , SpvR and growth S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11553591	9	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	808	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	32	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	11553591	9	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	808	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	32	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	12902215	3	ver/dev	Relationships between H-NS phase in the control of spvR , the	504	Relationships between H-NS , S , SpvR and growth phase in the control of spvR , the	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	14726232	2	ver/dev	Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , rowth phase in the control of spvR , the regulatory gene of peron .	165	[ 10 ] Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	16	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	14726232	2	ver/dev	Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , rowth phase in the control of spvR , the regulatory gene of he Salmonella plasmid virulence .	165	[ 10 ] Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	16	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	14726232	2	ver/dev	Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , pvR phase in the control of spvR , the regulatory gene of peron .	165	[ 10 ] Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	16	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	14726232	2	ver/dev	Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , pvR phase in the control of spvR , the regulatory gene of he Salmonella plasmid virulence .	165	[ 10 ] Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	16	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	16707690	40	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	720	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	29	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	16707690	40	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	720	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	29	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	17293430	29	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	601	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	17293430	29	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	601	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	24	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Norel , 1997 Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Norel , 1997 Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , L. Kowarz , 1997 Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , L. Kowarz , 1997 Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , 1997 Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , 1997 Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	31661351	26	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .	669	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	53	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	spvR	regulator	31661351	26	ver/dev	Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	669	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	53	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hilA	regulator	29857034	3	ver/dev	hilA are negatively regulated by SlyA	267	Presumptive genes involved in these pathways include sopD , sopE2 , and hilA , which belong to pathogenicity island-1 ( SPI-1 ) and are negatively regulated by SlyA .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	hilA	regulator	29857034	33	ver/dev	Direct regulation of hilA genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	12068808	6	ver/dev	In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress , mediating the reciprocal osmotic control of ompC .	69	In E. coli , OmpR is clearly involved in the cellular response to osmotic stress , mediating the reciprocal osmotic control of ompC and ompF ( Hall and Silhavy , 1981 ; Slauch and Silhavy , 1989 ; Tate et al. , 1988 ; Lan and Igo , 1998 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	regulator	12068808	45	ver/dev	Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompC is not clearly understood .	233	Phosphorylation of OmpR induces a conformational change in the protein ( Kenney et al. , 1995 ) , but how this change influ-ences OmpR control of ompC and ompF is not clearly understood ( Head et al. , 1998 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	regulator	12080060	6	ver/dev	In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress , mediating the reciprocal osmotic control of ompC .	69	In E. coli , OmpR is clearly involved in the cellular response to osmotic stress , mediating the reciprocal osmotic control of ompC and ompF ( Hall and Silhavy , 1981 ; Slauch and Silhavy , 1989 ; Tate et al. , 1988 ; Lan and Igo , 1998 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	regulator	12080060	45	ver/dev	Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompC is not clearly understood .	233	Phosphorylation of OmpR induces a conformational change in the protein ( Kenney et al. , 1995 ) , but how this change influ-ences OmpR control of ompC and ompF is not clearly understood ( Head et al. , 1998 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	regulator	15126450	5	ver/dev	Expression of the ompC is under the control of OmpR .	23	Expression of the ompC and ompF genes in S. enterica serovar Typhi is under the control of EnvZ and OmpR , a two-compo-nent signal transduction system encoded by the ompB ( ompR envZ ) locus .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	regulator	18361683	1	ver/dev	The two-component regulatory system OmpR = EnvZ regulates ompC in response to osmolarity changes in Salmonella .	257	The two-component regulatory system OmpR = EnvZ regulates the porin genes ompF and ompC in response to osmolarity changes in Salmonella ( Mills et al. , 1998 ) .	12	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	19609351	5	att	Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .	338	Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .	6	NON-CODING (NC) RNA SEQUENCES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	regulator	19759044	4	ver/dev	Transcription regulation of ompC by OmpR .	646	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	27	290–2.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	24720747	4	ver/dev	These results support the model where the LtrR protein directly induces ompR expression , upon which OmpR binds to the regulatory region of ompC to induce their synthesis in S. Typhi IMSS-1 .	100	These results support the model where the LtrR protein directly induces ompR expression , upon which OmpR binds to the regulatory region of ompC and ompF to induce their synthesis in S. Typhi IMSS-1 .	5	DETERMINATION OF THE LTRR-OMPR-OMPC-OMPF CASCADE FOR PORIN SYNTHESIS IN S. TYPHI	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompC	regulator	25875623	0	att	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .	18	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ompC	regulator	28553268	14	ver/dev	Transcription regulation of ompC by OmpR .	2120	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	34	ACKNOWLEDGMENTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-2 genes by SsrB resembles the reciprocal control of ompC transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-1 genes by SsrB resembles the reciprocal control of ompC transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	30524381	22	att	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( a SPI-2 structural gene ) .	271	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( a SPI-2 structural gene ) .	20	OMPR IS AN IMPORTANT GLOBAL REGULATOR OF THE BACTERIAL RESPONSE TO	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ompC	regulator	30524381	27	att	Three of these were ompF , ompC and tppB , i.e. , known OmpR-regulated genes .	295	Three of these were ompF , ompC and tppB , i.e. , known OmpR-regulated genes .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	gene	ompC	regulator	33751923	31	ver/dev	Transcription regulation of ompC by OmpR .	2518	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	204	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	regulator	33854491	20	ver/dev	Transcription regulation of ompC by OmpR .	582	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	25	THIS WORK WAS SUPPORTED BY GRANTS FROM THE DIRECCIÓN GENERAL AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB.2021.657404/ DE ASUNTOS DEL PERSONAL ACADÉMICO, DGAPA/UNAM (IN203618 FULL#SUPPLEMENTARY-MATERIAL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NhaR	gene	nhaA	regulator	22149171	47	ver/dev	Although IlvY bound its positive control NhaR bound its positive control P 1 nhaA .	340	Although IlvY bound its positive control PilvC and NhaR bound its positive control P 1 nhaA , neither protein bound PsdiA ( Fig .	18	ILVY, NHAR, AND FUR ARE INDIRECT ACTIVATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	flhDC	activator	26441883	4	ver/dev	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of flagellation by activation of the flagellar operon flhDC .	207	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility and flagellation by activation of the flagellar operon flhDC ( Hu et al. , 2009 ; Raczkowska et al. , 2011b ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	flhDC	activator	26441883	4	ver/dev	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility by activation of the flagellar operon flhDC .	207	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility and flagellation by activation of the flagellar operon flhDC ( Hu et al. , 2009 ; Raczkowska et al. , 2011b ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	flhDC	activator	32032766	4	ver/dev	The results showed that OmpR , activated the transcription of flhDC , whereas RpoS suppressed their expression .	195	The results showed that the regulators , OmpR and Fis , activated the transcription of AsfD and flhDC , whereas RpoS suppressed their expression .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	yjbE	regulator	34149657	3	ver/dev	The regulation of yjbE has been partially attributed to RpoS , respectively .	432	The regulation of yciE , yjbE , and ASPP has been partially attributed to RpoS , Rcs phosphorelay , and RpoN , respectively .	25	TIME: 11:13 # 11	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	acs	activator	26199328	3	ver/dev	Notably , during-growth-on-glucose , less Acs is made because Crp can not fully activate acs expression when cAMP levels are low .	291	Notably , during growth on glucose , less Acs is made because Crp can not fully activate acs expression when cyclic AMP ( cAMP ) levels are low ( 31 ) .	5	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CRP	gene	acs	activator	26199328	3	ver/dev	Notably , during-growth-on-glucose , less Acs is made because Crp can not fully activate acs expression when cyclic AMP levels are low .	291	Notably , during growth on glucose , less Acs is made because Crp can not fully activate acs expression when cyclic AMP ( cAMP ) levels are low ( 31 ) .	5	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CRP	gene	acs	activator	26705535	0	ver/dev	Notably , CRP activates acs .	85	Notably , the S. enterica catabolite repressor protein ( CRP ) activates expression pat and acs , but not cobB .	9	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvY	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	rfaG	regulator	26267246	8	ver/dev	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to Fig 5C , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting FlhDC stability .	115	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to the WT ( Fig 5C ) , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting FlhDC stability or mRNA translation .	8	CHARACTERIZATION OF MUTANTS WITH AN ALTERED MOTILITY PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	rfaG	regulator	26267246	8	ver/dev	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to the WT , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting FlhDC stability .	115	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to the WT ( Fig 5C ) , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting FlhDC stability or mRNA translation .	8	CHARACTERIZATION OF MUTANTS WITH AN ALTERED MOTILITY PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hns	repressor	12228306	0	ver/dev	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) .	322	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) and YMZ16 ( clyA hns ) ( solid bars ) carrying different constructs .	5	SEROVAR PARATYPHI A S3068/99 CLYASPA	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	repressor	12228306	0	ver/dev	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) _ carrying different constructs	322	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) and YMZ16 ( clyA hns ) ( solid bars ) carrying different constructs .	5	SEROVAR PARATYPHI A S3068/99 CLYASPA	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	repressor	12228306	0	ver/dev	H-NS-dependent repression of clyA hns .	322	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) and YMZ16 ( clyA hns ) ( solid bars ) carrying different constructs .	5	SEROVAR PARATYPHI A S3068/99 CLYASPA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	repressor	12228306	0	ver/dev	H-NS-dependent repression of clyA hns _ carrying different constructs	322	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) and YMZ16 ( clyA hns ) ( solid bars ) carrying different constructs .	5	SEROVAR PARATYPHI A S3068/99 CLYASPA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	repressor	18156266	0	ver/dev	Expression of STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	12	Expression of ompS1 , assT , and STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx and STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hns	repressor	19406898	2	ver/dev	an H-NS paralogue , was found to repress ompS1 in an hns background ; and a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	repressor	19406898	2	ver/dev	an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	repressor	21059643	5	ver/dev	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sseJ loci .	148	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA , sifB , and sseJ loci ( 13 , 14 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	21059643	5	ver/dev	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sifB .	148	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA , sifB , and sseJ loci ( 13 , 14 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	21059643	5	ver/dev	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA .	148	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA , sifB , and sseJ loci ( 13 , 14 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	25713562	10	ver/dev	The overexpression of H-NS repressed SPI-2 gene expression -LRB- comparing `` rpoE hns uninduced '' to `` rpoE hns '' -RRB- , however when σE was present , the repression of H-NS on SPI-2 was relieved -LRB- compare `` WT hns '' to `` rpoE hns '' -RRB- .	277	The overexpression of H-NS repressed SPI-2 gene expression ( comparing `` rpoE hns uninduced '' to `` rpoE hns induced '' ) , however when σE was present , the repression of H-NS on SPI-2 was relieved ( compare `` WT hns induced '' to `` rpoE hns induced '' ) .	12	SPI-2 APPARATUS AND EFFECTORS (B), PROTEIN SYNTHESIS (C), AND STRESS RESPONSE (D). RED REPRESENTS UP-REGULATION OF GENES BY ΣE WHILE GREEN REPRESENTS DOWN-REGULATION.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	31487966	5	ver/dev	i l t e freagexmpernests n2o5t ] siTgankfeicnatnotgyetahleer , reodurinretshueltdsoruebvleealmduttahnatt cHo-mNpSad e s ( i t i i f reirdecttolytrheeprWsTsedtrtahienexFpirgeussreon4Co ) f , yianedBicthartionugghthbaitndhnegdteolettsiopnroomoytaeerBreigniotnh.e hns mutant abolished the Pst induction , thus H-NS repression of Pst .	175	i l t e freagexmpernests ( inoengsaotifvpestcSoCnArBol ; gFengeusrwe4rBe ) n2o5t ] siTgankfeicnatnotgyetahleer , reodurinretshueltdsoruebvleealmduttahnatt cHo-mNpSad e s ( i t i i f reirdecttolytrheeprWsTsedtrtahienexFpirgeussreon4Co ) f , yianedBicthartionugghthbaitndhnegdteolettsiopnroomoytaeerBreigniotnh.e hns mutant abolished the Pst induction , thus H-NS repression of Pst required YaeB .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	31487966	5	ver/dev	i l t e gFengeusrwe4rBe n2o5t ] siTgankfeicnatnotgyetahleer , reodurinretshueltdsoruebvleealmduttahnatt cHo-mNpSad e s ( i t i i f reirdecttolytrheeprWsTsedtrtahienexFpirgeussreon4Co ) f , yianedBicthartionugghthbaitndhnegdteolettsiopnroomoytaeerBreigniotnh.e hns mutant abolished the Pst induction , thus H-NS repression of Pst .	175	i l t e freagexmpernests ( inoengsaotifvpestcSoCnArBol ; gFengeusrwe4rBe ) n2o5t ] siTgankfeicnatnotgyetahleer , reodurinretshueltdsoruebvleealmduttahnatt cHo-mNpSad e s ( i t i i f reirdecttolytrheeprWsTsedtrtahienexFpirgeussreon4Co ) f , yianedBicthartionugghthbaitndhnegdteolettsiopnroomoytaeerBreigniotnh.e hns mutant abolished the Pst induction , thus H-NS repression of Pst required YaeB .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	31487966	5	ver/dev	i l t e inoengsaotifvpestcSoCnArBol n2o5t ] siTgankfeicnatnotgyetahleer , reodurinretshueltdsoruebvleealmduttahnatt cHo-mNpSad e s ( i t i i f reirdecttolytrheeprWsTsedtrtahienexFpirgeussreon4Co ) f , yianedBicthartionugghthbaitndhnegdteolettsiopnroomoytaeerBreigniotnh.e hns mutant abolished the Pst induction , thus H-NS repression of Pst .	175	i l t e freagexmpernests ( inoengsaotifvpestcSoCnArBol ; gFengeusrwe4rBe ) n2o5t ] siTgankfeicnatnotgyetahleer , reodurinretshueltdsoruebvleealmduttahnatt cHo-mNpSad e s ( i t i i f reirdecttolytrheeprWsTsedtrtahienexFpirgeussreon4Co ) f , yianedBicthartionugghthbaitndhnegdteolettsiopnroomoytaeerBreigniotnh.e hns mutant abolished the Pst induction , thus H-NS repression of Pst required YaeB .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	32111072	11	ver/dev	Our results demonstrated that H-NS is a repressor of Usp synthesis as protein levels were higher from the E. coli and S. bongori native promoters in a hns defective strain compared to the wild type .	348	Our results demonstrated that H-NS is a repressor of Usp synthesis as protein levels were higher from the E. coli and S. bongori native promoters in a hns defective strain compared to the wild type .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	repressor	32209674	62	ver/dev	C. Ueguchi , M. Kakeda , T. Mizuno , Autoregulatory expression of the Escherichia coli hns gene : H-NS functions as a repressor of its own transcription .	740	C. Ueguchi , M. Kakeda , T. Mizuno , Autoregulatory expression of the Escherichia coli hns gene encoding a nucleoid protein : H-NS functions as a repressor of its own transcription .	6	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	repressor	32284321	0	ver/dev	We found that H-NS is the only repressor of the ltrR2 promoter since pKK8/ltrR2 -471 90 displayed the same activity in the hns lrp double mutant as in the single Δhns strain .	113	We found that H-NS is the only repressor of the ltrR2 promoter since the fusions pKK8/ltrRP2 -471 -1 and pKK8/ltrR2 -471 90 displayed the same activity in the hns lrp double mutant as in the single Δhns strain .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	repressor	32284321	0	ver/dev	We found that H-NS is the only repressor of the ltrR2 promoter since the fusions pKK8/ltrRP2 -471 -1 displayed the same activity in the hns lrp double mutant as in the single Δhns strain .	113	We found that H-NS is the only repressor of the ltrR2 promoter since the fusions pKK8/ltrRP2 -471 -1 and pKK8/ltrR2 -471 90 displayed the same activity in the hns lrp double mutant as in the single Δhns strain .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	yqhC	activator	16574345	0	att	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	179	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	15	3.1. MICROARRAY ANALYSIS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	yciR	repressor	25153529	3	ver/dev	yciR inhibit expression of CsgD .	130	The GGDEF/EAL domain protein STM1703 ( yciR ) and GGDEF domain proteins STM3611 ( yhjH ) and STM4264 ( yjcC ) each inhibit expression of CsgD and hence rdar morphotype development [ 57 ] .	8	GGDEF/EAL DOMAIN PROTEINS AND RDAR MORPHOTYPE DEVELOPMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilD	repressor	26300871	5	ver/dev	CpxR Represses hilD	349	CpxR Represses hilD and thus Indirectly Affects HilD-regulated Genes Several global regulators control the expression of the SPI-1 genes by directly affecting the expression , activity or concentration of	15	NLPE FROM THE T5-LAC PROMOTER OF PLASMID PCA-NLPE WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilD	repressor	26300871	8	ver/dev	the expression of the hilD-cat fusion _ revealing that CpxR represses hilD	370	The overexpression of CpxR reduced 50 % the expression of the hilD-cat fusion ( Figure 4A ) , revealing that CpxR represses hilD .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	Felis catus	0	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	hilD	repressor	26300871	9	ver/dev	CpxR could directly repress the transcription of hilD .	371	CpxR could directly repress the transcription of hilD or reduce post-transcriptionally the concentration of HilD and thus affect its positive autoregulation .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	hilD	repressor	26300871	17	ver/dev	our results _ indicating that CpxR represses the HilD-dependent expression of hilD	389	In agreement with our results indicating that CpxR represses the HilD-dependent expression of hilD and hilA , both the overexpression of CpxR and the absence of CpxA drastically reduced the production of SsrB-FLAG and SseB proteins ( Figures 1C , 3B ) , which are encoded in SPI-2 and whose expression is also dependent of HilD in the condition tested .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilD	repressor	26300871	23	ver/dev	FIGURE 4 CpxR represses the autoregulation of hilD .	422	FIGURE 4 | CpxR represses the autoregulation of hilD and thus negatively affects the expression of hilA .	17	CPXR AFFECTS STABILITY OF HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilD	repressor	30760616	6	ver/dev	CpxR also repressed SPI-1 genes by destabilizing its positive regulator , hilD .	291	CpxR also repressed SPI-1 genes by destabilizing its positive regulator , hilD ( 80 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	activator	11207562	2	auto	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) .	44	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	activator	16128395	0	ver/dev	indeed SpvR is known to activate the transcription of both the spvR	35	Based on amino acid sequence homologies , SpvR belongs to the LysR/MetR family of prokaryotic transcriptional activators ( Taira and Rhen , 1989a , b ; Caldwell and Gulig , 1991 ) , and indeed SpvR is known to activate the transcription of both the spvR and spvABCD transcriptional units ( Krause et al. , 1992 ; Sheehan and Dorman , 1998 ) .	4	MAIN	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
SpvR	gene	spvR	activator	23936152	13	ver/dev	Increased levels of spvR would then lead to increased expression of the spvABCD operon as SpvR is essential for activation of the spvA promoter .	439	Increased levels of spvR would then lead to increased expression of the spvABCD operon as SpvR is essential for activation of the spvA promoter and is known to be able to induce RpoS-independent expression from the spvA promoter [ 31 ] .	25	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SpvR	gene	spvR	activator	30143595	1	ver/dev	the DNA-binding SpvR protein acts as an essential activator of both spvR	31	While many global regulators can influence spv expression ( Fang et al. 1992 ; Kowarz et al. 1994 ; O'Byrne and Dorman 1994a , b ; Robbe-Saule et al. 1997 ; Marshall et al. 1999 ; Mangan et al. 2006 ) , the spvR gene that is located directly upstream of the spvABCD operon is thought to be transcribed separately ( Robbe-Saule et al. 1997 ; Wilson and Gulig 1998 ) and encodes the DNA-binding SpvR protein , which acts as an essential activator of both spvR and the spvABCD genes and is absolutely required for spv-mediated virulence in vivo ( Grob and Guiney 1996 ; Guilloteau et al. 1996 ; Sheehan and Dorman 1998 ) .	2	COPYRIGHT © 2018 BY THE GENETICS SOCIETY OF AMERICA DOI: HTTPS://DOI.ORG/10.1534/GENETICS.118.300822	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	hfq	repressor	22336758	11	ver/dev	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 background showed a clear downregulation of slightly reduced CsgD levels , whereby	122	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 which shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype ( Fig. 3B ) and slightly reduced CsgD levels , whereby	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	repressor	22336758	11	ver/dev	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 background showed a clear downregulation of Fig. 3B , whereby	122	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 which shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype ( Fig. 3B ) and slightly reduced CsgD levels , whereby	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	repressor	22336758	11	ver/dev	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 background showed a clear downregulation of the rdar morphotype , whereby	122	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 which shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype ( Fig. 3B ) and slightly reduced CsgD levels , whereby	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	repressor	22336758	14	ver/dev	Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with wild-type MAE52 , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant -LRB- Fig. 3C ; Fig .	128	Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with wild-type MAE52 ( Figs. 3C and S2 ) , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant ( Fig. 3C ; Fig .	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	repressor	22336758	14	ver/dev	Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with S2 , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant -LRB- Fig. 3C ; Fig .	128	Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with wild-type MAE52 ( Figs. 3C and S2 ) , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant ( Fig. 3C ; Fig .	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	repressor	22336758	14	ver/dev	Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with Figs. 3C , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant -LRB- Fig. 3C ; Fig .	128	Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with wild-type MAE52 ( Figs. 3C and S2 ) , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant ( Fig. 3C ; Fig .	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssaC	regulator	25875623	0	att	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .	18	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ssaC	regulator	30524381	22	att	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( a SPI-2 structural gene ) .	271	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( a SPI-2 structural gene ) .	20	OMPR IS AN IMPORTANT GLOBAL REGULATOR OF THE BACTERIAL RESPONSE TO	nan	1	L3	OTHER	Other	NEG	Other	Level 1
IclR	gene	yiaJ	repressor	25364573	0	ver/dev	Lastly , yiaJ is a repressor of transcription in the IclR family .	161	Lastly , yiaJ is a repressor of transcription in the IclR family , which is associated with control of some metabolic functions , multi-drug resistance , and quorum sensing [ 27 ] .	7	2.3. IDENTIFICATION OF GENES MORE HIGHLY TRANSCRIBED BY THE UK-1 DAM MUTANT AND UK-1 WT PARENT STRAIN REGARDLESS OF CULTURE CONDITION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	fliC	activator	31501286	27	ver/dev	Expression of fliC was increased by 40.4 % 36.7 % 2.6 % under these conditions , compared to treatment with the low ATc concentration , for MarA , respectively .	210	Expression of fliC was increased by 40.4 % 5.1 % and 36.7 % 2.6 % under these conditions , compared to treatment with the low ATc concentration , for MarA and Rob , respectively ( both P 3.9 10 7 , Student 's t test ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	fliC	activator	31501286	27	ver/dev	Expression of fliC was increased by 40.4 % 5.1 % 2.6 % under these conditions , compared to treatment with the low ATc concentration , for MarA , respectively .	210	Expression of fliC was increased by 40.4 % 5.1 % and 36.7 % 2.6 % under these conditions , compared to treatment with the low ATc concentration , for MarA and Rob , respectively ( both P 3.9 10 7 , Student 's t test ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	lpxR	regulator	27886269	27	ver/dev	In addition to HilD , the expression of lpxR in SPI-1-inducing conditions is positively regulated by SlyA .	169	In addition to HilD , the expression of lpxR in SPI-1-inducing conditions is positively regulated by SlyA , a MarR-like regulator63 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	activator	16777370	1	ver/dev	Fis , one of the major components of bacterial nucleoid , activated the stationary-phase-specific expression of ssaG when Salmonella was grown in LB media .	12	Fis , one of the major components of bacterial nucleoid , activated the stationary phase-specific expression of ssaG when Salmonella was grown in LB media .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	activator	16777370	3	ver/dev	All four Fis-binding sites were required for timely transcription activation of ssaG after Salmonella entered macrophage cells .	14	All four Fis-binding sites were required for timely transcription activation of ssaG after Salmonella entered macrophage cells .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	activator	16777370	8	ver/dev	In the present work , the effects of Fis on the expression of the ssaG gene , known to be induced by about 400-fold in the intracellular environment , were analyzed to understand the role of Fis in the regulation of the virulence genes of Salmonella in detail .	55	In the present work , the effects of Fis on the expression of the ssaG gene , known to be induced by about 400-fold in the intracellular environment [ 8 ] , were analyzed to understand the role of Fis in the regulation of the virulence genes of Salmonella in detail .	3	1. INTRODUCTION	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Fis	gene	ssaG	activator	16777370	20	ver/dev	To investigate the role of Fis in the activation of ssaG promoter inside the RAW 264.7 cells , pGLFP plasmid were used to measure the transcriptional activity of the promoter .	79	To investigate the role of Fis in the activation of ssaG promoter inside the RAW 264.7 cells , pGLFP plasmid containing egfp fused to the PssaGL and pGSFP plasmid containing egfp fused to the PssaGS were used to measure the transcriptional activity of the promoter .	7	2.3. FIS IS REQUIRED FOR TIMELY EXPRESSION OF SSAG AFTER INFECTION INTO EUKARYOTIC CELL	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	activator	16777370	21	ver/dev	These results suggest that all four Fis-binding sites are required for a timely induction of ssaG when Salmonella is responding to the activating signal inside animal cells .	87	These results suggest that Fis and all four Fis-binding sites are required for a timely induction of ssaG when Salmonella is responding to the activating signal inside animal cells .	7	2.3. FIS IS REQUIRED FOR TIMELY EXPRESSION OF SSAG AFTER INFECTION INTO EUKARYOTIC CELL	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	ssaG	activator	16777370	21	ver/dev	These results suggest that Fis are required for a timely induction of ssaG when Salmonella is responding to the activating signal inside animal cells .	87	These results suggest that Fis and all four Fis-binding sites are required for a timely induction of ssaG when Salmonella is responding to the activating signal inside animal cells .	7	2.3. FIS IS REQUIRED FOR TIMELY EXPRESSION OF SSAG AFTER INFECTION INTO EUKARYOTIC CELL	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	ssaG	activator	16777370	26	ver/dev	Although Fis levels drop precipitously during stationary-phases , Fis appears to be required for the activation of ssaG expression at the early stationary-phase .	111	Although Fis levels drop precipitously during late exponential and stationary phases [ 34 ] , Fis appears to be required for the activation of ssaG expression at the early stationary phase ( Fig. 1 ) .	9	3. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	ssaG	activator	16777370	26	ver/dev	Although Fis levels drop precipitously during late exponential , Fis appears to be required for the activation of ssaG expression at the early stationary-phase .	111	Although Fis levels drop precipitously during late exponential and stationary phases [ 34 ] , Fis appears to be required for the activation of ssaG expression at the early stationary phase ( Fig. 1 ) .	9	3. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	ssaG	activator	16777370	27	ver/dev	Johnson reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary-phase as was observed in the case of ssaG in our study .	112	Xu and Johnson [ 30 ] reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary phase as was observed in the case of ssaG in our study .	9	3. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	activator	16777370	27	ver/dev	Xu reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary-phase as was observed in the case of ssaG in our study .	112	Xu and Johnson [ 30 ] reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary phase as was observed in the case of ssaG in our study .	9	3. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LacI	gene	pspA	regulator	21134969	10	ver/dev	One explanation for why the impact of LacI was greater for the PssaG strain than the PpagC strain is that LacI interfered with the regulation of pspA expression from PssaG in-vivo .	373	One explanation for why the impact of LacI was greater for the PssaG strain than the PpagC strain is that LacI interfered with the regulation of pspA expression from PssaG in vivo .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	cpxA	activator	33613478	0	ver/dev	All the cpxA mutations significantly increased resistance to β-lactam due to CpxRA system activation via the phosphorylation of CpxR .	13	All the cpxA mutations significantly increased resistance to AGAs and β-lactams due to CpxRA system activation via the phosphorylation of CpxR .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CpxR	gene	cpxA	activator	33613478	0	ver/dev	All the cpxA mutations significantly increased resistance to AGAs due to CpxRA system activation via the phosphorylation of CpxR .	13	All the cpxA mutations significantly increased resistance to AGAs and β-lactams due to CpxRA system activation via the phosphorylation of CpxR .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CpxR	gene	cpxA	activator	33613478	1	ver/dev	Moreover , AckA-Pta-dependent activation of CpxR increased the antibiotic resistance of cpxA deletion mutants .	14	Moreover , AckA-Pta-dependent activation of CpxR increased the antibiotic resistance of cpxA deletion mutants .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	cpxA	activator	33613478	11	ver/dev	to determine whether the CpxA-mediated activation of CpxR also confers β-lactam resistance in S. Typhimurium , constitutively active mutants of cpxA were constructe	412	Here , to determine whether the CpxA-mediated activation of CpxR also confers AGAs and β-lactams resistance in S. Typhimurium , constitutively active mutants of cpxA ( JScpxA38 and JScpxA92 − 104 ) were constructed and the MICs of AGAs and β-lactams were measured .	14	ACKA-PTA-DEPENDENT ACTIVATION OF CPXR INCREASES ANTIBIOTIC RESISTANCE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	cpxA	activator	33613478	11	ver/dev	to determine whether the CpxA-mediated activation of CpxR also confers AGAs resistance in S. Typhimurium , constitutively active mutants of cpxA were constructe	412	Here , to determine whether the CpxA-mediated activation of CpxR also confers AGAs and β-lactams resistance in S. Typhimurium , constitutively active mutants of cpxA ( JScpxA38 and JScpxA92 − 104 ) were constructed and the MICs of AGAs and β-lactams were measured .	14	ACKA-PTA-DEPENDENT ACTIVATION OF CPXR INCREASES ANTIBIOTIC RESISTANCE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	glyA	activator	14643403	0	ver/dev	aa of the 216 aa long CsgD were shown to upregulate expression of the glyA gene	30	The 70 N-terminal amino acids ( aa ) of the 216 aa long CsgD were shown to upregulate expression of the glyA gene which encodes serine hydroxymethyltransferas	6	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	glyA	activator	17024490	15	ver/dev	Chirwa NT , Herrington MB Role of PurR in the activation of glyA by CsgD in Escherichia coli .	246	Chirwa NT , Herrington MB ( 2004 ) Role of MetR and PurR in the activation of glyA by CsgD in Escherichia coli K-12 .	19	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	glyA	activator	17024490	15	ver/dev	Chirwa NT , Herrington MB Role of MetR in the activation of glyA by CsgD in Escherichia coli .	246	Chirwa NT , Herrington MB ( 2004 ) Role of MetR and PurR in the activation of glyA by CsgD in Escherichia coli K-12 .	19	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliT	activator	21143315	4	ver/dev	Note also that activation of FlgM secretion allows s28 to increase transcription of fliT .	350	Note also that activation of FlgM secretion allows s28 to increase transcription of fliT .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliT	activator	21143315	4	ver/dev	Note also that activation of FlgM secretion allows s28 to increase transcription of fliT .	350	Note also that activation of FlgM secretion allows s28 to increase transcription of fliT .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
ArgR	gene	STM1630	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with tRNA hydroxylase S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1630	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with miaE S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1630	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with tRNA hydroxylase S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1630	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with miaE S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1630	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with tRNA hydroxylase S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1630	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with miaE S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
STM3124	gene	STM3122	activator	30648943	5	ver/dev	Taken together with the above-mentioned genetic analysis of sulfatase activity , these results demonstrate that STM3124 suggests that the presence of dopamine leads to transcriptional activation of STM3124 that , in turn , increases the expression of STM3122 .	212	Taken together with the above-mentioned genetic analysis of sulfatase activity , these results demonstrate that STM3124 regulates STM3122 and suggests that the presence of dopamine leads to transcriptional activation of STM3124 that , in turn , increases the expression of STM3122 .	15	PUTATIVE LUXR-TYPE TRANSCRIPTIONAL REGULATOR STM3124 IS REQUIRED FOR DOPAMINE INDUCTION OF SULFATASE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
IgaA	gene	yojN	regulator	15387821	1	ver/dev	To decipher the mechanism by which IgaA exerts negative control of the RcsC-YojN-RcsB system , isogenic strains , yojN genes were constructed .	103	To decipher the mechanism by which IgaA exerts negative control of the RcsC-YojN-RcsB system , isogenic strains carrying epitope tags in the 3 cents end of the chromosomal rcsC , rcsB and yojN genes were constructed .	7	IGAA CONTROLS THE RCSC-YOJN-RCSB SYSTEM AT A POST-TRANSLATIONAL LEVEL	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OxyR	gene	trxC	activator	12492857	5	att	We found induction of the OxyR-dependent trxC gene , encoding thioredoxin-2 .	176	We found induction of the OxyR-dependent trxC gene , encoding thioredoxin-2 .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	trxC	activator	12492857	5	ver/dev	We found induction of the OxyR-dependent trxC gene .	176	We found induction of the OxyR-dependent trxC gene , encoding thioredoxin-2 .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	trxC	activator	12492857	5	ver/dev	induction of the OxyR-dependent trxC gene _ encoding thioredoxin-2	176	We found induction of the OxyR-dependent trxC gene , encoding thioredoxin-2 .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rfaH	regulator	11682190	0	ver/dev	Moreover , the comparison of katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .	141	Moreover , the comparison of rfaH and katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS [ 27 ] .	14	3.2. THE RFAH GENE PRODUCT IS REQUIRED FOR NORMAL EXPRESSION OF LPS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rfaH	regulator	11682190	0	ver/dev	Moreover , the comparison of rfaH expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .	141	Moreover , the comparison of rfaH and katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS [ 27 ] .	14	3.2. THE RFAH GENE PRODUCT IS REQUIRED FOR NORMAL EXPRESSION OF LPS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rfaH	regulator	11682190	0	ver/dev	Moreover , the comparison of rfaH expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .	141	Moreover , the comparison of rfaH and katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS [ 27 ] .	14	3.2. THE RFAH GENE PRODUCT IS REQUIRED FOR NORMAL EXPRESSION OF LPS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	rfaH	regulator	14643636	0	ver/dev	In this study , we demonstrate that RpoS also modulates rfaH promoter activity as revealed by the absence of growth-dependent regulation of an rfaH -- O antigen production in a S. typhi rpoS mutant .	11	In this study , we demonstrate that RpoS also modulates rfaH promoter activity as revealed by the absence of growth-dependent regulation of an rfaH -- lacZ transcriptional fusion and O antigen production in a S. typhi rpoS mutant .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rfaH	regulator	14643636	0	ver/dev	In this study , we demonstrate that RpoS also modulates rfaH promoter activity as revealed by the absence of growth-dependent regulation of an rfaH -- lacZ-transcriptional-fusion antigen production in a S. typhi rpoS mutant .	11	In this study , we demonstrate that RpoS also modulates rfaH promoter activity as revealed by the absence of growth-dependent regulation of an rfaH -- lacZ transcriptional fusion and O antigen production in a S. typhi rpoS mutant .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rfaH	regulator	14643636	2	ver/dev	Thus , we conclude that both RpoS control the rfaH promoter activity and concomitantly , the production of O-specific LPS in S. typhi .	14	Thus , we conclude that both RpoS and RpoN control the rfaH promoter activity and concomitantly , the production of O-specific LPS in S. typhi .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	rfaH	regulator	14643636	3	ver/dev	that the alternative sigma factor RpoS , a global regulator of gene expression 38 S during the transition to stationary-phase , also controls the expression of the rfaH gene	50	In this study , we demonstrate that the alternative sigma factor RpoS ( s or s ) , a global regulator of gene expression 38 S during the transition to stationary phase [ 32 ] , also controls the expression of the rfaH gene , and that both RpoN and RpoS are involved in controlling the production of O antigen LPS in S. typhi .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rfaH	regulator	14643636	3	ver/dev	that the alternative sigma factor RpoS , a global regulator of gene expression 38 S during the transition to stationary-phase , also controls the expression of the rfaH gene	50	In this study , we demonstrate that the alternative sigma factor RpoS ( s or s ) , a global regulator of gene expression 38 S during the transition to stationary phase [ 32 ] , also controls the expression of the rfaH gene , and that both RpoN and RpoS are involved in controlling the production of O antigen LPS in S. typhi .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rfaH	regulator	14643636	4	ver/dev	Role of RpoS in the growth phase-dependent regulation of rfaH antigen production	69	Role of RpoS in the growth phase-dependent regulation of rfaH and O antigen production	4	2. RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rfaH	regulator	14643636	5	ver/dev	To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed strain M103 .	72	To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed strain M103 ( Table 1 ) , an isogenic derivative of S. typhi Ty2 that carries a deletion of the rpoS gene .	4	2. RESULTS AND DISCUSSION	Chlorobaculum macestae;Mycoplasma iners	0	L3	SPEC	Other	OTHER	New	Level 1
RpoS	gene	rfaH	regulator	14643636	5	ver/dev	To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed an isogenic derivative of S. typhi Ty2 .	72	To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed strain M103 ( Table 1 ) , an isogenic derivative of S. typhi Ty2 that carries a deletion of the rpoS gene .	4	2. RESULTS AND DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	New	Level 1
RpoS	gene	rfaH	regulator	15790293	17	ver/dev	RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .	422	RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi .	33	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rfaH	regulator	18706861	1	ver/dev	One reason for this phenomenon could be the fact that RpoS is involved in the growth-dependent regulation of rfaH transcription in S. typhi .	237	One reason for this phenomenon could be the fact that RpoS is involved in the growth-dependent regulation of rfaH transcription and O antigen expression in S. typhi ( Bittner et al. , 2004 ) .	12	IN VITRO EFFECT OF RPOS AND RFAH ON HEMOLYSIN EXPRESSION AND SECRETION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	rfaH	regulator	18706861	2	ver/dev	RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .	439	RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi .	22	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rfaH	regulator	19076233	11	ver/dev	Bittner M , Valvano MA & Contreras I RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .	183	Bittner M , Saldias S , Altamirano F , Valvano MA & Contreras I ( 2004 ) RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi .	20	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rfaH	regulator	21719537	3	ver/dev	RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .	209	RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi .	12	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HU	gene	ihfA	activator	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HU	gene	ihfA	activator	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between HU at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	envZ	activator	12753201	7	att	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	73	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	envZ	activator	15491370	22	ver/dev	In our previous study , we observed that the levels of activation of our transcriptional-fusions to spiC were similar in the absence of envZ , suggesting that EnvZ was signalling through OmpR for activation .	376	In our previous study , we observed that the levels of activation of our transcriptional fusions to ssrA/B or spiC were similar in the absence of ompR or envZ , suggesting that EnvZ was signalling through OmpR for activation ( Feng et al. , 2003 ) .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	envZ	activator	15491370	22	ver/dev	In our previous study , we observed that the levels of activation of our transcriptional-fusions to ssrA/B were similar in the absence of envZ , suggesting that EnvZ was signalling through OmpR for activation .	376	In our previous study , we observed that the levels of activation of our transcriptional fusions to ssrA/B or spiC were similar in the absence of ompR or envZ , suggesting that EnvZ was signalling through OmpR for activation ( Feng et al. , 2003 ) .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	envZ	activator	33952386	18	ver/dev	Interestingly , while the ompR mRNA level was not significantly influenced by the SNP in envZ , the total OmpR protein level was increased by the SNP in envZ -LRB- Fig .	425	Interestingly , while the ompR mRNA level was not significantly influenced by the SNP in envZ , the total OmpR protein level was increased by the SNP in envZ ( Fig .	10	DISCUSSION	nan	1	L2	OTHER	Other	NEG	Other	Level 1
Fis	gene	rpoS	repressor	17784910	29	ver/dev	This anti-correlation in the levels of RpoS proteins recalled an earlier observation that Fis is a repressor of rpoS gene transcription , at least in exponential-phase cultures .	542	This anti-correlation in the levels of the Fis and RpoS proteins recalled an earlier observation that Fis is a repressor of rpoS gene transcription , at least in exponential-phase cultures ( Hirsch and Elliott , 2005 ) .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	rpoS	repressor	17784910	29	ver/dev	This anti-correlation in the levels of the Fis recalled an earlier observation that Fis is a repressor of rpoS gene transcription , at least in exponential-phase cultures .	542	This anti-correlation in the levels of the Fis and RpoS proteins recalled an earlier observation that Fis is a repressor of rpoS gene transcription , at least in exponential-phase cultures ( Hirsch and Elliott , 2005 ) .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	rpoS	repressor	24885225	24	ver/dev	Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .	103	CRP and Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay using purified CRP activated with cAMP and the DNA corresponding to the taiA -- hlyE promoter region .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
Fis	gene	rpoS	repressor	24885225	36	ver/dev	Altogether , these results suggest that Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	125	Altogether , these results suggest that CRP and Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	rpoS	repressor	24885225	40	ver/dev	Fis participate in the repression of rpoS .	149	Figure 2 CRP and Fis participate in the repression of rpoS .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	rpoS	repressor	24885225	52	ver/dev	On the other hand , Fis precludes the RpoS accumulation by repressing the rpoS transcription .	206	On the other hand , Fis precludes the RpoS accumulation by repressing the rpoS transcription ( Figure 2 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	activator	12562806	5	att	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	201	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
SdiA	gene	srgE	activator	12562806	5	ver/dev	SdiA-dependent activation of srgE was observed with 0.5 % agar .	201	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	activator	12562806	5	ver/dev	SdiA-dependent activation of srgE was observed with 0.4 .	201	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	activator	12562806	5	ver/dev	SdiA-dependent activation of srgE was observed with 0.3 .	201	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	activator	12562806	5	ver/dev	SdiA-dependent activation of srgE was observed with data not shown .	201	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
SdiA	gene	srgE	activator	12562806	5	ver/dev	SdiA-dependent activation of srgE was observed with 0.7 % agar .	201	SdiA-dependent activation of srgE was observed with 0.3 , 0.4 , and 0.5 % agar but not with 0.7 % agar ( data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	activator	15130116	1	ver/dev	However , at 30 ∞ C , SdiA activates srgE regardless of the presence of AHLs .	133	However , at 30 ∞ C , SdiA activates srgE regardless of the presence of AHLs .	5	THE SALMONELLA SDIA SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	activator	18791004	1	att	Dose-response experiments with 14028/pCMPG5836 and BA612/pCMPG5836 confirmed that AHLs activate the expression of srgE in an SdiA-dependent fashion and that 3O-C7-HTL activates SdiA at lower concentrations than 3O-C7-HSL , as previously reported ( 29 ) .	86	Dose-response experiments with 14028/pCMPG5836 and BA612/pCMPG5836 confirmed that AHLs activate the expression of srgE in an SdiA-dependent fashion and that 3O-C7-HTL activates SdiA at lower concentrations than 3O-C7-HSL , as previously reported ( 29 ) .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	srgE	activator	18791004	0	ver/dev	In response to AHLs , SdiA activates two Salmonella-specific loci , srgE	48	In response to AHLs , SdiA activates two Salmonella-specific loci , srgE ( sdiA-regulated gene E ) and the rck ( resistance to complement kill-ing ) operon , but the exact function of SdiA in Salmonella remains unclear ( 1 , 62 ) .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	activator	20121449	0	ver/dev	In response to AHL under laboratory conditions , Salmonella SdiA activates the expression of the chromosomally encoded srgE gene .	47	In response to AHL under laboratory conditions , Salmonella SdiA activates the expression of the chromosomally encoded srgE gene and the rck operon , which is borne on the S. enterica sv .	2	J. T. NOEL,1 J. JOY,2 J. N. SMITH,3 M. FATICA,2 K. R. SCHNEIDER,2 B. M. M. AHMER,3 AND M. TEPLITSKI1 1SOIL AND WATER SCIENCE DEPARTMENT AND 2DEPARTMENT OF FOOD SCIENCE AND HUMAN NUTRITION, UNIVERSITY OF FLORIDA-IFAS, GAINESVILLE 32610, U.S.A.; 3DEPARTMENT OF MICROBIOLOGY, OHIO STATE UNIVERSITY, COLUMBUS 43210, U.S.A.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	activator	22149171	11	ver/dev	SdiA activates two operons in Salmonella in srgE on the chromosome .	57	SdiA activates two operons in Salmonella in response to AHL binding , rck on the pSLT virulence-associated plasmid and srgE on the chromosome ( Ahmer et al. 1998 ; Smith and Ahmer 2003 ) .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	activator	22610437	0	ver/dev	SdiA upregulates two loci in S. Typhimu-rium , resistance to complement killing operon , located on the Salmonella virulence plasmid , and srgE -LRB- sdiA-regulated gene -RRB- , a horizontally acquired gene located on the chromosome .	54	SdiA upregulates two loci in S. Typhimu-rium , the rck ( resistance to complement killing ) operon , located on the Salmonella virulence plasmid , and srgE ( sdiA-regulated gene ) , a horizontally acquired gene located on the chromosome ( 1 , 21 , 32 ) .	13	6 22	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	activator	26497459	2	ver/dev	as was the case for sdiA , suggesting that there was sufficient SdiA to activate srgE	297	Interestingly , resolution of srgE-tnpR was not significantly lower at 15 mM NaCl , as was the case for sdiA , suggesting that there was sufficient SdiA to activate srgE or that additional regulators could compensate for the lack of SdiAmediated regulation .	4	RESULTS IDENTIFICATION OF AHL ACTIVITY IN OYSTER TISSUE AND OYSTER-ASSOCI-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgE	activator	31468089	0	ver/dev	SdiA activates srgE expression	361	The gene sidA encodes an AHL receptor , SdiA ( a LuxR homolog ) , that activates srgE expression	26	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoH	activator	23960105	0	ver/dev	This tolerance appeared to be reflected in the upregulation of rpoH of the RpoS regulon .	59	This tolerance appeared to be reflected in the upregulation of stress genes ( rpoS , rpoH , and rpoE of the RpoS regulon ) that confers resistance to stationary cells exposed to a range of environmental stresses including in addition to heat , acids , osmotic shock , and starvation ( Loewen and Hengge-Aronis , 1994 ; Sirsat et al. , 2011a ) .	5	OF SALMONELLA AND SUBLETHAL HEAT EXPOSURE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	slyA	repressor	11882648	13	ver/dev	The region occupied by SlyA covers the 35 promoter elements , thus by binding at these sites SlyA denies RNA polymerase access to the promoter , thereby repressing slyA expression .	276	The region occupied by SlyA covers the 10 and 35 promoter elements , thus by binding at these sites SlyA denies RNA polymerase access to the promoter , thereby repressing slyA expression .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	slyA	repressor	11882648	13	ver/dev	The region occupied by SlyA covers the 10 promoter elements , thus by binding at these sites SlyA denies RNA polymerase access to the promoter , thereby repressing slyA expression .	276	The region occupied by SlyA covers the 10 and 35 promoter elements , thus by binding at these sites SlyA denies RNA polymerase access to the promoter , thereby repressing slyA expression .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	slyA	repressor	11882648	14	ver/dev	The size and location of the relatedness of the DNA sequences within the region indicated that at least five SlyA dimers bind at PslyA to repress slyA expression .	277	The size and location of the region of protection and the relatedness of the DNA sequences within the region indicated that at least five SlyA dimers bind at PslyA to repress slyA expression .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	slyA	repressor	11882648	14	ver/dev	The size and location of the region of protection indicated that at least five SlyA dimers bind at PslyA to repress slyA expression .	277	The size and location of the region of protection and the relatedness of the DNA sequences within the region indicated that at least five SlyA dimers bind at PslyA to repress slyA expression .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	emrR	activator	30992361	11	att	In contrast to PhoP-activated slyA transcription ( 5 , 21 ) , transcription of the emrR gene was not regulated by either PhoP/PhoQ system or SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains ( Fig. 3A , top panel ) .	114	In contrast to PhoP-activated slyA transcription ( 5 , 21 ) , transcription of the emrR gene was not regulated by either PhoP/PhoQ system or SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains ( Fig. 3A , top panel ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SprB	gene	slrP	activator	31484980	1	ver/dev	then , SprB directly activates expression of slrP .	11	then , SprB directly activates expression of several genes including yobH , slrP and ugtL .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SprB	gene	slrP	activator	31484980	4	ver/dev	SprB in turn activates expression of slrP	41	In this regulatory cascade , HilD induces expression of SprB , which in turn activates expression of several target genes including yobH , slrP and ugtL ; slrP and ugtL have been involved in Salmonella virulence .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SprB	gene	slrP	activator	31484980	38	ver/dev	Previous RNA-seq analyses indicate that SprB positively controls slrP .	184	Previous RNA-seq analyses indicate that HilD and SprB positively controls expression of several other genes in common , in addition to yobH , including slrP and ugtL28 , which have been involved in Salmonella virulence55 -- 59 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NadR	TU	nadA-pnuC	repressor	15968063	0	ver/dev	The NadR function represses the nadA-pnuC operon .	37	The NadR ( R ) function represses transcription of the nadB and pncB genes and the nadA-pnuC operon when NAD levels are high ( 7 , 37 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
ArgR	gene	fur	regulator	26944792	0	ver/dev	Putative regulation by ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of fur .	261	Putative regulation by the global regulators RcsB , Fur and ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of rcsDBC , fur and argR .	8	REGULATION OF TCF EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	hilA	activator	10844688	18	att	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
InvF	gene	hilA	activator	10844688	18	att	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
InvF	gene	hilA	activator	17060472	1	ver/dev	hilA transcription in turn activates the transcription of the InvF transcriptional regulator	278	Since HilD activates hilA transcription , which in turn activates the transcription of the InvF transcriptional regulator ( 2 ) , it was surprising that reduced transcription of the central regulator HilA was not detected by microarray analysis .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	hilA	activator	24018968	4	att	The luxS gene , which encodes a synthase that produces a quorum-sensing signal-molecule termed autoinducer ( AI-2 ) , is necessary for the growth-dependent induction of a subset of SPI1 genes , including invF and InvF-dependent genes , but not hilA [ 9 ] .	139	The luxS gene , which encodes a synthase that produces a quorum-sensing signal molecule termed autoinducer ( AI-2 ) , is necessary for the growth-dependent induction of a subset of SPI1 genes , including invF and InvF-dependent genes , but not hilA [ 9 ] .	14	STATIONARY PHASE UNDER SHAKING CULTURE CONDITIONS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FlhDC	gene	clpP	activator	12675803	3	ver/dev	Turnover of FlhDC by ClpXP protease 445 was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpP .	87	Turnover of FlhDC by ClpXP protease 445 was not changed , in contrast to the marked increase of bgalactosidase levels expressed from the fliC-lac fusion , by mutations in either clpX or clpP ( Tomoyasu et al. , 2002 ) .	6	LEVELS OF MASTER REGULATORS, FLHD AND FLHC, IN THE CLPXP PROTEASE-DEPLETED MUTANT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Sigma54	gene	rpoN	activator	12125817	11	att	Mutations in genes downstream of the rpoN gene ( encoding s54 ) of Klebsiella pneumoniae affect expression from s54-dependent promoters .	440	Mutations in genes downstream of the rpoN gene ( encoding s54 ) of Klebsiella pneumoniae affect expression from s54-dependent promoters .	29	REFERENCES	Klebsiella pneumoniae	0	L3	OTHER	Other	OTHER	New	Level 2
Sigma54	gene	rpoN	activator	12581721	11	att	Mutations in genes downstream of the rpoN gene ( encoding s54 ) of Klebsiella pneumoniae affect expression from s54-dependent promoters .	440	Mutations in genes downstream of the rpoN gene ( encoding s54 ) of Klebsiella pneumoniae affect expression from s54-dependent promoters .	29	REFERENCES	Klebsiella pneumoniae	0	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	sifA	regulator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sifA by both relief of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	sifA	regulator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sifA by both direct activation of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	sifA	regulator	21059643	16	ver/dev	Furthermore , DNase I footprinting suggests that SsrB directly competes for binding with H-NS at sifA .	292	Furthermore , DNase I footprinting suggests that SsrB directly competes for binding with H-NS at sifA ( supplemental Fig. 2 ) .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	sifA	regulator	30524381	47	ver/dev	the response regulator SsrB then regulates sifA	391	This type of indirect regulation has been observed in the OmpR regulation of the response regulator SsrB , which then regulates sifA ( Walthers et al. , 2011 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YncC	gene	katN	activator	20713450	8	ver/dev	that YncC are both able to induce expression of katN locus in E. coli K-12	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
YncC	gene	katN	activator	20713450	8	ver/dev	that YncC are both able to induce expression of katN locus in Salmonella	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
HilA	gene	hilD	regulator	21573071	9	ver/dev	the S. enterica hilD gene whose product is the most important regulator of the HilA activator	299	We show that the S. enterica hilD gene , whose product is the most important regulator of the HilA activator and therefore of SPI1 T3SS expression , contains a Fur binding site ( BoxA ) in the upstream region of PhilD ( 2191 to 2163 ) .	17	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagJ	regulator	19348639	0	ver/dev	pagJ are known to be regulated by PhoP ,56	254	The SPI-2 cluster is closely associated with three virulence-related genes ( pagJ , pagK , and phoN ) , which are known to be regulated by two virulenceassociated regulators , SlyA and PhoP ,56 that also regulate a number of SPI-2 genes .	14	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	pstS	regulator	12753201	50	ver/dev	A similar arrangement of binding sites has been observed in the regulation of pstS by PhoP in B. subtilis .	254	A similar arrangement of binding sites has been observed in the regulation of pstS by PhoP in B. subtilis ( Qi and Hulett , 1998 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	hns	repressor	17908208	36	ver/dev	S. Typhi where StpA represses only in an hns background	117	Our results indicate that indeed H-NS and StpA silence ompS1 expression in S. Typhi , where StpA represses only in an hns background .	9	B	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	hns	repressor	17908208	36	ver/dev	S. Typhi where StpA represses only in an hns background	117	Our results indicate that indeed H-NS and StpA silence ompS1 expression in S. Typhi , where StpA represses only in an hns background .	9	B	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	hns	repressor	19406898	2	ver/dev	StpA , was found to repress ompS1 in an hns background ; and a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	hns	repressor	19406898	2	ver/dev	StpA , was found to repress ompS1 in an hns background ; and LeuO , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	hns	repressor	19406898	7	ver/dev	This smaller effect could be due to the lowering of the affinity of the binding of StpA in an hns background , as shown in Fig. 5D .	103	This smaller effect could be due to the lowering of the affinity of the binding of StpA in an hns background , as shown in Fig. 5D .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	repressor	19843227	14	ver/dev	Because StpA potentially represses hns , we downregulated in a DstpA strain .	78	Because StpA potentially represses hns , we expected such genes to be upregulated in an hns mutant and downregulated in a DstpA strain .	7	IDENTIFICATION OF THE STPA REGULON	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
StpA	gene	hns	repressor	19843227	14	ver/dev	Because StpA potentially represses hns , we expected such genes to be upregulated in an hns mutant .	78	Because StpA potentially represses hns , we expected such genes to be upregulated in an hns mutant and downregulated in a DstpA strain .	7	IDENTIFICATION OF THE STPA REGULON	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	repressor	25375226	35	ver/dev	Point mutations M4T enhance StpA repression of select hns .	435	Point mutations A77D and M4T enhance StpA repression of select hns regulated loci .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	hns	repressor	25375226	35	ver/dev	Point mutations A77D enhance StpA repression of select hns .	435	Point mutations A77D and M4T enhance StpA repression of select hns regulated loci .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	hns	repressor	7635833	1	ver/dev	One possibility worth investigating is that the partial repression of the proU operon in media of low osmolality in hns mutants is mediated by the StpA protein .	158	One possibility worth investigating is that the partial repression of the proU operon in media of low osmolality in hns mutants is mediated by the StpA protein , which has 60 % amino acid sequence similarity to H-NS ( 27 ) .	4	RESULTS AND DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	katG	regulator	24239962	1	ver/dev	As shown in Fig. 5 , OxyR was able to bind to a DNA fragment corresponding to the coding region of the katG gene .	249	As shown in Fig. 5 , OxyR was able to bind to both promoter regions , and not to a DNA fragment corresponding to the coding region of the katG gene ( negative control ) .	16	3.3. RYHB-1 AND RYHB-2 ARE UPREGULATED BY OXYR IN RESPONSE TO H2O2	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
OxyR	gene	katG	regulator	24239962	1	ver/dev	As shown in Fig. 5 , OxyR was able to bind to both promoter regions corresponding to the coding region of the katG gene .	249	As shown in Fig. 5 , OxyR was able to bind to both promoter regions , and not to a DNA fragment corresponding to the coding region of the katG gene ( negative control ) .	16	3.3. RYHB-1 AND RYHB-2 ARE UPREGULATED BY OXYR IN RESPONSE TO H2O2	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
OxyR	gene	katG	regulator	29213059	0	ver/dev	The katG and ahpCF are regulated by OxyR , peroxide response regulator13 ,14 .	289	The katG and ahpCF are regulated by OxyR , peroxide response regulator13 ,14 .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	katG	regulator	30414454	2	ver/dev	The fact that katG is regulated by the OxyR regulon in E. coli indicates that there may be a similar situation in S. typhimurium -LSB- 28e30 -RSB- .	142	The fact that katG is regulated by the OxyR regulon in E. coli indicates that there may be a similar situation in S. typhimurium [ 28e30 ] .	16	HYDROGEN PEROXIDE SENSITIVITY.	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HU	gene	spvR	regulator	15790293	3	ver/dev	Genetic evidence has implicated HU in the control of SPI-1 virulence gene expression while IHF has been shown to bind to the promoter region of the spvR regulatory virulence gene on the 96-kb plasmid of S. Typhimurium where it has a positive effect in stationary-phase .	214	Genetic evidence has implicated HU in the control of SPI-1 virulence gene expression ( Schechter et al. , 2003 ) while IHF has been shown to bind to the promoter region of the spvR regulatory virulence gene on the 96-kb plasmid of S. Typhimurium where it has a positive effect in stationary phase ( Marshall et al. , 1999 ) .	13	NUCLEOID-ASSOCIATED PROTEINS	unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	sipA	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	leuO	repressor	24354910	7	ver/dev	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the absence of LeuO .	53	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO ( Dillon et al. , 2012 ) , we compared the expression of selected SPI-1 genes in the presence and in the absence of LeuO .	9	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	leuO	repressor	24354910	7	ver/dev	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the presence .	53	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO ( Dillon et al. , 2012 ) , we compared the expression of selected SPI-1 genes in the presence and in the absence of LeuO .	9	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	leuO	repressor	24354910	14	ver/dev	Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of OFF subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -	79	Single cell analysis of gene expression by flow cytometry ( Fig. 2 ) confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : ( i ) activation of leuO expression decreased the activity of a sipB : : GFP fusion , abolishing bistable SPI-1 expression ; ( ii ) lack of LeuO restored the wild type pattern of sipB : : GFP expression , indicating that SPI-1 downregulation was caused by LeuO indeed ; ( iii ) a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 ( OFF ) subpopulation , in agreement with the role of HilE as a SPI-1 repressor ( Baxter et al. , 2003 ) ; ( iv ) activation of leuO expression in a HilE − background yielded a small subpopulation of sipB - : : GFP ( OFF ) cells ; and ( v ) absence of both LeuO and HilE restored the wild type pattern of sipB : : GFP expression .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	leuO	repressor	24354910	14	ver/dev	Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -	79	Single cell analysis of gene expression by flow cytometry ( Fig. 2 ) confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : ( i ) activation of leuO expression decreased the activity of a sipB : : GFP fusion , abolishing bistable SPI-1 expression ; ( ii ) lack of LeuO restored the wild type pattern of sipB : : GFP expression , indicating that SPI-1 downregulation was caused by LeuO indeed ; ( iii ) a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 ( OFF ) subpopulation , in agreement with the role of HilE as a SPI-1 repressor ( Baxter et al. , 2003 ) ; ( iv ) activation of leuO expression in a HilE − background yielded a small subpopulation of sipB - : : GFP ( OFF ) cells ; and ( v ) absence of both LeuO and HilE restored the wild type pattern of sipB : : GFP expression .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	leuO	repressor	24354910	39	ver/dev	In the absence of HilE , activation of leuO transcription reduced Fig. 7B , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	147	In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three - to fourfold ( Fig. 7B ) , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	11	ACTIVATION OF LEUO TRANSCRIPTION INHIBITS EPITHELIAL CELL INVASION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
LeuO	gene	leuO	repressor	24354910	39	ver/dev	In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three - to fourfold , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	147	In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three - to fourfold ( Fig. 7B ) , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	11	ACTIVATION OF LEUO TRANSCRIPTION INHIBITS EPITHELIAL CELL INVASION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
SdiA	gene	luxS	regulator	12115054	3	ver/dev	that either SdiA regulates luxS	235	This could mean that either SdiA regulates flhC or luxS , or that there are multiple , quorum-sensing-independent systems capable of monitoring the changing environment of a growing population .	17	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
RpoS	gene	sdiA	regulator	22149171	53	ver/dev	RpoS may control the expression of a stationary-phase activator of sdiA .	359	RpoS may control the expression of a stationary-phase activator of sdiA .	19	RPOS-DEPENDENT SDIA EXPRESSION IN STATIONARY PHASE	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
SirA	TU	flhDC	regulator	11244064	15	ver/dev	The simplest hypothesis is that SirA represses the master regulator of the flagellar regulon flhDC gene fusions .	304	The simplest hypothesis is that SirA represses the master regulator of the flagellar regulon flhDC , which leads to decreased expression of all the flagellar gene fusions examined in this study .	7	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
DksA	gene	lacZ	activator	26039089	5	att	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	lacZ	activator	27065993	2	att	To independently test • NO - and DksA-dependent activation of sulfur assimilation and cysteine biosynthesis in Salmonella experiencing nitrosative-stress , the cysD promoter ( PcysD ) was cloned upstream of the promoterless lacZ gene in the plasmid pQF50 .	177	To independently test • NO - and DksA-dependent activation of sulfur assimilation and cysteine biosynthesis in Salmonella experiencing nitrosative stress , the cysD promoter ( PcysD ) was cloned upstream of the promoterless lacZ gene in the plasmid pQF50 .	12	RESULTS	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	mcpC	regulator	33441540	13	ver/dev	H-NS specifically bind to the regulatory region of mcpC	78	Thus , HilD and H-NS specifically bind to the regulatory region of mcpC and HilD is an antagonist of H-NS binding .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilD	activator	16045614	1	ver/dev	that HilC are each capable of independently inducing expression of the hilD genes	14	We demonstrate that HilC , HilD and RtsA are each capable of independently inducing expression of the hilC , hilD and rtsA genes , and that each can independently activate hilA .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	activator	16045614	20	ver/dev	We demonstrate that HilC are each capable of inducing expression of hilD .	82	We demonstrate that HilC , HilD and RtsA are each capable of inducing expression of hilC , hilD and rtsA .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilD	activator	16045614	21	ver/dev	HilC can independently induce expression of hilD	85	HilC , HilD and RtsA can independently induce expression of hilC , hilD and rtsA	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilD	activator	16045614	24	ver/dev	We wanted to determine if HilC could induce expression of hilD in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
HilC	gene	hilD	activator	16045614	28	ver/dev	HilC also induced expression of hilD .	131	RtsA , HilC and HilD also induced expression of hilC , hilD and rtsA ( Fig. 2 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilD	activator	16045614	29	ver/dev	HilC induced expression of hilD ~ 10 - to 12-fold .	133	RtsA , HilC and HilD induced expression of hilC approximately threeto fourfold and hilD ~ 10 - to 12-fold .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilD	activator	16045614	30	ver/dev	These data show that HilC are each capable of independently inducing expression of hilD , consistent with our model that HilC constitute a feed forward regulatory loop .	134	These data show that HilC , HilD and RtsA are each capable of independently inducing expression of hilC , hilD and rtsA , consistent with our model that HilC , HilD and RtsA constitute a feed forward regulatory loop ( Fig. 1 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	activator	16045614	69	ver/dev	We show that HilC can each independently activate expression of the hilD genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilD	activator	17208038	31	ver/dev	HilC are clearly able to induce hilD transcription .	159	HilC , HilD and RtsA , when overproduced are clearly able to induce hilD transcription .	11	REGULATION OF HILD	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilC	gene	hilD	activator	17993530	6	ver/dev	HilC are all also capable of activating expression of hilD independent of each other and comprise a complex feed forward regulatory loop .	39	HilC , HilD , and RtsA are all also capable of activating expression of hilC , hilD , and rtsA independent of each other and comprise a complex feed forward regulatory loop that controls hilA expression ( Fig. 1 ) ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	activator	17993530	21	ver/dev	HilC is known to independently activate hilD transcription	208	We then examined the effects of deleting fur , overproducing Fur , and overproducing HilC , which is known to independently activate hilD transcription ( 16 ) .	4	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilC	gene	hilD	activator	17993530	24	ver/dev	Figure 5A shows that hilD transcription was induced by both HilC in the hilD background .	214	Figure 5A shows that hilD transcription was induced by both Fur and HilC in the hilD background .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	activator	22479568	0	ver/dev	HilC can activate expression of hilD of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilD	activator	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilD	activator	32041797	5	ver/dev	HilC activate transcription of hilD , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilA	repressor	17074910	20	ver/dev	Given that both the csrB/C genes are required , we hypothesize that hilA gene expression requires the csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilA	repressor	17074910	20	ver/dev	Given that both sirA are required , we hypothesize that hilA gene expression requires the csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilA	repressor	34048498	24	ver/dev	Thus , our results suggest that in the absence of SirA the expression of hilA is repressed by two mechanisms : 1 -RRB- CsrA inhibits 2 -RRB- the diminished amount of	177	Thus , our results suggest that in the absence of SirA the expression of hilA is repressed by two mechanisms : 1 ) CsrA inhibits translation of the hilD mRNA and 2 ) the diminished amount of	9	HILE REPRESSES HILD-MEDIATED EXPRESSION OF SPI-1, SPI-2 AND SPI-5 GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilA	repressor	34048498	24	ver/dev	Thus , our results suggest that in the absence of SirA the expression of hilA is repressed by two mechanisms : 1 -RRB- CsrA inhibits translation of the hilD mRNA	177	Thus , our results suggest that in the absence of SirA the expression of hilA is repressed by two mechanisms : 1 ) CsrA inhibits translation of the hilD mRNA and 2 ) the diminished amount of	9	HILE REPRESSES HILD-MEDIATED EXPRESSION OF SPI-1, SPI-2 AND SPI-5 GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
KdgR	gene	lacZ	regulator	26682862	2	ver/dev	In soft-rot bacteria , binding of KdgR to KDG releases the protein from its operator sites ; however , in our experiments the addition of KDG to lacZ reporter fusions in kdgR-regulated genes did not relieve data not shown .	285	In soft-rot bacteria , binding of KdgR to KDG releases the protein from its operator sites ( 20 ) ; however , in our experiments the addition of KDG to lacZ reporter fusions in kdgR-regulated genes did not relieve the repression ( data not shown ) .	5	4	unidentified	1	L3	OTHER	Analysis	NEG	New	Level 1
KdgR	gene	lacZ	regulator	26682862	2	ver/dev	In soft-rot bacteria , binding of KdgR to KDG releases the protein from its operator sites ; however , in our experiments the addition of KDG to lacZ reporter fusions in kdgR-regulated genes did not relieve the repression .	285	In soft-rot bacteria , binding of KdgR to KDG releases the protein from its operator sites ( 20 ) ; however , in our experiments the addition of KDG to lacZ reporter fusions in kdgR-regulated genes did not relieve the repression ( data not shown ) .	5	4	nan	1	L3	OTHER	Other	NEG	New	Level 1
SsrB	gene	sciS	repressor	23690578	41	att	We considered the possibility of the SsrB-repressed sciS being such a gene because its inactivation was reported to increase Salmonella virulence in BALB/c mice infected orally ( 4 ) .	162	We considered the possibility of the SsrB-repressed sciS being such a gene because its inactivation was reported to increase Salmonella virulence in BALB/c mice infected orally ( 4 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella;Mus sp.	0.5	L1	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	orgB	repressor	18248433	1	ver/dev	those _ required for repression of orgB , other PhoP-activated genes	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	orgB	repressor	18248433	1	ver/dev	those _ required for repression of orgB , other PhoP-activated genes	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	sirA	regulator	33133465	2	ver/dev	sirA genes is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence-factors ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes	147	Typhimurium including pefI/srgC operon , srgE and sirA genes is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence factors which in turn will decrease the flagella formation ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes derived from genes located on the pathogenic islands 1 and 4.18,28-31	8	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SlyA	gene	STM2585	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FadD	gene	hilA	activator	27936347	1	ver/dev	The authors suggested that fatty acid and/or their derivatives , activated by FadD , may act as intracellular signals to regulate hilA expression , it has also been demonstrated that LCUFAs , present in the bacterial growth medium , exert a repressive action on the PhoP/PhoQ system activity .	281	The authors suggested that fatty acid and/or their derivatives , activated by FadD , may act as intracellular signals to regulate hilA expression and to increase expression of the SPI-1 Salmonella invasion genes .66,67 In addition , it was found that in E. coli and Sinorhizobium meliloti , FadD activates exogenous long-chain fatty acids ( LCFA ) , but also plays a major role in the activation of endogenous fatty acids released from membrane .68 Recently , it has also been demonstrated that long chain unsaturated free fatty acids ( LCUFAs ) , present in the bacterial growth medium , exert a repressive action on the PhoP/PhoQ system activity that is independent of the fatty acid b-oxidative pathway .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FadD	gene	hilA	activator	27936347	1	ver/dev	The authors suggested that fatty acid and/or their derivatives , activated by FadD , may act as intracellular signals to regulate hilA expression , it has also been demonstrated that long chain unsaturated free fatty-acids , present in the bacterial growth medium , exert a repressive action on the PhoP/PhoQ system activity .	281	The authors suggested that fatty acid and/or their derivatives , activated by FadD , may act as intracellular signals to regulate hilA expression and to increase expression of the SPI-1 Salmonella invasion genes .66,67 In addition , it was found that in E. coli and Sinorhizobium meliloti , FadD activates exogenous long-chain fatty acids ( LCFA ) , but also plays a major role in the activation of endogenous fatty acids released from membrane .68 Recently , it has also been demonstrated that long chain unsaturated free fatty acids ( LCUFAs ) , present in the bacterial growth medium , exert a repressive action on the PhoP/PhoQ system activity that is independent of the fatty acid b-oxidative pathway .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	invF	regulator	28704543	44	ver/dev	SsrB inversely regulates the expression of the invF -LRB- SPI-1 -RRB- and SPI-2 genes inside macrophages .	262	SsrB inversely regulates the expression of the invF ( SPI-1 ) and ssaG ( SPI-2 ) genes inside macrophages .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	invF	regulator	28704543	44	ver/dev	SsrB inversely regulates the expression of the invF -LRB- SPI-1 -RRB- and ssaG genes inside macrophages .	262	SsrB inversely regulates the expression of the invF ( SPI-1 ) and ssaG ( SPI-2 ) genes inside macrophages .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	activator	11918812	0	att	As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	116	As a first application of the two-colour flow cytometric technique , the in vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	6	IN VITRO CHARACTERIZATION OF TRANSCRIPTIONAL FUSIONS TO VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	14507376	3	att	In order to obtain direct evidence for this novel mode of PhoP regulation , we performed real time PCR analysis of pagC , a previously identified PhoP-activated gene .	145	In order to obtain direct evidence for this novel mode of PhoP regulation , we performed real time PCR analysis of pagC , a previously identified PhoP-activated gene .	8	PHOQ-DEPENDENT REGULATION OF PHOP-ACTIVATED GENES BY CATIONIC ANTIMICROBIAL PEPTIDES	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	pagC	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	pagC	activator	18270203	17	ver/dev	the pagC promoter region _ performed with increasing amounts of PhoP protein	176	B , DNase I footprinting analysis of the pagC promoter region performed with probes for the coding and noncoding strands and increasing amounts of PhoP protein ( 0 , 0.1 , 0.2 , 0.4 , and 0.8 M ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	activator	18270203	21	ver/dev	H-NS Remains Associated with the pagC Promoters under Inducing Conditions -- The PhoP proteins could activate transcription of the pagC genes by either displacing H-NS by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
PhoP	gene	pagC	activator	18270203	21	ver/dev	H-NS Remains Associated with the pagC Promoters under Inducing Conditions -- The PhoP proteins could activate transcription of the pagC genes by either displacing H-NS from their respective promoters not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
PhoP	gene	pagC	activator	18270203	70	ver/dev	Therefore , the role of PhoP in pagC transcription is 2-fold : as a direct transcriptional activator of the pagC promoter .	295	Therefore , the role of PhoP in pagC transcription is 2-fold : as a direct transcriptional activator of the pagC promoter and as a regulator of SlyA at transcriptional ( 23 , 24 ) and/or post-transcriptional ( 8 ) levels .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagC	activator	18620040	0	att	The mgtC and pagC genes are both PhoP-activated genes required for intramacrophage growth [ 2,5 -- 7 ] .	28	The mgtC and pagC genes are both PhoP-activated genes required for intramacrophage growth [ 2,5 -- 7 ] .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	19091955	0	att	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL and pagC , in Salmonella ( 2 , 3 , 9 -- 11 ) .	18	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL and pagC , in Salmonella ( 2 , 3 , 9 -- 11 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	activator	19091955	13	att	The pagD and pagC genes are PhoP-activated genes ( 9 ) located next to each other in the Salmonella chromosome but transcribed in opposite directions from a shared intergenic region .	86	The pagD and pagC genes are PhoP-activated genes ( 9 ) located next to each other in the Salmonella chromosome but transcribed in opposite directions from a shared intergenic region .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	19091955	29	att	SlyA functions independently when it forms a feedforward loop with the PhoP/PhoQ system , because the up-1 sequence that harbors only the PhoP box results in PhoP-dependent but SlyA-independent transcription of pagC ( Fig. 1 A ) .	186	SlyA functions independently when it forms a feedforward loop with the PhoP/PhoQ system , because the up-1 sequence that harbors only the PhoP box results in PhoP-dependent but SlyA-independent transcription of pagC ( Fig. 1 A ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	19091955	4	att	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	38	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus	0	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pagC	activator	19843227	44	att	( iii ) StpA transcriptionally represses PhoP-dependent genes ( e.g. pagC as shown ) both at MEP and LEP , and modulates resistance to cationic antimicrobial peptides ( CAMPs ) .	304	( iii ) StpA transcriptionally represses PhoP-dependent genes ( e.g. pagC as shown ) both at MEP and LEP , and modulates resistance to cationic antimicrobial peptides ( CAMPs ) .	15	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagC	activator	21396407	0	att	The PhoP-activated gene C ( pagC ) promoter of Salmonella is an inducible promoter , which is inhibited by Mg2 + in-vitro and activated after Salmonella phagocytosis by macrophages and dendritic cells in-vivo [ 52,53 ] .	264	The PhoP-activated gene C ( pagC ) promoter of Salmonella is an inducible promoter , which is inhibited by Mg2 + in vitro and activated after Salmonella phagocytosis by macrophages and dendritic cells in vivo [ 52,53 ] .	20	4. DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	23774596	0	att	The PhoP-activated gene pagC regulated by the PhoP / PhoQ system was identified as an IVI virulence protein in S. Typhi , and the PagC antibody was detected in sera from 11 of 14 patients , which shows that it has the potential to be developed as a diagnostic antigen ( 12 ) .	303	The PhoP-activated gene pagC regulated by the PhoP / PhoQ system was identified as an IVI virulence protein in S. Typhi , and the PagC antibody was detected in sera from 11 of 14 patients , which shows that it has the potential to be developed as a diagnostic antigen ( 12 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	pagC	activator	27886215	4	ver/dev	PhoP dephosphorylation subsequently inhibits the PhoPQ to activate the pagC in S. Choleraesuis	207	High concentration of Mg2 + might cause more PhoP dephosphorylation , which subsequently inhibits the PhoPQ to suppress the hilA and hilD , or to activate the pagC in S. Choleraesuis .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	activator	30373755	9	att	Specifically , using a - galactosidase reporter strain in which the promoter of the PhoP-activated pagC gene ( PpagC ) is transcriptionally fused to lac ( PpagC-lac ) on the chromosome , we determined that the PpagC activity was 4-fold higher in the mutant than in the wild type and that this upregulation appeared to require PhoP ( Fig. 6C ) .	190	Specifically , using a - galactosidase reporter strain in which the promoter of the PhoP-activated pagC gene ( PpagC ) is transcriptionally fused to lac ( PpagC-lac ) on the chromosome , we determined that the PpagC activity was 4-fold higher in the ΔSTM14_1829 mutant than in the wild type and that this upregulation appeared to require PhoP ( Fig. 6C ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagC	activator	30682134	18	att	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	225	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	31370702	0	att	SPI-11 includes the PhoP-activated genes pagD and pagC , which are involved in intramacrophage survival [ 40 ] ; pagD and pagC were downregulated 2.5 - and 2.6-fold in the lon mutant , respectively ( Supplementary Table 2 ) .	219	SPI-11 includes the PhoP-activated genes pagD and pagC , which are involved in intramacrophage survival [ 40 ] ; pagD and pagC were downregulated 2.5 - and 2.6-fold in the lon mutant , respectively ( Supplementary Table 2 ) .	15	LON REGULATES THE EXPRESSION OF SEVERAL SPIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	31611347	3	att	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ-transcriptional-fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	94	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ transcriptional fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	31611347	4	att	The inhibition action was calculated on the basis of the - galactosidase activity from lacZ-transcriptional-fusions to two different PhoP-activated genes ( virK and pagC ) and one PhoP-unrelated control reporter gene ( tppB ) .	129	The inhibition action was calculated on the basis of the - galactosidase activity from lacZ transcriptional fusions to two different PhoP-activated genes ( virK and pagC ) and one PhoP-unrelated control reporter gene ( tppB ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	33045730	18	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	pagC	activator	33045730	28	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	pagC	activator	33045730	39	att	Moreover , the site is necessary for PhoP activation in mildly acidic pH because the mRNA abundances of the PhoP-activated pagC and phoP genes were lower in an engineered strain deleted for the SsrB binding site ( Figure 3B ) than in the isogenic wild-type strain ( Figure 3E ) .	236	Moreover , the site is necessary for PhoP activation in mildly acidic pH because the mRNA abundances of the PhoP-activated pagC and phoP genes were lower in an engineered strain deleted for the SsrB binding site ( Figure 3B ) than in the isogenic wild-type strain ( Figure 3E ) .	26	SSRB ACTIVATES PHOP BY PROMOTING TRANSCRIPTION OF THE UGTL GENE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	activator	33045730	75	att	The mRNA abundance of the PhoP-activated ugtL , pagC and ssrB genes was similar among wild-type , ugtL-sifBmu mutant and ssrB null strains at 1 h post bacterial internalization by macrophages ( Figure 5B ) .	328	The mRNA abundance of the PhoP-activated ugtL , pagC and ssrB genes was similar among wild-type , ugtL-sifBmu mutant and ssrB null strains at 1 h post bacterial internalization by macrophages ( Figure 5B ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hlyE	activator	14996792	10	ver/dev	Previous studies have shown that H-NS contribute to hlyE expression when E. coli is grown on a solid medium .	72	Previous studies have shown that FNR , CRP , and H-NS contribute to hlyE expression when E. coli is grown on a solid medium ( 10 , 36 ) .	7	RESULTS	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hlyE	activator	14996792	14	ver/dev	Thus , we concluded that H-NS all contribute towards the regulation of hlyE expression .	83	Thus , we concluded that CRP , FNR , and H-NS all contribute towards the regulation of hlyE expression .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hlyE	activator	19835951	19	ver/dev	Thus , it is expected that H-NS mutants increase hlyE transcription via RpoS .	229	Thus , it is expected that H-NS mutants increase hlyE transcription via RpoS .	17	4. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hlyE	activator	30778340	0	ver/dev	S. Typhi 1hns where the hlyE transcript was highly abundant compared with the WT , showing that H-NS contributes to the repression of hlyE expression	173	The only exception was observed with S. Typhi 1hns , where the hlyE transcript was highly abundant compared with the WT , showing that H-NS contributes to the repression of hlyE expression ( Figure 1D ) .	16	GENERATION OF S. TYPHI HEMOLYTIC MUTANTS BY RANDOM INSERTIONAL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CysB	gene	cysD	activator	25637663	4	att	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	39	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	6	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sodCII	activator	22356617	4	att	Further , a mutation in the fliZ gene in E. coli has recently been shown to cause premature expression of RpoS-dependent genes ( Pesavento et al. , 2008 ) and in Salmonella overproduction of FliZ decreases expression of the RpoS-dependent genes , katE and sodCII ( Chubiz et al. , 2010 ) .	342	Further , a mutation in the fliZ gene in E. coli has recently been shown to cause premature expression of RpoS-dependent genes ( Pesavento et al. , 2008 ) and in Salmonella overproduction of FliZ decreases expression of the RpoS-dependent genes , katE and sodCII ( Chubiz et al. , 2010 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
TdcA	gene	tdcA	activator	21464594	8	ver/dev	If this region of TdcA is involved in an interaction with TdcR , this converged difference of Salmonella TdcA may explain the incomplete activation of tdcA under anaerobic conditions , even in the presence of TdcR in S. Typhimurium .	97	If this region of TdcA is involved in an interaction with TdcR , this converged difference of Salmonella TdcA may explain the incomplete activation of tdcA under anaerobic conditions , even in the presence of TdcR in S. Typhimurium ( Fig. 2 ) .	2	RECEIVED: OCTOBER 11, 2010 / REVISED: DECEMBER 24, 2010 / ACCEPTED: DECEMBER 25, 2010	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	tdcE	regulator	24272778	16	att	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	222	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	activator	17768242	13	att	We have demonstrated here that expression of the Salmonella P-type ATPase CopA is induced by copper ions in a CueR-dependent manner ( Figs 1 and 2 ) and that deletion of the copA gene affects copper tolerance under both aerobic and anaerobic conditions ( Table 3 ) .	286	We have demonstrated here that expression of the Salmonella P-type ATPase CopA is induced by copper ions in a CueR-dependent manner ( Figs 1 and 2 ) and that deletion of the copA gene affects copper tolerance under both aerobic and anaerobic conditions ( Table 3 ) .	9	THE SALMONELLA YEDW/YEDV SYSTEM IS NOT INVOLVED IN COPPER HOMEOSTASIS	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	activator	17768242	9	att	Expression of copA is induced by copper ions , in a CueR-dependent manner .	199	Expression of copA is induced by copper ions , in a CueR-dependent manner .	8	EXPRESSION OF COPA IN SALMONELLA IS DIRECTLY CONTROLLED BY CUER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	copA	activator	17768242	1	ver/dev	CueR directly stimulates the transcription of copA .	29	CueR directly stimulates the transcription of copA and cueO , coding for a P-type ATPase and a multicopper oxidase , respectively .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	copA	activator	17768242	6	ver/dev	This copper-dependent activation of copA was eliminated in a cueR null mutant , but not affected in a DgolS strain , confirming that CueR controls the expression of the Cu transporter CopA in Salmonella .	188	This copper-dependent activation of copA was eliminated in a cueR null mutant , but not affected in a DgolS strain , confirming that CueR controls the expression of the Cu ( I ) transporter CopA in Salmonella .	8	EXPRESSION OF COPA IN SALMONELLA IS DIRECTLY CONTROLLED BY CUER	Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
CueR	gene	copA	activator	17768242	9	ver/dev	Expression of copA is induced by copper ions , in a CueR-dependent manner .	199	Expression of copA is induced by copper ions , in a CueR-dependent manner .	8	EXPRESSION OF COPA IN SALMONELLA IS DIRECTLY CONTROLLED BY CUER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	copA	activator	20534583	1	ver/dev	CueR _ activating copA expression in response to gold	142	Notably in E. coli deletion of copA also had no affect on goldtolerance ( 42 ) or cytosolic gold levels ( 43 ) in LB medium , despite CueR activating copA expression in response to gold ( 42 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	copA	activator	20534583	1	ver/dev	CueR _ activating copA expression in response to gold	142	Notably in E. coli deletion of copA also had no affect on goldtolerance ( 42 ) or cytosolic gold levels ( 43 ) in LB medium , despite CueR activating copA expression in response to gold ( 42 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	copA	activator	23645605	0	att	cueR was introduced into L the chromosome of the S. Typhimurium 14028 strain replacing wild-type cueR , and the expression of the CueR-dependent copA : : lacZ reporter in cells grown in Luria-Bertani ( LB ) medium was determined in the presence or absence of either 40 M AuHCl4 or 1 mM CuSO4 ( Fig. 1B ) .	87	cueR was introduced into L the chromosome of the S. Typhimurium 14028 strain replacing wild-type cueR , and the expression of the CueR-dependent copA : : lacZ reporter in cells grown in Luria-Bertani ( LB ) medium was determined in the presence or absence of either 40 M AuHCl4 or 1 mM CuSO4 ( Fig. 1B ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	activator	23645605	3	att	The sensor proteins ' response was followed by measuring the expression of the CueR-dependent copA : : lacZ reporter in LB-medium in the absence or presence of either Au or Cu .	134	The sensor proteins ' response was followed by measuring the expression of the CueR-dependent copA : : lacZ reporter in LB medium in the absence or presence of either Au or Cu .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CueR	gene	copA	activator	34125582	3	ver/dev	CueR also activates the transcription of copA during copper-stress in S. enterica .	86	CueR also activates the transcription of cueO , copA , and cueP genes during copper stress in S. enterica ( 40 ) .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	copA	activator	34125582	4	ver/dev	Cu - bound CueR is the transcriptional activator for copA genes .	106	Cu ( I ) - bound CueR is the transcriptional activator for copA and cueO genes .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	def	repressor	19525399	0	ver/dev	Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in def mutant with a concomitant 50-fold reduction in deletion rate .	17	Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a lexA ( def ) mutant with a concomitant 50-fold reduction in deletion rate .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	rpoS	activator	23443158	12	ver/dev	In addition , DsrA may fall into Group I sRNAs , as it directly stimulates translation of rpoS mRNA , whereas it interferes with the expression of H-NS , which -- by repressing the expression of the flhDC repressor HdfR -- acts as an indirect activator of FlhDC expression .	160	In addition , DsrA may fall into Group I sRNAs , as it directly stimulates translation of rpoS mRNA , whereas it interferes with the expression of H-NS , which -- by repressing the expression of the flhDC repressor HdfR -- acts as an indirect activator of FlhDC expression .	6	3. SRNAS CONTRIBUTE TO INVERSE REGULATION OF FLAGELLA AND BIOFILM COMPONENTS IN DIFFERENT REGULATORY PATTERNS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
SpvR	gene	spvR	regulator	10874730	8	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .	626	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .	49	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11123690	29	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	355	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11207562	2	ver/dev	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , that of the spvABCD operon .	44	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11207562	2	ver/dev	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression of the spvABCD operon .	44	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11260470	9	ver/dev	Norel , F. Relationships between SpvR S phase in the control of spvR , the regulatory gene of operon .	482	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , s , SpvR and growth S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11260470	9	ver/dev	Norel , F. Relationships between SpvR S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	482	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , s , SpvR and growth S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	31	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11553591	9	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	808	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	32	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11553591	9	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	808	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	32	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	11705925	0	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	363	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	18	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	12011028	5	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	212	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	12	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	12902215	3	ver/dev	Relationships between SpvR phase in the control of spvR , the	504	Relationships between H-NS , S , SpvR and growth phase in the control of spvR , the	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	15256548	29	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	986	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	56	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	15790293	20	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	614	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	54	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	16430223	0	ver/dev	Grob , P. , and Guiney , D. G. In Vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR , J. Bacteriol .	274	Grob , P. , and Guiney , D. G. ( 1996 ) In Vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR , J. Bacteriol .	11	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	16707690	40	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	720	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	29	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	16707690	40	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	720	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	29	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	17293430	29	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	601	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	17293430	29	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	601	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	24	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	19447191	1	ver/dev	Gel mobility-shift assays revealed that the SpvR fusion proteins were able to bind 147-bp DNA fragments of spvR promoter regions , respectively .	80	Gel mobility shift assays revealed that the SpvR fusion proteins were able to bind to 125 - and 147-bp DNA fragments of the spvA and spvR promoter regions , respectively ( Grob and Guiney , 1996 ) .	5	4.1. SPVR	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SpvR	gene	spvR	regulator	19447191	21	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	206	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	13	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	24426086	0	ver/dev	SpvR binds to both the spvR .	33	SpvR binds to both the spvR and spvA promoters and is required for expression of the spvABCD genes [ 17 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	24426086	1	ver/dev	Grob P , Guiney DG In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter region of spvR .	162	Grob P , Guiney DG ( 1996 ) In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter region of spvA and spvR .	10	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	25080967	44	ver/dev	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	542	Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , and Norel , F. ( 1997 ) Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	38	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	12	ver/dev	As a result , in cells stochastically expressing a higher number of SpvR molecules , SpvR would be more prone to bind the spvR -LRB- establishing the positive feedback loop -RRB- , thereby activating spv expression .	235	As a result , in cells stochastically expressing a higher number of SpvR molecules , SpvR would be more prone to bind the spvR ( establishing the positive feedback loop ) and spvA promoter , thereby activating spv expression .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SpvR	gene	spvR	regulator	30143595	14	ver/dev	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and 1996 In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	406	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and D. G. Guiney , 1996 In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	26	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	14	ver/dev	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and D. G. Guiney In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .	406	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and D. G. Guiney , 1996 In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	26	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Norel , 1997 Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Norel , 1997 Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , L. Kowarz , 1997 Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , L. Kowarz , 1997 Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , 1997 Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	30143595	16	ver/dev	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , 1997 Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	535	https://doi.org/10.1016/j.ijmm.2004.11.004 Robbe-Saule , V. , F. Schaeffer , L. Kowarz , and F. Norel , 1997 Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	36	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	31661351	26	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .	669	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	53	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvR	regulator	31661351	26	ver/dev	Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .	669	Relationships between H-NS , sigma S , SpvR and growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence operon .	53	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	proP	activator	16332813	1	att	Fis activates the RpoS-dependent station-ary-phase expression of proP in Escherichia coli .	618	Fis activates the RpoS-dependent station-ary-phase expression of proP in Escherichia coli .	33	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	sspH	regulator	10844662	2	att	In the third multigene horizontal acquisition discovered ( Fig. 2 ) , an SsrB-regulated fusion ( srfH ) was found within a homologue of S. typhimurium type III secreted effectors sspH 1 ( P 10236 ) and sspH 2 ( P 10287 ) .	113	In the third multigene horizontal acquisition discovered ( Fig. 2 ) , an SsrB-regulated fusion ( srfH ) was found within a homologue of S. typhimurium type III secreted effectors sspH 1 ( P 10236 ) and sspH 2 ( P 10287 ) .	10	MOLECULAR CHARACTERIZATION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	fliZ	activator	32571967	10	att	Without proper assembly , flagellar regulatory systems are repressed by the anti-sigma factor FlgM , which remains intracellular and bound to the sigma factor FliA , leading to further repression of SPI1 via decreased expression of fliZ from the FliA-dependent promoter ( 35 , 76 , 77 ) .	216	Without proper assembly , flagellar regulatory systems are repressed by the anti-sigma factor FlgM , which remains intracellular and bound to the sigma factor FliA , leading to further repression of SPI1 via decreased expression of fliZ from the FliA-dependent promoter ( 35 , 76 , 77 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	fliZ	activator	32571967	7	att	The dsbA mutation also affects fliZ transcription independently of Rcs , presumably due to the inability to export FlgM , leading to decreased expression from the FliA-dependent promoter ( 35 ) .	137	The dsbA mutation also affects fliZ transcription independently of Rcs , presumably due to the inability to export FlgM , leading to decreased expression from the FliA-dependent promoter ( 35 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	New	Level 1
CRP	gene	acnA	activator	23637460	9	ver/dev	The activation of acnA expression by CRP indicate that these are conserved regulatory features in both bacteria .	241	The activation of acnA expression by CRP and SoxR and repression by FNR are in accord with observations reported for the E. coli acnA promoter ( Cunningham et al. , 1997 ; Fig. 3b ) and indicate that these are conserved regulatory features in both bacteria .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	acnA	activator	23637460	9	ver/dev	The activation of acnA expression by CRP are in accord with observations .	241	The activation of acnA expression by CRP and SoxR and repression by FNR are in accord with observations reported for the E. coli acnA promoter ( Cunningham et al. , 1997 ; Fig. 3b ) and indicate that these are conserved regulatory features in both bacteria .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	TU	acrAB	activator	15073288	10	ver/dev	Analysis of trans-criptional data demonstrated that there is no observed role for PhoP -- PhoQ in bile activation of acrAB ( data not shown ) .	277	Analysis of trans-criptional data demonstrated that there is no observed role for PhoP -- PhoQ or RpoS in bile activation of acrAB ( data not shown ) .	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoB	gene	phoB	activator	29693629	0	att	Furthermore , proteomic analysis of a mutant lacking phoB ( that encodes a key regulator of Pi shortage response ) suggested that only a small subset of the altered proteins upon Pi limitation was PhoB-dependent .	10	Furthermore , proteomic analysis of a mutant lacking phoB ( that encodes a key regulator of Pi shortage response ) suggested that only a small subset of the altered proteins upon Pi limitation was PhoB-dependent .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoB	gene	phoB	activator	29693629	1	ver/dev	Importantly , the full induction of NagB required the regulator PhoB as evidenced by the lower level of NagB in a phoB knockout mutant .	128	Importantly , the full induction of NagB required the regulator PhoB as evidenced by the lower level of NagB in a phoB knockout mutant .	13	3.1. PROTEOMIC ANALYSIS OF S. TYPHIMURIUM IN RESPONSE TO PI STARVATION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
ArcA	gene	cydA	activator	28575106	11	att	In addition , ArcA ( the regulator gene of the ArcAB system ) binding to the loiA promoter under low oxygen conditions was tested by EMSAs , with the ArcA-dependent cydA promoter used as a positive control [ 44,45 ] .	269	In addition , ArcA ( the regulator gene of the ArcAB system ) binding to the loiA promoter under low oxygen conditions was tested by EMSAs , with the ArcA-dependent cydA promoter used as a positive control [ 44,45 ] .	12	ACTIVATION OF LOIA EXPRESSION IN RESPONSE TO LOW O2 CONDITIONS IS MEDIATED BY THE ARCB/ARCA TWO-COMPONENT REGULATORY SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	ftsZ	activator	11425476	7	ver/dev	They also con cents rm previous reports that the RcsA protein is not involved in stimulation of ftsZ expression by RcsB .	149	They also con cents rm previous reports that the RcsA protein is not involved in stimulation of ftsZ expression by RcsB [ 4 ] .	9	3.3. E¡ECT OF MUCOID MUTATIONS ON THE EXPRESSION OF FTSZ GENE	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	ftsZ	activator	12757942	0	ver/dev	Moreover , RcsB activates transcription of the cell division genes ftsZ and ftsA by acting speci cents cally on one of the ftsA1p governing expression of the ftsQAZ cluster .	27	Moreover , RcsB activates transcription of the cell division genes ftsZ and ftsA by acting speci cents cally on one of the promoters ( ftsA1p ) governing expression of the ftsQAZ cluster [ 4 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ftsZ	activator	12757942	0	ver/dev	Moreover , RcsB activates transcription of the cell division genes ftsZ and ftsA by acting speci cents cally on one of the promoters governing expression of the ftsQAZ cluster .	27	Moreover , RcsB activates transcription of the cell division genes ftsZ and ftsA by acting speci cents cally on one of the promoters ( ftsA1p ) governing expression of the ftsQAZ cluster [ 4 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ftsZ	activator	33751923	21	ver/dev	When phosphorylated , RcsB binds RcsA to activate expression of ftsZ .	645	When phosphorylated , RcsB binds RcsA to activate expression of several genes , such as osmB , osmC , bdm , ftsZ , rprA , wza , and rcsA .	25	RCSBCD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
McbR	gene	katN	activator	20713450	8	ver/dev	that McbR are both able to induce expression of katN locus in E. coli K-12	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
McbR	gene	katN	activator	20713450	8	ver/dev	that McbR are both able to induce expression of katN locus in Salmonella	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
CsrA	TU	otsBA	repressor	30682134	26	ver/dev	In addition , CsrA repressed the translation of otsBA 3.0 - and 2.2-fold in S2 Table .	252	In addition , CsrA repressed the translation of otsBA 3.0 - and 2.2-fold in mLPM and LB , respectively ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	otsBA	repressor	30682134	26	ver/dev	In addition , CsrA repressed the translation of otsBA 3.0 - and 2.2-fold in LB , respectively .	252	In addition , CsrA repressed the translation of otsBA 3.0 - and 2.2-fold in mLPM and LB , respectively ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	otsBA	repressor	30682134	26	ver/dev	In addition , CsrA repressed the translation of otsBA 3.0 - and 2.2-fold in mLPM , respectively .	252	In addition , CsrA repressed the translation of otsBA 3.0 - and 2.2-fold in mLPM and LB , respectively ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	cas2	activator	21398529	1	att	To elucidate whether CRISPR is part of the casABCDE12 LeuO-dependent operon , the fusion plasmid pKK9-RR-casA-CRISPR ( 6.7 kb ) , containing the casA promoter region , the casA to cas2 genes , and the CRISPR sequences , was constructed and independently introduced into IMSS-1 / pFMTrc12 and IMSS-1 / pFMTrcleuO-50 .	141	To elucidate whether CRISPR is part of the casABCDE12 LeuO-dependent operon , the fusion plasmid pKK9-RR-casA-CRISPR ( 6.7 kb ) , containing the casA promoter region , the casA to cas2 genes , and the CRISPR sequences , was constructed and independently introduced into IMSS-1 / pFMTrc12 and IMSS-1 / pFMTrcleuO-50 .	4	RESULTS	unidentified plasmid	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	cas2	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas2 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
HilC	gene	tnpA	activator	28335027	11	att	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	768	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	tnpA	activator	28335027	12	att	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	770	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LuxS	gene	luxS	regulator	15790567	0	ver/dev	To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of pCMPG5643 , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	157	To explore the hypothesis that controlled synthesis of AI-2 at a given time point , and therefore tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter ( 34 ) ( pCMPG5643 ) , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	12	SYNTHETIC DPD COMPLEMENTS LSRA EXPRESSION IN S. TYPHIMURIUM LUXS MUTANT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LuxS	gene	luxS	regulator	15790567	0	ver/dev	To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of pCMPG5643 , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	157	To explore the hypothesis that controlled synthesis of AI-2 at a given time point , and therefore tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter ( 34 ) ( pCMPG5643 ) , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	12	SYNTHETIC DPD COMPLEMENTS LSRA EXPRESSION IN S. TYPHIMURIUM LUXS MUTANT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LuxS	gene	luxS	regulator	15790567	0	ver/dev	To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	157	To explore the hypothesis that controlled synthesis of AI-2 at a given time point , and therefore tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter ( 34 ) ( pCMPG5643 ) , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	12	SYNTHETIC DPD COMPLEMENTS LSRA EXPRESSION IN S. TYPHIMURIUM LUXS MUTANT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LuxS	gene	luxS	regulator	15790567	0	ver/dev	To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	157	To explore the hypothesis that controlled synthesis of AI-2 at a given time point , and therefore tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter ( 34 ) ( pCMPG5643 ) , resulted in restoration of Salmonella bio-film formation in the luxS mutant .	12	SYNTHETIC DPD COMPLEMENTS LSRA EXPRESSION IN S. TYPHIMURIUM LUXS MUTANT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
KdgR	gene	fruF	regulator	26682862	1	ver/dev	kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	fruF	regulator	26682862	1	ver/dev	kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	fruF	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	fruF	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
DksA	gene	dksA	regulator	20851888	1	ver/dev	To test whether these metabolic pathways are under the control of DksA , the lacZY fusions were transduced into the dksA mutant strain AV09294 .	77	To test whether these metabolic pathways are under the control of DksA , the lacZY fusions were transduced into the dksA mutant strain AV09294 .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
DksA	gene	dksA	regulator	22311927	0	ver/dev	Given the inhibitory effects of the DksA-dependent regulation of the transcription of amino-acid synthesis and transport , we tested whether the addition of amino-acids had any effect on the marked susceptibility of dksA mutant Salmonella strains to chemically generated NO .	127	Given the inhibitory effects of NO on amino acid biosynthetic pathways and the DksA-dependent regulation of the transcription of amino acid synthesis and transport , we tested whether the addition of amino acids had any effect on the marked susceptibility of dksA mutant Salmonella strains to chemically generated NO .	4	RESULTS	Salmonella	1	L3	SPEC	Other	OTHER	Other	Level 1
DksA	gene	dksA	regulator	26553464	5	ver/dev	To better understand how DksA affects biofilm These results indicated that DksA is a positive regulator of host cell invasion , we suggested that invasion phenotypes of the dksA mutant were at least the mid-logarithmic growth phase .	178	To better understand how DksA affects biofilm These results indicated that DksA is a positive regulator of formation , motility , and host cell invasion , we determined by genes belong to the SPI-1 and the motility-chemotaxis regu-means of RT-PCR the expression of representative SPI-1 , lons and suggested that the impaired motility , biofilm forma-SPI-2 , flagellar ( motility ) , and biofilm-associated genes during tion , and invasion phenotypes of the dksA mutant were at least the mid-logarithmic growth phase .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	dksA	regulator	26553464	5	ver/dev	To better understand how DksA affects biofilm These results indicated that DksA is a positive regulator of motility , we suggested that invasion phenotypes of the dksA mutant were at least the mid-logarithmic growth phase .	178	To better understand how DksA affects biofilm These results indicated that DksA is a positive regulator of formation , motility , and host cell invasion , we determined by genes belong to the SPI-1 and the motility-chemotaxis regu-means of RT-PCR the expression of representative SPI-1 , lons and suggested that the impaired motility , biofilm forma-SPI-2 , flagellar ( motility ) , and biofilm-associated genes during tion , and invasion phenotypes of the dksA mutant were at least the mid-logarithmic growth phase .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	dksA	regulator	26553464	5	ver/dev	To better understand how DksA affects biofilm These results indicated that DksA is a positive regulator of formation , we suggested that invasion phenotypes of the dksA mutant were at least the mid-logarithmic growth phase .	178	To better understand how DksA affects biofilm These results indicated that DksA is a positive regulator of formation , motility , and host cell invasion , we determined by genes belong to the SPI-1 and the motility-chemotaxis regu-means of RT-PCR the expression of representative SPI-1 , lons and suggested that the impaired motility , biofilm forma-SPI-2 , flagellar ( motility ) , and biofilm-associated genes during tion , and invasion phenotypes of the dksA mutant were at least the mid-logarithmic growth phase .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrA	repressor	12753201	41	ver/dev	conditions under which either ssrA was repressed by OmpR	236	However , in the present study , we did not find conditions under which either ssrA or ssrB was repressed by OmpR ( see below ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	hns	regulator	31333620	3	ver/dev	Our previous study also showed that H-NS is essential for establishing the Mg2 + - responsive transcriptional regulation of the PhoP regulon in Salmonella because deletion of the hns gene abolished the transcriptional repression of PhoP/PhoQ-activated genes in the millimolar levels of Mg2 + .	58	Our previous study also showed that H-NS is essential for establishing the Mg2 + - responsive transcriptional regulation of the PhoP regulon in Salmonella because deletion of the hns gene abolished the transcriptional repression of PhoP/PhoQ-activated genes in the millimolar levels of Mg2 + ( Kong et al. , 2008 ) .	3	INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MetR	gene	hmp	activator	17024490	4	ver/dev	Under aerobic conditions , and presumably anoxic conditions also , MetR activates hmp gene expression in response to NO per se .	42	Under aerobic conditions , and presumably anoxic conditions also , MetR ( a methionine biosynthesis transcriptional regulator ) activates hmp gene expression in response to nitrosothiols but not to NO per se ( Membrillo-Her-nández et al. 1998 ) .	4	INTRODUCTION	nan	1	L3	SPEC	Other	OTHER	New	Level 1
MetR	gene	hmp	activator	17024490	4	ver/dev	Under aerobic conditions , and presumably anoxic conditions also , MetR activates hmp gene expression in response to nitrosothiols per se .	42	Under aerobic conditions , and presumably anoxic conditions also , MetR ( a methionine biosynthesis transcriptional regulator ) activates hmp gene expression in response to nitrosothiols but not to NO per se ( Membrillo-Her-nández et al. 1998 ) .	4	INTRODUCTION	nan	1	L3	SPEC	Other	OTHER	New	Level 1
MetR	gene	hmp	activator	20829289	0	ver/dev	In Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
MetR	gene	hmp	activator	20829289	0	ver/dev	In E. coli , five transcription factors have been implicated : hmp transcription is activated by MetR .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
MetR	gene	hmp	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser ' : nitrosation of modulation of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser ' : nitrosation of homocysteine of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser ' : nitrosation of modulation of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser ' : nitrosation of homocysteine of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser ' : nitrosation of modulation of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	activator	26443513	3	ver/dev	A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser ' : nitrosation of homocysteine of MetR binding to the glyA-hmp intergenic region .	763	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	STM4118	regulator	15681155	13	att	To determine whether the PmrA-regulated genes identified herein affect lipid-A structure ( particularly for STM4118 , which demonstrated somewhat decreased PM resistance ) , purified lipid-A from each mutant ( PmrA background ) was compared to that of the C parental strain for the presence of Ara4N .	241	To determine whether the PmrA-regulated genes identified herein affect lipid A structure ( particularly for STM4118 , which demonstrated somewhat decreased PM resistance ) , purified lipid A from each mutant ( PmrA background ) was compared to that of the C parental strain for the presence of Ara4N .	12	3.3. ANALYSIS OF RESISTANCE AND LPS PHENOTYPES	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	STM4118	regulator	15681155	16	ver/dev	Using site directed mutagenesis , Marchal et al. demonstrated that the fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM4118 promoters .	261	Using site directed mutagenesis , Marchal et al. [ 35 ] demonstrated that the third and fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 , STM1253 and STM4118 promoters .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM4118	regulator	15681155	16	ver/dev	Using site directed mutagenesis , Marchal et al. demonstrated that the third positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM4118 promoters .	261	Using site directed mutagenesis , Marchal et al. [ 35 ] demonstrated that the third and fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 , STM1253 and STM4118 promoters .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM4118	regulator	15866924	0	att	Here we demonstrate that the PmrA-regulated STM4118 ( cptA ) gene is necessary for the addition of pEtN to the LPS core .	7	Here we demonstrate that the PmrA-regulated STM4118 ( cptA ) gene is necessary for the addition of pEtN to the LPS core .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RstA	gene	rstA	regulator	18792679	4	ver/dev	the genes are directly controlled by the response regulator RstA to affect gene expression only when the organism experiences the simultaneous presence of the signals activate low Mg2 + to generate PhoP-P protein for binding to the rstA promoter	140	For example , the RstA/RstB two-component system is upregulated by the PhoP protein at a transcriptional level ( Fig. 3 ) .29,44.57 Because response regulators bind to DNA in vivo only when phosphorylated , one would expect the genes that are directly controlled by the response regulator RstA to affect gene expression only when the organism experiences the simultaneous presence of the signals that activate the sensors PhoQand RstB : low Mg2 + to generate PhoP-P protein for binding to the rstA promoter and the still unknown signal activating the RstB to generate RstA-P .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	rstA	regulator	18792679	4	ver/dev	the genes are directly controlled by the response regulator RstA to affect gene expression only when the organism experiences the simultaneous presence of the signals activate the sensors PhoQand RstB + to generate PhoP-P protein for binding to the rstA promoter	140	For example , the RstA/RstB two-component system is upregulated by the PhoP protein at a transcriptional level ( Fig. 3 ) .29,44.57 Because response regulators bind to DNA in vivo only when phosphorylated , one would expect the genes that are directly controlled by the response regulator RstA to affect gene expression only when the organism experiences the simultaneous presence of the signals that activate the sensors PhoQand RstB : low Mg2 + to generate PhoP-P protein for binding to the rstA promoter and the still unknown signal activating the RstB to generate RstA-P .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	STM2303	activator	26039089	7	att	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	164	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrHFIJKLM	regulator	12438352	26	att	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	334	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrHFIJKLM	regulator	12438352	3	att	Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .	46	Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrHFIJKLM	regulator	12438352	26	ver/dev	PmrA has been shown to bind pmrHFIJKLM .	334	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrHFIJKLM	regulator	12730171	0	ver/dev	PmrA regulates the transcription of the pmrHFIJKLM operon .	27	PmrA regulates the transcription of the pmrHFIJKLM operon , which in turn adds 4-aminoarabinose ( L-Ara4N ) residues to the lipid A portion of LPS ( 14 , 32 , 33 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrHFIJKLM	regulator	15866924	9	ver/dev	PmrA controls the expression of pmrHFIJKLM .	220	PmrA controls the expression of pmrE and pmrHFIJKLM , which encode enzymes involved in producing Ara4N substitutions on lipid A ( 16 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrHFIJKLM	regulator	19332669	0	ver/dev	After being phosphorylated by PmrB , PmrA can effectively bind to the transcriptional sites of pmrHFIJKLM .	37	After being phosphorylated by PmrB , PmrA can effectively bind to the transcriptional sites of other genes ( pmrE , pmrHFIJKLM , and pmrC ) and activate their transcription .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrHFIJKLM	regulator	23166721	0	att	The PmrA-regulated pmrHFIJKLM operon mediates 4-amino-4-deoxy-L-arabinose ( Ara4N ) production and attachment to the lipid-A of LPS .	12	The PmrA-regulated pmrHFIJKLM operon mediates 4-amino-4-deoxy-L-arabinose ( Ara4N ) production and attachment to the lipid A of LPS .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrHFIJKLM	regulator	23166721	1	att	Activation of the S. Typhimurium PmrA-regulated pmrE gene and the pmrHFIJKLM operon leads to aminoarabinose ( Ara4N ) production and its attachment to lipid-A [ 11,12 ] .	42	Activation of the S. Typhimurium PmrA-regulated pmrE gene and the pmrHFIJKLM operon leads to aminoarabinose ( Ara4N ) production and its attachment to lipid A [ 11,12 ] .	4	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	osmY	repressor	19843227	21	ver/dev	the osmY genes were repressed by StpA at LEP	124	This is exemplified by the osmY and otsAB genes , which were repressed by StpA at the MEP stage of growth , but not at LEP .	9	STPA REPRESSES S38-ACTIVATED GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	osmY	repressor	19843227	21	ver/dev	the osmY genes were repressed by StpA at the MEP stage of growth	124	This is exemplified by the osmY and otsAB genes , which were repressed by StpA at the MEP stage of growth , but not at LEP .	9	STPA REPRESSES S38-ACTIVATED GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	katE	repressor	30682134	34	ver/dev	Additional qRT-PCR experiments found that CsrA repressed accumulation of katE mRNA in both mLPM .	275	Additional qRT-PCR experiments found that CsrA repressed accumulation of katE mRNA in both mLPM and LB ( Fig 6A ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	katE	repressor	30682134	34	ver/dev	Additional qRT-PCR experiments found that CsrA repressed accumulation of katE mRNA in both Fig 6A .	275	Additional qRT-PCR experiments found that CsrA repressed accumulation of katE mRNA in both mLPM and LB ( Fig 6A ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	katE	repressor	30682134	34	ver/dev	Additional qRT-PCR experiments found that CsrA repressed accumulation of katE mRNA in both LB .	275	Additional qRT-PCR experiments found that CsrA repressed accumulation of katE mRNA in both mLPM and LB ( Fig 6A ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hfq	regulator	29417203	13	ver/dev	The regulation of OmpR on hfq may be in a indirect manner .	131	The regulation of OmpR on hfq may be in a direct or indirect manner .	14	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	hfq	regulator	29417203	13	ver/dev	The regulation of OmpR on hfq may be in a direct manner .	131	The regulation of OmpR on hfq may be in a direct or indirect manner .	14	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssaM	activator	17630976	38	att	Our results indicated that transcription of ssaL and ssaM are indeed coupled in an SsrB-dependent manner ( Fig. 7B ) .	299	Our results indicated that transcription of ssaL and ssaM are indeed coupled in an SsrB-dependent manner ( Fig. 7B ) .	10	IDENTIFICATION OF SSRB-REGULATED GENES ON SPI-2	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssaM	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaM .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaM	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaM .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaM	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaM .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaM	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaM .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaM	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaM .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaM	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaM .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Sigma28	gene	flk	activator	9765570	0	att	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	invF	activator	11123690	17	ver/dev	Using a genetic approach , Fis was shown to be necessary for the induction of invF expression , genes .	151	Using a genetic approach , Fis was shown to be necessary for the induction of hilA and invF expression , genes that encode two positive regulators of several SPI-1 genes .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	invF	activator	11123690	25	ver/dev	Fis activates a chromosomal invF : : Tn5lacZY reporter in the absence of HilA .	202	Fis activates a chromosomal invF : : Tn5lacZY reporter in the absence of HilA .	11	BACTERIAL STRAINS AND PLASMIDS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
H	gene	proV	regulator	15966862	8	att	This resembles the situation observed for the H-NS-regulated proU operon where H-NS binds to the DRE ( downstream-regul-atory element ) within the proV structural gene [ 50 ] .	257	This resembles the situation observed for the H-NS-regulated proU operon where H-NS binds to the DRE ( downstream-regul-atory element ) within the proV structural gene [ 50 ] .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	phoP	regulator	30524381	45	ver/dev	A more likely explanation is that OmpR directly regulates phoP , in agreement with , where OmpR was shown to bind to the phoP promoter .	389	A more likely explanation is that OmpR directly regulates phoP , in agreement with ( Quinn et al. , 2014 ) , where OmpR was shown to bind to the phoP promoter .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sopA	activator	23419780	7	ver/dev	InvF are transcription activators of effectors downregulates sopA .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	fliC	repressor	12791144	7	ver/dev	flgE Hook protein ( first module ) flgG Cell-distal portion of basal body rod flgK Hook -- filament junction protein 1 ( second module ) flgL Hook -- filament junction protein flgM Anti-FliA ( antisigma ) factor ; also known as RflB protein flgN Believed to be export chaperone for FlgK and FlgL fliA Sigma F ( sigma-28 ) factor of RNA polymerase , transcription of late genes fliC Flagellin , filament structural protein ( second module ) fliD Filament-capping protein ; enables filament assembly fliT Possible export chaperone for FliD fliZ Putative regulator of FliA fljA Repressor of fliC fljB Phase 2 flagellin ( filament structural protein ) motA Proton conductor component of motor motB Enables flagellar motor rotation Aerotaxis/chemotaxis aer Aerotaxis sensor receptor , senses cellular redox state or proton motive force cheA Sensory kinase , transduces signal between chemosignal receptors and CheB and cheB Methyl esterase cheW Purine-binding chemotaxis protein ; regulation cheY Chemotaxis regulator , transmits chemoreceptor signals to flagellar motor cheZ Chemotactic response ; CheY protein phosphatase tsr Methyl-accepting chemotaxis protein I , serine sensor receptor	129	flgE Hook protein ( first module ) flgG Cell-distal portion of basal body rod flgK Hook -- filament junction protein 1 ( second module ) flgL Hook -- filament junction protein flgM Anti-FliA ( antisigma ) factor ; also known as RflB protein flgN Believed to be export chaperone for FlgK and FlgL fliA Sigma F ( sigma 28 ) factor of RNA polymerase , transcription of late genes fliC Flagellin , filament structural protein ( second module ) fliD Filament-capping protein ; enables filament assembly fliT Possible export chaperone for FliD fliZ Putative regulator of FliA fljA Repressor of fliC fljB Phase 2 flagellin ( filament structural protein ) motA Proton conductor component of motor motB Enables flagellar motor rotation Aerotaxis/chemotaxis aer Aerotaxis sensor receptor , senses cellular redox state or proton motive force cheA Sensory kinase , transduces signal between chemosignal receptors and CheB and cheB Methyl esterase cheW Purine-binding chemotaxis protein ; regulation cheY Chemotaxis regulator , transmits chemoreceptor signals to flagellar motor cheZ Chemotactic response ; CheY protein phosphatase tsr Methyl-accepting chemotaxis protein I , serine sensor receptor	6	REGULATION OF INVASION GENES BY CSRA	Calophysus macropterus	0	L1	SPEC	Fact	OTHER	Other	Level 1
FliA	gene	fliC	repressor	23977202	0	ver/dev	The loss of virulence in FlgM defective Salmonella requires fliC , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	165	The loss of virulence in FlgM defective Salmonella requires fliA and fliC [ 35 ] , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	24	IN VITRO CHARACTERIZATION OF FLGM-DEFICIENT SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	fliC	repressor	8631681	1	ver/dev	wild-type strains of S. typhimurium were indistinguishable , as were inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype	6	In this investigation , we observed that ( i ) the in vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
CRP	gene	aniC	activator	10692151	4	ver/dev	J.W. Cyclic-AMP-receptor-protein are required for anaerobic induction of aniC in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	aniC	activator	10692151	4	ver/dev	J.W. Cyclic-AMP-receptor-protein are required for acid-pH induction of aniC in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	aniC	activator	17906148	9	ver/dev	Cyclic-AMP-receptor-protein are required for anaerobic induction of aniC in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	aniC	activator	17906148	9	ver/dev	Cyclic-AMP-receptor-protein are required for acid-pH induction of aniC in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM2123	activator	16629664	35	ver/dev	On the other hand , STM2123 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a post-transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM2123	activator	16629664	35	ver/dev	On the other hand , STM2123 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a post-transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM2123	activator	16629664	35	ver/dev	On the other hand , STM2123 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM2123	activator	16629664	35	ver/dev	On the other hand , STM2123 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM2123	activator	26655751	3	ver/dev	For example , although both STM2123 and STM3388 are important for CsgD expression , STM2123 contributes early in in-vitro biofilm formation , while STM3388 is involved later .	47	For example , although both STM2123 and STM3388 are important for CsgD expression , STM2123 contributes early in in vitro biofilm formation , while STM3388 is involved later ( 13 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	scsD	activator	29866803	9	att	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper-stress .	211	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper stress .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	gltA	regulator	30524381	30	ver/dev	OmpR regulation of gltA also appeared in a ChIP-seq analysis of S. Typhi .	312	OmpR regulation of gltA also appeared in a ChIP-seq analysis of S. Typhi ( Perkins et al. , 2013 ) .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
OmpR	gene	gltA	regulator	30524381	33	ver/dev	FIGURE 7 OmpR binds to the gltA promoter .	332	FIGURE 7 | OmpR binds to the gltA promoter .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HU	gene	ihfB	activator	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfB .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HU	gene	ihfB	activator	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between HU at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfB .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Fis	gene	cadA	repressor	15256548	10	ver/dev	While it may be tempting to speculate that repression of cadA transcription by Fis may represent a step in the expression of virulence in S. typhimurium , it is not known if lysine decarboxylase activity plays any role in S. typhimurium virulence .	648	While it may be tempting to speculate that repression of cadA transcription by Fis may represent a step in the expression of virulence in S. typhimurium , it is not known if lysine decarboxylase activity plays any role in S. typhimurium virulence .	14	GENES INVOLVED IN METABOLISM AND TRANSPORT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Fact	NEG	Other	Level 1
YdgT	gene	pefA	regulator	31661351	17	ver/dev	While the precise mechanism of pef fimbriae regulation by YdgT remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefA since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs .	344	While the precise mechanism of pef fimbriae regulation by Hha and YdgT remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefB and pefA since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs [ 24 ] .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	slrP	activator	25182488	22	att	( B ) Alignment of the promoter region of slrP and six PhoP-activated genes with a similar architecture .	310	( B ) Alignment of the promoter region of slrP and six PhoP-activated genes with a similar architecture .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slrP	activator	25182488	11	ver/dev	To study if PhoP was a direct activator of slrP transcription , first we analyzed the promoter region of this gene .	246	To study if PhoP was a direct activator of slrP transcription , first we analyzed the promoter region of this gene .	3	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	slrP	activator	29555922	18	ver/dev	Additionally , PhoP positively regulate the expression of the slrP gene .	270	Additionally , HilD and PhoP positively and independently regulate the expression of the slrP gene , in SPI-1-inducing growth conditions , PhoP directly and HilD by an unknown mechanism37 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slrP	activator	29555922	19	ver/dev	In SPI-2-inducing growth-conditions , PhoP also positively controls the slrP gene independently of HilD37 ,56 .	281	In SPI-2-inducing growth conditions , PhoP also positively controls transcription of the orgBC operon and the slrP gene independently of HilD37 ,56 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	dsrA	repressor	22804842	29	ver/dev	LeuO has also been shown to repress the small RNA dsrA in E. coli	416	Transcriptional activation by LeuO is well documented but LeuO has also been shown to repress the acid stress regulator cadC , the small RNA dsrA and the fimAICDFGH operon in E. coli ( Shi and Bennett , 1995 ; Repoila and Gottesman , 2001 ; Shimada et al. , 2011 ) .	8	GENOME-WIDE PREDICTION AND VALIDATION OF LEUO BINDING SITES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	hilD	regulator	17208038	13	ver/dev	These results showed that , whereas OmpR-mediated regulation of hilA expression was dampened in a DhilC DrtsA background , regulation was blocked only in strains missing HilD , suggesting that OmpR controls SPI1 expression by regulating hilD expression .	101	These results showed that , whereas OmpR-mediated regulation of hilA expression was dampened in a DhilC DrtsA background , regulation was blocked only in strains missing HilD , suggesting that OmpR controls SPI1 expression by regulating hilD expression [ 19 ] .	7	ENVZ/OMPR	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	hilD	regulator	23370732	2	ver/dev	Increased OmpR can be recruited to bind to hilD promoters , in a process .	154	Increased OmpR can be recruited to bind to hilC and hilD promoters ( PhilC and PhilD ) , in a process that stimulates hilC transcription but restrains hilD [ 9 ] .	8	REGULATORS OF THE EXPRESSION OF SPI-1 PROTEINS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
OmpR	gene	hilD	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilD , the main regulators of pathogenicity islands 2 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilD	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilD , the main regulators of pathogenicity islands 2 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilD	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilD , the main regulators of pathogenicity islands 1 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilD	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilD , the main regulators of pathogenicity islands 1 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	crl	regulator	17293430	22	ver/dev	We reasoned that because Crl participates in the negative regulation by S , a crl mutant should display a competitive advantage over the wild-type strain .	314	We reasoned that because Crl participates in the negative regulation by S , a crl mutant should display a competitive advantage over the wild-type strain .	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Crl	gene	crl	regulator	17293430	25	ver/dev	The finding that the crl mutant had an advantage over the wild-type strain for fitness in stationary-phase indicated that Crl contributes to negative regulation by S .	371	The finding that the crl mutant had an advantage over the wild-type strain for growth on succinate and fitness in stationary phase ( Fig. 6 to 8 ) indicated that Crl contributes to negative regulation by S .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Crl	gene	crl	regulator	17293430	25	ver/dev	The finding that the crl mutant had an advantage over the wild-type strain for growth-on-succinate in stationary-phase indicated that Crl contributes to negative regulation by S .	371	The finding that the crl mutant had an advantage over the wild-type strain for growth on succinate and fitness in stationary phase ( Fig. 6 to 8 ) indicated that Crl contributes to negative regulation by S .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
AraC	gene	araC	regulator	1848842	1	ver/dev	Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli .	547	Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli .	23	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	araC	regulator	24272778	53	ver/dev	Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli .	688	Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli .	41	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	lacZ	repressor	30252837	3	ver/dev	A fliC : : lacZ fusion was repressed by StdEF in the presence of FlhDC only , suggesting that StdEF-mediated repression of flhDC transcription may be transmitted to downstream genes in the flagellar regulon .	206	A fliC : : lacZ fusion was repressed by StdEF in the presence of FlhDC only ( Fig 4 , panel D ) , suggesting that StdEF-mediated repression of flhDC transcription may be transmitted to downstream genes in the flagellar regulon .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	symE	regulator	30201777	18	att	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	194	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Escherichia coli	0.5	L3	OTHER	Other	NEG	Other	Level 1
FlhD	gene	fliA	activator	16430704	0	ver/dev	In turn , fliA is positively controlled by the gene products FlhD .	79	In turn , fliA is positively controlled by the gene products FlhD and FlhC , which are encoded by the sole operon lying at the apex of the hierarchy .	5	THE SALMONELLA DNAK MUTANT IS DEFECTIVE IN FLAGELLUM BIOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhD	gene	fliA	activator	16430704	1	ver/dev	The FlhD proteins act together in an FlhD2C2 hetero-tetramer to activate the σ70 promoter of fliA gene .	86	The FlhD and FlhC proteins act together in an FlhD2C2 hetero-tetramer to activate the σ70 promoter of fliA gene ( Ikebe et al. , 1999 ) .	5	THE SALMONELLA DNAK MUTANT IS DEFECTIVE IN FLAGELLUM BIOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FhlA	gene	yghW	activator	28373272	4	ver/dev	However , since operon is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between yghW .	331	However , since the hydrogenase 2 ( hypO-hybABCDE ) operon is differentially expressed under conditions that favor fermentation ( 60 , 61 ) , we hypothesized that FhlA , a bEBP that is activated by the fermentation product formate ( 62 ) , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO and yghW ( Pinter-hypO-yghW ) and thereby modulates expression of the hydrogenase 2 operon ( Fig. 3B ) .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FhlA	gene	yghW	activator	28373272	4	ver/dev	However , since the hydrogenase 2 -LRB- hypO-hybABCDE -RRB- is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between yghW .	331	However , since the hydrogenase 2 ( hypO-hybABCDE ) operon is differentially expressed under conditions that favor fermentation ( 60 , 61 ) , we hypothesized that FhlA , a bEBP that is activated by the fermentation product formate ( 62 ) , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO and yghW ( Pinter-hypO-yghW ) and thereby modulates expression of the hydrogenase 2 operon ( Fig. 3B ) .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	araE	repressor	25991823	8	ver/dev	As AraC activates araE transcription , suppression in an AraCˉ background might be caused by a decrease of intracellular L-arabinose due to lack of AraE permease .	216	As AraC activates araE transcription , suppression in an AraCˉ background might be caused by a decrease of intracellular L-arabinose due to lack of AraE permease .	13	SPI-1 REPRESSION BY L-ARABINOSE IS INDEPENDENT OF ARAC	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SirA	gene	csrB	repressor	16949866	17	ver/dev	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA .	301	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	ugd	regulator	12438352	26	att	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	334	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	ugd	regulator	12438352	3	att	Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .	46	Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ugd	regulator	12438352	26	ver/dev	PmrA has been shown to bind ugd .	334	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	ugd	regulator	12519186	8	ver/dev	The ugd gene product participates in multiple cellular activities , suggesting that regulatory systems other than PhoP -- PmrA -- PmrB might also control ugd expression .	33	The ugd gene product participates in multiple cellular activities , suggesting that regulatory systems other than PhoP -- PhoQ and PmrA -- PmrB might also control ugd expression .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	ugd	regulator	15205413	0	att	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid-A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	7	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	ugd	regulator	19076233	6	att	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	138	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	14	INACTIVATION OF RPON INDUCES PM RESISTANCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	ompS1	repressor	17908208	31	ver/dev	StpA repressed ompS1 expression in a mutant hns background	95	StpA repressed ompS1 expression in a mutant hns background	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	repressor	19406898	2	ver/dev	StpA , was found to repress ompS1 in an hns background ; and a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	ompS1	repressor	19406898	2	ver/dev	StpA , was found to repress ompS1 in an hns background ; and LeuO , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	metF	activator	21768276	2	ver/dev	The MetR protein acts as an activator for the transcription of metF .	727	The MetR protein acts as an activator for the transcription of metE , metA , metF , and metH ( 93 ) .	8	TRANSCRIPTION STM3773 PUTATIVE TRANSCRIPTIONAL REGULATOR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	spiC	activator	12753201	35	ver/dev	From the data , it is apparent that both SsrB activate the transcriptional-fusions to spiC .	222	From the data shown in Fig. 2C , it is apparent that both OmpR and SsrB activate the transcriptional fusions to spiC .	11	THE SSRA/B REGION CONTAINS TWO PROMOTERS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	spiC	activator	12874347	3	ver/dev	In contrast , the activation of the spiC promoter was shown to require SsrB .	289	In contrast , the activation of the spiC promoter was shown to require SsrB and to be modulated by PhoP ( 9 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	spiC	activator	15491370	4	ver/dev	The response regulator SsrB , in turn , is autoregulated , activating spiC	37	The response regulator SsrB , in turn , is autoregulated , activating ssrB , ssrA and spiC ( Feng et al. , 2003 ) , as well as other genes located both inside and outside of	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	spiC	activator	15491370	9	ver/dev	SsrB , in turn , activates spiC .	88	SsrB , in turn , activates ssrB , ssrA and spiC ( ssaB ) as well as additional genes , including srfH .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	hfq	regulator	24018968	6	att	The Hfq-dependent stationary-phase expression of SPI1 genes was also clearly observed in an InvF-regulated gene , sipC : a sipC : : lacZ chromosomal fusion expressed 3,761 ± 292 and 1,120 ± 12 Miller units of β-galactosidase at 4 and 12 h p.i. , respectively , in wild-type cells , whereas the sipC : : lacZ fusion in ∆ hfq cells expressed 1,486 ± 192 and 830 ± 67 Miller units of β-galactosidase at the same time points ( data	177	The Hfq-dependent stationary-phase expression of SPI1 genes was also clearly observed in an InvF-regulated gene , sipC : a sipC : : lacZ chromosomal fusion expressed 3,761 ± 292 and 1,120 ± 12 Miller units of β-galactosidase at 4 and 12 h p.i. , respectively , in wild-type cells , whereas the sipC : : lacZ fusion in ∆ hfq cells expressed 1,486 ± 192 and 830 ± 67 Miller units of β-galactosidase at the same time points ( data	14	STATIONARY PHASE UNDER SHAKING CULTURE CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sseA	activator	30682134	18	ver/dev	SlyA activates sseA expression in a PhoP-dependent manner , and only in LB was S2 Table .	225	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sseA	activator	30682134	18	ver/dev	SlyA activates sseA expression in a PhoP-dependent manner , and only in LB was their translation .	225	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	lacZ	activator	23645605	0	att	cueR was introduced into L the chromosome of the S. Typhimurium 14028 strain replacing wild-type cueR , and the expression of the CueR-dependent copA : : lacZ reporter in cells grown in Luria-Bertani ( LB ) medium was determined in the presence or absence of either 40 M AuHCl4 or 1 mM CuSO4 ( Fig. 1B ) .	87	cueR was introduced into L the chromosome of the S. Typhimurium 14028 strain replacing wild-type cueR , and the expression of the CueR-dependent copA : : lacZ reporter in cells grown in Luria-Bertani ( LB ) medium was determined in the presence or absence of either 40 M AuHCl4 or 1 mM CuSO4 ( Fig. 1B ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	lacZ	activator	23645605	3	att	The sensor proteins ' response was followed by measuring the expression of the CueR-dependent copA : : lacZ reporter in LB-medium in the absence or presence of either Au or Cu .	134	The sensor proteins ' response was followed by measuring the expression of the CueR-dependent copA : : lacZ reporter in LB medium in the absence or presence of either Au or Cu .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Fur	gene	entE	repressor	24858080	11	ver/dev	To confirm the repression by an expected behaviour for a Fur-regulated locus -- we employed a strain carrying an entE : .	376	To confirm this induction as well as the repression by Fe ( II ) -- an expected behaviour for a Fur-regulated locus ( Tsolis et al. , 1995 ) -- we employed a strain carrying an entE : : MudJ transcriptional fusion ( Table S1 ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hfq	repressor	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	sopE	regulator	21168230	2	ver/dev	SprB , regulates the expression of sopE .	212	SprB , a transcriptional regulator , is encoded within the SPI1 and regulates the expression of sipC , sptP , avrA , sopB and sopE ( Eichelberg et al. , 1999 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	pcgL	activator	31333620	6	ver/dev	It also provided an explanation for the H-NSHA-WT protein heterogeneously produced from plasmid upregulation of these PhoP/PhoQ-dependent genes due to the pUHE21-hns-HA reduced the transcription of the pcgL , T13 phosphorylation of H-NS .	340	It also provided an explanation for the H-NSHA-WT protein heterogeneously produced from plasmid upregulation of these PhoP/PhoQ-dependent genes due to the pUHE21-hns-HA reduced the transcription of the pcgL , pagC , T13 phosphorylation of H-NS .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	New	Level 2
FimZ	gene	fimZ	activator	25547794	0	att	Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does not affect fimZ expression but does upregulate hilE in an FimZ-dependent manner .	12	Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does not affect fimZ expression but does upregulate hilE in an FimZ-dependent manner .	1	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FimZ	gene	fimZ	activator	25547794	23	auto	One possible explanation of this finding is that the pstS mutation increases protein levels of FimZ , potentially activating transcription of its own gene , consistent with previous work by Yeh et al. ( 43 ) .	240	One possible explanation of this finding is that the pstS mutation increases protein levels of FimZ , potentially activating transcription of its own gene , consistent with previous work by Yeh et al. ( 43 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	yddX	regulator	27601571	28	ver/dev	Moreover , RcsB regulates yddX in E. coli .	254	Moreover , RcsB regulates yddX in E. coli ( 51 ) .	3	RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	fljB	regulator	24031550	0	ver/dev	underlying the expressional regulation of fljB , gene deletion mutants of the regulators FliA were constructed in this study .	8	underlying the expressional regulation of fljB : z66 , gene deletion mutants of the regulators FliA , FlhDC , and OmpR were constructed in this study .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	fljB	regulator	24031550	6	ver/dev	To investigate whether fljB is regulated by FliA	245	To investigate whether fljB : z66 is regulated by FlhDC and FliA	5	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilC	gene	dam	regulator	21984608	0	ver/dev	It is interesting to note that several regulators of HilC , were found in significantly lower levels in the dam mutant .	135	It is interesting to note that several regulators of T3SS1 , such as HilA , HilC , HilD , and InvF , were found in significantly lower levels in the dam mutant .	5	TRANSCRIPTIONAL AND TRANSLATIONAL REGULATION DURING INVASION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilE	gene	hilE	repressor	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilE	repressor	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilE	repressor	24354910	47	ver/dev	A genetic screen for loss-of-function mutations provided evidence that the hilE gene is necessary for LeuOmediated repression of an hypothesis confirmed upon directed construction of a HilE − muta .	195	A genetic screen for loss-of-function mutations that restored SPI-1 expression in the presence of LeuO provided evidence that the hilE gene is necessary for LeuOmediated repression of SPI-1 , an hypothesis confirmed upon directed construction of a HilE − mutant .	12	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
Sigma54	gene	fliK	activator	19942438	2	att	Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni .	495	Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni .	18	REFERENCES	Campylobacter jejuni	0	L3	OTHER	Other	OTHER	Other	Level 2
CspE	gene	cspB	activator	24056458	0	ver/dev	this effect was reflected by induction of cspB and proteins ( CspE ) in response to preadaptation to cold-stress	146	Cold stress genes and proteins regulate membrane fluidity and resume protein synthesis ( 18 ) , and this effect was reflected by induction of cold stress genes ( cspB and cspD ) and proteins ( CspA , CspE , and CspC ) in response to preadaptation to cold stress .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	igaA	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	activator	11292737	3	ver/dev	DksA appears to positively regulate the expression of rpoS at the level of translation .	378	DksA appears to positively regulate the expression of rpoS at the level of translation .	7	2	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	regulator	12068808	15	auto	Although the evidence suggests that OmpR can regulate its own expression , OmpR autoregulation could be indirect , with OmpR controlling the expression of a second gene , the product of which directly controls the ompR promoter .	134	Although the evidence suggests that OmpR can regulate its own expression , OmpR autoregulation could be indirect , with OmpR controlling the expression of a second gene , the product of which directly controls the ompR promoter .	9	OMPR BINDS TO ITS OWN PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	12068808	48	auto	The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .	254	The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12068808	16	ver/dev	Consequently , DNA mobility-shift assays were performed to determine whether OmpR actually binds to the ompR promoter region .	135	Consequently , DNA mobility shift assays were performed to determine whether OmpR actually binds to the ompR promoter region .	9	OMPR BINDS TO ITS OWN PROMOTER	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	12068808	18	ver/dev	The results clearly demonstrate that phosphorylated OmpR protein binds to the ompR promoter region with a greater affinity than that of unphosphorylated OmpR .	137	The results presented in Fig. 6 clearly demonstrate that phosphorylated OmpR protein binds to the ompR promoter region with a greater affinity than that of unphosphorylated OmpR .	9	OMPR BINDS TO ITS OWN PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12068808	22	ver/dev	In vitro DNA footprinting experiments were then conducted to determine which of the three potential OmpR binding sites in the ompR promoter are actually bound by OmpR .	152	In vitro DNA footprinting experiments were then conducted to determine which of the three potential OmpR binding sites in the ompR promoter are actually bound by OmpR .	10	OMPR FOOTPRINT	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	12068808	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12068808	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12068808	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12068808	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12080060	15	auto	Although the evidence suggests that OmpR can regulate its own expression , OmpR autoregulation could be indirect , with OmpR controlling the expression of a second gene , the product of which directly controls the ompR promoter .	134	Although the evidence suggests that OmpR can regulate its own expression , OmpR autoregulation could be indirect , with OmpR controlling the expression of a second gene , the product of which directly controls the ompR promoter .	9	OMPR BINDS TO ITS OWN PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	12080060	48	auto	The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .	254	The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12080060	16	ver/dev	Consequently , DNA mobility-shift assays were performed to determine whether OmpR actually binds to the ompR promoter region .	135	Consequently , DNA mobility shift assays were performed to determine whether OmpR actually binds to the ompR promoter region .	9	OMPR BINDS TO ITS OWN PROMOTER	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	12080060	18	ver/dev	The results clearly demonstrate that phosphorylated OmpR protein binds to the ompR promoter region with a greater affinity than that of unphosphorylated OmpR .	137	The results presented in Fig. 6 clearly demonstrate that phosphorylated OmpR protein binds to the ompR promoter region with a greater affinity than that of unphosphorylated OmpR .	9	OMPR BINDS TO ITS OWN PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12080060	22	ver/dev	In vitro DNA footprinting experiments were then conducted to determine which of the three potential OmpR binding sites in the ompR promoter are actually bound by OmpR .	152	In vitro DNA footprinting experiments were then conducted to determine which of the three potential OmpR binding sites in the ompR promoter are actually bound by OmpR .	10	OMPR FOOTPRINT	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	12080060	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12080060	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12080060	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	12080060	59	ver/dev	the ompR promoter region serve as internal controls for spurious binding of OmpR	371	The resulting 1084 bp DNA fragment was purified ( BioRad Quick Kleen ) and digested with BglII and HincII to produce a 545 bp product containing the ompR promoter region and two other fragments ( a 344 bp fragment containing the OmpR ORF and a 195 bp fragment ) , which serve as internal controls for spurious binding of OmpR .	20	ELECTROPHORETIC MOBILITY SHIFT ASSAYS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	regulator	19609351	5	att	Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .	338	Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .	6	NON-CODING (NC) RNA SEQUENCES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	regulator	23159630	0	ver/dev	Since previous studies have demonstrated that OmpR is a regulator of Agf expression , we decided to determine whether the TnphoA insertion in 2 final candidate mutants is in the ompR gene .	167	Since previous studies have demonstrated that OmpR is a regulator of Agf expression [ 8 ] , we decided to determine whether the TnphoA insertion in 2 final candidate mutants is in the ompR gene .	12	3.1. IDENTIFICATION OF A S. TYPHIMURIUM MUTANT DEREGULATING AGF EXPRESSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	24720747	14	ver/dev	The ompR mutant was also complemented with the ompR coding region from Escheri-chia coli under the control of pQE60ompR ; this construct was used since it is identical to the S. Typhi OmpR protein .	219	The ompR mutant was also complemented with the ompR coding region from Escheri-chia coli under the control of an IPTG-inducible promoter ( pQE60ompR ) ; this construct was used since it is identical to the S. Typhi OmpR protein .	7	LTRR-DEPENDENT AND -INDEPENDENT OMPR PROMOTERS ARE INVOLVED IN OMPR SYNTHESIS FOR OMPC AND OMPF PRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	regulator	24720747	14	ver/dev	The ompR mutant was also complemented with the ompR coding region from Escheri-chia coli under the control of an IPTG-inducible promoter ; this construct was used since it is identical to the S. Typhi OmpR protein .	219	The ompR mutant was also complemented with the ompR coding region from Escheri-chia coli under the control of an IPTG-inducible promoter ( pQE60ompR ) ; this construct was used since it is identical to the S. Typhi OmpR protein .	7	LTRR-DEPENDENT AND -INDEPENDENT OMPR PROMOTERS ARE INVOLVED IN OMPR SYNTHESIS FOR OMPC AND OMPF PRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	regulator	29214489	9	ver/dev	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to RNA polymerase .	107	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase .	13	CADC INTERACTS DIRECTLY WITH OMPR	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	29214489	9	ver/dev	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter .	107	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase .	13	CADC INTERACTS DIRECTLY WITH OMPR	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	regulator	29417203	9	ver/dev	Thus , OmpR only directly regulates two , i.e. , ompR , of the four genes .	112	Thus , OmpR only directly regulates two , i.e. , tviA and ompR , of the four genes tested .	13	AUTOREGULATION AND RECIPROCAL REGULATION OF OMPR AND HFQ	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompR	regulator	30663891	4	ver/dev	Besides its role in osmotic-stress , OmpR it is the major regulator of acid-induced stationary-phase ATR , since ompR mutants lead to sensitive stationary-phase cells , with almost no inducible ATR .	288	Besides its role in osmotic stress , OmpR it is the major regulator of acid-induced stationary-phase ATR , since ompR mutants lead to sensitive stationary-phase cells , with almost no inducible ATR ( Bang et al. , 2000 ) .	11	4.2.1 ACID TOLERANCE RESPONSE (ATR)	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ompR	regulator	33799446	7	ver/dev	Interestingly , several studies have connected OmpR with Salmonella virulence , mainly through the regulation of the SPI-1-and SPI-2-encoded genes , thereby observing that ompR mutants are highly attenuated in mice .	144	Interestingly , several studies have connected OmpR with Salmonella virulence , mainly through the regulation of the SPI-1-and SPI-2-encoded genes , thereby observing that ompR mutants are highly attenuated in mice [ 82,94 -- 97 ] .	6	3.2. SPECIFIC STRESS RESPONSES 3.2.1. ACID STRESS	Salmonella;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	regulator	33854491	10	ver/dev	Due to the fact that only a few transcriptional factors have been implicated in the control of ompR in Salmonella , such as OmpR , the data contribute to the understanding of the regulatory network .	261	Due to the fact that only a few transcriptional factors have been implicated in the control of ompR in Salmonella , such as LtrR , H-NS , and OmpR ( autoregulation ; Bang et al. , 2002 ; Villarreal et al. , 2014 ) , the data obtained contribute to the understanding of the regulatory network that controls the activity of this master regulator .	19	DISCUSSION	Salmonella	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SirA	gene	spf	regulator	33162952	1	ver/dev	Interestingly , it has been described that SirA can bind to the promoter region of spf , suggesting that SirA might be regulating Spot 42 .	133	Interestingly , it has been described that SirA can bind to the promoter region of spf ( Zere et al. , 2015 ) , suggesting that SirA might be regulating Spot 42 .	8	THE SRNA SPOT 42 POSITIVELY REGULATES CSRC	Leiostomus xanthurus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
FimY	gene	fimA	activator	24462182	31	ver/dev	Since FimY are both required to activate fimA , it is possible that these two proteins form a complex to bind the promoter of fimA .	245	Since FimY and FimZ are both required to activate fimA ( Swenson and Clegg , 1992 ) , it is possible that these two proteins form a complex to bind the promoter of fimA .	17	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Sigma32	gene	ibpB	regulator	12125817	9	ver/dev	Transcription of the ibpB heat-shock gene is under control of s32 , a third regulon of heat-shock response .	397	Transcription of the ibpB heat-shock gene is under control of s32 - and s54-promoters , a third regulon of heat-shock response .	26	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma32	gene	ibpB	regulator	12581721	9	ver/dev	Transcription of the ibpB heat-shock gene is under control of s32 , a third regulon of heat-shock response .	397	Transcription of the ibpB heat-shock gene is under control of s32 - and s54-promoters , a third regulon of heat-shock response .	26	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	STM3968	activator	15681155	9	att	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	206	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	11	3. RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	STM3968	activator	15681155	31	ver/dev	In addition , the lack of consensus PmrA-binding sites in the promoters of STM3968 suggested that these genes may be indirectly activated by PmrA .	339	In addition , the lack of consensus PmrA-binding sites in the promoters of STM1257 , STM3968 , STM4568 and STM0459 suggested that these genes may be indirectly activated by PmrA .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsAB	gene	rcsA	regulator	29186528	5	ver/dev	the rcsA promoter is autoregulated by RcsB in the so named RcsAB box	172	We selected these regions since P1flhDC accounts for the RcsB box while a similar consensus sequence is observed in the rcsA promoter , which is autoregulated by RcsA and RcsB in the so named RcsAB box ( 4,40 ) ( Supplementary Figure S6B ) .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsAB	gene	rcsA	regulator	29186528	5	ver/dev	the rcsA promoter is autoregulated by RcsA in the so named RcsAB box	172	We selected these regions since P1flhDC accounts for the RcsB box while a similar consensus sequence is observed in the rcsA promoter , which is autoregulated by RcsA and RcsB in the so named RcsAB box ( 4,40 ) ( Supplementary Figure S6B ) .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sopD	repressor	29857034	5	ver/dev	In accordance with the RNA-seq analysis , suggesting that sopD is downregulated by SlyA .	273	In accordance with the RNA-seq analysis , where expression levels in WT showed a log2 fold-change of 2.2 compared to the mutant , suggesting that sopD is downregulated by SlyA .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	sopD	repressor	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopD were negatively regulated by SlyA , with DslyA expression increased five-times , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sopD	repressor	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopD were negatively regulated by SlyA , with DslyA expression increased two , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	fliA	repressor	26553464	11	ver/dev	E. coli strains increased motility , possibly due to the inhibition of fliA promoters by DksA -LRB- 14 , on 19 October 2021 by 132.24	215	E. coli strains lacking dksA were shown to express higher levels of che-motaxis and flagellum genes , resulting in overproduction of flagellin , hyperflagellated cells , and increased motility , possibly due to the inhibition of flhDC and fliA promoters by DksA ( 14 , loaded from https://journals.asm.org/journal/iai on 19 October 2021 by 132.24	6	DISCUSSION	Escherichia coli	0	L1	SPEC	Other	OTHER	New	Level 1
DksA	gene	fliA	repressor	26553464	11	ver/dev	the inhibition of fliA promoters by DksA ( 14 , _ loaded from https://journals.asm.org/journal/iai	215	E. coli strains lacking dksA were shown to express higher levels of che-motaxis and flagellum genes , resulting in overproduction of flagellin , hyperflagellated cells , and increased motility , possibly due to the inhibition of flhDC and fliA promoters by DksA ( 14 , loaded from https://journals.asm.org/journal/iai on 19 October 2021 by 132.24	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	nlpD	activator	33251260	14	ver/dev	the upstream nlpD gene _ contributing to basal level expression of RpoS in exponential phase	342	Transcription regulation is primarily from the rpoS promoter , embedded within the upstream nlpD gene contributing to basal level expression of RpoS in exponential phase ( 30 , 31 ) .	18	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FNR	gene	pilV	repressor	27601577	0	ver/dev	Moreover , downregulation of pilV expression in the absence of FNR was not observed under data not shown , consistent with the inactive form of FNR under aerobiosis .	108	Moreover , downregulation of pilV and pilS expression in the absence of FNR was not observed under aerobic growth conditions ( data not shown ) , consistent with the inactive form of FNR under aerobiosis ( 24 ) .	4	2	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	pilV	repressor	27601577	0	ver/dev	Moreover , downregulation of pilV expression in the absence of FNR was not observed under aerobic-growth-conditions , consistent with the inactive form of FNR under aerobiosis .	108	Moreover , downregulation of pilV and pilS expression in the absence of FNR was not observed under aerobic growth conditions ( data not shown ) , consistent with the inactive form of FNR under aerobiosis ( 24 ) .	4	2	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	pilV	repressor	27601577	4	ver/dev	Under microaerobic conditions , the absence of FNR resulted in a downregulation of pilV , demonstrating the integration of the pilus gene expression with the global metabolic regulatory setup of Salmonella .	224	Under microaerobic conditions , the absence of FNR resulted in a downregulation of pilV , pilS , and pilT transcription and lower pESI conjugation , demonstrating the integration of the pilus gene expression with the global metabolic regulatory setup of Salmonella .	5	DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
RtsA	gene	hilD	repressor	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxR	gene	acnA	regulator	23637460	0	ver/dev	that acnA expression was regulated by SoxR , oxidative-stress .	17	that acnA expression was regulated by the cyclic-AMP receptor protein ( CRP , glucose starvation ) , the fumarate nitrate reduction regulator ( FNR , oxygen starvation ) , the ferric uptake regulator ( Fur , iron starvation ) and the superoxide response protein ( SoxR , oxidative stress ) .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	acnA	regulator	23637460	2	ver/dev	Expression of S. Typhimurium acnA is regulated by SoxR	218	Expression of S. Typhimurium acnA is regulated by CRP, FNR, Fur and SoxR	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrHFIJKLM	regulator	33106344	17	att	A similar outcome was observed in a mutant with mutation of a PhoP-regulated operon of pmrHFIJKLM , which is responsible for lipid-A modification , which was sensitive to PMB in S. Typhimurium ( 49 ) .	429	A similar outcome was observed in a mutant with mutation of a PhoP-regulated operon of pmrHFIJKLM , which is responsible for lipid A modification , which was sensitive to PMB in S. Typhimurium ( 49 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	11755416	6	ver/dev	First , HilD , binds directly to several sites within de-represses hilA expression .	159	First , HilD , an AraC/XylS family member , binds directly to several sites within PhilA and de-represses hilA expression ( [ 52 ] ; L. Schechter and C. Lee , unpublished observations ) .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	11755416	6	ver/dev	First , HilD , binds directly to several sites within PhilA hilA expression .	159	First , HilD , an AraC/XylS family member , binds directly to several sites within PhilA and de-represses hilA expression ( [ 52 ] ; L. Schechter and C. Lee , unpublished observations ) .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	12453229	7	ver/dev	The expression of hilA is itself controlled by two additional SPI-1 regulators : HilD .	68	The expression of hilA is itself controlled by two additional SPI-1 regulators : HilC and HilD ( Eichelberg et al. , 1999 ; Schechter et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	12535071	9	ver/dev	HilD bind the same regions upstream of hilA .	53	In vitro , HilD and HilC bind the same regions upstream of hilA ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	12791144	4	ver/dev	Both HilC and HilD are positive regulators of hilA expression .	41	Both HilC and HilD are positive regulators of hilA expression ( Schechter et al. , 1999 ; Lostroh et al. , 2000 ; Lucas and Lee , 2001 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	15661008	0	ver/dev	HilD are positive regulators of hilA expression	19	We found that HilC and HilD , which are positive regulators of hilA expression , accumulate in Lon-depleted cells , and that the enhancement of SPI1 expression that occurs in a lon-disrupted mutant is not observed in the lon hilC hilD triple null mutant .	4	SUMMARY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	15661008	2	ver/dev	HilD have been shown to bind to URS of hilA .	48	HilC and HilD have been shown to bind to the upstream repressing sequence ( URS ) of hilA and counteract the repression ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	15661008	2	ver/dev	HilD have been shown to bind to the upstream repressing sequence of hilA .	48	HilC and HilD have been shown to bind to the upstream repressing sequence ( URS ) of hilA and counteract the repression ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	15661008	8	ver/dev	HilD bind directly to the upstream sequence of hilA .	84	HilC and HilD bind directly to the upstream sequence of hilA and derepress the transcription of PhilA .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	15661008	20	ver/dev	As shown in Fig. 8 , the increased effect of Lon depletion on hilA expression was abolished by depletion of both HilC and HilD , suggesting that both proteins are also involved in regulation of SPI1 by Lon under SPI1-repressing conditions .	236	As shown in Fig. 8 , the increased effect of Lon depletion on hilA expression was abolished by depletion of both HilC and HilD , suggesting that both proteins are also involved in regulation of SPI1 by Lon under SPI1-repressing conditions .	8	DIFFERENTIAL RESPONSES OF HILC AND HILD IN SPI1 EXPRESSION TO ENVIRONMENTAL STIMULI	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	15661008	23	ver/dev	HilD can independently bind the hilA promoter .	267	HilC and HilD can independently bind and activate the hilA promoter ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	15765064	35	ver/dev	HilD , directly bind the Salmonella typhimurium hilA promoter .	410	HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	26	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	16045614	19	ver/dev	a model in which expression of hilA is controlled by the combined action of HilD	81	Based on our genetic analyses , and taking into account the published results outlined above , we present a model in which expression of hilA is controlled by the combined action of HilC , HilD and RtsA , each of which can independently bind upstream of hilA to induce its expression ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	16045614	19	ver/dev	a model in which expression of hilA is controlled by the combined action of HilD	81	Based on our genetic analyses , and taking into account the published results outlined above , we present a model in which expression of hilA is controlled by the combined action of HilC , HilD and RtsA , each of which can independently bind upstream of hilA to induce its expression ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	16045614	61	ver/dev	HilD is required for EnvZ/OmpR regulation of hilA It was previously concluded that the EnvZ/OmpR two-component system functioned through hilC to regulate expression of invasion genes .	399	HilD is required for EnvZ/OmpR regulation of hilA It was previously concluded that the EnvZ/OmpR two-component system functioned through hilC to regulate expression of invasion genes ( Lucas and Lee , 2001 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	16045614	72	ver/dev	HilD bind to overlapping sites in the hilA promoter .	470	HilC and HilD bind to overlapping sites in the hilA promoter ( Olekhnovich and Kadner , 2002 ) .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	16045614	95	ver/dev	Lee , C.A. Roles of HilD in regulation of hilA expression in Salmonella enterica sero-var Typhimurium .	742	Lucas , R.L. , and Lee , C.A. ( 2001 ) Roles of HilC and HilD in regulation of hilA expression in Salmonella enterica sero-var Typhimurium .	27	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	17208038	1	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilD .	51	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD and RtsA [ 23 -- 25 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17208038	2	ver/dev	Studies have shown PheU that HilD can each individually bind to the hilA promoter	55	Studies have shown PheU that HilC , HilD and RtsA can each individually bind to the hilA promoter , and deletions of hilC , hilD or rtsA cause a decrease in expression of hilA [ 19 ,23 -- 25 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	hilA	regulator	17208038	6	ver/dev	HilD , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by the sic/sip operon -- in a fashion independent of HilA .	67	HilC , HilD and RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through , the sic/sip operon -- in a fashion independent of HilA [ 15,16,25,27 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17208038	6	ver/dev	HilD , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through -- in a fashion independent of HilA .	67	HilC , HilD and RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through , the sic/sip operon -- in a fashion independent of HilA [ 15,16,25,27 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilA by HilD .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17208038	35	ver/dev	It also demonstrates EnvZ/OmpR control of hilA through HilD .	204	It also demonstrates BarA/SirA and EnvZ/OmpR control of hilA through HilD .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	hilA	regulator	17208038	35	ver/dev	It also demonstrates BarA/SirA control of hilA through HilD .	204	It also demonstrates BarA/SirA and EnvZ/OmpR control of hilA through HilD .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	hilA	regulator	17208038	36	ver/dev	Schechter LM , Lee CA : HilD , directly bind the Salmonella typhimurium hilA promoter .	237	Schechter LM , Lee CA : AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	17575908	0	ver/dev	HilD were described to influence the expression of hilA .	34	HilD and HilC were described to influence the expression of hilA ( Rakeman et al. 1999 ) .	2	ABBREVIATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17575908	4	ver/dev	SCHECHTER L.M. , LEE C.A. : HilD , directly bind the Salmonella typhimurium hilA promoter .	261	SCHECHTER L.M. , LEE C.A. : AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	14	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	17675384	9	ver/dev	To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilD-lac chromosomal fusions .	125	To test whether the RtsA , HilC , and HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac , hilC-lac , and hilD-lac chromosomal fusions ( 13 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	17675384	9	ver/dev	To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilC-lac .	125	To test whether the RtsA , HilC , and HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac , hilC-lac , and hilD-lac chromosomal fusions ( 13 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	17675384	9	ver/dev	To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac .	125	To test whether the RtsA , HilC , and HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac , hilC-lac , and hilD-lac chromosomal fusions ( 13 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	17993530	3	ver/dev	Expression of hilA is directly controlled by three AraC-like activators : HilD .	35	Expression of hilA is directly controlled by three AraC-like activators : HilC , HilD , and RtsA ( 18 , 42 , 47 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17993530	12	ver/dev	In this work , we demonstrated that Fur regulates expression of hilA via control of HilD .	61	In this work , we demonstrated that Fur regulates expression of hilA via control of HilD .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	17993530	16	ver/dev	To further test the requirement for HilD for Fur-mediated regulation of hilA , we examined the effects of Fur overexpression in strains .	195	To further test the requirement for HilD for Fur-mediated regulation of hilA , we examined the effects of Fur overexpression in strains containing the hilA-lac fusion , with and without hilC , hilD , or rtsA .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	hilA	regulator	17993530	18	ver/dev	This provides clear genetic evidence that HilD is absolutely required for Fur regulation of hilA .	198	This provides clear genetic evidence that HilD is absolutely required for Fur regulation of hilA .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	17993530	20	ver/dev	Given that HilD is required for Fur regulation of hilA , it seemed possible that Fur regulates hilD expression in some manner .	206	Given that HilD is required for Fur regulation of hilA , it seemed possible that Fur regulates hilD expression in some manner .	4	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	18792679	5	ver/dev	HilD directly controls expression ofthe hilA gene .61,62	160	The molecular mechanism by which this occurs remains unclear and appears to involve an AraC-like regulator named HilD that directly controls expression ofthe hilA gene .61,62	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	19003447	0	ver/dev	Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilD .	38	Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilD , HilC and RtsA , which in a complex arrangement of feedback and feedforward loops bring about maximal induction of HilA ( Altier 2005 ; Jones 2005 ; Ellermeier and Slauch 2007 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	19003447	1	ver/dev	Of these regulators , HilD can be considered as the most important single regulator of the hilA promoter since the hilD knockout strain shows nearly basal levels of HilA under inducing conditions .	39	Of these regulators , HilD can be considered as the most important single regulator of the hilA promoter ( PhilA ) since the hilD knockout strain shows nearly basal levels of HilA under inducing conditions ( Lucas and Lee 2001 ; Boddicker et al. 2003 ; Ellermeier et al. 2005 ) .	5	INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	19537165	3	ver/dev	Earlier work on mathematical modeling of regulation of expression of hilA by HilD was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .	44	Earlier work on mathematical modeling of regulation of expression of hilA by HilC , HilD and RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop [ Maithreye and Mande , 2007 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	21168230	4	ver/dev	In turn , hilA is regulated by HilD .	343	In turn , hilA is regulated by HilD and HilC ( Schechter and Lee , 2001 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	22479568	0	ver/dev	HilD can activate expression of rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	23442379	0	ver/dev	Schechter LM , Lee CA : HilD , directly bind the Salmonella typhimurium hilA promoter .	568	Schechter LM , Lee CA : AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	30	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	23504014	3	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilD .	24	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD , and RtsA ( 14 -- 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	24929817	1	ver/dev	HilD mutually regulate the hilA gene expression	166	HilC and HilD mutually regulate the hilA gene expression	9	SURVIVAL AND PROPHAGE INDUCTION OF LYSOGENIC S. TYPHIMURIUM EXPOSED TO GASTROINTESTINAL JUICES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	25182488	2	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilD .	19	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD , and RtsA ( 8 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	25991823	26	ver/dev	Schechter , L. M. , and C. A. Lee , 2001 AraC/XylS family members , HilD , directly bind the Salmonella typhi-murium hilA promoter .	633	Schechter , L. M. , and C. A. Lee , 2001 AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhi-murium hilA promoter .	44	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	26300871	13	ver/dev	These results suggest that CpxR represses hilA by affecting the autoregulation of HilD .	375	These results suggest that CpxR represses hilA and thus the other SPI-1 genes by affecting the autoregulation of HilD .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	hilA	regulator	26300871	29	ver/dev	HilD directly regulates hilA	464	Furthermore , we demonstrate that CpxR-P negatively affects the transcription of the SPI-1 genes hilD and hilA , but only in the presence of HilD , which would be expected , since the expression of HilD is autoregulated and HilD directly regulates hilA ( Golubeva et al. , 2012 ; Fàbrega and Vila , 2013 ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	26561851	2	ver/dev	The transcription of hilA is regulated by HilD .	172	The transcription of hilA is regulated by HilD , an important activator that controls cross-talk between SPI1 and SPI2 expression [ 55,58 ] .	7	THE PRIMARY TRANSCRIPTOME OF INTRA-MACROPHAGE S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	26810370	3	ver/dev	HilD plays a major role in the regulation of hilA	245	Expression of hilA is coordinately controlled by the HilD / HilC/RtsA complex , and HilD plays a major role in the regulation of hilA .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	26810370	3	ver/dev	Expression of hilA is coordinately controlled by the HilD / HilC/RtsA complex	245	Expression of hilA is coordinately controlled by the HilD / HilC/RtsA complex , and HilD plays a major role in the regulation of hilA .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	27341691	18	att	The C-terminal domain of RNAPa has been shown to be important for transcription of HilD-regulated genes in-vivo , as the mutation of leucine 289 to phenylalanine within this domain fails to induced hilA expression , similarly to a hilD null mutant	292	The C-terminal domain of RNAPa has been shown to be important for transcription of HilD-regulated genes in vivo , as the mutation of leucine 289 to phenylalanine within this domain fails to induced hilA expression , similarly to a hilD null mutant	11	SALMONELLA TO MAXIMIZE ITS VIRULENCE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	27341691	8	att	Additionally , this strain harbored a HilD-regulated hilA ' - lacZ fusion that allowed us to monitor HilD activity .	166	Additionally , this strain harbored a HilD-regulated hilA ' - lacZ fusion that allowed us to monitor HilD activity .	8	PAT CONTROLS HILD STABILITY	Varanus togianus	0	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	27565525	0	ver/dev	Differential expression of hilA , is influenced by HilD	361	Differential expression of hilA , that encodes the transcriptional activator of the SPI1 structural genes , is influenced by three AraC-like regulators ( HilD , HilC , and RtsA ) and each of them can activate the hilD , hilC , rtsA , and hilA genes that form a complex feed-forward regulatory loop ( Golubeva et al. , 2012 ; Lim et al. , 2012 ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	27886269	8	ver/dev	the hilA genes are controlled by HilD indirectly , respectively	85	As controls , the expression of cat transcriptional fusions of the hilA and ssaG genes , which are controlled by HilD directly and indirectly , respectively , were also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	27886269	8	ver/dev	the hilA genes are controlled by HilD directly , respectively	85	As controls , the expression of cat transcriptional fusions of the hilA and ssaG genes , which are controlled by HilD directly and indirectly , respectively , were also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	28329249	4	ver/dev	HilD , can bind to the promoters of hilA .	91	HilD , a member of the AraC/XylS family , can bind to the promoters of hilA and invF [ 4 , 19 ] .	12	INVOLVEMENT OF K297 IN HILD’S DNA-BINDING ABILITY	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	28329249	13	ver/dev	EMSA was used to test the binding of the indicated concentrations of HilD to 6 ' - FAM -- labeled hilA promoter .	147	EMSA was used to test the binding of the indicated concentrations of HilD ( lanes 2 -- 5 , 7 -- 10 , 12 -- 15 , 17 -- 20 , 22 -- 25 ) to 6 ' - FAM -- labeled hilA promoter .	13	K297 ACETYLATION MAINTAINING HILD STABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	28329249	17	ver/dev	HilD is a dominant regulator of hilA transcription	189	HilD is a dominant regulator of hilA transcription , and HilC and RtsA amplify its expression [ 27 ] .	15	MODULATION BY PAT ON HILD K297 ACETYLATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	28426789	0	ver/dev	HilD plays a major role in regulating hilA expression .	55	HilD plays a major role in regulating hilA expression .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via an unknown regulation of HilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	unidentified	1	L3	OTHER	Analysis	NEG	New	Level 1
HilD	gene	hilA	regulator	28575106	6	ver/dev	As the expression of hilA is directly controlled by HilD , we tested whether LoiA regulates HilA through any of these three regulators .	177	As the expression of hilA is directly controlled by HilD , HilC and RtsA , we tested whether LoiA regulates HilA through any of these three regulators .	9	LOIA ACTIVATES EXPRESSION OF HILA GENE THROUGH ACTIVATING HILD	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	28704543	29	ver/dev	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on hilA .	206	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on hilA ( S3A , S3B , S3C and S3D Fig ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	28704543	29	ver/dev	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on S3A , S3D Fig .	206	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on hilA ( S3A , S3B , S3C and S3D Fig ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	28704543	29	ver/dev	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on S3A , S3C Fig .	206	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on hilA ( S3A , S3B , S3C and S3D Fig ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	28704543	29	ver/dev	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on S3A , S3B Fig .	206	Interestingly , the mutations we created within the hilA-cat-100 +6 fusion also affected the regulation and binding of HilD on hilA ( S3A , S3B , S3C and S3D Fig ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	29018419	3	ver/dev	HilD , binds directly to several sites within the hilA promoter .	332	HilD , an AraC/XylS family member , binds directly to several sites within the hilA promoter and derepresses gene expression , which in turn results in the expression of other associated virulence genes .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	29229736	2	ver/dev	Given that expression of hilA , significantly increases in bile , we investigated if HilD is posttranscriptionally regulated by bile in S. Typhi .	212	Given that expression of hilA , a gene directly regulated by HilD , significantly increases in bile , we investigated if HilD is posttranscriptionally regulated by bile in S. Typhi .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	29229736	5	ver/dev	In terms of understanding how S. Typhimurium differ with regard to SPI-1 expression in bile , our results , in combination with previous findings , dem-onstrate that HilD is differentially regulated by hilA .	256	In terms of understanding how S. Typhi and S. Typhimurium differ with regard to SPI-1 expression in bile , our results , in combination with previous findings ( 23 ) , dem-onstrate that HilD is differentially regulated by bile at the level of protein stability ( consistent with the idea that HilD is controlled largely at the posttranscriptional level [ 40 ] ) , resulting in significant differences in the expression of downstream genes , including the SPI-1 master regulator , hilA ( Fig. 7 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	29229736	5	ver/dev	In terms of understanding how S. Typhi differ with regard to SPI-1 expression in bile , our results , in combination with previous findings , dem-onstrate that HilD is differentially regulated by hilA .	256	In terms of understanding how S. Typhi and S. Typhimurium differ with regard to SPI-1 expression in bile , our results , in combination with previous findings ( 23 ) , dem-onstrate that HilD is differentially regulated by bile at the level of protein stability ( consistent with the idea that HilD is controlled largely at the posttranscriptional level [ 40 ] ) , resulting in significant differences in the expression of downstream genes , including the SPI-1 master regulator , hilA ( Fig. 7 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	30716090	46	ver/dev	Transcription of hilA is controlled by HilD .	464	Transcription of hilA is controlled by a complex feed-forward loop including RtsA , HilC and HilD [ 46 ] .	25	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	30941426	2	ver/dev	the promoter activity of hilA _ suggesting that HilD is an essential positive regulator of hilA transcription in Salmonella Typhimurium	213	Deleting hilD completely abolished the promoter activity of hilA , suggesting that HilD is an essential positive regulator of hilA transcription in Salmonella Typhimurium .	24	NON-OPTIMAL TRANSLATIONAL FIDELITY IMPAIRS HOST-CELL INTERAC- TIONS AND ANIMAL INFECTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	31182495	3	ver/dev	electrophoretic-mobility-shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	31182495	3	ver/dev	Genetic analyses suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	regulator	31428589	1	ver/dev	The feed-forward regulatory loop of HilC -- RtsA -- HilD is the most important core part of the regulatory networks to control the transcription of hilA , while HilA is the central regulator of SPI-1 .	150	The feed-forward regulatory loop of HilC -- RtsA -- HilD is the most important core part of the regulatory networks to control the transcription of hilA , while HilA is the central regulator of SPI-1 ( Ellermeier et al. , 2005 ; Dieye et al. , 2007 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31428589	15	ver/dev	a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression through the degradation of HilD .	202	Lon protease , a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression and intracellular survival after the invasion of epithelial cells through the degradation of HilC and HilD ( Boddicker and Jones , 2004 ; Takaya et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31484980	2	ver/dev	HilD controls expression of hilA through a feed-forward loop that it forms with RtsA , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over RtsA30 ,31 .	32	HilD controls expression of hilA directly or through a feed-forward loop that it forms with HilC and RtsA , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over HilC and RtsA30 ,31 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31484980	2	ver/dev	HilD controls expression of hilA through a feed-forward loop that it forms with HilC , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over HilC30 ,31 .	32	HilD controls expression of hilA directly or through a feed-forward loop that it forms with HilC and RtsA , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over HilC and RtsA30 ,31 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31484980	2	ver/dev	HilD controls expression of hilA directly that it forms with RtsA , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over RtsA30 ,31 .	32	HilD controls expression of hilA directly or through a feed-forward loop that it forms with HilC and RtsA , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over HilC and RtsA30 ,31 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31484980	2	ver/dev	HilD controls expression of hilA directly that it forms with HilC , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over HilC30 ,31 .	32	HilD controls expression of hilA directly or through a feed-forward loop that it forms with HilC and RtsA , encoded within and outside SPI-1 , respectively ; although these three AraC-like regulators recognize the same DNA motif , HilD is dominant over HilC and RtsA30 ,31 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31484980	11	ver/dev	DNA fragments were also assessed in these assays as negative controls , respectively ; HilD binds to hilA .	73	DNA fragments carrying the regulatory region of hilA or sopB were also assessed in these assays as positive and negative controls , respectively ; HilD binds to hilA but not to sopB25 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	31484980	11	ver/dev	DNA fragments were also assessed in these assays as positive controls , respectively ; HilD binds to hilA .	73	DNA fragments carrying the regulatory region of hilA or sopB were also assessed in these assays as positive and negative controls , respectively ; HilD binds to hilA but not to sopB25 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	32041797	0	ver/dev	Expression of hilA is positively regulated by three homologous transcriptional regulators , HilD , .	9	Expression of hilA is positively regulated by three homologous transcriptional regulators , HilD , HilC , and RtsA , belonging to the AraC/XylS family .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	32041797	2	ver/dev	Expression of hilA is regulated by the combined actions of three AraC-like transcriptional activators , HilD , .	30	Expression of hilA is regulated by the combined actions of three AraC-like transcriptional activators , HilD , HilC , and RtsA ( 17 -- 19 ) , each of which is capable of inducing transcription of the hilD , hilC , and rtsA genes .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	33101243	5	ver/dev	HilD is also able to bind to the promoters of hilA to active SPI-1 .	242	HilD is also able to bind to the promoters of hilA and invF to active SPI-1 ( Schechter and Lee , 2001 ) .	25	MYRICANOL INTERFERES WITH THE DNA-BINDING ABILITY OF HILD	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilA	regulator	33101243	7	ver/dev	The EMSA results suggest that HilD protein does bind specifically to the hilA promoters as described .	260	The EMSA results suggest that HilD protein does bind specifically to the hilA and invF promoters as described ( Akbar et al. , 2003 ; Bustamante et al. , 2008 ) .	25	MYRICANOL INTERFERES WITH THE DNA-BINDING ABILITY OF HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	hilA	regulator	33177235	0	ver/dev	The DNA binding protein HilD is a dominant regulator of hilA transcription .	212	The DNA binding protein HilD is a dominant regulator of hilA transcription ( 39 ) and also directly activates transcription of the flagellar master operon flhDC ( 40 ) .	4	THE AUTHORS DECLARE NO COMPETING INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	33593291	9	ver/dev	yeast extract in a ΔhilE mutant HilD is the master regulator of hilA expressio	98	HilC and RtsA are not involved in repressing hilA expression by acetate and yeast extract in a ΔhilE mutant HilD is the master regulator of hilA expression .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	33617591	0	ver/dev	Originally identified in Xylella fastidiosa as a diffusible signal factor for quorum-sensing , this fatty acid directly interacts with HilD transcriptional regulator of Salmonella , and prevents hilA activation , thus inhibiting Salmonella invasion .	38	Originally identified in Xylella fastidiosa as a diffusible signal factor for quorum sensing , this fatty acid directly interacts with HilD , the master transcriptional regulator of Salmonella , and prevents hilA activation , thus inhibiting Salmonella invasion .	6	A DIFFUSIBLE SIGNAL FACTOR OF THE INTESTINE	Xylella fastidiosa;Salmonella;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced less effectively , by Fig 1A .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced less effectively , by 22 % .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced significantly , by Fig 1A .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced significantly , by 22 % .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to hilA under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced less effectively , by Fig 1A .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to hilA under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced less effectively , by 22 % .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to hilA under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced significantly , by Fig 1A .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	33617591	3	ver/dev	Using a luxCDABE reporter fusion to hilA under the control of HilD , we found that LCFAs reduced hilA gene expression by 3.6-fold , while those from the caecum reduced significantly , by 22 % .	77	Using a luxCDABE reporter fusion to hilA , an essential SPI-1 invasion regulator under the control of HilD , we found that LCFAs extracted from the murine colon reduced hilA gene expression when added to growing cultures of Salmonella by 3.6-fold , while those from the caecum reduced significantly , but less effectively , by 22 % ( Fig 1A ) .	9	THE INVASION-REPRESSING SIGNAL FACTOR C2-HDA IS PRESENT IN THE MURINE INTESTINE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	regulator	33617591	17	ver/dev	HilD , K293A remained bound to the hilA promoter despite the presence of Fig 5 .	178	HilD , which is impaired for binding to c2-HDA , K293A remained bound to the hilA promoter despite the presence of 30 μM c2-HDA ( Fig 5B ) .	11	BINDING OF C2-HDA TO SPECIFIC HILD RESIDUES DICTATES ITS STABILITY AND CAPACITY TO BIND TARGET DNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	33617591	17	ver/dev	HilD , K293A remained bound to the hilA promoter despite the presence of 30 μM c2-HD .	178	HilD , which is impaired for binding to c2-HDA , K293A remained bound to the hilA promoter despite the presence of 30 μM c2-HDA ( Fig 5B ) .	11	BINDING OF C2-HDA TO SPECIFIC HILD RESIDUES DICTATES ITS STABILITY AND CAPACITY TO BIND TARGET DNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	regulator	34202800	14	ver/dev	PhoP specifically binds the hilA promoter to block the binding of HilD as a repression mechanism	329	PhoP specifically binds the hilA promoter to block the binding of HilD , HilC , and RtsA activators as a repression mechanism [ 126 ]	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	regulator	34424033	2	ver/dev	Expression of hilA is controlled by the transcription factors HilD ,	18	Expression of hilA is controlled by the transcription factors HilD ,	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of Fig 1A , upregulation of hdfR transcription by StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of Fig 1A , upregulation of hdfR transcription by StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of Fig 1A , upregulation of hdfR transcription by StdE may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of Fig 1A , upregulation of hdfR transcription by StdE may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of std expression , upregulation of hdfR transcription by StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of std expression , upregulation of hdfR transcription by StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of std expression , upregulation of hdfR transcription by StdE may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of std expression , upregulation of hdfR transcription by StdE may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	activator	31216025	3	ver/dev	Formation of the StdON subpopulation thus requires both HdfR : HdfR activate StdE activates hdfR transcription .	225	Formation of the StdON subpopulation thus requires both StdEF and HdfR ( Figure 4B , lower panel ) , suggesting the existence of a network of positive feedback : StdF and HdfR activate std transcription and StdE activates hdfR transcription .	25	TRANSCRIPTIONAL ACTIVATION OF STD BY HDFR	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HdfR	gene	hdfR	activator	31216025	3	ver/dev	Formation of the StdON subpopulation thus requires both HdfR : HdfR activate std transcription activates hdfR transcription .	225	Formation of the StdON subpopulation thus requires both StdEF and HdfR ( Figure 4B , lower panel ) , suggesting the existence of a network of positive feedback : StdF and HdfR activate std transcription and StdE activates hdfR transcription .	25	TRANSCRIPTIONAL ACTIVATION OF STD BY HDFR	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HdfR	gene	hdfR	activator	31216025	3	ver/dev	Formation of the StdON subpopulation thus requires both StdEF : HdfR activate std transcription activates hdfR transcription .	225	Formation of the StdON subpopulation thus requires both StdEF and HdfR ( Figure 4B , lower panel ) , suggesting the existence of a network of positive feedback : StdF and HdfR activate std transcription and StdE activates hdfR transcription .	25	TRANSCRIPTIONAL ACTIVATION OF STD BY HDFR	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by HdfR , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdF synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by HdfR , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdF synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by HdfR , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by HdfR , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by StdF , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdF synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by StdF , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdF synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by StdF , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	hdfR	activator	31216025	7	ver/dev	Transcription of hdfR is activated by StdE and transcription of std is activated by StdF , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE synthesis .	353	Transcription of hdfR is activated by StdE ( Figure 3 ) and transcription of std is activated by StdF and by HdfR ( Figures 2 and 4 ) , thereby creating a complex feedback loop : StdE is necessary for HdfR synthesis and HdfR is necessary for StdE and StdF synthesis .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	STM1250	regulator	31396489	1	ver/dev	Interestingly , STM1250 is also regulated by Fis .	332	Interestingly , STM1250 is also regulated by Fis , a global regulator of virulence genes ( Wang et al. , 2013 ) .	17	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SprB	gene	sopB	regulator	21168230	2	ver/dev	SprB , regulates the expression of sopB .	212	SprB , a transcriptional regulator , is encoded within the SPI1 and regulates the expression of sipC , sptP , avrA , sopB and sopE ( Eichelberg et al. , 1999 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	sirA	activator	11162188	1	ver/dev	The fliZ mutation did not have a significant effect on the sirA expression , indicating that FliZ control of the hilA expression is not mediated by transcriptional activation of the sirA gene .	110	The fliZ mutation did not have a significant effect on the sirA expression , indicating that FliZ control of the hilA expression is not mediated by transcriptional activation of the sirA gene .	6	TRANSCRIPTION OF THE VIRULENCE-ASSOCIATED GENES IN THE FLIZ MUTANT	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
BolA	gene	dacC	regulator	30524381	26	ver/dev	In another study , dacC was regulated by BolA .	293	In another study , dacC was shown to be essential for E. coli cell morphology and was regulated by BolA ( Santos et al. , 2002 ) .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YdgT	gene	pefB	regulator	31661351	17	ver/dev	While the precise mechanism of pef fimbriae regulation by YdgT remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefB since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs .	344	While the precise mechanism of pef fimbriae regulation by Hha and YdgT remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefB and pefA since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs [ 24 ] .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
TyrR	gene	hyaB	activator	10692151	4	ver/dev	TyrR are required for anaerobic induction of hyaB in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	hyaB	activator	10692151	4	ver/dev	TyrR are required for acid-pH induction of hyaB in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	hyaB	activator	17906148	9	ver/dev	TyrR are required for anaerobic induction of hyaB in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	hyaB	activator	17906148	9	ver/dev	TyrR are required for acid-pH induction of hyaB in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	hilE	activator	21478311	1	ver/dev	It has also been demonstrated that FimZ can induce hilE .	278	It has also been demonstrated that FimZ can induce hilE , which is a negative regulator of SPI1 ( 5 , 50 ) .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FimZ	gene	hilE	activator	25547794	0	att	Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does not affect fimZ expression but does upregulate hilE in an FimZ-dependent manner .	12	Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does not affect fimZ expression but does upregulate hilE in an FimZ-dependent manner .	1	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FimZ	gene	hilE	activator	25547794	6	ver/dev	In our studies , we showed that FimZ upregulates hilE expression , thereby playing a significant role in whether hilA is expressed or not .	64	In our studies , we showed that FimZ upregulates hilE expression , thereby playing a significant role in whether hilA is expressed or not .	2	MAIN	nan	1	L2	SPEC	Investigation	OTHER	Other	Level 1
FimZ	gene	hilE	activator	27564394	6	att	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	hilE	activator	27564394	0	ver/dev	The hilE gene is transcriptionally activated by the regulator of fimbrial gene expression , FimZ .	152	The hilE gene is transcriptionally activated by the regulator of fimbrial gene expression , FimZ [ 29 ] , and HilE interacts with the HilD protein to repress hilA transcription [ 52 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	hilE	activator	27564394	6	ver/dev	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	hilE	activator	27777572	1	ver/dev	FimZ alone can enhance the expression of hilE .	367	FimZ alone can enhance the expression of hilE , a repressor of SPI-1 gene expression .	21	MENAQUINONE REVERSES THE EFFECT OF YQIC DELETION ON EXPRESSION OF TYPE-1	nan	1	L2	OTHER	Other	OTHER	New	Level 1
FimZ	gene	hilE	activator	29378886	33	ver/dev	FimZ should lead to increased expression of hilE -LRB- not tested -RRB-	270	Deletion of invS leads to increased levels of FimZ , which should lead to increased expression of hilE ( not tested ) .	5	DISCUSSION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FimZ	gene	hilE	activator	31428589	11	ver/dev	FimZ enhances the expression of hilE .	181	FimZ enhances the expression of hilE , which negatively regulates hilD .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	invF	repressor	17178790	15	ver/dev	In contrast , RcsB under low-osmolarity conditions , acting in association with the viaB locus-encoded TviA protein , negatively controls the transcription of invF .	345	In contrast , RcsB under low-osmolarity conditions , acting in association with the viaB locus-encoded TviA protein , negatively controls the transcription of iagA , invF , and sipB ( encoding proteins involved in cell invasion ) ( 1 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	bfr	activator	17302823	0	att	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	bfr	activator	17302823	1	att	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Other	OTHER	Other	Level 1
Fur	gene	bfr	activator	17302823	0	ver/dev	Thus , the S. Typhimu-rium bfr are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	bfr	activator	17302823	1	ver/dev	Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
Fur	gene	bfr	activator	17302823	1	ver/dev	Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
RstA	gene	fhuA	repressor	18790861	20	ver/dev	Under the same growth-conditions , the RstA protein was unable to repress transcription of fhuA .	158	Under the same growth conditions , the RstA protein was unable to repress transcription of fhuA ( Fig. 1C ) , which resembled the result in LB medium treated with the iron chelator ( Fig. 1B ) .	4	RESULTS	nan	1	L2	OTHER	Other	NEG	Other	Level 1
CRP	gene	melR	regulator	21148209	33	ver/dev	This mechanism has been described for the tandem regulation of the melR promoters in E. coli ; in both cases , a second sequence located upstream are relevant for CRP transcriptional activation .	270	This mechanism has been described for the tandem regulation of the cdd and melR promoters in E. coli ; in both cases , a sequence close to the 235 and a second sequence located upstream are relevant for CRP transcriptional activation ( Busby et al. , 1994 ; Savery et al. , 1996 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	melR	regulator	21148209	33	ver/dev	This mechanism has been described for the tandem regulation of the melR promoters in E. coli ; in both cases , a sequence close to the 235 are relevant for CRP transcriptional activation .	270	This mechanism has been described for the tandem regulation of the cdd and melR promoters in E. coli ; in both cases , a sequence close to the 235 and a second sequence located upstream are relevant for CRP transcriptional activation ( Busby et al. , 1994 ; Savery et al. , 1996 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	sseA	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	gogB	activator	15843015	3	att	In contrast , gogB expression under SPI-1-inducing conditions was not co-regulated with other HilA-dependent virulence genes encoded within SPI-1 .	247	In contrast , gogB expression under SPI-1-inducing conditions was not co-regulated with other HilA-dependent virulence genes encoded within SPI-1 .	8	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FNR	gene	pflC	regulator	21887378	1	ver/dev	Furthermore , Fnr is involved in regulation of pflC , encoding the ` pyruvate formate lyase activase II ' and ` putative formate acetyltransferase 2 ' respectively , that were also identified from in IVET screening .	374	Furthermore , Fnr is involved in regulation of pflC and pflD , encoding the ` pyruvate formate lyase activase II ' and ` putative formate acetyltransferase 2 ' respectively , that were also identified from in IVET screening .	19	QUORUM SENSING AND ANAEROBIC GROWTH	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	thiM	activator	30742606	0	att	For example , translational repression of thiMD genes caused by the binding of TPP to thiM riboswitch promotes Rho-dependent premature termination in a region located between codons 20 and 34 of thiM [ 13 ] .	54	For example , translational repression of thiMD genes caused by the binding of TPP to thiM riboswitch promotes Rho-dependent premature termination in a region located between codons 20 and 34 of thiM [ 13 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	thiM	activator	30742606	0	att	For example , translational repression of thiMD genes caused by the binding of TPP to thiM riboswitch promotes Rho-dependent premature termination in a region located between codons 20 and 34 of thiM [ 13 ] .	54	For example , translational repression of thiMD genes caused by the binding of TPP to thiM riboswitch promotes Rho-dependent premature termination in a region located between codons 20 and 34 of thiM [ 13 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	arcA	regulator	11238977	0	att	When , finally , the RpoS-controlled stationary-phase of growth is reached , arcA is suppressed in an RpoS-dependent fashion .	17	When , finally , the RpoS-controlled stationary phase of growth is reached , arcA is suppressed in an RpoS-dependent fashion .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	hfq	regulator	29417203	14	ver/dev	DksA , plays a role in regulating hfq gene expression	132	Studies with Shigella flexneri show that DksA , a pleiotropic regulator , plays a role in regulating hfq gene expression and this regulation is important for virulence [ 37 ] .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
ChbR	gene	chiP	activator	24450479	18	ver/dev	Altogether , these observations suggested that the residual chiP induction by chitobiose in the ΔchiX background is unlikely to be due to direct activation by ChbR at the chiP promoter .	89	Altogether , these observations suggested that the residual chiP induction by chitobiose in the ΔchiX background is unlikely to be due to direct activation by ChbR at the chiP promoter .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
ChbR	gene	chiP	activator	24450479	18	ver/dev	Altogether , these observations suggested that the residual chiP induction by chitobiose in the ΔchiX background is unlikely to be due to direct activation by ChbR at the chiP promoter .	89	Altogether , these observations suggested that the residual chiP induction by chitobiose in the ΔchiX background is unlikely to be due to direct activation by ChbR at the chiP promoter .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
ChbR	gene	chiP	activator	24450479	20	ver/dev	From the data in Fig. 3 , it is apparent that inactivation of the ChbR repressor completely prevents residual chiP induction by chitobiose in ΔchiX background in E. coli as it does in Salmonella .	99	From the data in Fig. 3 , it is apparent that inactivation of the ChbR repressor completely prevents residual chiP induction by chitobiose in ΔchiX background in E. coli as it does in Salmonella .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
ChbR	gene	chiP	activator	24450479	21	ver/dev	Given that the E. coli sequence lacks the ChbR binding site and shows no binding to the purified protein in-vitro , these findings suggest that the ChbR requirement for the residual induction of chiP by chitobiose is independent of ChbR binding to the chiP promoter region .	100	Given that the E. coli sequence lacks the ChbR binding site and shows no binding to the purified protein in vitro ( see above ) , these findings suggest that the ChbR requirement for the residual induction of chiP by chitobiose is independent of ChbR binding to the chiP promoter region .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	Escherichia coli	0	L2	SPEC	Analysis	NEG	Other	Level 1
ChbR	gene	chiP	activator	24450479	25	ver/dev	Final proof that the ChbR binding site at − 180 in Sal-monella is not implicated in chitobiose induction of chiP came from replacing the ChbR binding site in Salmonella with h 11 -- lacZ fusion construct on the chromosome .	113	Final proof that the ChbR binding site at − 180 in Sal-monella is not implicated in chitobiose induction of chiP came from replacing the ChbR binding site in Salmonella with 11 bp derived from the equivalent region in E. coli in cis in the chiP -- lacZ fusion construct on the chromosome .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	Salmonella;Salmonella;Salmonella	1	L2	OTHER	Other	NEG	Other	Level 1
ChbR	gene	chiP	activator	24450479	29	ver/dev	Thus the ChbR requirement for chiP induction can be simply explained based on its essential role in activation of the chb operon .	120	Thus the ChbR requirement for chiP induction can be simply explained based on its essential role in activation of the chb operon .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
ChbR	gene	chiP	activator	24450479	37	ver/dev	Intriguingly , while footprint analysis confirmed such binding , we obtained no evidence for a ChbR involvement in chiP induction other than its indirect role as activator of chbBCARFG transcription .	172	Intriguingly , while footprint analysis confirmed such binding , we obtained no evidence for a ChbR involvement in chiP induction other than its indirect role as activator of chbBCARFG transcription .	8	DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
ChbR	gene	chiP	activator	24450479	38	ver/dev	Furthermore , replacement of the ChbR binding site in the Salmonella chiP promoter region with the sequence did not affect chiP induction by chitobiose to any significant extent .	174	Furthermore , replacement of the ChbR binding site in the Salmonella chiP promoter region with the sequence found at the corresponding position in E. coli did not affect chiP induction by chitobiose to any significant extent .	8	DISCUSSION	Salmonella	1	L2	OTHER	Other	NEG	New	Level 1
ChbR	gene	chiP	activator	24450479	47	ver/dev	Activation of chbBCA expression by ChbR is essential to relieve ChiX repression of chiP .	220	Activation of chbBCA expression by ChbR is essential to relieve ChiX repression of chiP .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	cpxP	activator	16574345	0	att	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	179	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	15	3.1. MICROARRAY ANALYSIS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	hlyE	regulator	14996792	14	ver/dev	Thus , we concluded that H-NS all contribute towards the regulation of hlyE expression .	83	Thus , we concluded that CRP , FNR , and H-NS all contribute towards the regulation of hlyE expression .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hlyE	regulator	14996792	25	ver/dev	H-NS binds at two regions of the hlyE promoter with high affinity .	127	H-NS binds at two regions of the hlyE promoter with high affinity .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hlyE	regulator	14996792	28	ver/dev	To investigate how much of this extensive H-NS protection is required for the observed regulation of hlyE expression , we used two approaches as follows .	130	To investigate how much of this extensive H-NS protection is required for the observed regulation of hlyE expression , we used two approaches as follows .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hlyE	regulator	14996792	54	ver/dev	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both csiD genes in E. coli is stimulated by H-NS .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hlyE	regulator	14996792	54	ver/dev	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both the malT in E. coli is stimulated by H-NS .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hlyE	regulator	14996792	62	ver/dev	In summary , we have shown that the H-NS-mediated regulation of hlyE expression in E. coli K-12 is more complex than was previously suggested because H-NS can negatively to hlyE expression .	274	In summary , we have shown that the H-NS-mediated regulation of hlyE expression in E. coli K-12 is more complex than was previously suggested because H-NS can contribute positively as well as negatively to hlyE expression .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hlyE	regulator	14996792	62	ver/dev	In summary , we have shown that the H-NS-mediated regulation of hlyE expression in E. coli K-12 is more complex than was previously suggested because H-NS can contribute positively .	274	In summary , we have shown that the H-NS-mediated regulation of hlyE expression in E. coli K-12 is more complex than was previously suggested because H-NS can contribute positively as well as negatively to hlyE expression .	8	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hlyE	regulator	17259627	39	ver/dev	For example , E. coli hlyE -LRB- also known as sheA -RRB- , is regulated positively by the nucleoid-structuring protein H-NS .	365	For example , E. coli hlyE ( also known as clyA and sheA ) , which encodes a novel pore-forming toxin , is regulated positively by the global transcriptional factors FNR ( fumarate and nitrate reduction ) and CRP ( cAMP receptor protein ) and by SlyA , and negatively by the nucleoid-structuring protein H-NS ( Wyborn et al. , 2004 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	gene	hlyE	regulator	17259627	39	ver/dev	For example , E. coli hlyE -LRB- also known as clyA -RRB- , is regulated positively by the nucleoid-structuring protein H-NS .	365	For example , E. coli hlyE ( also known as clyA and sheA ) , which encodes a novel pore-forming toxin , is regulated positively by the global transcriptional factors FNR ( fumarate and nitrate reduction ) and CRP ( cAMP receptor protein ) and by SlyA , and negatively by the nucleoid-structuring protein H-NS ( Wyborn et al. , 2004 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	gene	hlyE	regulator	19204896	10	ver/dev	Lithgow JK , Haider F , Roberts IS , Green J H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .	178	Lithgow JK , Haider F , Roberts IS , Green J ( 2007 ) Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .	8	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hlyE	regulator	19229334	13	ver/dev	Lithgow JK , Haider F , Roberts IS , Green J H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .	923	Lithgow JK , Haider F , Roberts IS , Green J ( 2007 ) Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .	25	AUTHOR CONTRIBUTIONS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hlyE	regulator	19763423	2	ver/dev	H-NS nucleoprotein complexes control hlyE expre	407	SlyA and H-NS nucleoprotein complexes control hlyE expre	12	REPUBLIC OF KOREA.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hlyE	regulator	25916986	4	ver/dev	H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .	573	Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .	58	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	tehB	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	rcsC	activator	12519186	22	att	On the other hand , the tolB mutant produced two S1 products : the large PmrA-dependent product , and a small product whose presence is RcsB dependent because it was produced at higher levels in a mutant harbouring a constitutive allele of rcsC -- rcsC11 ( Costa and Anton , 2001 ) , and it was not detected in RNA harvested from rcsB and tolB rcsB mutants ( Fig. 4A ) .	73	On the other hand , the tolB mutant produced two S1 products : the large PmrA-dependent product , and a small product whose presence is RcsB dependent because it was produced at higher levels in a mutant harbouring a constitutive allele of rcsC -- rcsC11 ( Costa and Anton , 2001 ) , and it was not detected in RNA harvested from rcsB and tolB rcsB mutants ( Fig. 4A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SlyA	gene	sopE2	regulator	29857034	33	ver/dev	Direct regulation of sopE2 genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	sopE2	regulator	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopE2 were negatively regulated by SlyA , with DslyA expression increased five-times , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sopE2	regulator	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopE2 were negatively regulated by SlyA , with DslyA expression increased two , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagJ	regulator	19348639	0	ver/dev	pagJ are known to be regulated by SlyA	254	The SPI-2 cluster is closely associated with three virulence-related genes ( pagJ , pagK , and phoN ) , which are known to be regulated by two virulenceassociated regulators , SlyA and PhoP ,56 that also regulate a number of SPI-2 genes .	14	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	ssaG	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FadR	gene	fabA	regulator	27004424	4	ver/dev	Conversely , FadR , stimulates UFA biosynthesis by binding to the fabA end fabB promoter .	45	Conversely , another transcription regulator , FadR , stimulates UFA biosynthesis by binding to the fabA end fabB promoter .	5	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YdiV	TU	flhDC	repressor	24706743	1	ver/dev	The known posttranscriptional inhibitors of flhDC expression included in this study were YdiV .	126	The known transcriptional and posttranscriptional inhibitors of flhDC expression included in this study were EcnR , RscB , LrhA , FliT , DskA , and YdiV .	4	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
YdiV	TU	flhDC	repressor	24706743	1	ver/dev	The known transcriptional inhibitors of flhDC expression included in this study were YdiV .	126	The known transcriptional and posttranscriptional inhibitors of flhDC expression included in this study were EcnR , RscB , LrhA , FliT , DskA , and YdiV .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
YdiV	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliT , YdiV .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	invG	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	flhD	repressor	23676436	0	ver/dev	In addition to controlling SPI1 expression , HilA represses expression of flhD expression .	29	In addition to controlling SPI1 expression , HilA induces expression of SPI4 and SPI5 , and represses expression of the SPI2 genes and flhD expression ( Thijs et al. , 2007 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EmrR	gene	pagC	regulator	30992361	13	att	We chose some bioactive phenolic compounds ( 39 ) and investigated their effects on transcription of EmrR-regulated pagC gene on the premise that EmrR could sense one of these molecules .	118	We chose some bioactive phenolic compounds ( 39 ) and investigated their effects on transcription of EmrR-regulated pagC gene on the premise that EmrR could sense one of these molecules .	3	RESULTS	nan	1	L1	OTHER	Other	OTHER	New	Level 1
EmrR	gene	pagC	regulator	30992361	33	ver/dev	-LRB- Left -RRB- The pagC promoter forms a `` derepression state '' after binding to EmrR .	261	( Left ) The pagC promoter forms a `` derepression state '' after binding to EmrR .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	yigN	activator	30760616	1	att	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	148	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
NadR	gene	nadB	regulator	15805524	4	ver/dev	We confirmed the previous evidence that purified NadR protein binds nadB operator sequence in the absence of ATP with or without Fig. 3A .	174	We confirmed the previous evidence ( 25 ) that purified NadR protein binds nadB operator sequence in the absence of ATP with or without NAD ( Fig. 3A ) .	4	RESULTS	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
NadR	gene	nadB	regulator	15805524	4	ver/dev	We confirmed the previous evidence that purified NadR protein binds nadB operator sequence in the absence of ATP with or without NAD .	174	We confirmed the previous evidence ( 25 ) that purified NadR protein binds nadB operator sequence in the absence of ATP with or without NAD ( Fig. 3A ) .	4	RESULTS	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
LsrR	gene	sdiA	regulator	30286813	0	ver/dev	In Salmonella Typhimurium , sdiA are regulated by the transcription factor LsrR .	254	In Salmonella Typhimurium , sdiA and srgE are regulated by the transcription factor LsrR .	13	DISCUSSION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	rck	regulator	15130116	9	ver/dev	Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates accessory factors -LRB- rck , pefI , srgA -RRB- .	223	Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates accessory factors that may contribute to intestinal survival or colonization ( rck , pefI , srgA ) and other genes of unknown function ( srgB -- E ) .	5	THE SALMONELLA SDIA SYSTEM	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CspE	gene	rpoS	regulator	32159509	11	ver/dev	Phadtare S , Inouye M. Role of CspE in regulation of expression of rpoS , the stress response proteins in Escherichia coli .	380	Phadtare S , Inouye M. Role of CspC and CspE in regulation of expression of rpoS and UspA , the stress response proteins in Escherichia coli .	29	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	nsrR	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	bolA	regulator	11238977	6	ver/dev	Growth phase-regulated expression of bolA of stationary-phase Escherichia coli cells is controlled by the novel sigma factor RpoS .	342	Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells is controlled by the novel sigma factor RpoS .	13	IUCHI, S., CHEPURI, V., FU, H. A., GENNIS, R. B. & LIN, E. C. (1990B).	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	gudT	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1344	regulator	19376870	9	ver/dev	-LRB- A to D -RRB- The expression of the master regulator of rdar morphotype expression , CsgD , in the STM1344 mutant was downregulated in comparison to that in wild-type S. Typhimurium UMR1 .	231	( A to D ) The expression of the rdar morphotype ( A ) , calcofluor white binding capability ( indicative of cellulose expression ) ( B ) , extracellular matrix component curli fimbriae ( C ) , and the master regulator of rdar morphotype expression , CsgD ( D ) , in the STM1344 mutant was downregulated in comparison to that in wild-type S. Typhimurium UMR1 .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	regulator	19376870	28	ver/dev	STM1344 positively affects the expression of the major regulator of CsgD , through the downregulation of the expression of the phosphodiesterases STM1703 and STM3611 .	342	STM1344 positively affects the expression of the major regulator of the multicellular rdar morphotype behavior , CsgD , through the downregulation of the expression of the phosphodiesterases STM1703 and STM3611 ( 37 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	regulator	19691499	0	ver/dev	Römlin , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	536	Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , and Römling , U. ( 2009a ) A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	35	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	regulator	19691499	0	ver/dev	Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	536	Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , and Römling , U. ( 2009a ) A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	35	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	regulator	24127899	45	ver/dev	Römlin , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	586	Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , and Römling , U. ( 2009 ) A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	44	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	regulator	24127899	45	ver/dev	Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	586	Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , and Römling , U. ( 2009 ) A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .	44	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	regulator	25824832	11	ver/dev	A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility in Salmonella enterica serovar Typhimurium .	782	A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility in Salmonella enterica serovar Typhimurium .	41	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	tnpA	activator	28335027	12	att	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	770	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	invA	regulator	14633100	0	att	virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .	15	virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .	1	ABSTRACT	Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	invA	regulator	14633100	0	att	virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .	15	virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .	1	ABSTRACT	Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	invA	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	invA	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	invA	regulator	14633100	3	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	190	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	invA	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	invA	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	cfa	activator	15632439	2	att	38 S suggested that the CFA synthesis during the stationary-phase is due to the increased transcription of cfa mediated by the RpoS-dependent promoter in E. coli .	43	38 S suggested that the CFA synthesis during the stationary phase is due to the increased transcription of cfa mediated by the RpoS-dependent promoter in E. coli .	3	MAIN	Cell fusing agent virus;Cell fusing agent virus;Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	cfa	activator	15632439	3	att	In E. coli , it has been suggested that the initiation of CFA synthesis at the entry to the stationary-phase is due to the increased transcription of cfa by the RpoS-dependent promoter ( P2 ) whereas the s - dependent promoter ( P1 ) is responsible 70 for the low level of CFA synthesis in exponentially growing cultures ( Eichel et al. , 1999 ; Wang & Cronan , 1994 ) .	225	In E. coli , it has been suggested that the initiation of CFA synthesis at the entry to the stationary phase is due to the increased transcription of cfa by the RpoS-dependent promoter ( P2 ) whereas the s - dependent promoter ( P1 ) is responsible 70 for the low level of CFA synthesis in exponentially growing cultures ( Eichel et al. , 1999 ; Wang & Cronan , 1994 ) .	8	A CFA MUTANT IS UNABLE TO PRODUCE CFAS	Escherichia coli;Cell fusing agent virus;Cell fusing agent virus;Cell fusing agent virus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	ptsN	activator	33853321	7	ver/dev	CRP induces ptsN transcription by binding to its promoter .	123	CRP induces ptsN transcription by binding to its promoter .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	ptsN	activator	33853321	18	ver/dev	Thus , CRP promotes pdu expression in two ways : by transcriptional activation of the ptsN gene .	280	Thus , CRP promotes pdu expression in two ways : by directly increasing transcription of the pdu operon and by transcriptional activation of the ptsN gene .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	rmf	activator	30760616	5	ver/dev	In addition , CpxR induces expression of the ribosome modulation factor rmf to inhibit translation .	290	In addition , CpxR induces expression of the ribosome modulation factor rmf and ribosomeassociated inhibitor A ( raiA ) to inhibit translation ( 76 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ompR	activator	12068808	55	att	These include ( i ) increasing OmpR levels through autoinduction in which OmpR-P overcomes H-NS repression of ompR ; ( ii ) binding of OmpR-P to specific ATR genes ; and ( iii ) an undefined effect of acid-pH on OmpR-P-dependent ATR gene promoters .	282	These include ( i ) increasing OmpR levels through autoinduction in which OmpR-P overcomes H-NS repression of ompR ; ( ii ) binding of OmpR-P to specific ATR genes ; and ( iii ) an undefined effect of acid pH on OmpR-P-dependent ATR gene promoters .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ompR	activator	12068808	24	ver/dev	A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR-P -LRB- as indicated -RRB- for 2 h at room temperature .	166	A radiolabelled ompR promoter DNA fragment and two control fragments ( 5000 c.p.m. ) were incubated with increasing quantities of OmpR or OmpR-P ( as indicated ) for 2 h at room temperature and assayed for an electrophoretic mobility shift .	10	OMPR FOOTPRINT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR-P	gene	ompR	activator	12080060	55	att	These include ( i ) increasing OmpR levels through autoinduction in which OmpR-P overcomes H-NS repression of ompR ; ( ii ) binding of OmpR-P to specific ATR genes ; and ( iii ) an undefined effect of acid-pH on OmpR-P-dependent ATR gene promoters .	282	These include ( i ) increasing OmpR levels through autoinduction in which OmpR-P overcomes H-NS repression of ompR ; ( ii ) binding of OmpR-P to specific ATR genes ; and ( iii ) an undefined effect of acid pH on OmpR-P-dependent ATR gene promoters .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ompR	activator	12080060	24	ver/dev	A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR-P -LRB- as indicated -RRB- for 2 h at room temperature .	166	A radiolabelled ompR promoter DNA fragment and two control fragments ( 5000 c.p.m. ) were incubated with increasing quantities of OmpR or OmpR-P ( as indicated ) for 2 h at room temperature and assayed for an electrophoretic mobility shift .	10	OMPR FOOTPRINT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliZ	gene	fliZ	activator	25161191	6	ver/dev	Rather , the FliA loop contributes to bistability by ensuring that expression of FliZ is strongly enhanced by FlhD4C2 due to fliZ .	229	Rather , the FliA loop contributes to bistability by ensuring that expression of FliZ is strongly enhanced by FlhD4C2 due to fliZ being transcribed from a hybrid class 2/3 promoter .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliZ	gene	fliZ	activator	25972986	1	att	However , as stress in introduced in the surroundings , the FliZ-dependent feedback is much more sensitive and as a result , the fliZ mutant exhibits a much steeper decline in class 2 and class 3 expression ( Fig. 3a , b ) .	310	However , as stress in introduced in the surroundings , the FliZ-dependent feedback is much more sensitive and as a result , the fliZ mutant exhibits a much steeper decline in class 2 and class 3 expression ( Fig. 3a , b ) .	6	STEADY STATE CLASS 2 AND CLASS 3 EXPRESSIONS AT VARIOUS NUTRITIONAL LEVELS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	STM3611	activator	24127899	27	ver/dev	FlhD4C2 suppresses rdar biofilm formation through activation of STM3611 expression by the class 2 sigma factor FliA .	258	FlhD4C2 suppresses rdar biofilm formation and CsgD expression through activation of STM3611 expression by the class 2 sigma factor FliA ( Jonas et al. , 2010 ) .	11	FUNCTIONAL FLAGELLA AND CHEMOTAXIS ARE REQUIRED FOR INVASION OF HT-29 CELLS BY S. TYPHIMURIUM UMR1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	STM1269	regulator	15681155	16	ver/dev	Using site directed mutagenesis , Marchal et al. demonstrated that the fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 promoters .	261	Using site directed mutagenesis , Marchal et al. [ 35 ] demonstrated that the third and fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 , STM1253 and STM4118 promoters .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM1269	regulator	15681155	16	ver/dev	Using site directed mutagenesis , Marchal et al. demonstrated that the third positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 promoters .	261	Using site directed mutagenesis , Marchal et al. [ 35 ] demonstrated that the third and fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 , STM1253 and STM4118 promoters .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
DksA	gene	ssrB	activator	29930310	24	att	Transcriptional control of a small RNA could mediate the DksA-dependent post-transcriptional activation of ssrB .	193	Transcriptional control of a small RNA could mediate the DksA-dependent post-transcriptional activation of ssrB .	4	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
DksA	gene	ssrB	activator	29930310	25	att	Further investigations are needed to elucidate whether DsrA or a small RNA contribute to the DksA-dependent activation of ssrB .	195	Further investigations are needed to elucidate whether DsrA or a small RNA contribute to the DksA-dependent activation of ssrB .	4	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	ssrB	activator	29930310	2	ver/dev	Collectively , these findings indicate that ppGpp relieves the negative regulation , whereas DksA activates ssrB gene expression post-transcriptionally .	13	Collectively , these findings indicate that ( p ) ppGpp relieves the negative regulation associated with the AT-rich discriminator region in the promoter of the horizontally-acquired ssrA gene , whereas DksA activates ssrB gene expression post-transcriptionally .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
DksA	gene	ssrB	activator	29930310	8	ver/dev	We examined whether DksA participate in the transcriptional activation of the ssrB genes .	80	We examined whether DksA and ( p ) ppGpp participate in the transcriptional activation of the ssrA and ssrB genes that encode the master two-component regulatory system that activates SPI2 expression .	3	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	New	Level 1
DksA	gene	ssrB	activator	29930310	24	ver/dev	Transcriptional control of a small RNA could mediate the DksA-dependent post-transcriptional activation of ssrB .	193	Transcriptional control of a small RNA could mediate the DksA-dependent post-transcriptional activation of ssrB .	4	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
DksA	gene	ssrB	activator	29930310	25	ver/dev	Further investigations are needed to elucidate whether a small RNA contribute to the DksA-dependent activation of ssrB .	195	Further investigations are needed to elucidate whether DsrA or a small RNA contribute to the DksA-dependent activation of ssrB .	4	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	ssrB	activator	29930310	25	ver/dev	Further investigations are needed to elucidate whether DsrA contribute to the DksA-dependent activation of ssrB .	195	Further investigations are needed to elucidate whether DsrA or a small RNA contribute to the DksA-dependent activation of ssrB .	4	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	yjfP	regulator	30760616	7	ver/dev	In addition , the esterase yjfP were also positively regulated by CpxR in egg white .	292	In addition , the major facilitator superfamily member tsgA , the esterase yjfP , and a putative membrane-bound redox modulator alx were also positively regulated by CpxR in egg white ( 78 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	kgtP	regulator	29857034	33	ver/dev	Direct regulation of kgtP genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with Venus , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with Venus , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with yfp , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with yfp , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with Venus , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with Venus , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with yfp , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC with yfp , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	repressor	31501286	23	ver/dev	MarA homologs repress flhDC expression posttranscriptionally .	204	MarA homologs repress flhDC expression posttranscriptionally .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	flhDC	repressor	31501286	25	ver/dev	This approach allowed detection of possible posttranscriptional effects on flhDC expression , since reductions in flagellar expression and motility could not occur through transcriptional repression of the native flhDC promoter when MarA was ectopically expressed .	207	This approach allowed detection of possible posttranscriptional effects on flhDC expression , since reductions in flagellar expression and motility could not occur through transcriptional repression of the native flhDC promoter when MarA , SoxS , Rob , or RamA was ectopically expressed .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
MarA	TU	flhDC	repressor	31501286	36	ver/dev	FIG 3 Production of MarA _ resulting in posttranscriptional repression of flhDC	269	FIG 3 Production of MarA , SoxS , Rob , and RamA resulting in posttranscriptional repression of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	flhDC	repressor	31501286	46	ver/dev	In the case of MarA , this largely occurs through binding repression of the flhDC promoter .	447	In the case of MarA and Rob , this largely occurs through binding repression of the flhDC promoter .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	invF	activator	28704543	43	ver/dev	Together , these results show that SsrB simultaneously induces the expression of invF , respectively , inside Fig 8D .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	invF	activator	28704543	43	ver/dev	Together , these results show that SsrB simultaneously induces the expression of invF , respectively , inside macrophages .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilD	activator	16045614	48	ver/dev	In contrast , the presence of a hilD mutation completely blocked SirA induction of Fig. 5A .	292	In contrast , the presence of a hilD mutation completely blocked SirA induction of rtsA and hilC ( Fig. 5A ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilD	activator	16045614	48	ver/dev	In contrast , the presence of a hilD mutation completely blocked SirA induction of rtsA .	292	In contrast , the presence of a hilD mutation completely blocked SirA induction of rtsA and hilC ( Fig. 5A ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilD	activator	17208038	30	att	With the exception of the SirA-dependent csr system , we have not yet identified any of these intermediaries , nor do we know if the remaining systems function through a single intermediary or if each system controls hilD independently .	158	With the exception of the SirA-dependent csr system , we have not yet identified any of these intermediaries , nor do we know if the remaining systems function through a single intermediary or if each system controls hilD independently .	11	REGULATION OF HILD	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilD	activator	17208038	18	ver/dev	Thus SirA induction of csrBC prevents CsrA action , indirectly activating hilD expression post-transcriptionally .	112	Thus SirA induction of csrBC prevents CsrA action , indirectly activating hilD expression post-transcriptionally [ 43 ] .	8	BARA/SIRA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilD	activator	17208038	18	ver/dev	Thus SirA induction of csrBC prevents CsrA action , indirectly activating hilD expression post-transcriptionally .	112	Thus SirA induction of csrBC prevents CsrA action , indirectly activating hilD expression post-transcriptionally [ 43 ] .	8	BARA/SIRA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilD	activator	24500522	1	ver/dev	SirA , positively regulates hilD .	170	The global response regulator , SirA , positively regulates the expression of hilA , hilC , and hilD encoded within SPI-1 and SPI-2 ( Teplitski et al. 2006 ; Martínez et al. 2011 ) .	19	VIABILITY AND MOTILITY OF S. TYPHIMURIUM EXPOSED TO THE SIMULATED INTESTINAL CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilD	activator	28575106	3	ver/dev	SirA , independently of BarA , also activates hilD in response to the high acetate concentration .	91	SirA , independently of BarA , also activates hilD in response to the high acetate concentration ( 10 -- 30 mM ) found in the distal ileum [ 24 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
GcvA	gene	gcvB	activator	23376784	2	ver/dev	GcvA interacts with both σ subuni of RNA polymerase to activate e the Escherichia coli gcvB ge .	552	GcvA interacts with both the α and σ subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon .	29	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	prgHIJK	repressor	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the prgs prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	prgHIJK	repressor	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the PhoP-repressed genes prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rpoS	regulator	17725620	1	ver/dev	These results indicate that phoP may control the expression of the rpoS gene , as substantiated by previous reports that PhoP controls the expression of rpoS gene .	247	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	20	LF1036 4.49 LF1037 7.58	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhD	TU	flhDC	activator	33751923	11	ver/dev	Expression of flhDC is activated by QseBC and , as expected , QseBC is unable to activate fliA transcription in the absence of FlhD .	434	Expression of flhDC is activated by QseBC and , as expected , QseBC is unable to activate fliA transcription in the absence of FlhD ( Sperandio et al. 2002 ) .	11	QSECB	nan	1	L2	OTHER	Other	NEG	Other	Level 1
OxyR	gene	mntH	regulator	21722794	6	ver/dev	In addition , mntH is controlled by the hydrogen-peroxide sensor OxyR .	562	In addition , mntH is controlled by the hydrogen peroxide sensor OxyR ( Kehres et al. , 2002a ; Ikeda et al. , 2005 ) causing its expression to also be induced in response to intracellular hydrogen peroxide stress .	18	4.1.1. MNTH AND SITABCD (ALIAS MNTABCD)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	virB	activator	11123690	30	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	370	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	32	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	11123690	30	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .	370	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	32	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	17908208	86	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	519	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	24	ACKNOWLEDGEMENTS	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	17908208	86	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .	519	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	24	ACKNOWLEDGEMENTS	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	24354910	64	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	507	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF and repression by H-NS .	46	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	24354910	64	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF by H-NS .	507	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF and repression by H-NS .	46	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	25566242	22	ver/dev	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	455	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	54	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	activator	25566242	22	ver/dev	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .	455	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	54	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	relA	activator	16905537	9	att	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	197	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sopE2	regulator	27601571	19	ver/dev	Thus , many of the target genes of RtsA association of InvF with sites upstream of sopE2 regulated by a countersilencing mechanism .	212	Thus , many of the target genes of HilD , HilC , and RtsA association of InvF with sites upstream of sopE2 and STM14_1486 are likely regulated by a countersilencing mechanism .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sopE2	regulator	27601571	19	ver/dev	Thus , many of the target genes of HilC of InvF with sites upstream of sopE2 regulated by a countersilencing mechanism .	212	Thus , many of the target genes of HilD , HilC , and RtsA association of InvF with sites upstream of sopE2 and STM14_1486 are likely regulated by a countersilencing mechanism .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sopE2	regulator	27601571	19	ver/dev	Thus , many of the target genes of HilD of InvF with sites upstream of sopE2 regulated by a countersilencing mechanism .	212	Thus , many of the target genes of HilD , HilC , and RtsA association of InvF with sites upstream of sopE2 and STM14_1486 are likely regulated by a countersilencing mechanism .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sopE2	regulator	27601571	23	ver/dev	RNA-seq data for InvF confirm direct regulation of Our RNA-seq data identified 23 direct target genes sopE2 ( Fig. 2 ; see also Fig .	228	ChIP-seq and RNA-seq data for InvF confirm direct regulation of Our ChIP-seq and RNA-seq data identified 23 direct target genes sopE2 ( Fig. 2 ; see also Fig .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
InvF	gene	sopE2	regulator	27601571	23	ver/dev	ChIP-seq data for InvF confirm direct regulation of Our ChIP-seq data identified 23 direct target genes sopE2 ( Fig. 2 ; see also Fig .	228	ChIP-seq and RNA-seq data for InvF confirm direct regulation of Our ChIP-seq and RNA-seq data identified 23 direct target genes sopE2 ( Fig. 2 ; see also Fig .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilE	gene	hilD	repressor	24354910	16	ver/dev	Because HilE is a negative regulator of hilD , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level .	83	Because HilE is a negative regulator of hilD ( Baxter et al. , 2003 ) , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level , which in turn might inhibit HilD activity .	9	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilE	gene	hilD	repressor	28335027	10	ver/dev	post-translational repression by HilE dampens hilD activation	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilD	repressor	34048498	25	ver/dev	It is reasonable to suggest that when SirA counteracts the CsrA-mediated repression of hilD , higher levels of HilE would be required to negatively control the activity of HilD .	179	It is reasonable to suggest that when SirA counteracts the CsrA-mediated repression of hilD , higher levels of HilE would be required to negatively control the activity of HilD , which can be reached with the positive regulation of the hilE expression by SirA .	9	HILE REPRESSES HILD-MEDIATED EXPRESSION OF SPI-1, SPI-2 AND SPI-5 GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	hilE	activator	24354910	1	ver/dev	In vivo analyses indicate that LeuO activates hilE transcription .	24	In vivo analyses using β-galactosidase fusions indicate that LeuO activates hilE transcription .	7	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the occurrence of autogenous activation of hilD transcription .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in accordance with two well known facts .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	24354910	23	ver/dev	LeuO activates hilE transcription	107	LeuO activates hilE transcription	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	24354910	24	ver/dev	that LeuO may activate hilE expression	108	A tentative model for LeuO-mediated downregulation of SPI-1 via HilE and HilD is that LeuO may activate hilE expression , and that HilE-mediated inhibition of HilD activity ( Baxter et al. , 2003 ) may contribute to SPI-1 downregulation .	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
LeuO	gene	hilE	activator	24354910	24	ver/dev	that LeuO may activate hilE expression	108	A tentative model for LeuO-mediated downregulation of SPI-1 via HilE and HilD is that LeuO may activate hilE expression , and that HilE-mediated inhibition of HilD activity ( Baxter et al. , 2003 ) may contribute to SPI-1 downregulation .	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
LeuO	gene	hilE	activator	24354910	25	ver/dev	To test whether LeuO is an activator of a hilE : : lacZ translational fusion was constructed on the Salmonella chromosome .	109	To test whether LeuO is an activator of hilE expression , a hilE : : lacZ translational fusion was constructed on the Salmonella chromosome .	10	LEUO ACTIVATES HILE TRANSCRIPTION	Salmonella	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	hilE	activator	24354910	25	ver/dev	To test whether LeuO is an activator of hilE expression : : lacZ translational fusion was constructed on the Salmonella chromosome .	109	To test whether LeuO is an activator of hilE expression , a hilE : : lacZ translational fusion was constructed on the Salmonella chromosome .	10	LEUO ACTIVATES HILE TRANSCRIPTION	Salmonella	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	hilE	activator	24354910	37	ver/dev	The observation that LeuO downregulates SPI expression thus raised the question of whether activation of hilE transcription by LeuO might inhibit epithelial cell invasion .	142	The observation that LeuO downregulates SPI expression thus raised the question of whether activation of hilE transcription by LeuO might inhibit epithelial cell invasion .	11	ACTIVATION OF LEUO TRANSCRIPTION INHIBITS EPITHELIAL CELL INVASION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
LeuO	gene	hilE	activator	24354910	49	ver/dev	that LeuO might activate hilE transcription	199	We thus considered that LeuO might activate hilE transcription , and that HilE might repress SPI-1 via HilD inactivation .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
LeuO	gene	hilE	activator	24354910	50	ver/dev	LeuO activates transcription of hilE	200	The existence of a LeuO-HilE-HilD ` pathway ' of SPI-1 repression in S. enterica serovar Typhimurium is supported by several lines of evidence : ( i ) lack of HilE relieves LeuO-mediated repression of SPI-1 ( Fig. 2 ) ; ( ii ) activation of leuO transcription decreases the level of HilD protein ( Fig. 3 ) ; ( iii ) the HilD protein decrease caused by LeuO is suppressed by a hilE mutation ( Fig. 3 ) ; and ( iv ) LeuO activates transcription of hilE ( Fig. 5 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	24354910	53	ver/dev	a tentative model is that activation of hilE transcription by LeuO might boost SPI-1 repression , perhaps under conditions .	208	SPI-1 repressor , a tentative model is that activation of hilE transcription by LeuO might boost SPI-1 repression , perhaps under conditions in which H-NS fails to do so .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	hilE	activator	24354910	53	ver/dev	SPI-1 repressor is that activation of hilE transcription by LeuO might boost SPI-1 repression , perhaps under conditions .	208	SPI-1 repressor , a tentative model is that activation of hilE transcription by LeuO might boost SPI-1 repression , perhaps under conditions in which H-NS fails to do so .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	hilE	activator	25182488	7	ver/dev	that the transcriptional regulator LeuO directly activates transcription of hilE	235	It was shown previously that Lon protease degrades HilD ( 40 ) and that the transcriptional regulator LeuO directly activates transcription of hilE ( 41 ) , whose product inhibits HilD activity ( 42 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	25182488	24	ver/dev	previous findings _ indicating that LeuO mediates SPI1 downregulation mainly through activation of the transcription of hilE , a gene	331	This is consistent with HilD being a substrate for the Lon protease ( 40 ) and with previous findings indicating that LeuO mediates SPI1 downregulation mainly through activation of the transcription of hilE , a gene encoding a HilD inhibitor ( 41 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	hilE	activator	25547794	20	ver/dev	The LysR-type regulator LeuO has been shown to activate hilE transcription to repress HilD activity .	212	The LysR-type regulator LeuO has been shown to activate hilE transcription to repress HilD activity ( 58 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	hilE	activator	25566242	16	ver/dev	the major one involves the induction of hilE transcription by LeuO	130	Two different modes of action were found : the major one that involves the induction of hilE transcription by LeuO ( Figure 1 ) and another one that was HilE-independent .	7	LEUO HAS SEVERAL FUNCTIONS IN VIVO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	31428589	9	ver/dev	LeuO inhibits the expression of SPI-1 mainly by directly activating the promoter of hilE .	175	LeuO inhibits the expression of SPI-1 mainly by directly activating the promoter of hilE and via an unknown HilE-independent mechanism ( Espinosa and Casadesús , 2014 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	activator	34202800	33	ver/dev	Moreover , LeuO suppresses SPI-1 expression by direct activation of the hilE promoter .	498	Moreover , LeuO suppresses SPI-1 expression by direct activation of the hilE promoter and an unknown mechanism independent of the HilE protein .	18	3.7.2. LEUO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	orgB	activator	18248433	1	att	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	orgB	activator	23504014	16	att	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	277	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	orgB	activator	25182488	12	att	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	250	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	20363312	5	ver/dev	Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .	222	Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is dependent on FliA and FlhDC and regulated by OmpR .	13	REFERENCES	unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	20717675	4	ver/dev	Xu S , Zou X , Sheng X et al Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .	391	Xu S , Zou X , Sheng X et al ( 2010 ) Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is dependent on FliA and FlhDC and regulated by OmpR .	21	REFERENCES	unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	22179129	8	ver/dev	Xu S , Zou X , Sheng X et al Expression of fljB : z66 on a novel linear plasmid of salmonella enterica serovar Typhi is regulated by OmpR .	251	Xu S , Zou X , Sheng X et al ( 2010 ) Expression of fljB : z66 on a novel linear plasmid of salmonella enterica serovar Typhi is dependent on FliA and FlhDC and regulated by OmpR .	22	REFERENCES	unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	24031550	0	ver/dev	underlying the expressional regulation of fljB , gene deletion mutants of OmpR were constructed in this study .	8	underlying the expressional regulation of fljB : z66 , gene deletion mutants of the regulators FliA , FlhDC , and OmpR were constructed in this study .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	24031550	4	ver/dev	that OmpR regulates the expression of fljB	47	that OmpR regulates the expression of fljB : z66 and affects the More than 90 kinds of flagellin have been identified in expression and secretion of FljB : z66 in different osmotic	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	fljB	regulator	24723031	0	ver/dev	Xu S , Zou X , Sheng X et al Expression of fljB : z66 on a novel linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .	154	Xu S , Zou X , Sheng X et al ( 2010 ) Expression of fljB : z66 on a novel linear plasmid of Salmonella enterica serovar Typhi is dependent on FliA and FlhDC and regulated by OmpR .	15	REFERENCES	unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	33952386	24	ver/dev	Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .	557	Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is dependent on fliA and flhDC and regulated by OmpR .	21	REFERENCES	unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	regulator	34340061	11	ver/dev	Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .	626	Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is dependent on FliA and FlhDC and regulated by OmpR .	38	REFERENCES	unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	rob	regulator	22752112	4	ver/dev	The expression of rob is negatively regulated by SoxS in response to sodium salicylate and paraquat , respectively .	29	The expression of rob is negatively regulated by MarA and SoxS in response to sodium salicylate and paraquat , respectively ( Pomposiello et al. 2001 ; Michán et al. 2002 ; Schneiders and Levy 2006 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	rob	regulator	22752112	9	ver/dev	rob is negatively regulated by SoxS	200	rob is negatively regulated by MarA and SoxS	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	rob	regulator	22752112	13	ver/dev	SoxS bind the promoter region of rob	231	MarA and SoxS bind the promoter region of rob	16	MARA AND SOXS BIND THE PROMOTER REGION OF ROB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	rob	regulator	22752112	21	ver/dev	other studies _ performed in E. coli where rob was shown to be negatively regulated by both SoxS by a direct interaction with its promoter region	304	Our results are in agreement with other studies performed in E. coli where rob was shown to be negatively regulated by both MarA and SoxS by a direct interaction with its promoter region ( Schneiders and Levy 2006 ; Michán et al. 2002 ) .	17	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	rob	regulator	22752112	22	ver/dev	EMSAs _ demonstrating that SoxS bind to the promoter region of rob , indicating that the repression exerted by SoxS is due to a direct interaction with the DNA	308	DNA-protein interaction was confirmed by EMSAs demonstrating that MarA and SoxS bind to the promoter region of rob ( Fig. 4b , c ) , indicating that the repression exerted by MarA and SoxS is due to a direct interaction with the DNA ( Table 3 ) .	17	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	leuABCD	regulator	17908208	6	ver/dev	also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region	44	Furthermore , expression of LeuO has been found to affect the expression of several genes influenced by mutations in hns : LeuO relieved silencing of the bgl operon , the operon involved in the utilization of certain b-glucosides ( Ueguchi et al. , 1998 ) ; suppressed the effect of an hns mutation on cadC , which codes for the activator of the acid-inducible lysine decarboxylase ( Shi and Bennet , 1995 ) ; and also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene and the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region ( Chen et al. , 2001 ; 2003 ) .	3	B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	arcA	activator	17906148	3	ver/dev	It has been shown that FNR can upregulate arcA expression in E. coli .	251	It has been shown that FNR can upregulate arcA expression in E. coli ( Compan & Touati , 1994 ) .	7	ANOXIC REGULATION OF HYDROGENASE PROMOTERS	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
FNR	gene	arcA	activator	17906148	8	ver/dev	Anaerobic activation of arcA transcription in Escherichia coli : roles of Fnr .	370	Anaerobic activation of arcA transcription in Escherichia coli : roles of Fnr and ArcA .	12	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	arcA	activator	24018968	18	ver/dev	Anaerobic activation of arcA transcription in Escherichia coli : roles of Fnr .	305	Anaerobic activation of arcA transcription in Escherichia coli : roles of Fnr and ArcA .	21	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	arcA	activator	29937757	20	ver/dev	Anaerobic activation of arcA transcription in Escherichia coli : roles of Fnr .	628	Anaerobic activation of arcA transcription in Escherichia coli : roles of Fnr and ArcA .	27	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB-BglJ	gene	leuO	activator	22804842	17	ver/dev	LeuO is known to activate bglJ in E. coli while RcsB-BglJ heterodimers activate leuO transcription .	336	LeuO is known to activate bglJ in E. coli ( Stratmann et al. , 2008 ) while RcsB-BglJ heterodimers activate leuO transcription ( Stratmann et al. , 2012 ) .	8	GENOME-WIDE PREDICTION AND VALIDATION OF LEUO BINDING SITES	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
RcsB-BglJ	gene	leuO	activator	22804842	39	ver/dev	Schnetz , K. RcsB-BglJ activates the Escherichia coli leuO gene .	760	Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , and Schnetz , K. ( 2012 ) RcsB-BglJ activates the Escherichia coli leuO gene , encoding an H-NS antagonist and pleiotropic regulator of virulence determinants .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB-BglJ	gene	leuO	activator	22804842	39	ver/dev	Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , , K. RcsB-BglJ activates the Escherichia coli leuO gene .	760	Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , and Schnetz , K. ( 2012 ) RcsB-BglJ activates the Escherichia coli leuO gene , encoding an H-NS antagonist and pleiotropic regulator of virulence determinants .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB-BglJ	gene	leuO	activator	24354910	63	ver/dev	Schnetz , K. RcsB-BglJ activates the Escherichia coli leuO gene .	501	Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , and Schnetz , K. ( 2012 ) RcsB-BglJ activates the Escherichia coli leuO gene , encoding an H-NS antagonist and pleiotropic regulator of virulence determinants .	46	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB-BglJ	gene	leuO	activator	24354910	63	ver/dev	Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , , K. RcsB-BglJ activates the Escherichia coli leuO gene .	501	Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , and Schnetz , K. ( 2012 ) RcsB-BglJ activates the Escherichia coli leuO gene , encoding an H-NS antagonist and pleiotropic regulator of virulence determinants .	46	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB-BglJ	gene	leuO	activator	24659766	25	ver/dev	RcsB-BglJ activates the Escherichia coli leuO gene .	516	RcsB-BglJ activates the Escherichia coli leuO gene , encoding an H-NS antagonist and pleiotropic regulator of virulence determinants .	38	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB-BglJ	gene	leuO	activator	29186528	17	ver/dev	RcsB-BglJ activates the Escherichia coli leuO gene .	534	RcsB-BglJ activates the Escherichia coli leuO gene , encoding an H-NS antagonist and pleiotropic regulator of virulence determinants .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
DksA	gene	zwf	activator	20851888	5	att	Genes encoding glucose-6-phosphate dehydrogenase ( zwf ) , isocitrate dehydrogenase ( icdA ) , and malic enzyme ( maeB ) responsible for the generation of NADPH , and the sucAB-encoded subunits of - oxaloacetate dehydrogenase associated with generation of NADH all showed DksA-dependent regulation ( Fig. 3A , bold red font ) .	178	Genes encoding glucose-6-phosphate dehydrogenase ( zwf ) , isocitrate dehydrogenase ( icdA ) , and malic enzyme ( maeB ) responsible for the generation of NADPH , and the sucAB-encoded subunits of - oxaloacetate dehydrogenase associated with generation of NADH all showed DksA-dependent regulation ( Fig. 3A , bold red font ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	hns	activator	12068808	31	ver/dev	Mutants defective in hns exhibited high , constitutive levels of OmpR not subject to further induction by acid shock .	189	Mutants defective in hns exhibited high , constitutive levels of OmpR not subject to further induction by acid shock ( Fig. 8A , lanes 3 and 4 ) .	10	OMPR FOOTPRINT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hns	activator	12080060	31	ver/dev	Mutants defective in hns exhibited high , constitutive levels of OmpR not subject to further induction by acid shock .	189	Mutants defective in hns exhibited high , constitutive levels of OmpR not subject to further induction by acid shock ( Fig. 8A , lanes 3 and 4 ) .	10	OMPR FOOTPRINT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	yddX	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , yddX are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Fis	gene	cat	activator	15256548	2	att	Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .	259	Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .	7	TRANSCRIPTIONAL PROFILING OF SL1344 AND SL1344FIS : : CAT	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Felis catus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	dksA	repressor	21507083	1	ver/dev	As ppGpp regulation may require DksA , we also tested whether inactivation of dksA would result in a decreased resistance towards streptomycin .	299	As ppGpp regulation may require certain cofactors such as DksA ( Paul et al. , 2005 ) , we also tested whether inactivation of dksA would result in a decreased resistance towards streptomycin .	10	GROWTH ON MINIMAL MEDIA INCREASES STREPTOMYCIN RESISTANCE IN CLINICAL ISOLATES OF SALMONELLA	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
HilE	gene	tetA	regulator	29378886	3	ver/dev	The rtsA gene was under the control of a tetA promoter , hilD was deleted , and HilE was overexpressed as indicated .	67	The rtsA gene was under the control of a tetA promoter , hilD was left unaltered or deleted , and HilE was overexpressed as indicated .	3	KEYWORDS SALMONELLA, SPI1, HILD, HILE	Hypostomus robinii	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	tetA	regulator	29378886	3	ver/dev	The rtsA gene was under the control of a tetA promoter , hilD was left unaltered , and HilE was overexpressed as indicated .	67	The rtsA gene was under the control of a tetA promoter , hilD was left unaltered or deleted , and HilE was overexpressed as indicated .	3	KEYWORDS SALMONELLA, SPI1, HILD, HILE	Hypostomus robinii	0	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	cspH	activator	15235764	16	ver/dev	Fis somewhat increased the expression of cspH upon nutritional up-shift .	173	Fis somewhat increased the expression of cspH upon nutritional up-shift .	16	FIS AFFECTS THE EXPRESSION OF CSPH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	proV	regulator	15966862	5	ver/dev	These results agree well with those for the proU operon when H-NS binds within the proV operon .	185	These results agree well with those for the proU operon when H-NS binds within the proV operon [ 21 ] .	12	H-NS BINDS TO THE HILC PROMOTER AND STRUCTURAL GENE IN A TEMPERATURE-DEPENDENT MANNER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	proV	regulator	15966862	8	ver/dev	the H-NS-regulated proU operon where H-NS binds to downstream-regul-atory element within the proV structural gene	257	This resembles the situation observed for the H-NS-regulated proU operon where H-NS binds to the DRE ( downstream-regul-atory element ) within the proV structural gene [ 50 ] .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	proV	regulator	15966862	8	ver/dev	the H-NS-regulated proU operon where H-NS binds to the DRE within the proV structural gene	257	This resembles the situation observed for the H-NS-regulated proU operon where H-NS binds to the DRE ( downstream-regul-atory element ) within the proV structural gene [ 50 ] .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	proV	regulator	25375226	36	ver/dev	four H-NS _ regulated proV	436	Transcript levels of four H-NS regulated genes , proV , ssrA , yciG and hilA , were measured by reverse transcriptase QPCR in a Dhns/DstpA strain expressing StpAWT or the variants StpAM4T , StpAA77D and StpAF21C .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	proV	regulator	27564394	18	ver/dev	the hemX gene were used as negative control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	proV	regulator	27564394	18	ver/dev	the hemX gene were used as positive control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	proV	regulator	27564394	18	ver/dev	The proV promoter were used as negative control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	proV	regulator	27564394	18	ver/dev	The proV promoter were used as positive control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	barA	regulator	20656781	0	ver/dev	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of carbon storage .	344	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of the BarA ( SirA ) TCS in control of T3SS-1 , motility , biofilm formation and carbon storage ( Mondragón et al. , 2006 ; Teplitski et al. , 2003 ) .	7	JONES ET AL. (1992)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	barA	regulator	20656781	0	ver/dev	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of biofilm formation .	344	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of the BarA ( SirA ) TCS in control of T3SS-1 , motility , biofilm formation and carbon storage ( Mondragón et al. , 2006 ; Teplitski et al. , 2003 ) .	7	JONES ET AL. (1992)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	barA	regulator	20656781	0	ver/dev	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of motility .	344	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of the BarA ( SirA ) TCS in control of T3SS-1 , motility , biofilm formation and carbon storage ( Mondragón et al. , 2006 ; Teplitski et al. , 2003 ) .	7	JONES ET AL. (1992)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	barA	regulator	20656781	0	ver/dev	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of T3SS-1 .	344	The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of the BarA ( SirA ) TCS in control of T3SS-1 , motility , biofilm formation and carbon storage ( Mondragón et al. , 2006 ; Teplitski et al. , 2003 ) .	7	JONES ET AL. (1992)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompS1	activator	17908208	65	att	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter ( Fernández-Mora et al. , 2004 ) , the induction of ompS1 can occur independent of OmpR .	257	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter ( Fernández-Mora et al. , 2004 ) , the induction of ompS1 can occur independent of OmpR .	13	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	spiC	regulator	12874347	1	ver/dev	This surprising result suggested that the spiC promoter in pCS192 is at least partially regulated by Mg2 through a PhoP .	219	This surprising result suggested that the spiC promoter in pCS192 is at least partially regulated by Mg2 through a PhoP - and PhoQ-independent pathway .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	regulator	15765064	29	ver/dev	Efforts in our laboratory to demonstrate binding of purified HilE protein to the hilA promoter have failed , however , recent work demonstrated that the HilE protein interacts with HilD , using a bacterial two-hybrid assay .	159	Efforts in our laboratory to demonstrate binding of purified HilE protein to the hilA promoter have failed , however , recent work demonstrated that the HilE protein interacts with HilD , using a bacterial two-hybrid assay ( Baxter et al. , 2003 ) .	7	NEGATIVE REGULATORS OF INVASION	hybrid	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilE	gene	hilA	regulator	16045614	87	ver/dev	colleagues have identified HilE as a negative regulator of hilA transcription .	565	Jones and colleagues have identified HilE as a negative regulator of hilA transcription ( Fahlen et al. , 2000 ; Baxter et al. , 2003 ; Baxter and Jones , 2005 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	regulator	16045614	87	ver/dev	Jones have identified HilE as a negative regulator of hilA transcription .	565	Jones and colleagues have identified HilE as a negative regulator of hilA transcription ( Fahlen et al. , 2000 ; Baxter et al. , 2003 ; Baxter and Jones , 2005 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	regulator	17208038	25	ver/dev	In E. coli , a hilA was regulated by HilE only when HilD protein was present .	142	In E. coli , a hilA -- lacZY fusion was regulated by HilE only when HilD protein was present .	10	HILE	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	regulator	17208038	26	ver/dev	Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE .	143	Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE [ 49 ] .	10	HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	regulator	17208038	26	ver/dev	Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE .	143	Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE [ 49 ] .	10	HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	regulator	25547794	8	ver/dev	To determine the effects of HilE on the regulation of hilA via PhoPQ , we conducted a - galactosidase assay : : lacZY expression .	100	To determine the effects of HilE on the regulation of hilA via PhoPQ , we conducted a - galactosidase assay examining the effect of an hilE mutation on hilA : : lacZY expression when phoQ is constitutively expressed .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilE	gene	hilA	regulator	29378886	2	ver/dev	Fahlen et al. identified HilE as a negative regulator of hilA transcription provided bacterial two-hybrid data .	52	Fahlen et al. identified HilE as a negative regulator of hilA transcription , and Baxter et al. provided bacterial two-hybrid data indicating that HilE directly interacts with HilD protein ( 5 , 21 ) .	3	KEYWORDS SALMONELLA, SPI1, HILD, HILE	hybrid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	regulator	31428589	4	ver/dev	HilE is the most important negative regulator of hilA expression .	156	HilE is the most important negative regulator of hilA expression .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	regulator	33593291	7	ver/dev	the wild typ is consistent with HilE being a negative regulator of hilA expressio	85	In the case of formate , expression was higher in the ΔhilE mutant than in the wild type , which is consistent with HilE being a negative regulator of hilA expression .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	regulator	33593291	16	ver/dev	These results would naively suggest that HilE is a positive regulator of hilA expression .	122	These results would naively suggest that HilE is a positive regulator of hilA expression .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	regulator	33593291	19	ver/dev	Therefore , we hypothesized that loss of HilE is somehow affecting the expression of some other regulator of hilA expression .	125	Therefore , we hypothesized that loss of HilE is somehow affecting the expression of some other regulator of hilA expression .	6	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SirA	gene	hilC	regulator	16045614	8	ver/dev	Although it has been proposed that SirA directly controls expression of both hilC , it was also determined that HilC was not required for SirA to control hilA expression .	54	Although it has been proposed that SirA directly controls expression of both hilA and hilC ( Teplitski et al. , 2003 ) , it was also determined that HilC was not required for SirA to control hilA expression ( Lucas and Lee , 2001 ) .	4	INTRODUCTION	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
SirA	gene	hilC	regulator	16045614	43	ver/dev	Our model suggests that SirA could control expression of hilC by regulating the expression of a single regulator .	243	Our model ( Fig. 1 ) suggests that SirA could control expression of hilC , hilD and rtsA by either independently activating each gene or by regulating the expression of a single regulator .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SirA	gene	hilC	regulator	16045614	43	ver/dev	Our model suggests that SirA could control expression of hilC by either independently activating each gene .	243	Our model ( Fig. 1 ) suggests that SirA could control expression of hilC , hilD and rtsA by either independently activating each gene or by regulating the expression of a single regulator .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SirA	gene	hilC	regulator	16045614	49	ver/dev	This suggests that SirA regulates expression of hilC via HilD .	294	This suggests that SirA regulates expression of rtsAB and hilC via HilD .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	regulator	16045614	79	ver/dev	This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both the hilC .	550	This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both the hilC and hilA , but not the hilD , promoters ( Teplitski et al. , 2003 ) .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	regulator	16949866	9	ver/dev	Once phosphorylated , SirA directly binds the hilC promoters .	60	Once phosphorylated , SirA directly binds the hilA and hilC promoters and contributes to Salmonella enteropathogenesis in a bovine model ( Ahmer et al. , 1999a ; Teplitski et al. , 2003 ) .	5	CORRESPONDING AUTHOR. TEL.: +1 352 392 1951X254; FAX: +1 352 392 3902.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	regulator	16949866	30	ver/dev	SirA controls these genes by directly binding hilC regulatory genes .	455	SirA controls these genes by directly binding and activating the hilA and hilC regulatory genes that are encoded within the horizontal acquisition , SPI1 ( Teplitski et al. , 2003 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	regulator	17074910	19	ver/dev	However , this may seem unexpected , as SirA can directly bind hilC , so SirA would be expected to activate these genes independently of csrC .	510	However , this may seem unexpected , as SirA can directly bind the hilA , hilC and fimA promoters , so SirA would be expected to activate these genes independently of csrB and csrC .	10	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	regulator	17074910	19	ver/dev	However , this may seem unexpected , as SirA can directly bind hilC , so SirA would be expected to activate these genes independently of csrB .	510	However , this may seem unexpected , as SirA can directly bind the hilA , hilC and fimA promoters , so SirA would be expected to activate these genes independently of csrB and csrC .	10	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	regulator	17208038	20	ver/dev	Conversely , previously published gel-shift data suggested that SirA is able to bind to the promoters of hilC .	121	Conversely , previously published gel-shift data [ 44 ] suggested that SirA is able to bind to the promoters of hilC and hilA , but not to that of hilD .	8	BARA/SIRA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	regulator	17208038	22	ver/dev	Whereas SirA might bind to the hilC promoters during in-vitro gel-shift experiments , genetic data shows that SirA is incapable of directly activating these promoters ; SirA binding to DNA in-vitro does not represent activation .	123	Whereas SirA might bind to the hilA and hilC promoters during in vitro gel-shift experiments , genetic data shows that SirA is incapable of directly activating these promoters ; SirA binding to DNA in vitro does not represent activation .	8	BARA/SIRA	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
SirA	gene	hilC	regulator	19537165	6	ver/dev	To check if both regulators are important , the regulation of hilC gene expression by SirA is considered to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	106	To check if both regulators are important , the regulation of hilC gene expression by HilD and SirA is considered to function as an AND gate , and to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	regulator	19537165	6	ver/dev	To check if both regulators are important , the regulation of hilC gene expression by SirA is considered to function as gate , this dependency is taken as an OR gate .	106	To check if both regulators are important , the regulation of hilC gene expression by HilD and SirA is considered to function as an AND gate , and to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilC	regulator	19537165	6	ver/dev	To check if both regulators are important , the regulation of hilC gene expression by SirA is considered to function as an , this dependency is taken as an OR gate .	106	To check if both regulators are important , the regulation of hilC gene expression by HilD and SirA is considered to function as an AND gate , and to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilC	regulator	19537165	7	ver/dev	Scenario-3: Regulation of the network by SirA via hilC in combination with regulation through HilD	253	Scenario-3: Regulation of the network by SirA via hilC and hilA in combination with regulation through HilD	16	SCENARIO-3: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA IN COMBINATION WITH REGULATION THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	regulator	24929817	0	ver/dev	SirA , directly regulates the hilC genes at the top of the invasion cascade .	165	SirA , a global regulator necessary for enteropathogenesis , directly regulates the hilA and hilC genes at the top of the invasion cascade ( Prouty and gunn 2000 ; Teplitski et al. 2006 ) .	9	SURVIVAL AND PROPHAGE INDUCTION OF LYSOGENIC S. TYPHIMURIUM EXPOSED TO GASTROINTESTINAL JUICES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PutA	gene	putA	activator	8483946	3	ver/dev	the putA gene downstream of the lacIq gene _ allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside	58	Plasmid pPC34 is a derivative of pCKR101 ( 11 ) that contains the putA gene downstream of the tac promoter and the lacIq gene , allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PutA	gene	putA	activator	8483946	3	ver/dev	the putA gene downstream of the tac promoter _ allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside	58	Plasmid pPC34 is a derivative of pCKR101 ( 11 ) that contains the putA gene downstream of the tac promoter and the lacIq gene , allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PutA	gene	putA	activator	8483946	4	ver/dev	the putA gene downstream of the lacIq gene _ allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside	116	Plasmid pPC34 is a derivative of pCKR101 ( 11 ) that contains the putA gene downstream of the tac promoter and the lacIq gene , allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PutA	gene	putA	activator	8483946	4	ver/dev	the putA gene downstream of the tac promoter _ allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside	116	Plasmid pPC34 is a derivative of pCKR101 ( 11 ) that contains the putA gene downstream of the tac promoter and the lacIq gene , allowing induction of PutA expression by isopropyl 8-D-thiogalactopyranoside .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	degP	activator	29685984	1	ver/dev	Phosphorylated CpxR increases the expression of degP .	32	Phosphorylated CpxR increases the expression of degP , which encodes a periplasmic protease that degrades misfolded proteins , allowing bacteria to cope with misfolded-protein-related envelope stress ( 6 -- 8 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	activator	11207562	2	ver/dev	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression of the spvABCD operon .	44	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	activator	11553591	2	ver/dev	SpvR positively regulates the plasmid-encoded spvABCD operon	348	SpvR , which positively regulates the plasmid-encoded spvABCD operon ( 27 ) , is also needed for systemic disease ( 41 ) .	6	DISCUSSION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	activator	16128395	0	ver/dev	indeed SpvR is known to activate the transcription of both spvABCD transcriptional units	35	Based on amino acid sequence homologies , SpvR belongs to the LysR/MetR family of prokaryotic transcriptional activators ( Taira and Rhen , 1989a , b ; Caldwell and Gulig , 1991 ) , and indeed SpvR is known to activate the transcription of both the spvR and spvABCD transcriptional units ( Krause et al. , 1992 ; Sheehan and Dorman , 1998 ) .	4	MAIN	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
SpvR	gene	spvABCD	activator	19447191	0	ver/dev	SpvR induces the expression of the spvABCD operon .	79	SpvR induces the expression of the spvABCD operon and its own expression in the stationary phase of bacterial growth and inside the macrophages .	5	4.1. SPVR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	activator	30143595	1	ver/dev	the DNA-binding SpvR protein acts as an essential activator of the spvABCD genes	31	While many global regulators can influence spv expression ( Fang et al. 1992 ; Kowarz et al. 1994 ; O'Byrne and Dorman 1994a , b ; Robbe-Saule et al. 1997 ; Marshall et al. 1999 ; Mangan et al. 2006 ) , the spvR gene that is located directly upstream of the spvABCD operon is thought to be transcribed separately ( Robbe-Saule et al. 1997 ; Wilson and Gulig 1998 ) and encodes the DNA-binding SpvR protein , which acts as an essential activator of both spvR and the spvABCD genes and is absolutely required for spv-mediated virulence in vivo ( Grob and Guiney 1996 ; Guilloteau et al. 1996 ; Sheehan and Dorman 1998 ) .	2	COPYRIGHT © 2018 BY THE GENETICS SOCIETY OF AMERICA DOI: HTTPS://DOI.ORG/10.1534/GENETICS.118.300822	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	cdtB	regulator	29324231	7	ver/dev	Using ChIP , we determined that H-NS strongly binds both the cdtB promoter regions .	151	Using ChIP , we determined that H-NS strongly binds both the pltB and the cdtB promoter regions , indicating that H-NS directly silences the typhoid toxin genes ( Figure 4A ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
TyrR	gene	ompF	regulator	32514543	2	ver/dev	multiple antibiotic resistance protein MarA transcriptional regulatory protein TyrR invasion response-regulator cys regulon transcriptional activator possible LysR-family transcriptional regulatory protein sensor protein PhoQ fatty acid-fatty acyl responsive DNA-binding protein right origin-binding protein histone-like DNA-binding protein HU-alpha DNA repair protein exodeoxyribonuclease large subunit exodeoxyribonuclease I putative ATP-dependent helicase DNA-binding protein HU-beta endonuclease I possibly cell division cell division protein cell division protein cell division protein tryptophanyl-tRNA synthetase host factor-I protein small RNA regulator of ompF expression polynucleotide phosphorylase	123	multiple antibiotic resistance protein MarA transcriptional regulatory protein TyrR invasion response-regulator cys regulon transcriptional activator possible LysR-family transcriptional regulatory protein sensor protein PhoQ fatty acid-fatty acyl responsive DNA-binding protein right origin-binding protein histone-like DNA-binding protein HU-alpha DNA repair protein exodeoxyribonuclease large subunit exodeoxyribonuclease I putative ATP-dependent helicase DNA-binding protein HU-beta endonuclease I ATP-dependent DNA helicase DNA helicase II lipoprotein ; possibly cell division cell division protein cell division protein cell division protein tryptophanyl-tRNA synthetase host factor-I protein small RNA regulator of ompF expression polynucleotide phosphorylase conserved hypothetical protein tRNA-Pro putative aminotransferase conserved hypothetical protein	15	GENES INVOLVED IN DNA BINDING AND REPAIR	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Lrp	gene	lrp	activator	12067346	22	ver/dev	Effect of lrp mutations on conjugal plasmid transfer Together , the results suggest that Lrp might act as an activator of conjugal plasmid transfer .	119	Effect of lrp mutations on conjugal plasmid transfer Together , the results described in the former sections suggest that Lrp might act as an activator of conjugal plasmid transfer .	5	DELETION ANALYSIS OF THE TRAJ UAS: EFFECT ON TRAJ EXPRESSION	unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	lrp	activator	12067346	26	ver/dev	This magnification of the difference in the absence of fertility inhibition further supports the model that Lrp acts as an activator of pSLT plasmid transfer : a FinO - plasmid is no longer derepressed when an lrp mutation reduces traJ transcription .	143	This magnification of the difference in the absence of fertility inhibition further supports the model that Lrp acts as an activator of pSLT plasmid transfer : a FinO - plasmid is no longer derepressed when an lrp mutation reduces traJ transcription .	6	DISCUSSION	unidentified plasmid;unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	lrp	activator	18599829	5	ver/dev	When leucine was added to the MOPS culture , the level of lrp-gfp expression increased by between 1.5 - and 2-fold , provided the Lrp protein was present ; leucine did not have this effect in the lrp knockout mutant .	127	When leucine was added to the MOPS culture , the level of lrp-gfp expression increased by between 1.5 - and 2-fold , provided the Lrp protein was present ; leucine did not have this effect in the lrp knockout mutant ( Fig. 2b ) .	6	NEGATIVE AUTOREGULATION OF LRP TRANSCRIPTION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
LexA	gene	uvrC	regulator	19525399	5	att	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	175	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	3	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	mgtA	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CusR	gene	cueO	regulator	34125582	5	ver/dev	cueO _ regulated by CusR	249	As expected , the known copper efflux and detoxification genes copA , cueO , and cusCFBA , regulated by CueR and CusR , are upregulated in E. coli during growth in copper-supplemented media .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LysR	gene	ompS2	regulator	15126450	24	ver/dev	Moreover , the LeuO activator of the LysR family was identified as a regulator for ompS2 .	273	Moreover , the LeuO activator of the LysR family was identified ( 21 ) as a regulator for ompS2 .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OxyR	gene	ahpC	activator	25425233	0	att	To determine whether DalS-deficient bacteria allowed a higher concentration of enzymatic hydrogen-peroxide product to form from DAO , we constructed an S. Typhimurium reporter strain , previously validated to report hydrogen-peroxide stress , by fusing the OxyR-dependent ahpC promoter ( 18 , 19 ) to luxCDABE from Photorhabdus luminescens .	60	To determine whether DalS-deficient bacteria allowed a higher concentration of enzymatic hydrogen peroxide product to form from DAO , we constructed an S. Typhimurium reporter strain , previously validated to report hydrogen peroxide stress , by fusing the OxyR-dependent ahpC promoter ( 18 , 19 ) to luxCDABE from Photorhabdus luminescens .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Photorhabdus luminescens	0.5	L3	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	ahpC	activator	25425233	1	att	To confirm that this killing phenotype was linked to DAO-dependent hydrogen-peroxide stress , we infected neutrophils with the wild type and dalS mutants carrying the OxyR-dependent ahpC reporter in the presence or absence of CBIO .	77	To confirm that this killing phenotype was linked to DAO-dependent hydrogen peroxide stress , we infected neutrophils with the wild type and dalS mutants carrying the OxyR-dependent ahpC reporter in the presence or absence of CBIO .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pbgP	repressor	22921935	6	ver/dev	By 120 min , the PmrA-dependent lipid-A modifications were wild-type Salmonella and expressed lower amounts of pbgP transcript than Figures 6B .	141	By 120 min , the PmrA-dependent lipid A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	repressor	22921935	6	ver/dev	By 120 min , the PmrA-dependent lipid-A modifications were wild-type Salmonella and expressed lower amounts of pbgP transcript than the ugd mutant .	141	By 120 min , the PmrA-dependent lipid A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	repressor	22921935	6	ver/dev	By 120 min , the PmrA-dependent lipid-A modifications were visible Salmonella and expressed lower amounts of pbgP transcript than Figures 6B .	141	By 120 min , the PmrA-dependent lipid A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	repressor	22921935	6	ver/dev	By 120 min , the PmrA-dependent lipid-A modifications were visible Salmonella and expressed lower amounts of pbgP transcript than the ugd mutant .	141	By 120 min , the PmrA-dependent lipid A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	marT	activator	26561851	1	att	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	159	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	7	THE PRIMARY TRANSCRIPTOME OF INTRA-MACROPHAGE S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Zur	gene	rpmE2	regulator	24858080	12	att	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	408	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	STM1055	activator	17379730	5	ver/dev	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA .	362	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA , which is also involved in the regulation of virulence genes such as mig-14 , sopD2 and virK ( Brumell et al. , 2003 ; Ho et al. , 2002 ; Navarre et al. , 2005 ) .	14	GIFSY-1 AND GIFSY-2 PROPHAGES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FruR	gene	crp	activator	21388802	4	ver/dev	FruR activates crp expression .	170	FruR activates crp expression and represses rpoS and SPI2 genes .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FruR	gene	crp	activator	2203752	7	ver/dev	With regard to transcriptional regulation of thefru operon , the results summarized here and previously , as well as unpublished results -LRB- Cao and Saier -RRB- suggest that the fru regulon in S. typhimurium is complex ; that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru -LRB- Cao and Saier , unpublished results -RRB- ; that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; that it may be regulated at the transcriptional level by two or more distinct mechanisms -LRB- possibly involving two distinct inducers , fructose-i-phos-phate and fructose -RRB- which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .	452	With regard to transcriptional regulation of thefru operon , the results summarized here and previously ( 6 ) , as well as unpublished results ( Cao and Saier ) suggest ( i ) that the fru regulon in S. typhimurium is complex ; ( ii ) that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru ( Cao and Saier , unpublished results ) ; ( iii ) that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; ( iv ) that it may be regulated at the transcriptional level by two or more distinct mechanisms ( possibly involving two distinct inducers , fructose-i-phos-phate and fructose ) which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and ( v ) that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	ssrA	activator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in bacteria ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	activator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in LB medium ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	activator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in Bertani medium ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	activator	16999831	7	ver/dev	We wished to examine the contribution of Fis to ssrA gene expression in bacteria .	105	We wished to examine the contribution of Fis to ssrA gene expression in bacteria growing in macrophage .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
Fis	gene	ssrA	activator	16999831	17	ver/dev	Our data establish a role for the Fis protein in the upregulation of the ssrA gene when S. Typhimurium grows in macrophage .	188	Our data establish a role for the Fis protein in the upregulation of the ssrA gene when S. Typhimurium grows in macrophage .	15	GFP FLUORESCENCE INTENSITY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	activator	20861532	5	ver/dev	Fis is required for activation of ssrA expression in murine macrophages through DNA relaxation .	530	Fis is required for activation of ssrA expression in murine macrophages through DNA relaxation [ 56 ] .	12	3.2.1 SPI PATHWAY VALIDATION BY NETWORK ENRICHMENT ANALYSIS OF SALMONELLA GENE EXPRESSION TIME-COURSE DURING MACROPHAGE INFECTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	cadC	regulator	25875623	8	ver/dev	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC .	248	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC and cadB .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	cadC	regulator	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in SCV of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadC	regulator	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in the Salmonellacontaining vacuole of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadC	regulator	29214489	15	ver/dev	Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC , leading to cytoplasmic acidification .	163	Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC and cadB promo-ters , leading to cytoplasmic acidification and reduced flagellation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	mgtA	regulator	33045730	50	ver/dev	Control experiments showed that no detectable binding to the DNA region upstream of mgtA not bound by H-NS .	249	Control experiments showed that the SsrB binding site mutant retained normal H-NS binding to the STM14 3310 DNA ( Figure 3F ) , one of the genes most tightly bound by H-NS ( 50 ) , and no detectable binding to the DNA region upstream of mgtA ( Figure 3F ) , a PhoP-activated gene not bound by H-NS ( 50 ) .	27	SSRB ANTAGONIZES THE GENE SILENCER H-NS IN THE UGTL PRO- MOTER REGION	nan	1	L2	OTHER	Other	NEG	New	Level 1
PhoP	TU	prgHIJK	activator	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	prgHIJK	activator	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the prgs prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	prgHIJK	activator	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the PhoP-repressed genes prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hmpA	activator	18350168	2	att	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	294	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	ssrA	regulator	10998173	4	ver/dev	Falkow , S. OmpR regulates the two-component system ssrA ± ssrB in Salmo-nella pathogenicity island 2 .	632	Lee , A.K. , Detweiler , C.S. , and Falkow , S. ( 2000 ) OmpR regulates the two-component system ssrA ± ssrB in Salmo-nella pathogenicity island 2 .	22	N.A., AND FIERER, J. (1995) BIOLOGY AND CLINICAL SIGNIFICANCE OF VIRULENCE PLASMIDS IN SALMONELLA SEROVARS. CLIN INFECT DIS 21: S146±S151.	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	10998173	4	ver/dev	Lee , A.K. , Detweiler , C.S. , , S. OmpR regulates the two-component system ssrA ± ssrB in Salmo-nella pathogenicity island 2 .	632	Lee , A.K. , Detweiler , C.S. , and Falkow , S. ( 2000 ) OmpR regulates the two-component system ssrA ± ssrB in Salmo-nella pathogenicity island 2 .	22	N.A., AND FIERER, J. (1995) BIOLOGY AND CLINICAL SIGNIFICANCE OF VIRULENCE PLASMIDS IN SALMONELLA SEROVARS. CLIN INFECT DIS 21: S146±S151.	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	11886586	0	ver/dev	OmpR binds directly to the promoter of ssrA .	72	OmpR binds directly to the promoter of ssrA , which is in turn required for the expression of SPI-2 genes ( 23,39 ) .	9	SPI-2	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	12753201	3	ver/dev	Phosphorylation of OmpR has a large effect on DNA binding at ssrA	50	Phosphorylation of OmpR has a large effect on DNA binding at ssrA , and OmpR-P also binds to the ssrB region .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	12753201	16	ver/dev	Phosphorylation of OmpR stimulates DNA binding to ssrA We next measured equilibrium binding of OmpR to the ssrA-1 binding site .	137	Phosphorylation of OmpR stimulates DNA binding to ssrA We next measured equilibrium binding of OmpR and OmpR-P to the ssrA-1 binding site ( Fig. 5 ) .	6	PRIMER EXTENSION OF SSRA AND SSRB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	12753201	26	ver/dev	OmpR did not examine the effect of OmpR phosphorylation on DNA binding at ssrA	169	Our results extend the findings from a previous study on DNA binding by OmpR that did not examine the effect of OmpR phosphorylation on DNA binding at ssrA ( Lee et al. , 2000 ) .	9	PHOSPHORYLATION OF OMPR INCREASES ITS AFFINITY FOR SSRA	nan	1	L3	OTHER	Investigation	NEG	New	Level 1
OmpR	gene	ssrA	regulator	12753201	39	ver/dev	that OmpR binds directly to the ssrA to affect their expression	228	In the present work , we have demonstrated that OmpR binds directly to the ssrA and ssrB regulatory regions to affect their expression and that regulation requires the sensor kinase EnvZ .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	15491370	5	ver/dev	Previous results from gene fusions suggest that regulation of ssrA by OmpR is distinct .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrA	regulator	15491370	5	ver/dev	Previous results from gene fusions suggest that regulation of ssrA by OmpR is uncoupled .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrA	regulator	15491370	5	ver/dev	Previous results from primer-extension analysis suggest that regulation of ssrA by OmpR is distinct .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	synthetic construct	0	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrA	regulator	15491370	5	ver/dev	Previous results from primer-extension analysis suggest that regulation of ssrA by OmpR is uncoupled .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	synthetic construct	0	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrA	regulator	17259627	3	ver/dev	OmpR binds to both ssrA	41	OmpR binds to both ssrA and ssrB promoters in vitro ( Feng et al. , 2003 , 2004 ; Lee et al. , 2000 ) , and PhoP is directly involved in ssrB transcription and the protein levels of SsrA posttranscriptionally ( Bijlsma & Groisman , 2005 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	19609351	4	ver/dev	Other examples of genes include ssrA known regulators of SPI-2 previously reported to be influenced by OmpR	320	Other examples of genes identified by ssRNA-seq include ssrA and ssrB ( expression ratios of 0.09 and 0.31 respectively ) known regulators of SPI-2 previously reported to be influenced by OmpR	6	NON-CODING (NC) RNA SEQUENCES	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	gene	ssrA	regulator	19609351	4	ver/dev	Other examples of genes include ssrA known regulators of SPI-2 previously reported to be influenced by OmpR	320	Other examples of genes identified by ssRNA-seq include ssrA and ssrB ( expression ratios of 0.09 and 0.31 respectively ) known regulators of SPI-2 previously reported to be influenced by OmpR	6	NON-CODING (NC) RNA SEQUENCES	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	gene	ssrA	regulator	19759044	2	ver/dev	previous work in Salmonella has shown that phosphorylated OmpR can bind to either sensor kinase gene ssrA within SPI-2	390	Furthermore , the 56 local activator for SPI-2 , ssrA , was increased in expression after triclosan exposure , and previous work in Salmonella has shown that phosphorylated OmpR can bind to either sensor kinase gene ssrA or ssrB within SPI-2 and activate expression .	23	DISCUSSION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
OmpR	gene	ssrA	regulator	24079299	3	ver/dev	In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrA genes .	123	In low osmolarity conditions , OmpR and/or OmpR-P ( phosphorylayted OmpR present in low levels ) can bind to the upstream regions of ssrA and ssrB genes .	5	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
OmpR	gene	ssrA	regulator	26880544	1	ver/dev	Under low osmolality , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	regulator	26880544	1	ver/dev	Under acidic pH , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	regulator	27404739	2	ver/dev	The global regulator OmpR regulates positively SsrAB directly by binding to the ssrA promoter .	154	The global regulator OmpR regulates positively SsrAB directly by binding to the ssrA promoter .	8	A PROCEDURE TO IDENTIFY PEPTIDES WITH AMP ACTIVITY 5 OF 11	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	27404739	2	ver/dev	The global regulator OmpR regulates positively SsrAB directly by binding to the ssrA promoter .	154	The global regulator OmpR regulates positively SsrAB directly by binding to the ssrA promoter .	8	A PROCEDURE TO IDENTIFY PEPTIDES WITH AMP ACTIVITY 5 OF 11	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	27564394	5	ver/dev	OmpR directly regulates expression from the ssrA promoter .	245	OmpR binds to and directly regulates expression from the ssrA promoter [ 99 ] , while , in conjunction with the nucleoid-associated protein Fis , OmpR primes SPI2 genes for expression while S. Typhimurium is still in the host intestinal lumen [ 112 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	29751061	1	ver/dev	For example , OmpR promotes SPI-2 expression by directly binding to both the ssrA .	235	For example , OmpR promotes SPI-2 expression by directly binding to both the ssrA and ssrB promoters [ 16 ] ; PhoP activates SPI-2 transcription by directly binding to the ssrB promoter and controls SsrA levels post-transcriptionally [ 15 ] ; SlyA , HilD and Fis proteins can bind to the ssrA promoter to regulate SPI-2 genes [ 19,20,22 ] , and PmrA represses SPI-2 gene transcription through directly binding to the ssrB promoter [ 18 ] .	19	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	regulator	33751923	7	ver/dev	OmpR also regulates the transcription of ssrA , genes .	385	OmpR also regulates the transcription of ssrA and ssrB , genes encoding another TCS that is also required for the expression of SPI-2 genes and Salmonella survival inside host cells , by direct binding to the promoter of ssrA ( Lee , Detweiler , et al. 2000 ) ( Lee , Detweiler , et al. 2000 ; Leonhartsberger et al. 2001 ) .	9	ENVZ-OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	yhjH	activator	22336758	29	ver/dev	Indeed , deletion of yhjH in the arcZ mutant lead to 3-fold upregulation of CsgD levels ( Fig. 6D ; Fig .	286	Indeed , deletion of yhjH in the arcZ mutant lead to 3-fold upregulation of CsgD levels ( Fig. 6D ; Fig .	2	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by EnvZ through SsrB -- both protein pairs being two-component regulators -- and not by PhoQ .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by EnvZ through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoQ .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	ssaH	regulator	17630976	11	ver/dev	There was no evidence of SsrB binding at ssaH .	116	There was no evidence of SsrB binding at ssaH and ssaR .	5	THE ISOLATED C-TERMINUS OF SSRB (SSRBC) BINDS TO MULTIPLE TARGETS WITHIN SPI-2	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
CpxR	gene	pmrD	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrD at the CpxR box-like sequences .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	pmrD	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrD at the CpxR box-like sequences .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	pmrD	regulator	32620947	6	ver/dev	CpxR binds directly to the promoters of CRRGs pmrD at the CpxR box-like sites	86	CpxR binds directly to the promoters of CRRGs phoPQ, pmrC, pmrH and pmrD at the CpxR box-like sites	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	pmrD	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the pmrD promoters .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	pmrD	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the pmrD promoters .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	pmrD	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrD at the CpxR box-like sequences .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrD	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrD at the CpxR box-like sequences .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrD	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of CRRGs , binding directly to pmrD promoters of box-type CpxR sequences .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	pmrD	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of colistin resistance-related genes , binding directly to pmrD promoters of box-type CpxR sequences .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	rpoS	activator	19843227	41	att	The negative effect of StpA on s38 levels at MEP does not occur during LEP as StpA-dependent control of s38 stability is probably compensated at the rpoS mRNA level .	300	The negative effect of StpA on s38 levels at MEP does not occur during LEP as StpA-dependent control of s38 stability is probably compensated at the rpoS mRNA level .	15	DISCUSSION	nan	1	L2	SPEC	Other	NEG	Other	Level 1
SsrB	TU	flhDC	regulator	30355489	2	ver/dev	SsrB Binds to the flhDC Promoter in STM	90	SsrB Binds to the flhDC Promoter in STM	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	TU	flhDC	regulator	30355489	5	ver/dev	Although we found that purified HilD bound equally well to SBG flhDC promoters , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa , thus ruling out a competitive inhibition by SsrB .	97	Although we found that purified HilD bound equally well to the STM and SBG flhDC promoters ( Figure S3B ) , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa ( Figure S3C ) , thus ruling out a competitive inhibition by SsrB .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	TU	flhDC	regulator	30355489	5	ver/dev	Although we found that purified HilD bound equally well to the STM , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa , thus ruling out a competitive inhibition by SsrB .	97	Although we found that purified HilD bound equally well to the STM and SBG flhDC promoters ( Figure S3B ) , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa ( Figure S3C ) , thus ruling out a competitive inhibition by SsrB .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	csgD	activator	16313619	6	att	The results showed that the bapA mRNA level was significantly downregulated in the mlrA mutant strain and that bapA activation through MlrA was exclusively CsgD-dependent , because bapA transcription levels in csgD mutant and csgD mutant complemented with MlrA were comparable ( Fig. 7 ) .	246	The results showed that the bapA mRNA level was significantly downregulated in the mlrA mutant strain and that bapA activation through MlrA was exclusively CsgD-dependent , because bapA transcription levels in csgD mutant and csgD mutant complemented with MlrA were comparable ( Fig. 7 ) .	10	TRANSCRIPTIONAL REGULATION OF BAPA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	csgD	activator	20545866	21	att	B. Expression of CsgD-dependent genes in the S. Typhimurium strains UMR1 ( wt ) , MAE52 ( 3-fold increased csgD expression ) and MAE50 ( DcsgD ) .	118	B. Expression of CsgD-dependent genes in the S. Typhimurium strains UMR1 ( wt ) , MAE52 ( 3-fold increased csgD expression ) and MAE50 ( DcsgD ) .	7	CSGD IS CRUCIAL FOR THE TRANSCRIPTION OF CSGBA AND ADRA IN VITRO	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	csgD	activator	32604994	1	ver/dev	The activation of CsgD in-vitro has been well-defined , with limiting nutrients necessary to activate csgD transcription .	43	The activation of CsgD in vitro has been well-defined , with growth conditions of low osmolarity , lower temperatures and limiting nutrients necessary to activate csgD transcription [ 29 ] .	4	1. INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	osmC	regulator	12519186	48	att	RcsB-regulated genes can be divided into those that are RcsA dependent , such as the cps genes ( Gottesman et al. , 1985 ) ( Fig. 3 ) , and those that are RcsA independent , such as the ftsZ ( Carballes et al. , 1999 ; Costa and Anton , 2001 ) and osmC ( Davalos-Garcia et al. , 2001 ) genes .	136	RcsB-regulated genes can be divided into those that are RcsA dependent , such as the cps genes ( Gottesman et al. , 1985 ) ( Fig. 3 ) , and those that are RcsA independent , such as the ftsZ ( Carballes et al. , 1999 ; Costa and Anton , 2001 ) and osmC ( Davalos-Garcia et al. , 2001 ) genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	cat	regulator	30414454	4	ver/dev	These results indicated that the cat gene is regulated by RpoS .	234	These results indicated that the cat gene is regulated by RpoS .	20	3.5. CAT GENE IS REGULATED BY RPOS	Felis catus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	map	activator	30201777	27	att	( B ) The RNA repair operon map is shown with the 70-type promoter for the dinJ-yafQ operon , dinJp , and the potential promoters for RtcR-dependent expression of the dinJ-yafQ operon : the 54-dependent promoter for the RNA repair operon ( rsrp ) and the E 54 binding site within rtcA .	267	( B ) The RNA repair operon map is shown with the 70-type promoter for the dinJ-yafQ operon , dinJp , and the potential promoters for RtcR-dependent expression of the dinJ-yafQ operon : the 54-dependent promoter for the RNA repair operon ( rsrp ) and the E 54 binding site within rtcA .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsA	regulator	29186528	5	ver/dev	the rcsA promoter is autoregulated by RcsA in the so named RcsAB box	172	We selected these regions since P1flhDC accounts for the RcsB box while a similar consensus sequence is observed in the rcsA promoter , which is autoregulated by RcsA and RcsB in the so named RcsAB box ( 4,40 ) ( Supplementary Figure S6B ) .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	flhDC	regulator	26441883	17	ver/dev	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , SlyA with the P5 promoters .	361	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / EcnR , the Spi-1-encoded regulator RtsB , the LysR-type regulator LrhA ( RovM in Yersinia ) , and SlyA ( RovA in Yersinia ) with the P1 and P5 promoters being the main regulatory targets ( Yanagihara et al. , 1999 ; Wang et al. , 2007 ; Singer et al. , 2013 ; Mouslim and Hughes , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	flhDC	regulator	26441883	17	ver/dev	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , SlyA with the P1 promoters .	361	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / EcnR , the Spi-1-encoded regulator RtsB , the LysR-type regulator LrhA ( RovM in Yersinia ) , and SlyA ( RovA in Yersinia ) with the P1 and P5 promoters being the main regulatory targets ( Yanagihara et al. , 1999 ; Wang et al. , 2007 ; Singer et al. , 2013 ; Mouslim and Hughes , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	10568808	2	ver/dev	Although induction of the cysteine regulon occurred near the end of exponential phase , the stationary-phase sigma factor RpoS was not involved in the phenomenon since a r derivative of strain DA1964 carrying mutation rpoS : : a null allele of the rpoS gene , showed the same behavior as the corresponding rpoS1 isogenic strain .	79	Although induction of the cysteine regulon occurred near the end of exponential phase , the stationary-phase sigma factor RpoS was not involved in the phenomenon since a r derivative of strain DA1964 carrying mutation rpoS : : Ap , a null allele of the rpoS gene [ 7 ] , showed the same behavior as the corresponding rpoS1 isogenic strain .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	activator	10568808	2	ver/dev	Although induction of the cysteine regulon occurred near the end of exponential phase , the stationary-phase sigma factor RpoS was not involved in the phenomenon since a r derivative of strain DA1964 carrying mutation rpoS : : Ap , showed the same behavior as the corresponding rpoS1 isogenic strain .	79	Although induction of the cysteine regulon occurred near the end of exponential phase , the stationary-phase sigma factor RpoS was not involved in the phenomenon since a r derivative of strain DA1964 carrying mutation rpoS : : Ap , a null allele of the rpoS gene [ 7 ] , showed the same behavior as the corresponding rpoS1 isogenic strain .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	activator	11101680	0	att	A majority of stress-sensitive DT 104 and PT 4 strains harboured mutations in the rpoS gene or showed reduced expression of the RpoS protein as measured indirectly using the RpoS-dependent spvR } A `` : : luxCDABE fusion .	53	A majority of stress-sensitive DT 104 and PT 4 strains harboured mutations in the rpoS gene or showed reduced expression of the RpoS protein as measured indirectly using the RpoS-dependent spvR } A `` : : luxCDABE fusion .	3	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium DT104	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	rpoS	activator	11101680	3	att	In the five sensitive DT 104 and PT 4 strains examined , three harboured mutations in the rpoS gene , while two DT 104 strains had intact rpoS genes and one of those demonstrated a reduced level of RpoS-dependent spvR } A `` : : luxCDABE expression .	332	In the five sensitive DT 104 and PT 4 strains examined , three harboured mutations in the rpoS gene , while two DT 104 strains had intact rpoS genes and one of those demonstrated a reduced level of RpoS-dependent spvR } A `` : : luxCDABE expression .	8	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium DT104;Salmonella enterica subsp. enterica serovar Typhimurium DT104	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	11101680	8	att	Thus , the role of the rpoS gene is dependent on the host environment , and while virulence in mice and survival in the environment is highly RpoS-dependent , invasion into day-old chicks may not require RpoS .	362	Thus , the role of the rpoS gene is dependent on the host environment , and while virulence in mice and survival in the environment is highly RpoS-dependent , invasion into day-old chicks may not require RpoS .	8	DISCUSSION	Mus sp.	0	L1	SPEC	Analysis	NEG	New	Level 1
RpoS	gene	rpoS	activator	11673423	2	att	As explained above , all lac expression values were obtained in , and are reported for , pairs of isogenic rpoS and rpoS deriv-atives , whose difference has been taken to represent the in-vivo activity of the RpoS-dependent proU P1 promoter under the particular test conditions ; by these criteria , the plasmid vectors pMU575 and pMU2385 carrying the promoterless lacZ reporter gene displayed insignificant RpoS-dependent lac expression under any of the conditions tested in this study ( data not shown ) .	97	As explained above , all lac expression values were obtained in , and are reported for , pairs of isogenic rpoS and rpoS deriv-atives , whose difference has been taken to represent the in vivo activity of the RpoS-dependent proU P1 promoter under the particular test conditions ; by these criteria , the plasmid vectors pMU575 and pMU2385 carrying the promoterless lacZ reporter gene displayed insignificant RpoS-dependent lac expression under any of the conditions tested in this study ( data not shown ) .	6	RESULTS	unidentified plasmid;unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	rpoS	activator	11681212	4	ver/dev	Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are low in ions found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	248	Such conditions may occur when the patho-gen invades host cells as in vivo measurements suggest that Salmonella-containing vacuoles are acidic and low in Mg2 + ions [ 36 , 37 ] found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	22	4 DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	11681212	4	ver/dev	Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are low in Mg2 found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	248	Such conditions may occur when the patho-gen invades host cells as in vivo measurements suggest that Salmonella-containing vacuoles are acidic and low in Mg2 + ions [ 36 , 37 ] found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	22	4 DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	11681212	4	ver/dev	Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are acidic in ions found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	248	Such conditions may occur when the patho-gen invades host cells as in vivo measurements suggest that Salmonella-containing vacuoles are acidic and low in Mg2 + ions [ 36 , 37 ] found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	22	4 DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	11681212	4	ver/dev	Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are acidic in Mg2 found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	248	Such conditions may occur when the patho-gen invades host cells as in vivo measurements suggest that Salmonella-containing vacuoles are acidic and low in Mg2 + ions [ 36 , 37 ] found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .	22	4 DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	12406731	9	att	We found no significant changes in 25 RpoS-dependent genes in either the wild type or the rpoS mutant in response to low-shear MMG .	257	We found no significant changes in 25 RpoS-dependent genes in either the wild type or the rpoS mutant in response to low-shear MMG .	6	DISCUSSION	nan	1	L2	OTHER	Other	NEG	New	Level 1
RpoS	gene	rpoS	activator	14723688	1	ver/dev	In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .	39	In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .	5	PRESENT ADDRESS: E. KOMITOPOULOU, LEATHERHEAD FOOD INTERNATIONAL LIMITED, RANDALLS ROAD, LEATHERHEAD, SURREY KT22 7RY, UK.	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	14723688	1	ver/dev	In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .	39	In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .	5	PRESENT ADDRESS: E. KOMITOPOULOU, LEATHERHEAD FOOD INTERNATIONAL LIMITED, RANDALLS ROAD, LEATHERHEAD, SURREY KT22 7RY, UK.	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	14723688	1	ver/dev	In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .	39	In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .	5	PRESENT ADDRESS: E. KOMITOPOULOU, LEATHERHEAD FOOD INTERNATIONAL LIMITED, RANDALLS ROAD, LEATHERHEAD, SURREY KT22 7RY, UK.	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	15819634	4	att	Chen , C.Y. , Eckmann , L. , Libby , S.J. , Fang , F.C. , Okamoto , S. , Kagnoff , M.F. , et al. ( 1996 ) Expression of Salmonella typhimurium rpoS and RpoS-dependent genes in the intracellular environment of eukaryotic cells .	583	Chen , C.Y. , Eckmann , L. , Libby , S.J. , Fang , F.C. , Okamoto , S. , Kagnoff , M.F. , et al. ( 1996 ) Expression of Salmonella typhimurium rpoS and RpoS-dependent genes in the intracellular environment of eukaryotic cells .	27	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoS	activator	16023758	12	ver/dev	In E. coli , the genes overlap with those of the RpoS regulon although induction of rpoS itself is not enough for the increased acid resistance observed since rpoS did not protect E. coli from subsequent exposure to pH 3 .	354	In E. coli , the genes induced by SCFA overlap with those of the RpoS regulon although induction of rpoS itself is not enough for the increased acid resistance observed since rpoS induced by osmotic shock by NaCl or sodium acetate did not protect E. coli from subsequent exposure to pH 3 [ 143 ] .	18	3.5.3. SCFA	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	activator	16625049	0	att	Recent studies have shown that rpoS and RpoS-dependent genes are	22	Recent studies have shown that rpoS and RpoS-dependent genes are	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	16816180	4	att	For insertion within the rpoS RBS , it was important that the recipient strain also contained katE-lac [ op ] , an RpoS-dependent reporter fusion .	123	For insertion within the rpoS RBS , it was important that the recipient strain also contained katE-lac [ op ] , an RpoS-dependent reporter fusion .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	16816180	2	ver/dev	DsrA is necessary for activation of rpoS translation in response to osmotic shock , while RprA increases RpoS both in response to a constitutively active rcsC allele , indicating a role in cell envelope stress .	22	DsrA is necessary for activation of rpoS translation in response to low temperature and osmotic shock ( 27 ) , while RprA increases RpoS both in response to osmotic shock ( 29 ) and in response to a constitutively active rcsC allele , indicating a role in cell envelope stress ( 15 , 29 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	16816180	2	ver/dev	DsrA is necessary for activation of rpoS translation in response to osmotic shock , while RprA increases RpoS both in response to osmotic shock to a constitutively active rcsC allele , indicating a role in cell envelope stress .	22	DsrA is necessary for activation of rpoS translation in response to low temperature and osmotic shock ( 27 ) , while RprA increases RpoS both in response to osmotic shock ( 29 ) and in response to a constitutively active rcsC allele , indicating a role in cell envelope stress ( 15 , 29 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	16816180	2	ver/dev	DsrA is necessary for activation of rpoS translation in response to low-temperature shock , while RprA increases RpoS both in response to a constitutively active rcsC allele , indicating a role in cell envelope stress .	22	DsrA is necessary for activation of rpoS translation in response to low temperature and osmotic shock ( 27 ) , while RprA increases RpoS both in response to osmotic shock ( 29 ) and in response to a constitutively active rcsC allele , indicating a role in cell envelope stress ( 15 , 29 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	16816180	2	ver/dev	DsrA is necessary for activation of rpoS translation in response to low-temperature shock , while RprA increases RpoS both in response to osmotic shock to a constitutively active rcsC allele , indicating a role in cell envelope stress .	22	DsrA is necessary for activation of rpoS translation in response to low temperature and osmotic shock ( 27 ) , while RprA increases RpoS both in response to osmotic shock ( 29 ) and in response to a constitutively active rcsC allele , indicating a role in cell envelope stress ( 15 , 29 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	17178790	2	ver/dev	However , rpoS might also contribute to the virulence of this serotype because RpoS strains of serotype Typhi are less cytotoxic than RpoS strains	49	However , rpoS might also contribute to the virulence of this serotype because RpoS strains of serotype Typhi are less cytotoxic than RpoS strains , but RpoS strains survive better inside resting THP-1 macrophages without apoptosis induction and have higher capacities for resistance in the macrophage ( 34 ) .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	17178790	3	ver/dev	V-W form RpoS Aps Cys VW form rpoS Ap RpoS Apr Cys V form rpoS Ap RpoS Apr Cys Trp V form PrpoS183 : : TTaraC PBADrpoS Cys Trp VW form induced by arabinose PrpoS183 : : TTaraC PBAD rpoS RpoS Cys V form PrpoS183 :	70	V-W form RpoS Aps Cys VW form rpoS Ap RpoS Apr Cys V form rpoS Ap RpoS Apr Cys Trp V form PrpoS183 : : TTaraC PBADrpoS Cys Trp VW form induced by arabinose PrpoS183 : : TTaraC PBAD rpoS RpoS Cys V form PrpoS183 : : TTaraC PBAD rpoS Cys VW form induced by arabinose tviABCDE10 Cys Vi Vi-phageS RpoS W form tviABCDE10 Cys Trp Vi Vi-phageS RpoS W form tviABCDE10 Cys Vi Vi-phageS RpoS W form rpoS Ap RpoS Apr thi-1 thr-1 leuB6 fhuA21 lacY1 glnV44 asdA4 recA1 RP42-Tc : : M	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoS	activator	17178790	3	ver/dev	TTaraC PBAD rpoS Cys VW form _ induced by arabinose tviABCDE10 Cys Vi Vi-phageS RpoS W form tviABCDE10 Cys Trp Vi Vi-phageS RpoS W form tviABCDE10 Cys Vi Vi-phageS RpoS W form rpoS Ap RpoS Apr thi-1 thr-1 leuB6 fhuA21 lacY1 glnV44 asdA4 recA1 RP42-Tc : : M	70	V-W form RpoS Aps Cys VW form rpoS Ap RpoS Apr Cys V form rpoS Ap RpoS Apr Cys Trp V form PrpoS183 : : TTaraC PBADrpoS Cys Trp VW form induced by arabinose PrpoS183 : : TTaraC PBAD rpoS RpoS Cys V form PrpoS183 : : TTaraC PBAD rpoS Cys VW form induced by arabinose tviABCDE10 Cys Vi Vi-phageS RpoS W form tviABCDE10 Cys Trp Vi Vi-phageS RpoS W form tviABCDE10 Cys Vi Vi-phageS RpoS W form rpoS Ap RpoS Apr thi-1 thr-1 leuB6 fhuA21 lacY1 glnV44 asdA4 recA1 RP42-Tc : : M	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoS	activator	17784910	33	ver/dev	Presumably , the posttranscriptional mechanisms responsible for regulation of RpoS protein expression were sufficiently robust to withstand our attempts at overwhelming them through ectopic transcriptional upregulation of the rpoS gene .	548	Presumably , the posttranscriptional mechanisms responsible for regulation of RpoS protein expression were sufficiently robust to withstand our attempts at overwhelming them through ectopic transcriptional upregulation of the rpoS gene .	14	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	19745516	4	ver/dev	However , rpoS might also contribute to the virulence of this serotype because RpoS strains of S. Typhi are -- cytotoxic than RpoS strains	93	However , rpoS might also contribute to the virulence of this serotype because RpoS strains of S. Typhi are less + -- cytotoxic than RpoS strains , but RpoS strains survive better inside resting THP-1 macrophages without apoptosis induction [ 50 ] .	10	EFFECT OF RPOS ON VI SYNTHESIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	19835951	18	ver/dev	H-NS-deficient mutants strongly increased RpoS due to enhanced rpoS translation .	228	H-NS-deficient mutants strongly increased RpoS due to enhanced rpoS translation and a dramatic reduction ( or even abolition ) in RpoS proteolysis [ 64 ] .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L Fig. 4A .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L NaCl LB broth .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt Fig. 4A .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt NaCl LB broth .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L Fig. 4A .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L NaCl LB broth .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt Fig. 4A .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	activator	19940937	3	ver/dev	At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt NaCl LB broth .	225	At exponential phase , when RpoS level should be very low in an rpoS + strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt or in 0.3 mol/L NaCl LB broth ( Fig. 4A ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L2	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rpoS	activator	20003355	1	att	Transcriptomic comparison of biofilm and planktonic-cells showed that rpoS was highly expressed in both populations , and that several RpoS-activated genes showed biofilm-specific patterns of expression .	227	Transcriptomic comparison of biofilm and planktonic cells showed that rpoS was highly expressed in both populations , and that several RpoS-activated genes showed biofilm-specific patterns of expression .	7	INACTIVATION OF SSRA AND RPOS ALTERS BIOFILM FORMATION IN S. TYPHIMURIUM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	22256797	7	ver/dev	In this study , we investigated effect of rpoS disruption and expression on intracellular levels of RpoS during induction of VBNC state , using S. Typhimurium strain LT2 .	303	In this study , we investigated effect of rpoS disruption and expression on VBNC state and intracellular levels of RpoS during induction of VBNC state , using S. Oranienburg , S. Dublin , and S. Typhimurium strain LT2 .	15	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	22256797	7	ver/dev	In this study , we investigated effect of rpoS disruption and expression on intracellular levels of RpoS during induction of VBNC state , using S. Dublin .	303	In this study , we investigated effect of rpoS disruption and expression on VBNC state and intracellular levels of RpoS during induction of VBNC state , using S. Oranienburg , S. Dublin , and S. Typhimurium strain LT2 .	15	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	22256797	7	ver/dev	In this study , we investigated effect of rpoS disruption and expression on intracellular levels of RpoS during induction of VBNC state , using S. Oranienburg .	303	In this study , we investigated effect of rpoS disruption and expression on VBNC state and intracellular levels of RpoS during induction of VBNC state , using S. Oranienburg , S. Dublin , and S. Typhimurium strain LT2 .	15	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	0	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	29	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	0	Unknown	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 RprA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	2	ver/dev	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25	51	However , whereas OxyS negatively influences RpoS abundance ,15 DsrA , RprA and ArcZ all upregulate RpoS protein lev-els .16 -20 Post-transcriptional activation of RpoS by these sRNAs relies on de-sequestration of an intramolecular base-pairing within the rpoS 5 ' UTR , a process which increases transcript stability and facilitates translation initiation .21 The importance of post-transcriptionally acting sRNAs for rpoS translation is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium and E. coli recruited multiple sRNAs to control rpoS translation , however , the degree of regulation by the above mentioned sRNAs varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development and c-di-GMP signaling has been studied in great detail ,6,25	1	INTRODUCTION	Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	22336758	21	ver/dev	To further distinguish between the contribution of RpoS to rdar morphotype expression , we compared the phenotype of an arcZ mutant with an rpoS mutant in the MAE52 strain background .	229	To further distinguish between the contribution of RpoS and ArcZ to csgD and rdar morphotype expression , we compared the phenotype of an arcZ mutant with an rpoS mutant in the MAE52 strain background .	2	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoS	activator	22356617	0	att	The expression patterns of rpoS and the two well-known RpoS-dependent genes , osmY and yciF , were assessed by qRT-PCR , which showed a similar immobilization-specific induction ( Fig. 6A and data not shown ) .	286	The expression patterns of rpoS and the two well-known RpoS-dependent genes , osmY and yciF , were assessed by qRT-PCR , which showed a similar immobilization-specific induction ( Fig. 6A and data not shown ) .	8	LINKING THE METABOLOMIC AND TRANSCRIPTOMIC DATA SHOWS A SHIFT FROM AEROBIC TO ANAEROBIC METABOLISM	unidentified	1	L3	OTHER	Fact	NEG	Other	Level 1
RpoS	gene	rpoS	activator	23960105	0	ver/dev	This tolerance appeared to be reflected in the upregulation of rpoS of the RpoS regulon .	59	This tolerance appeared to be reflected in the upregulation of stress genes ( rpoS , rpoH , and rpoE of the RpoS regulon ) that confers resistance to stationary cells exposed to a range of environmental stresses including in addition to heat , acids , osmotic shock , and starvation ( Loewen and Hengge-Aronis , 1994 ; Sirsat et al. , 2011a ) .	5	OF SALMONELLA AND SUBLETHAL HEAT EXPOSURE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	24985365	1	ver/dev	To further investigate the potential contribution of RpoS to growth during hyperosmotic-stress , a rpoS deletion mutant was generated , M-09DrpoS .	135	To further investigate the potential contribution of RpoS to growth during hyperosmotic stress , a rpoS deletion mutant was generated , M-09DrpoS .	11	RESULTS AND DISCUSSION	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	33799446	2	att	However , the transcription SPI-9 operon genes , which contribute to adherence to epithelial cells , increases under low pH and high-osmolarity in an RpoS-dependent manner in S. Typhi [ 46 ] and Nickerson and Curtis observed that a rpoS mutant of S. Typhimurium exhibited wild-type abilities to attach itself to and invade Int-407 cells and J774 macrophage-like cells [ 47 ] .	104	However , the transcription SPI-9 operon genes , which contribute to adherence to epithelial cells , increases under low pH and high osmolarity in an RpoS-dependent manner in S. Typhi [ 46 ] and Nickerson and Curtis observed that a rpoS mutant of S. Typhimurium exhibited wild-type abilities to attach itself to and invade Int-407 cells and J774 macrophage-like cells [ 47 ] .	4	1. INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	33799446	3	att	It has also been reported that rpoS and RpoS-dependent genes are highly expressed upon entry into macrophages and epithelial cells [ 38,48 ] , that RpoS induces the expression of SEF14 fimbriae [ 49 ] , and that RpoS is required for the expression of the plasmid encoded spv genes , which , in turn , are required for intracellular growth in deep lymphoid organs such as the spleen and the liver , and which are associated with strains causing non-typhoid bacteremia [ 50 -- 53 ] .	105	It has also been reported that rpoS and RpoS-dependent genes are highly expressed upon entry into macrophages and epithelial cells [ 38,48 ] , that RpoS induces the expression of SEF14 fimbriae [ 49 ] , and that RpoS is required for the expression of the plasmid encoded spv genes , which , in turn , are required for intracellular growth in deep lymphoid organs such as the spleen and the liver , and which are associated with strains causing non-typhoid bacteremia [ 50 -- 53 ] .	4	1. INTRODUCTION	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rpoS	activator	33799446	4	att	These latter results would at least partially explain why deletion of rpoS or altered rpoS alleles leads to a decrease in Salmonella lethality in mice [ 54 ] , and why S. Typhimurium rpoS mutants demonstrated a decreased ability to colonize murine Peyer 's patches after oral inoculation as compared to its wild-type virulent parent strain , which indicates that RpoS-dependent gene expression was required for the initial stages of systemic infection [ 47 ] .	106	These latter results would at least partially explain why deletion of rpoS or altered rpoS alleles leads to a decrease in Salmonella lethality in mice [ 54 ] , and why S. Typhimurium rpoS mutants demonstrated a decreased ability to colonize murine Peyer 's patches after oral inoculation as compared to its wild-type virulent parent strain , which indicates that RpoS-dependent gene expression was required for the initial stages of systemic infection [ 47 ] .	4	1. INTRODUCTION	Salmonella;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	activator	8045891	10	ver/dev	The rpoS mutation resulted in a two - to threefoldhigher level of induction of a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	99	The rpoS mutation resulted in a two - to threefoldhigher level of induction of stiB during P starvation and a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	steA	activator	23504014	24	att	( C ) Alignment of the promoter regions of steA and six PhoP-activated genes with a similar architecture ( 49 ) .	322	( C ) Alignment of the promoter regions of steA and six PhoP-activated genes with a similar architecture ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steA	activator	23504014	26	att	Here , we show that steA possesses a PhoP-activated promoter with a PhoP box located 12 nucleotides upstream of the 10 hexamer , resembling promoters with architecture I .	343	Here , we show that steA possesses a PhoP-activated promoter with a PhoP box located 12 nucleotides upstream of the 10 hexamer , resembling promoters with architecture I .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steA	activator	23504014	8	att	MgrB regulates expression of steA in a PhoP-dependent manner .	244	MgrB regulates expression of steA in a PhoP-dependent manner .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steA	activator	23504014	7	ver/dev	These results establish that regulation of steA by PhoQ/PhoP suggest that PhoP could be a direct activator of steA .	243	These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system and suggest that PhoP could be a direct activator of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	steA	activator	23504014	7	ver/dev	These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system .	243	These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system and suggest that PhoP could be a direct activator of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
PhoP	gene	steA	activator	23504014	14	ver/dev	Results suggest that PhoP could be a direct activator of steA transcription .	266	Results shown in previous sections suggest that PhoP could be a direct activator of steA transcription .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	steA	activator	23504014	27	ver/dev	that PhoP directly activates steA	346	Several lines of evidence suggest that PhoP directly activates steA and that the proposed PhoP binding site is functional .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steA	activator	25182488	12	att	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	250	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	bfr	repressor	30682134	31	ver/dev	In addition to its effects on genes , CsrA repressed translation of bfr in LB , respectively -LRB- S2 Table -RRB- .	267	In addition to its effects on genes involved in iron acquisition , CsrA repressed translation of genes encoding the iron storage proteins ftnB ( 13 - and 5.6-fold ) , dps ( 5.1 - and 2.6-fold ) , and bfr ( 2.7-fold and not significant ) in mLPM and LB , respectively ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	bfr	repressor	30682134	31	ver/dev	In addition to its effects on genes , CsrA repressed translation of bfr in mLPM , respectively -LRB- S2 Table -RRB- .	267	In addition to its effects on genes involved in iron acquisition , CsrA repressed translation of genes encoding the iron storage proteins ftnB ( 13 - and 5.6-fold ) , dps ( 5.1 - and 2.6-fold ) , and bfr ( 2.7-fold and not significant ) in mLPM and LB , respectively ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	regulator	11254626	1	att	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	208	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	6	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	20824208	0	ver/dev	rck operons are controlled by the Salmonella N-Acyl homoserine lactone receptor SdiA	201	In addition to the tra and spv genes , pSLT carries pef and rck operons that are controlled by the Salmonella N-Acyl homoserine lactone receptor SdiA [ 39 ] .	11	CRYPTIC GENES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	20824208	0	ver/dev	rck operons are controlled by the Salmonella N-Acyl homoserine lactone receptor SdiA	201	In addition to the tra and spv genes , pSLT carries pef and rck operons that are controlled by the Salmonella N-Acyl homoserine lactone receptor SdiA [ 39 ] .	11	CRYPTIC GENES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	22149171	5	att	AHL-dependent expression of the SdiA-regulated gene rck correlated to the observed sdiA transcriptional changes in regulator mutants .	13	AHL-dependent expression of the SdiA-regulated gene rck correlated to the observed sdiA transcriptional changes in regulator mutants .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	regulator	22149171	56	att	To test whether observed differences in sdiA expression among mutants and media conditions resulted in actual differences in SdiA levels , SdiA-regulated rck expression was measured .	365	To test whether observed differences in sdiA expression among mutants and media conditions resulted in actual differences in SdiA levels , SdiA-regulated rck expression was measured .	20	REGULATORY INPUT AT THE SDIA PROMOTER AFFECTS SDIA OUTPUT	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
SdiA	gene	rck	regulator	25080967	1	ver/dev	To decipher the regulation of rck by SdiA , we first confirmed the operon organization of the pefI-srgC locus .	13	To decipher the regulation of rck by SdiA , we first confirmed the operon organization of the pefI-srgC locus .	3	SUMMARY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25080967	10	ver/dev	These results demonstrate that the transcriptional regulation of rck by SdiA previously observed also modulates Rck protein expression .	84	These results demonstrate that the transcriptional regulation of rck by SdiA previously observed ( Ahmer et al. , 1998 ; Smith and Ahmer , 2003 ) also modulates Rck protein expression .	6	RCK PROTEIN EXPRESSION IS TEMPERATURE- AND SDIA-AHLS-DEPENDENT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25080967	11	ver/dev	We thus decided to further characterize the mechanism of transcriptional regulation of rck by SdiA .	85	We thus decided to further characterize the mechanism of transcriptional regulation of rck by SdiA .	6	RCK PROTEIN EXPRESSION IS TEMPERATURE- AND SDIA-AHLS-DEPENDENT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25080967	17	ver/dev	Different rck regulation by SdiA between S. Typhimurium is due to differences in the promoter region of the pefI-srgC operon	180	Different rck regulation by SdiA between S. Enteritidis and S. Typhimurium is due to differences in the promoter region of the pefI-srgC operon	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25080967	17	ver/dev	Different rck regulation by SdiA between S. Enteritidis is due to differences in the promoter region of the pefI-srgC operon	180	Different rck regulation by SdiA between S. Enteritidis and S. Typhimurium is due to differences in the promoter region of the pefI-srgC operon	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25080967	18	ver/dev	The PefIP2 promoters are absent in S. Enteritidis , suggesting a mechanism of regulation of rck expression by SdiA different between these two sero-types .	187	The PefIP1 and PefIP2 promoters described above for S. Typhimurium are absent in S. Enteritidis , suggesting a mechanism of regulation of rck expression by SdiA different between these two sero-types .	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
SdiA	gene	rck	regulator	25080967	18	ver/dev	The PefIP1 promoters are absent in S. Enteritidis , suggesting a mechanism of regulation of rck expression by SdiA different between these two sero-types .	187	The PefIP1 and PefIP2 promoters described above for S. Typhimurium are absent in S. Enteritidis , suggesting a mechanism of regulation of rck expression by SdiA different between these two sero-types .	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
SdiA	gene	rck	regulator	25080967	20	ver/dev	This result demonstrates that the regulation of rck expression by SdiA is different between these two serotypes .	191	This result demonstrates that the regulation of rck expression by SdiA is different between these two serotypes .	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25080967	24	ver/dev	As our results were not supporting an involvement of SdiA in the transcriptional regulation of rck at low-temperature , we searched for another regulatory mechanism .	234	As our results were not supporting an involvement of SdiA in the transcriptional regulation of rck at low temperature , we searched for another regulatory mechanism .	12	H-NS NEGATIVELY REGULATES RCK EXPRESSION AT 25°C AND AT 37°C	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SdiA	gene	rck	regulator	25080967	27	ver/dev	In this study , we first confirmed that the transcriptional regulation of rck by SdiA resulted in an increase of Rck protein expression .	257	In this study , we first confirmed that the transcriptional regulation of rck by SdiA described earlier ( Ahmer et al. , 1998 ; Smith and Ahmer , 2003 ) resulted in an increase of Rck protein expression .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	rck	regulator	25299072	1	ver/dev	Encoding an outer membrane protein , the rck gene on the virulence plasmid of some serotypes of Salmonella was regulated by SdiA .	84	Encoding an outer membrane protein , the rck gene on the virulence plasmid of some serotypes of Salmonella was regulated by SdiA .	4	INTRODUCTION	unidentified plasmid;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	26442936	1	att	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that carries seven genes and the srgE gene ( 30 , 50 ) .	105	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that carries seven genes and the srgE gene ( 30 , 50 ) .	8	AI-1 SIGNALING IN SALMONELLA	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	26443762	1	att	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 19 , 35 ) .	93	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 19 , 35 ) .	8	AI-1 SIGNALING IN SALMONELLA	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	regulator	29763730	0	ver/dev	Abed et al. also showed that the promoter region of the rck operon , located on the S. enterica serovar Typhimurium ATCC 14018 plasmid , is regulated by the SdiA protein in the presence of AHL .	35	Abed et al. [ 15 ] also showed that the promoter region of the rck operon , located on the S. enterica serovar Typhimurium ATCC 14018 plasmid , is regulated by the SdiA protein in the presence of AHL .	3	MAIN	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Gardnerella vaginalis;unidentified plasmid	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	invF	activator	16045614	51	ver/dev	SirA induction of invF requires HilD Previous evidence suggested that SirA required the entire SPI1 TTSS	299	SirA induction of hilA and invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA and thus the entire SPI1 TTSS	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	invF	activator	16045614	51	ver/dev	SirA induction of invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA	299	SirA induction of hilA and invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA and thus the entire SPI1 TTSS	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	invF	activator	16045614	78	ver/dev	In support of our model , we demonstrate that SirA induction of invF requires the presence of HilD .	549	In support of our model , we demonstrate that SirA induction of hilC , rtsA , hilA and invF requires the presence of HilD .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
NsrR	gene	yeaR	repressor	24021902	0	att	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	77	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	narK	regulator	29857034	19	ver/dev	narK -LRB- are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	sodA	regulator	19460824	15	ver/dev	Examination of the sequence revealed that SoxS binds with high affinity in a manner characteristic of class I promoters in the sodA promoters of E. coli .	190	Examination of the sequence associated with the PQ-inducible ompW promoter revealed that SoxS binds with high affinity in a manner characteristic of class I promoters in the forward orientation , such as the zwf and sodA promoters of E. coli .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	sodA	regulator	19917752	0	ver/dev	SoxS _ regulated , including sodA	266	Among the genes that were upregulated in 104-cip , a number were SoxS regulated , including acnA , fpr , ribA , sodA , lpxC , and soxS itself .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	regulator	21193816	5	ver/dev	SoxS is involved in the LsrR-mediated regulation of the sodA gene .	210	SoxS is involved in the LsrR-mediated regulation of the sodA gene .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FadR	gene	fabA	activator	27004424	4	ver/dev	Conversely , FadR , stimulates UFA biosynthesis by binding to the fabA end fabB promoter .	45	Conversely , another transcription regulator , FadR , stimulates UFA biosynthesis by binding to the fabA end fabB promoter .	5	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	rcsA	activator	23443158	7	att	DsrA ( downstream region of rcsA ) was initially discovered as an antagonist of H-NS-dependent transcriptional repression .	120	DsrA ( downstream region of rcsA ) was initially discovered as an antagonist of H-NS-dependent transcriptional repression .	5	2.1. SRNA-MEDIATED REGULATION OF THE FLAGELLAR CASCADE—FLHDC MRNA AS A MAJOR SITE FOR SRNA ACTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	spiC	regulator	12753201	32	ver/dev	spiC is regulated by both SsrB	205	spiC is regulated by both OmpR and SsrB	9	PHOSPHORYLATION OF OMPR INCREASES ITS AFFINITY FOR SSRA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	mdtA	repressor	22173828	9	ver/dev	The BaeR D61A protein showed lower aYnity for the mdtA promoter at the same concentrations	159	The BaeR D61A protein showed lower aYnity for the mdtA promoter at the same concentrations used for the native BaeR protein ( Fig. 4c ) , and even after phosphorylating BaeR D61A , the aYnity was lower than that observed for BaeR-P , indicating that phosphorylation of residue Asp 61 is important for BaeR binding to DNA ( Fig. 4d ) .	19	BAER–P BINDS TO THE MDTA PROMOTER REGION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LexA	gene	umuD	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	umuD	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	siiA	activator	27601571	18	ver/dev	scription activation of protein-coding genes outside SPI-1 overlap Table S1 -RRB- , suggesting that failure to detect binding of InvF by regions _ bound by H-NS -LRB- HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites , , siiA , mcpC , epitope tags	210	scription activation of protein-coding genes outside SPI-1 overlap Table S1 ) , suggesting that failure to detect binding of InvF by regions that are likely bound by H-NS ( HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites associated with regulation of lpxR , STM14_5184 , siiA , mcpC , epitope tags .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	dsbA	activator	32571967	7	att	The dsbA mutation also affects fliZ transcription independently of Rcs , presumably due to the inability to export FlgM , leading to decreased expression from the FliA-dependent promoter ( 35 ) .	137	The dsbA mutation also affects fliZ transcription independently of Rcs , presumably due to the inability to export FlgM , leading to decreased expression from the FliA-dependent promoter ( 35 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	New	Level 1
FliA	gene	fliA	repressor	23977202	0	ver/dev	The loss of virulence in FlgM defective Salmonella requires fliA , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	165	The loss of virulence in FlgM defective Salmonella requires fliA and fliC [ 35 ] , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	24	IN VITRO CHARACTERIZATION OF FLGM-DEFICIENT SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	fljB	regulator	33799446	11	ver/dev	Thus , whereas in E. coli K12 it is well established that RpoS to a lesser extent fljB , were positively controlled by Rpo , resulting in a decreased motility in a rpoS deletion mutant , even though transcription of the flhDC gene were slightly upregulated in a Salmonella ∆ rpoS strain .	340	Thus , whereas in E. coli K12 it is well established that RpoS downregulates the expression of flagella , results from Lévi-Meyrueis et al. , ( 2014 ) indicate that the flagellin genes fliC , and to a lesser extent fljB , were positively controlled by RpoS , resulting in a decreased motility in a rpoS deletion mutant , even though transcription of the flhDC genes encoding the master regulator of flagellar synthesis were slightly upregulated in a Salmonella ∆ rpoS strain [ 42 ] .	16	4. IMPACT OF STRESS RESISTANCE RESPONSES ON OTHER ASPECTS OF SALMONELLA PHYSIOLOGY	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	pagC	activator	19202096	3	att	pagC and sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	335	pagC and sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	pagC	activator	33045730	76	att	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	333	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sipC	activator	21722794	2	att	Fur also positively regulates other HilA-dependent genes ( invF and sipC ) involved in invasion , by repressing the expression of H-NS ( Troxell et al. , 2011 ) .	444	Fur also positively regulates other HilA-dependent genes ( invF and sipC ) involved in invasion , by repressing the expression of H-NS ( Troxell et al. , 2011 ) .	11	3.1. TRANSCRIPTIONAL REGULATION BY FUR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sipC	activator	26386070	2	att	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	262	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	assT	repressor	18156266	0	ver/dev	Expression of assT was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	12	Expression of ompS1 , assT , and STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx and STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	assT	repressor	18156266	28	ver/dev	The transcriptional profile was consistent with the hypothesis that H-NS represses the expression of assT , .	298	The transcriptional profile obtained was consistent with the hypothesis that H-NS represses the expression of ompS1 ( 5 ) ( Fig. 2c ) , assT ( Fig. 2b ) , and STY307O ( Fig. 2a ) , suggesting that the STY3070-STY3064 operon also belongs to the H-NS regulon .	5	FIG. 2	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HNS	gene	assT	repressor	18156266	42	ver/dev	The results of our experiments concur with the concept that H-NS represses the expression of assT in Salmonella serovar Typhi .	351	The results of our experiments concur with the concept that H-NS represses the expression of STY3070 , assT , and ompS1 in Salmonella serovar Typhi ( Fig. 2a to c ) .	6	DISCUSSION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	assT	repressor	18156266	43	ver/dev	Previous studies also showed that assT are repressed by H-NS in Salmo-nella serovar Typhimurium .	352	Previous studies also showed that assT and ompS1 are repressed by H-NS in Salmo-nella serovar Typhimurium and Salmonella serovar Typhi , respectively ( 13 , 37 ) .	6	DISCUSSION	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	assT	repressor	22343301	0	ver/dev	The H-NS nucleoid protein repressed the expression of the assT transcriptional units .	8	The H-NS nucleoid protein repressed the expression of the assT-dsbL-dsbI LeuO-dependent operon , as well as of the assT transcriptional units .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	assT	repressor	22343301	16	ver/dev	assT transcriptional activation in repression by H-NS .	157	assT transcriptional activation in N-minimal medium and repression by H-NS .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	assT	repressor	22343301	19	ver/dev	Since previous reports have shown that H-NS negatively regulates assT transcription in S. Typhi IMSS-1 , the assT transcriptional-fusions were analyzed in an hns background , in N-minimal-medium .	167	Since previous reports have shown that H-NS negatively regulates assT transcription in S. Typhi IMSS-1 ( 26 , 42 , 49 ) , the assT transcriptional fusions were analyzed in an hns background , in N-minimal medium ( Fig. 4 ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	assT	repressor	22343301	21	ver/dev	In contrast , low levels of assT expression were detected in the absence of P2 , in a STYhns99 strain , suggesting that the upstream PLeuO promoter activity is also repressed by the H-NS global regulator in N-minimal-medium .	182	In contrast , low levels of assT expression were detected in the absence of P1 and P2 , in a STYhns99 strain , suggesting that the upstream PLeuO promoter activity is also repressed by the H-NS global regulator in N-minimal medium .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	assT	repressor	22343301	21	ver/dev	In contrast , low levels of assT expression were detected in the absence of P1 , in a STYhns99 strain , suggesting that the upstream PLeuO promoter activity is also repressed by the H-NS global regulator in N-minimal-medium .	182	In contrast , low levels of assT expression were detected in the absence of P1 and P2 , in a STYhns99 strain , suggesting that the upstream PLeuO promoter activity is also repressed by the H-NS global regulator in N-minimal medium .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	dps	repressor	30682134	33	ver/dev	Thus , repression of dps by CsrA may be more closely related to repression of the oxidative-stress response than to iron storage .	272	Thus , repression of ftnB and dps by CsrA may be more closely related to repression of the oxidative stress response than to iron storage .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	dps	repressor	30682134	33	ver/dev	Thus , repression of dps by CsrA may be more closely related to repression of the oxidative-stress response than to iron storage .	272	Thus , repression of ftnB and dps by CsrA may be more closely related to repression of the oxidative stress response than to iron storage .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
SlyA	gene	pagC	activator	18270203	3	att	Thus , to understand this process , we investigated the expression of the PhoP - and SlyA-dependent ugtL and pagC genes , which are normally bound by the H-NS protein ( 4 , 5 ) .	37	Thus , to understand this process , we investigated the expression of the PhoP - and SlyA-dependent ugtL and pagC genes , which are normally bound by the H-NS protein ( 4 , 5 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	activator	18270203	21	ver/dev	H-NS Remains Associated with the pagC Promoters under Inducing Conditions -- The SlyA proteins could activate transcription of the pagC genes by either displacing H-NS by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
SlyA	gene	pagC	activator	18270203	21	ver/dev	H-NS Remains Associated with the pagC Promoters under Inducing Conditions -- The SlyA proteins could activate transcription of the pagC genes by either displacing H-NS from their respective promoters not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
SlyA	gene	pagC	activator	19091955	5	att	A direct repeat , TAAAT - ( 6 nt ) - TCAAC , referred to as `` the reverse PhoP box , '' was identified in the ugtL promoter ( 2 ) , which is conserved in another PhoP and SlyA-dependent gene , pagC ( shown as TAAAT - ( 6 nt ) - TAAAC in Fig. 1A ) ( 13 , 14 ) .	58	A direct repeat , TAAAT - ( 6 nt ) - TCAAC , referred to as `` the reverse PhoP box , '' was identified in the ugtL promoter ( 2 ) , which is conserved in another PhoP and SlyA-dependent gene , pagC ( shown as TAAAT - ( 6 nt ) - TAAAC in Fig. 1A ) ( 13 , 14 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	activator	19091955	19	ver/dev	Transcriptional activation of pagC is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in Fig. 3C .	100	Transcriptional activation of pagD and pagC is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in the relA spoT mutant harboring pYS1109 ( Fig. 3C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Iris germanica	0	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	activator	19091955	19	ver/dev	Transcriptional activation of pagC is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in the relA spoT mutant harboring pYS1109 .	100	Transcriptional activation of pagD and pagC is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in the relA spoT mutant harboring pYS1109 ( Fig. 3C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Iris germanica;Leiostomus xanthurus	0	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	activator	29857034	10	ver/dev	Moreover , the pagC gene is positively regulated by SlyA .	290	Moreover , the pagC gene that encodes a membrane protein involved in bacterial virulence is positively regulated by SlyA .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	activator	29857034	13	ver/dev	Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression .	299	Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression ( Fig. 3G ) .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	activator	29857034	14	ver/dev	Within the virulence coincident genes , we determined that pagC is positively regulated by SlyA .	309	Within the virulence coincident genes , we determined that pagC is positively regulated by SlyA , which is consistent with previous reports [ 7,13,14 ] .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	activator	29857034	32	ver/dev	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of Fig. 4G , suggesting that SlyA positively regulates pagC expression .	367	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM ( Fig. 4G ) , suggesting that SlyA positively and directly regulates pagC expression , which is similar to previous findings [ 7,13,14 ] .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagC	activator	29857034	32	ver/dev	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM , suggesting that SlyA positively regulates pagC expression .	367	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM ( Fig. 4G ) , suggesting that SlyA positively and directly regulates pagC expression , which is similar to previous findings [ 7,13,14 ] .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagC	activator	30682134	18	ver/dev	SlyA activates pagC expression in a PhoP-dependent manner , and only in LB was S2 Table .	225	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	activator	30682134	18	ver/dev	SlyA activates pagC expression in a PhoP-dependent manner , and only in LB was their translation .	225	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	activator	30992361	18	att	We found that the EmrR-stimulated pagC transcription in the ΔemrR ΔslyA mutant carrying plasmid pemrR-FLAG was 7.1-fold reduced by 1 mM dopamine , whereas the SlyA-stimulated transcription in this mutant carrying pslyA-FLAG was not influenced ( Fig. 3D ) .	136	We found that the EmrR-stimulated pagC transcription in the ΔemrR ΔslyA mutant carrying plasmid pemrR-FLAG was 7.1-fold reduced by 1 mM dopamine , whereas the SlyA-stimulated transcription in this mutant carrying pslyA-FLAG was not influenced ( Fig. 3D ) .	3	RESULTS	unidentified plasmid;Iris germanica;Iris germanica	0.5	L3	OTHER	Other	NEG	Other	Level 1
SlyA	gene	pagC	activator	30992361	15	ver/dev	As a matter of fact , our previous study revealed that SlyA , at a high level , could stimulate deficient transcription of both pagC genes .	130	As a matter of fact , our previous study revealed that SlyA , at a high level that could not be attained physiologically in a wild-type cell , could stimulate deficient transcription of both pagC and pagD genes caused by an absence of the positive signal , i.e. , alarmine-guanosine pentaphosphate ( 23 ) .	3	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
SlyA	gene	pagC	activator	31333620	0	att	According to our previous studies , transcription of many horizontally acquired genetic loci such as the ugtL and pagC genes are governed by a PhoP/PhoQ - and SlyA-dependent feedforward regulatory loop ( Shi et al. , 2004b ; Zhao et al. , 2008 ) .	55	According to our previous studies , transcription of many horizontally acquired genetic loci such as the ugtL and pagC genes are governed by a PhoP/PhoQ - and SlyA-dependent feedforward regulatory loop ( Shi et al. , 2004b ; Zhao et al. , 2008 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
FimY	gene	fimZ	activator	24462182	9	ver/dev	Our results suggested that FimY may function as a DNA-binding protein to activate fimZ .	53	Our results suggested that FimY may function as a DNA-binding protein to activate fimZ .	4	1. INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FimY	gene	fimZ	activator	24462182	19	ver/dev	FimY was previously reported to activate fimZ	219	FimY was previously reported to activate fimZ and its own promoters , but no DNA-binding activity was demonstrated ( Saini et al. , 2009 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	cat	regulator	31484980	6	ver/dev	To confirm the regulation of yobH by HilD , a transcriptional-fusion of the intergenic region upstream of yobH to the cat reporter gene was constructed in the pKK232-8 plasmid .	50	To confirm the regulation of yobH by HilD , a transcriptional fusion of the intergenic region upstream of yobH to the cat ( chloramphenicol acetyl transferase ) reporter gene was constructed in the pKK232-8 plasmid .	3	RESULTS	Felis catus;unidentified plasmid	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hmp	repressor	17024490	3	ver/dev	Thus repression of hmp transcription by active Fnr is lifted in the presence of its congeners .	41	Thus repression of hmp transcription by active Fnr is lifted in the presence of NO and its congeners .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hmp	repressor	17024490	3	ver/dev	Thus repression of hmp transcription by active Fnr is lifted in the presence of NO .	41	Thus repression of hmp transcription by active Fnr is lifted in the presence of NO and its congeners .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hmp	repressor	20829289	0	ver/dev	In Salmonella , five transcription factors have been implicated : hmp transcription is repressed by FNR .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
FNR	gene	hmp	repressor	20829289	0	ver/dev	In E. coli , five transcription factors have been implicated : hmp transcription is repressed by FNR .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	lacZ	regulator	27341691	8	att	Additionally , this strain harbored a HilD-regulated hilA ' - lacZ fusion that allowed us to monitor HilD activity .	166	Additionally , this strain harbored a HilD-regulated hilA ' - lacZ fusion that allowed us to monitor HilD activity .	8	PAT CONTROLS HILD STABILITY	Varanus togianus	0	L3	OTHER	Other	OTHER	Other	Level 2
ArcA	gene	barA	repressor	32392214	31	att	This is because similar fluorescence was displayed by wild-type and barA mutant Salmonella harboring transcriptional-fusions between a promoterless gfp gene and the promoter of the ArcA-repressed lldP gene ( S16 Fig ) .	327	This is because similar fluorescence was displayed by wild-type and barA mutant Salmonella harboring transcriptional fusions between a promoterless gfp gene and the promoter of the ArcA-repressed lldP gene ( S16 Fig ) .	17	BARA IS DISPENSABLE FOR ACTIVATION OF THE REGULATORS ARCA, OMPR, AND PHOP UNDER CONDITIONS IN WHICH IT ACTIVATES RCSB	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	orgBC	regulator	29555922	16	ver/dev	HilD also independently regulate the expression of the orgBC SPI-1 operon .	267	HilD and PhoP also positively and independently regulate the expression of the orgBC SPI-1 operon , in SPI-1-inducing growth conditions , PhoP directly and HilD through HilA8 ,56 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	sbmC	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	yaeB	regulator	31487966	3	ver/dev	EMSAs revealed that H-NS bound specifically to yaeB promoter , but 2.4 .	169	Electrophoretic mobility shift assays ( EMSAs ) revealed that H-NS bound specifically to the hns promoter ( positive control ) and yaeB promoter , but 2.4 .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	yaeB	regulator	31487966	3	ver/dev	Electrophoretic mobility-shift assays revealed that H-NS bound specifically to yaeB promoter , but 2.4 .	169	Electrophoretic mobility shift assays ( EMSAs ) revealed that H-NS bound specifically to the hns promoter ( positive control ) and yaeB promoter , but 2.4 .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	yaeB	regulator	31487966	16	ver/dev	Figures S7 and S8 supported our conclusion that the regulation of yaeB is mediated by H-NS	313	We sequenced the rpoS and phoP genes of the hns mutant generated in this study and WT strain and found that mutations did not occur in phoP and rpoS loci ( Figures S7 and S8 ) , which supported our conclusion that the regulation of yaeB is mediated by H-NS .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	yaeB	regulator	31487966	16	ver/dev	rpoS loci supported our conclusion that the regulation of yaeB is mediated by H-NS	313	We sequenced the rpoS and phoP genes of the hns mutant generated in this study and WT strain and found that mutations did not occur in phoP and rpoS loci ( Figures S7 and S8 ) , which supported our conclusion that the regulation of yaeB is mediated by H-NS .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	yaeB	regulator	31487966	16	ver/dev	phoP loci supported our conclusion that the regulation of yaeB is mediated by H-NS	313	We sequenced the rpoS and phoP genes of the hns mutant generated in this study and WT strain and found that mutations did not occur in phoP and rpoS loci ( Figures S7 and S8 ) , which supported our conclusion that the regulation of yaeB is mediated by H-NS .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	fliA	activator	23977202	0	att	The loss of virulence in FlgM defective Salmonella requires fliA and fliC [ 35 ] , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	165	The loss of virulence in FlgM defective Salmonella requires fliA and fliC [ 35 ] , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	24	IN VITRO CHARACTERIZATION OF FLGM-DEFICIENT SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	dsrA	repressor	25566242	5	ver/dev	Both cadC and dsrA are repressed by H-NS .	68	Both cadC and dsrA are repressed by H-NS ( 55 , 56 ) .	4	LEUO HISTORY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sdiA	regulator	22149171	15	ver/dev	Thus , the CRP binding site was converted to the CRP consensus sequence , resulting in increased sdiA expression .	248	Thus , the CRP binding site was converted to the CRP consensus sequence , resulting in increased sdiA expression .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	sdiA	regulator	22149171	23	ver/dev	Because CRP is a regulator of carbon metabolism , the effects of different carbon sources were tested on sdiA expression .	260	Because CRP is a regulator of carbon metabolism , the effects of different carbon sources were tested on sdiA expression .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sdiA	regulator	22149171	32	ver/dev	sdiA is regulated by CRP	286	Because sdiA is regulated by CRP , and carbon source affects the activity of CRP , the promoter mutant b1-d4 , which lacks a CRP binding site , was tested in a strain carrying leuO : pBAD .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sdiA	regulator	22149171	41	ver/dev	that CRP regulates sdiA	320	Because it was shown that CRP regulates sdiA and that an active Rcs-system-making capsule may be altering carbon metabolism in the cell , interactions between CRP and the Rcs system were examined .	17	THE RCS PHOSPHORELAY NEGATIVELY REGULATES SDIA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	gene	lacZ	activator	16430704	15	ver/dev	expression of activity of FlhC proteins in initiating the transcription of fliA-fused lacZ gene after induction of IPTG-controlled flhDC genes in cells depleted either of DnaK or of both DnaK and ClpP .	224	Accumulation and expression of activity of FlhD and FlhC proteins in initiating the transcription of fliA-fused lacZ gene after induction of IPTG-controlled flhDC genes in cells depleted either of DnaK or of both DnaK and ClpP .	7	PHYSICAL INTERACTION OF FLHD, FLHC AND DNAK PROTEINS IN VIVO	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilC	gene	hns	regulator	17675384	12	ver/dev	To evaluate the role of the activators HilD and HilC in the regulation of rtsA transcription , the single-copy rtsA-lac transcriptional-fusion was tested in the hilD hilC background in the presence and absence of hns mutations .	231	To evaluate the role of the activators HilD and HilC in the regulation of rtsA transcription , the single-copy rtsA-lac transcriptional fusion was tested in the hilD hilC background in the presence and absence of hha and hns mutations ( Fig. 8 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	invC	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	ppiA	regulator	24858080	7	att	Our microarray data revealed the activation of at least five CpxR-controlled genes ( including ppiA ) when Salmonella was grown in the presence of CuSO4 in both SLB and M9 , as well as in the presence of ZnSO4 in SLB ( Fig. 1 , Table S3 ) .	289	Our microarray data revealed the activation of at least five CpxR-controlled genes ( including ppiA ) when Salmonella was grown in the presence of CuSO4 in both SLB and M9 , as well as in the presence of ZnSO4 in SLB ( Fig. 1 , Table S3 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ydgT	activator	16301528	7	ver/dev	Inactivation of ssrB in the ydgT background resulted in complete loss of virulence during systemic infection , consistent with the finding that deletion of ydgT does not override the requirement of SsrB for transcriptional activation of the SPI-2 pathogenicity island .	92	Inactivation of ssrB in the ydgT background resulted in complete loss of virulence during systemic infection , consistent with the finding that deletion of ydgT does not override the requirement of SsrB for transcriptional activation of the SPI-2 pathogenicity island .	5	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	sefA	regulator	25217722	0	ver/dev	It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sefA	regulator	25217722	0	ver/dev	It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	macB	repressor	24169575	0	ver/dev	macB transcript levels are elevated in 12 h postinfection , consistent with potential rapid inactivation of PhoP .	211	macA and macB transcript levels are elevated in mRNA isolated from Salmonella-infected J774 macrophage-like cells at later time points , including 4 , 8 , and 12 h postinfection ( 73 , 74 ) , consistent with potential rapid inactivation of PhoP and with our data .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	macB	repressor	24169575	0	ver/dev	macB transcript levels are elevated in 8 h postinfection , consistent with potential rapid inactivation of PhoP .	211	macA and macB transcript levels are elevated in mRNA isolated from Salmonella-infected J774 macrophage-like cells at later time points , including 4 , 8 , and 12 h postinfection ( 73 , 74 ) , consistent with potential rapid inactivation of PhoP and with our data .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	macB	repressor	24169575	0	ver/dev	macB transcript levels are elevated in 4 h postinfection , consistent with potential rapid inactivation of PhoP .	211	macA and macB transcript levels are elevated in mRNA isolated from Salmonella-infected J774 macrophage-like cells at later time points , including 4 , 8 , and 12 h postinfection ( 73 , 74 ) , consistent with potential rapid inactivation of PhoP and with our data .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
STM2361	gene	STM2360	activator	29024617	2	ver/dev	Given the significant induction of STM2361 under acid shock conditions , STM2360 genes within the operon may have roles in acid stress response .	49	Given the significant induction of STM2361 under acid shock conditions , STM2360 and other genes within the operon may have roles in acid stress response .	5	MAIN	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
NorR	gene	hcp	regulator	22039967	0	ver/dev	These genes are regulated by hcp and NorR -LRB- norV -RRB- ,	114	These genes are regulated by the cytoplasmic NO-responsive transcription factors NsrR ( hmp and hcp ) and NorR ( norV ) ,	8	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NtrC	gene	glnA	activator	27583250	0	att	NtrC-dependent transcription of target genes ( Table 1 ) allows the cell to assimilate low levels of ammonia and utilize alternative nitrogen sources in nutrient-limited environments ; NtrC-regulated glnA ( glutamine synthetase ) and glnHQ ( glutamine transport ) together contribute to S. Typhimurium virulence in a mouse model and increased survival in macrophages ( Klose and Mekalanos , 1997 ) .	224	NtrC-dependent transcription of target genes ( Table 1 ) allows the cell to assimilate low levels of ammonia and utilize alternative nitrogen sources in nutrient-limited environments ; NtrC-regulated glnA ( glutamine synthetase ) and glnHQ ( glutamine transport ) together contribute to S. Typhimurium virulence in a mouse model and increased survival in macrophages ( Klose and Mekalanos , 1997 ) .	8	NTRC (GLNG)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus musculus	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	fliZ	repressor	22479568	6	ver/dev	coworkers showed that HilD protein level , was significantly decreased by the deletion of fliZ .	195	Kage and coworkers showed that HilD protein level , when expressed from a constitutive promoter , was significantly decreased by the deletion of fliZ .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	fliZ	repressor	22479568	6	ver/dev	Kage showed that HilD protein level , was significantly decreased by the deletion of fliZ .	195	Kage and coworkers showed that HilD protein level , when expressed from a constitutive promoter , was significantly decreased by the deletion of fliZ .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FimW	gene	fimY	repressor	24462182	7	ver/dev	FimW inhibition of type 1 fimbrial production may be mediated by repression of the promoter activity of fimY .	36	FimW inhibition of type 1 fimbrial production may be mediated by consumption of the positive regulator , FimZ or by physical interactions , or may be mediated by repression of the promoter activity of fimY ( Saini et al. , 2009 ; Tinker et al. , 2001 ) .	4	1. INTRODUCTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FimW	gene	fimY	repressor	24462182	7	ver/dev	FimW inhibition of type 1 fimbrial production may be mediated by repression of the promoter activity of fimY .	36	FimW inhibition of type 1 fimbrial production may be mediated by consumption of the positive regulator , FimZ or by physical interactions , or may be mediated by repression of the promoter activity of fimY ( Saini et al. , 2009 ; Tinker et al. , 2001 ) .	4	1. INTRODUCTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	ugtL	activator	31484980	1	ver/dev	then , SprB directly activates expression of ugtL .	11	then , SprB directly activates expression of several genes including yobH , slrP and ugtL .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SprB	gene	ugtL	activator	31484980	4	ver/dev	SprB in turn activates expression of ugtL	41	In this regulatory cascade , HilD induces expression of SprB , which in turn activates expression of several target genes including yobH , slrP and ugtL ; slrP and ugtL have been involved in Salmonella virulence .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	mcpC	regulator	27564394	9	ver/dev	mcpC , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HilA	gene	mcpC	regulator	27564394	9	ver/dev	mcpC , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
MntR	TU	sitABCD	repressor	17555437	1	ver/dev	In the presence of Mn , MntR represses the expression of sitABCD , through direct binding of specific sites within the promoter regions of these genes .	270	In the presence of Mn ( 2 + ) , MntR represses the expression of mntH and sitABCD , through direct binding of specific sites within the promoter regions of these genes .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	oafA	regulator	10844662	1	att	Downstream of oafA , but within the same horizontal acquisition , is the site of a second SsrB-regulated fusion ( srfE ) , within an msgA ( macrophage survival gene ) 29 homologue ( P 10 ; Fig. 2 ) .	108	Downstream of oafA , but within the same horizontal acquisition , is the site of a second SsrB-regulated fusion ( srfE ) , within an msgA ( macrophage survival gene ) 29 homologue ( P 10 ; Fig. 2 ) .	10	MOLECULAR CHARACTERIZATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	spvR	repressor	21388802	7	ver/dev	spvR transcription is repressed by PhoP .	209	spvR transcription is activated by Hnr , CRP , RpoE , HimD and CsrA and is repressed by PhoP .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	hilA	repressor	26300871	13	ver/dev	These results suggest that CpxR represses hilA by affecting the autoregulation of HilD .	375	These results suggest that CpxR represses hilA and thus the other SPI-1 genes by affecting the autoregulation of HilD .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilA	repressor	26300871	17	ver/dev	our results _ indicating that CpxR represses the HilD-dependent expression of hilA	389	In agreement with our results indicating that CpxR represses the HilD-dependent expression of hilD and hilA , both the overexpression of CpxR and the absence of CpxA drastically reduced the production of SsrB-FLAG and SseB proteins ( Figures 1C , 3B ) , which are encoded in SPI-2 and whose expression is also dependent of HilD in the condition tested .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilA	repressor	30716090	39	ver/dev	therefore CpxR would be able to inhibit hilA expression	412	In this case , CpxR would remain in an activated phosphorylated state in the absence of CpxA and therefore CpxR would be able to inhibit hilA expression .	25	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
EutR	gene	ssrB	activator	26565973	12	att	To test our findings within the complexities of the in-vivo environment , we assessed EutR-dependent regulation of ssrB using single strain infections and purified S. Typhimurium RNA from harvested spleens .	208	To test our findings within the complexities of the in vivo environment , we assessed EutR-dependent regulation of ssrB using single strain infections and purified S. Typhimurium RNA from harvested spleens .	11	EUTR SIGNALING DURING SYSTEMIC INFECTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
EutR	gene	ssrB	activator	28357338	4	att	Our findings suggest a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , an abundant and integral component of host cell membranes , with SCV-specific signals to efficiently and temporally regulate SPI-2 expression .	79	Our findings suggest a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , an abundant and integral component of host cell membranes , with SCV-specific signals to efficiently and temporally regulate SPI-2 expression .	4	MAIN	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	activator	28357338	4	ver/dev	a model in which EutR-dependent activation of ssrB temporally regulate SPI-2 expression	79	Our findings suggest a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , an abundant and integral component of host cell membranes , with SCV-specific signals to efficiently and temporally regulate SPI-2 expression .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EutR	gene	ssrB	activator	28357338	4	ver/dev	a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , with SCV-specific signals to efficiently	79	Our findings suggest a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , an abundant and integral component of host cell membranes , with SCV-specific signals to efficiently and temporally regulate SPI-2 expression .	4	MAIN	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
EutR	gene	ssrB	activator	28357338	4	ver/dev	a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate an integral component of host cell membranes , with SCV-specific signals to efficiently	79	Our findings suggest a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , an abundant and integral component of host cell membranes , with SCV-specific signals to efficiently and temporally regulate SPI-2 expression .	4	MAIN	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
EutR	gene	ssrB	activator	28357338	4	ver/dev	a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate an abundant component of host cell membranes , with SCV-specific signals to efficiently	79	Our findings suggest a model in which EutR-dependent activation of ssrB enables Salmo-nella to incorporate ethanolamine , an abundant and integral component of host cell membranes , with SCV-specific signals to efficiently and temporally regulate SPI-2 expression .	4	MAIN	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	cat	repressor	15256548	2	att	Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .	259	Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .	7	TRANSCRIPTIONAL PROFILING OF SL1344 AND SL1344FIS : : CAT	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Felis catus	0.5	L2	SPEC	Analysis	OTHER	New	Level 1
ArgR	gene	miaE	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with miaE S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	miaE	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with miaE S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	miaE	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with miaE S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
Rho	gene	hisG	activator	22895254	8	att	However , the effect appears to be specific to the chiPQ system , as it is not observed at a different Rho-dependent polarity site in the hisG gene of Salmonella ( Supplemental Fig .	239	However , the effect appears to be specific to the chiPQ system , as it is not observed at a different Rho-dependent polarity site in the hisG gene of Salmonella ( Supplemental Fig .	9	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
SlyA	gene	fruK	regulator	29857034	33	ver/dev	Direct regulation of fruK genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HdfR	gene	seqA	activator	33475482	0	ver/dev	HdfR acts as an activator of std expression in seqA mutant strain .	39	HdfR is repressed by H-NS and acts as an activator of std expression in a dam or seqA mutant strain [ 8 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	STM1485	repressor	30763640	9	ver/dev	These results support the assumption that RcsB activation represses STM1485 transcription .	131	These results support the assumption that RcsB activation represses STM1485 transcription .	11	3.1. RCSB MODULATES THE STM1485 EXPRESSION IN A PH-DEPENDENT PATHWAY	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	STM1485	repressor	30763640	41	ver/dev	This data confirms that RcsB represses STM1485 transcription .	190	This data confirms that RcsB represses STM1485 transcription and suggests that such effect could occur by competing with RstA for the binding site .	14	3.5. COMBINED EFFECTS OF RCSB AND RSTA REGULATORS ON STM1485 GENE TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	STM1485	repressor	30763640	62	ver/dev	Our results demonstrated that Salmonella is able to survive the pancreatic fluid possibly due to the RcsB repression of STM1485 gene .	290	Our results demonstrated that Salmonella is able to survive the pancreatic fluid possibly due to the RcsB repression of STM1485 gene .	16	4. DISCUSSION	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	clpP	repressor	25123657	15	ver/dev	10 °C was correct , it was likely that the cold-resistant clpP suppressor mutants would have lower levels of RpoS than the clpP mutant .	173	10 °C was correct , it was likely that the cold-resistant clpP suppressor mutants would have lower levels of RpoS than the clpP mutant .	6	RESULT AND DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	nmpC	regulator	29857034	16	ver/dev	These studies are in agreement with our results that gene nmpC -LRB- -RRB- is regulated by SlyA .	315	These studies are in agreement with our results that gene nmpC ( STM14_1898 ) is regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , the global regulator ss .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , phosphate regulation .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , PhoB .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , osmoregulation .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , OmpR .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , s32 of heat-shock response .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	uspA	activator	17081727	2	ver/dev	In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , RpoH .	73	In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter and is independent of RpoS , PhoB ( phosphate regulation ) , OmpR ( osmoregulation ) , RpoH ( s32 of heat-shock response ) and the global regulator ss [ 4 ] .	7	2.3. USPA IS INDUCED DURING STATIONARY PHASE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	acrE	repressor	34278432	0	ver/dev	described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177	53	The acrD and acrA genes were amplified from S. Typhimurium SL1344 by PCR and cloned into pHSG398 and pACYC177 plasmids , respectively , as described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177 and obtain sufficient expression , a forward primer was designed containing the trc promoter and the acrE ribosomal binding site	9	PLASMID CONSTRUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	acrE	repressor	34278432	0	ver/dev	described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177	53	The acrD and acrA genes were amplified from S. Typhimurium SL1344 by PCR and cloned into pHSG398 and pACYC177 plasmids , respectively , as described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177 and obtain sufficient expression , a forward primer was designed containing the trc promoter and the acrE ribosomal binding site	9	PLASMID CONSTRUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	acrE	repressor	34278432	0	ver/dev	described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177	53	The acrD and acrA genes were amplified from S. Typhimurium SL1344 by PCR and cloned into pHSG398 and pACYC177 plasmids , respectively , as described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177 and obtain sufficient expression , a forward primer was designed containing the trc promoter and the acrE ribosomal binding site	9	PLASMID CONSTRUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	acrE	repressor	34278432	0	ver/dev	described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177	53	The acrD and acrA genes were amplified from S. Typhimurium SL1344 by PCR and cloned into pHSG398 and pACYC177 plasmids , respectively , as described previously .22 Expression of the acrE gene is repressed by H-NS .13 Therefore , to clone acrE into pACYC177 and obtain sufficient expression , a forward primer was designed containing the trc promoter and the acrE ribosomal binding site	9	PLASMID CONSTRUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FlhD	gene	STM1697	regulator	24127899	1	ver/dev	Like STM1344 , STM1697 suppresses the transcription of class 3 flagella regulon genes by binding to FlhD .	15	Like STM1344 , STM1697 suppresses the transcription of class 2 and class 3 flagella regulon genes by binding to FlhD , a component of the master regulator of the flagella regulon FlhD4C2 and act additively under numerous conditions .	2	SUMMARY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	24127899	1	ver/dev	Like STM1344 , STM1697 suppresses the transcription of class 2 flagella regulon genes by binding to FlhD .	15	Like STM1344 , STM1697 suppresses the transcription of class 2 and class 3 flagella regulon genes by binding to FlhD , a component of the master regulator of the flagella regulon FlhD4C2 and act additively under numerous conditions .	2	SUMMARY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	25437188	45	ver/dev	Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .	552	STM1344 ( YdiV ) and Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis [ 168,174 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	26655751	4	ver/dev	Both STM1344 and STM1697 suppress class 3 flagellum regulon genes by binding to FlhD	382	Both STM1344 and STM1697 suppress transcription of class 2 and class 3 flagellum regulon genes by binding to FlhD ( 58 ) , and we posit that both genes play a role in leaf persistence via motility .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	26655751	4	ver/dev	Both STM1344 and STM1697 suppress transcription of class 2 by binding to FlhD	382	Both STM1344 and STM1697 suppress transcription of class 2 and class 3 flagellum regulon genes by binding to FlhD ( 58 ) , and we posit that both genes play a role in leaf persistence via motility .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	1	ver/dev	A 2.0 Å resolution STM1697 -- FlhD structure reveals that STM1697 binds the same region of FlhD as STM134 .	24	A 2.0 Å resolution STM1697 -- FlhD structure reveals that STM1697 binds the same region of FlhD as STM1344 , but with weaker affinity .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	13	ver/dev	complementation experiments demonstrated that STM1697 regulates virulence phenotypes through its interaction with FlhD .	59	Gene knockout and complementation experiments demonstrated that STM1697 regulates flagellar formation and virulence phenotypes through its interaction with FlhD .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	13	ver/dev	complementation experiments demonstrated that STM1697 regulates flagellar formation through its interaction with FlhD .	59	Gene knockout and complementation experiments demonstrated that STM1697 regulates flagellar formation and virulence phenotypes through its interaction with FlhD .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	13	ver/dev	Gene knockout demonstrated that STM1697 regulates virulence phenotypes through its interaction with FlhD .	59	Gene knockout and complementation experiments demonstrated that STM1697 regulates flagellar formation and virulence phenotypes through its interaction with FlhD .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	13	ver/dev	Gene knockout demonstrated that STM1697 regulates flagellar formation through its interaction with FlhD .	59	Gene knockout and complementation experiments demonstrated that STM1697 regulates flagellar formation and virulence phenotypes through its interaction with FlhD .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	55	ver/dev	Therefore , we hypothesize that , when STM1697 binds to the FlhD subunits of steric exclusion prevents-70 RNA polymerase from binding to template DNA , thus blocking transcription .	243	Therefore , we hypothesize that , when STM1697 binds to the FlhD subunits of the FlhD4C2 complex , steric exclusion prevents 70 RNA polymerase from binding to template DNA , thus blocking transcription ( Figure 5B ) .	26	THE BINDING OF STM1697 TO FLHD4C2 RESTRAINS RNA POLY- MERASE RECRUITMENT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FlhD	gene	STM1697	regulator	28973452	55	ver/dev	Therefore , we hypothesize that , when STM1697 binds to the FlhD subunits of the FlhD4C2 complex prevents-70 RNA polymerase from binding to template DNA , thus blocking transcription .	243	Therefore , we hypothesize that , when STM1697 binds to the FlhD subunits of the FlhD4C2 complex , steric exclusion prevents 70 RNA polymerase from binding to template DNA , thus blocking transcription ( Figure 5B ) .	26	THE BINDING OF STM1697 TO FLHD4C2 RESTRAINS RNA POLY- MERASE RECRUITMENT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FlhD	gene	STM1697	regulator	28973452	64	ver/dev	The STM1697 mutants were unable to bind to FlhD in-vitro , as shown above .	275	The STM1697 mutants expressed by Mut-1 and Mut-2 were unable to bind to FlhD in vitro , as shown above .	27	THE STM1697 SUPPRESSION OF CELL MOTILITY IS MEDIATED BY ITS INTERACTION WITH FLHD	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
FlhD	gene	STM1697	regulator	28973452	74	ver/dev	STM1697 then binds to the peripheral FlhD of the FlhD4C2 complex .	345	STM1697 then binds to the peripheral FlhD of the FlhD4C2 complex , which restrains the recruitment of RNA polymerase by steric exclusion .	29	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1697	regulator	28973452	75	ver/dev	STM1697 then binds to the peripheral FlhD of the FlhD4C2 complex .	352	STM1697 then binds to the peripheral FlhD of the FlhD4C2 complex , which restrains the recruitment of RNA polymerase , repressing the expression of flagellar genes .	30	MODEL FOR STM1697-DEPENDENT FLAGELLAR REGULATION DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	sipB	regulator	10899868	1	ver/dev	Under conditions of low-osmolarity , the transcription of sipB is negatively controlled by the RcsB regulator , acting in concert with the TviA protein .	322	Under conditions of low osmolarity , the transcription of iagA , invF , and sipB ( encoding proteins involved in cell invasion ) is negatively controlled by the RcsB regulator , acting in concert with the TviA protein , which is encoded by tviA within the viaB locus .	6	CVD 908-HTRA 9/10 A (90) 10 CVD 909B 3/8 B (38) 62 PBS 10/10 C (100) 0	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	sipB	regulator	19901065	1	ver/dev	The transcription of sipB genes is negatively controlled by the RcsB regulator .	29	The transcription of the iagA , invF , and sipB genes is negatively controlled by the RcsB regulator ( 2 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrB	activator	12898222	14	ver/dev	gyrB promoter DNA was incubated with increasing concentrations of Fis protein prior to digestion with DNase I .	183	Radiolabelled gyrA ( A ) or gyrB ( C ) promoter DNA was incubated with increasing concentrations of Fis protein prior to digestion with DNase I .	15	EXPRESSION OF THE FIS PROTEIN IN E. COLI AND S. ENTERICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrB	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over TopA levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	gyrB	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	slrP	regulator	25182488	27	att	The distal half of this motif is very similar to the consensus sequence previously defined for a subset of PhoP-regulated genes that contain a promoter pattern known as architecture I ( 48 ) , whereas the other half of the motif is not conserved in slrP .	341	The distal half of this motif is very similar to the consensus sequence previously defined for a subset of PhoP-regulated genes that contain a promoter pattern known as architecture I ( 48 ) , whereas the other half of the motif is not conserved in slrP .	3	RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PhoP	gene	slrP	regulator	25182488	10	ver/dev	Direct regulation of slrP expression by PhoP .	244	Direct regulation of slrP expression by PhoP .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slrP	regulator	25182488	13	ver/dev	The level of expression of the lac fusions indicated that these fragments contained the motifs necessary for PhoP regulation of slrP .	253	The level of expression of the lac fusions indicated that these fragments contained the motifs necessary for transcription and PhoP regulation of slrP ( Fig. 7A ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	slrP	regulator	25182488	15	ver/dev	As seen in Fig. 7B , PhoP was able to bind to the promoters of slrP .	258	As seen in Fig. 7B , PhoP was able to bind to the promoters of slrP and slyB but not to the phoN promoter .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	slrP	regulator	25182488	18	ver/dev	FIG 7 PhoP binds to the promoter of slrP .	289	FIG 7 PhoP binds to the promoter of slrP .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slrP	regulator	25182488	26	ver/dev	slot blot-based experiments _ showing binding of PhoP to DNA fragments containing the promoter region of slrP	339	Support for this hypothesis was obtained from in vitro slot blot-based experiments showing binding of PhoP to DNA fragments containing the promoter region of slrP ( Fig. 7 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	slrP	regulator	27886269	26	ver/dev	Similarly , the expression of slrP , also encoding an effector protein , is controlled by the response regulator PhoP in SPI-2-inducing conditions32 .	165	Similarly , the expression of slrP , also encoding an effector protein secreted through both T3SS-1 and T3SS-2 , is controlled by HilD in SPI-1-inducing conditions and by the response regulator PhoP in SPI-2-inducing conditions32 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slrP	regulator	29555922	18	ver/dev	Additionally , PhoP independently regulate the expression of the slrP gene .	270	Additionally , HilD and PhoP positively and independently regulate the expression of the slrP gene , in SPI-1-inducing growth conditions , PhoP directly and HilD by an unknown mechanism37 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	clpV	regulator	31383745	1	ver/dev	These observations suggest that H-NS might synergistically control clpV expression in S. Typhimurium .	257	These observations suggest that Fur and H-NS might synergistically control clpV expression in S. Typhimurium .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	mgtCBR	activator	26231375	5	ver/dev	When the PhoP/PhoQ two component system is activated by low Mg transcribes mgtCBR messenger RNAs .	73	When the PhoP/PhoQ two component 2 + system is activated by low Mg , phosphorylated PhoP binds to the promoter region of the mgtCBR operon and transcribes mgtCBR messenger RNAs ( Soncini et al. , 1996 ; Shin and Groisman , 2005 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCBR	activator	26231375	5	ver/dev	When the PhoP/PhoQ two component system is activated by low Mg binds to the promoter region of the mgtCBR operon .	73	When the PhoP/PhoQ two component 2 + system is activated by low Mg , phosphorylated PhoP binds to the promoter region of the mgtCBR operon and transcribes mgtCBR messenger RNAs ( Soncini et al. , 1996 ; Shin and Groisman , 2005 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCBR	activator	26231375	5	ver/dev	When the PhoP/PhoQ two component 2 is activated by low Mg transcribes mgtCBR messenger RNAs .	73	When the PhoP/PhoQ two component 2 + system is activated by low Mg , phosphorylated PhoP binds to the promoter region of the mgtCBR operon and transcribes mgtCBR messenger RNAs ( Soncini et al. , 1996 ; Shin and Groisman , 2005 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCBR	activator	26231375	5	ver/dev	When the PhoP/PhoQ two component 2 is activated by low Mg binds to the promoter region of the mgtCBR operon .	73	When the PhoP/PhoQ two component 2 + system is activated by low Mg , phosphorylated PhoP binds to the promoter region of the mgtCBR operon and transcribes mgtCBR messenger RNAs ( Soncini et al. , 1996 ; Shin and Groisman , 2005 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCBR	activator	26561851	1	att	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	159	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	7	THE PRIMARY TRANSCRIPTOME OF INTRA-MACROPHAGE S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCBR	activator	29802740	1	att	In addition , the accumulation of the mgtCBR mRNA is subject to regulation by turnover by a 1.2 kb-long antisense RNA , AmgR , that is generated from a PhoP-dependent promoter located between mgtC and mgtB and can hybridize to the sense mRNA across the mgtM , mgtP and mgtC coding sequences ( Lee and Groisman , 2010 ) .	49	In addition , the accumulation of the mgtCBR mRNA is subject to regulation by turnover by a 1.2 kb-long antisense RNA , AmgR , that is generated from a PhoP-dependent promoter located between mgtC and mgtB and can hybridize to the sense mRNA across the mgtM , mgtP and mgtC coding sequences ( Lee and Groisman , 2010 ) .	3	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	mgtCBR	activator	30602583	3	att	Among those , a PhoP-activated cis-antisense RNA ( AmgR ) constitutes a negative-feedback loop to counteract mgtCBR expression in an Hfq - and RNase E-dependent manner .	525	Among those , a PhoP-activated cis-antisense RNA ( AmgR ) constitutes a negative-feedback loop to counteract mgtCBR expression in an Hfq - and RNase E-dependent manner .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	repressor	12396235	9	ver/dev	These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , .	106	These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25375226	28	ver/dev	increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25688233	0	ver/dev	The HilA protein decreases in expression of the hilA gene typically decrease on invasion .	117	The HilA protein is the master regulator of SPI-1 , and increases or decreases in expression of the hilA gene typically have a corresponding increase or decrease on invasion ( Lee et al. , 1992 ) .	16	DIFFERENTIAL EXPRESSION OF THE HILA GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	repressor	25688233	0	ver/dev	The HilA protein decreases in expression of the hilA gene typically have a corresponding increase .	117	The HilA protein is the master regulator of SPI-1 , and increases or decreases in expression of the hilA gene typically have a corresponding increase or decrease on invasion ( Lee et al. , 1992 ) .	16	DIFFERENTIAL EXPRESSION OF THE HILA GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ptsN	regulator	30967459	7	att	We further verified the EIIANtr 's regulatory effects on PhoP-activated genes using quantitative reverse transcription-PCR ( qRT-PCR ) : the ptsN mutant displayed 3 - to 7-fold-higher transcript levels of PhoP-regulated genes than the wild type ( Fig. 3A ) .	132	We further verified the EIIANtr 's regulatory effects on PhoP-activated genes using quantitative reverse transcription-PCR ( qRT-PCR ) : the ptsN mutant displayed 3 - to 7-fold-higher transcript levels of PhoP-regulated genes than the wild type ( Fig. 3A ) .	3	RESULTS	Terfezia eliocrocae	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ptsN	regulator	30967459	6	ver/dev	the phoP mutant _ harboring a plasmid expressing PhoP under the control of an IPTG-inducible promoter with deletions of the ptsN or ptsN	110	( A and B ) Western blot analysis of crude extracts prepared from Salmonella expressing EIIANtr-FLAG from the normal chromosomal location ( ptsN-FLAG ) , an isogenic phoP mutant , and the phoP mutant harboring a plasmid expressing PhoP under the control of an IPTG-inducible promoter ( A ) and Salmonella strains with deletions of the ptsN or ptsN and phoP genes harboring a plasmid expressing EIIANtr-FLAG from an IPTG-inducible promoter ( B ) .	3	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ptsN	regulator	30967459	6	ver/dev	an isogenic phoP mutant _ harboring a plasmid expressing PhoP under the control of an IPTG-inducible promoter with deletions of the ptsN or ptsN	110	( A and B ) Western blot analysis of crude extracts prepared from Salmonella expressing EIIANtr-FLAG from the normal chromosomal location ( ptsN-FLAG ) , an isogenic phoP mutant , and the phoP mutant harboring a plasmid expressing PhoP under the control of an IPTG-inducible promoter ( A ) and Salmonella strains with deletions of the ptsN or ptsN and phoP genes harboring a plasmid expressing EIIANtr-FLAG from an IPTG-inducible promoter ( B ) .	3	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	fliA	activator	24992093	4	ver/dev	FlhDC , activates transcription of fliA .	124	FlhDC , the master regulator of flagellar gene expression , activates transcription of class II flagellar genes , such as fliA and fliZ [ 45,46 ] .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
BasR	gene	dgkA	activator	28923603	0	ver/dev	Activation of dgkA gene is ensured by the two-basic regulator BasR , combining dgkA function of phospholipid .	214	Activation of dgkA gene is ensured by the two-basic regulator BasR , combining dgkA function of phospholipid converting to lipopolysaccharide modifications .	18	3.2.1. PLSB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	spiR	regulator	26441883	1	ver/dev	PhoP also controls expression of Spi-2 by binding to the ssrB promoter the 5 ′ - UTR of the spiR transcript .	73	PhoP also controls expression of Salmonella pathogenicity island-2 ( Spi-2 ) by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	spiR	regulator	26441883	1	ver/dev	PhoP also controls expression of Salmonella pathogenicity island-2 by binding to the ssrB promoter the 5 ′ - UTR of the spiR transcript .	73	PhoP also controls expression of Salmonella pathogenicity island-2 ( Spi-2 ) by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	spiR	regulator	26441883	37	ver/dev	The response regulator PhoP controls Spi-2 by binding to the ssrB promoter the 5 ′ - UTR of the spiR transcript .	479	The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Bijlsma and Groisman , 2005 ) .	10	REGULATORY CIRCUITS CONTROLLING LATER STAGES OF INFECTION AND DEFENSE SYSTEMS AGAINST THE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	spiR	regulator	33045730	4	ver/dev	Transcription of spiR genes is regulated by PhoP .	29	Transcription of the horizontally acquired ssrB and spiR genes is regulated by several ancestral regulators , including SlyA ( 20 ) , OmpR ( 6 ) , and PhoP ( 7 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	ssrAB	activator	29555922	1	ver/dev	When Salmonella is grown in minimal media , the expression of the ssrAB operon , is induced by the MarR-like regulator SlyA of HilD8 ,45 .	42	When Salmonella is grown in minimal media , the expression of the ssrAB operon , and thus the SPI-2 genes , is induced by other regulators such as the MarR-like regulator SlyA and the two-component systems OmpR/EnvZ and PhoP/PhoQ , independently of HilD8 ,45 .	2	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	ssrAB	activator	30718301	12	ver/dev	In this work , we determine how the ancestral regulators SlyA and OmpR induce the expression of the S. Typhimurium ssrAB operon under different growth-conditions .	52	In this work , we determine how the ancestral regulators SlyA and OmpR and the acquired regulator HilD induce the expression of the S. Typhimurium ssrAB operon under different growth conditions .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	TU	ssrAB	activator	30718301	54	ver/dev	Previous studies have demonstrated that SlyA induces the expression of ssrAB .	169	Previous studies have demonstrated that SlyA induces the expression of ssrAB and several other genes during growth in minimal medium ( 27 , 42 , 59 ) .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	TU	ssrAB	activator	30718301	55	ver/dev	We found that SlyA induces the expression of ssrAB during-growth in LB .	170	We found that SlyA induces the expression of ssrAB during growth in LB , which is consistent with previous reports indicating that the overexpression of SlyA induces the expression of ssrAB in LB ( 25 , 28 ) , as well as with results from a previous transcriptomic analysis supporting the idea that SlyA positively regulates ssrAB and several other genes during growth in LB ( 36 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	TU	ssrAB	activator	30718301	55	ver/dev	We found that SlyA induces the expression of ssrAB during-growth with results from a previous transcriptomic analysis .	170	We found that SlyA induces the expression of ssrAB during growth in LB , which is consistent with previous reports indicating that the overexpression of SlyA induces the expression of ssrAB in LB ( 25 , 28 ) , as well as with results from a previous transcriptomic analysis supporting the idea that SlyA positively regulates ssrAB and several other genes during growth in LB ( 36 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	ssrAB	activator	30718301	55	ver/dev	a previous transcriptomic analysis _ supporting the idea that SlyA positively regulates ssrAB other genes during-growth in LB	170	We found that SlyA induces the expression of ssrAB during growth in LB , which is consistent with previous reports indicating that the overexpression of SlyA induces the expression of ssrAB in LB ( 25 , 28 ) , as well as with results from a previous transcriptomic analysis supporting the idea that SlyA positively regulates ssrAB and several other genes during growth in LB ( 36 ) .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	TU	ssrAB	activator	30718301	56	ver/dev	Our results show that SlyA induces the expression of ssrAB during-growth in LB by counteracting H-NS-mediated repression .	174	Our results show that SlyA induces the expression of ssrAB during growth in LB by counteracting H-NS-mediated repression .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	TU	ssrAB	activator	30718301	60	ver/dev	Our results indicate that SlyA also induces the expression of ssrAB during-growth in N-MM by counteracting H-NS-mediated repression .	179	Our results indicate that SlyA also induces the expression of ssrAB during growth in N-MM by counteracting H-NS-mediated repression .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	csgD	activator	26880544	6	ver/dev	Surprisingly , the SsrB response regulator positively regulated the formation of biofilms by activating csgD expression in the absence of any phos-pho-donors .	71	Surprisingly , the SsrB response regulator positively regulated the formation of biofilms by activating csgD expression in the absence of any phos-pho-donors .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	csgD	activator	26880544	12	ver/dev	Unphosphorylated SsrB activates csgD expression	202	Unphosphorylated SsrB activates csgD expression	9	UNPHOSPHORYLATED SSRB ACTIVATES CSGD EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	csgD	activator	26880544	13	ver/dev	An obvious null hypothesis was therefore to test whether SsrB -LRB- in its unphosphorylated state -RRB- , activated the expression of csgD .	205	An obvious null hypothesis was therefore to test whether SsrB ( in its unphosphorylated state ) , activated the expression of csgD .	9	UNPHOSPHORYLATED SSRB ACTIVATES CSGD EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	csgD	activator	26880544	18	ver/dev	Thus , we strengthened our prediction of a role for SsrB in the activation of csgD expression by acting as an anti-H-NS molecule .	229	Thus , we strengthened our prediction of a role for SsrB in the activation of csgD expression by acting as an anti-H-NS molecule .	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	csgD	activator	26880544	46	ver/dev	We show that under biofilm-inducing conditions , unphosphorylated SsrB is sufficient to activate the expression of csgD .	342	We show that under biofilm-inducing conditions , unphosphorylated SsrB is sufficient to activate the expression of csgD .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgA	repressor	16714543	1	ver/dev	H-NS _ mediated transcriptional repression of csgA in Escherichia coli	713	The RpoS sigma factor relieves H-NS mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	30	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	STM1808	repressor	24021902	0	att	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	77	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DnaA	gene	dam	regulator	20132031	0	ver/dev	the control of the DnaA binding to oriC can be related with the partial reestablishment of the replication asynchrony _ observed at every dam mutant	275	However , Makise et al. ( 2002 ) have reported that UFAs increase membrane fluidity , which may be important for the control of the DnaA binding to oriC in vitro and can be related with the partial reestablishment of the replication asynchrony observed at every seqA and dam mutant ( Lobner-Olesen and Von Freiesleben , 1996 ) .	14	MEMBRANE PHL COMPOSITION OF S. ENTERICA SEROVAR TYPHIMURIUM: EFFECTS OF SEQA AND DAM MUTATIONS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
DnaA	gene	dam	regulator	20132031	0	ver/dev	the control of the DnaA binding to oriC in-vitro _ observed at every dam mutant	275	However , Makise et al. ( 2002 ) have reported that UFAs increase membrane fluidity , which may be important for the control of the DnaA binding to oriC in vitro and can be related with the partial reestablishment of the replication asynchrony observed at every seqA and dam mutant ( Lobner-Olesen and Von Freiesleben , 1996 ) .	14	MEMBRANE PHL COMPOSITION OF S. ENTERICA SEROVAR TYPHIMURIUM: EFFECTS OF SEQA AND DAM MUTATIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pagA	regulator	12438352	3	att	Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .	46	Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	spoT	activator	19091955	28	att	This phenotype is not associated with the PhoP/PhoQ system because transcriptional levels of PhoP-dependent but SlyA-independent genes , such as pcgL , are reduced 2-fold overall in a relA spoT mutant ( data not shown ) .	183	This phenotype is not associated with the PhoP/PhoQ system because transcriptional levels of PhoP-dependent but SlyA-independent genes , such as pcgL , are reduced 2-fold overall in a relA spoT mutant ( data not shown ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	spoT	activator	19091955	4	att	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	38	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus	0	L3	OTHER	Other	NEG	Other	Level 1
CRP	gene	yihU	activator	21148209	14	att	In order to determine the CRP-dependent sequences involved in the transcriptional activation of yihU , we constructed transcriptional-fusions encompassing different lengths of the yihU -- yshA promoter region ( Fig. 5a ) .	180	In order to determine the CRP-dependent sequences involved in the transcriptional activation of yihU , we constructed transcriptional fusions encompassing different lengths of the yihU -- yshA promoter region ( Fig. 5a ) .	9	TWO CRP BOXES MEDIATE YIHU TRANSCRIPTIONAL ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	yihU	activator	21148209	14	ver/dev	the CRP-dependent sequences _ involved in the transcriptional activation of yihU	180	In order to determine the CRP-dependent sequences involved in the transcriptional activation of yihU , we constructed transcriptional fusions encompassing different lengths of the yihU -- yshA promoter region ( Fig. 5a ) .	9	TWO CRP BOXES MEDIATE YIHU TRANSCRIPTIONAL ACTIVATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	yihU	activator	21148209	23	ver/dev	Hence , we expected that if CRP complex positively regulated the yihU , its activity should decrease in medium supplemented-with-glucose as the carbon source .	241	Hence , we expected that if the cAMP -- CRP complex positively regulated the yihU -- yshA operon , its activity should decrease in medium supplemented with glucose as the carbon source .	11	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HNS	gene	pefA	repressor	31661351	20	ver/dev	The promoter upstream of pefA is repressed by H-NS	353	The promoter upstream of pefA is repressed by H-NS and the RNA binding protein CsrA stabilizes the pefACDorf5orf6 transcript .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	rpoS	repressor	31563538	11	ver/dev	our results _ assuming that with a high level of carbon source , RstA represses the expression of rpoS	210	These data could explain our results , assuming that with a high level of carbon source , RstA represses the expression of rpoS and consequently affects narZ transcription .	13	3.4. RSTA ALSO CONTROLS NARZ TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	gene	flhD	activator	16430704	6	ver/dev	The FlhC levels were determined by immunoblotting analysis at various times after flhD transcription was induced by 50 µM IPTG .	171	The FlhD and FlhC levels were determined by immunoblotting analysis at various times after flhD and flhC transcription was induced by 50 µM IPTG .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	sopB	regulator	11244064	5	ver/dev	SirA-dependent regulation of serovar Typhimurium sopB .	101	SirA-dependent regulation of serovar Typhimurium sopB and flagellar regulon components during chemotaxing through three different types of 0.3 % motility agar plates ( T , TS , and LB ) at 37 °C .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	regulator	11244064	6	ver/dev	SirA-dependent regulation of serovar Typhimurium sopB .	184	SirA-dependent regulation of serovar Typhimurium sopB and flagellar regulon promoter fusions in shaking liquid medium .	6	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	regulator	11244064	13	ver/dev	SirA-dependent regulation of sopB chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar .	286	SirA-dependent regulation of sopB and flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar containing kanamycin and X-Gal at 37 °C .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	regulator	11418329	1	ver/dev	A screen revealed that SirA regulates not only expression of SPI1-encoded genes but also the transcription of SPI5-encoded sopB .	253	A screen using reporter gene fusions revealed that SirA regulates not only expression of SPI1-encoded genes but also the transcription of SPI5-encoded sopB [ 58 ] .	13	7. REGULATION OF SPI1 AND SPI2 GENE EXPRESSION	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
PhoP	gene	pgtE	activator	15225317	16	att	Thus , we investigated the role of the PhoP-activated pagP and pgtE genes , because they had been implicated in resistance to the alpha-helical peptide C18G ( Guo et al. , 1998 ; Guina et al. , 2000 ) .	170	Thus , we investigated the role of the PhoP-activated pagP and pgtE genes , because they had been implicated in resistance to the alpha-helical peptide C18G ( Guo et al. , 1998 ; Guina et al. , 2000 ) .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	pgtE	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	pgtE	activator	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pgtE	activator	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- pgtE .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	mgtA	regulator	27849575	1	ver/dev	Transcription of mgtA is regulated at translation of mgtL , which governs folding of the 5 ′ LR mRNA and Rho-dependent terminati .	62	Transcription of mgtA is regulated at two steps : activation of the promoter by PhoP , which is phosphorylated by PhoQ in response to low [ Mg2 + ] and other periplasmic signals ( inset 1 ) ( 4 ) , and translation of mgtL ( encoded by nucleotides 71 -- 124 ) ( 12 ) , which governs folding of the 5 ′ LR mRNA and Rho-dependent termination .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgB	regulator	16707690	30	ver/dev	Indeed , it has been suggested , although it has never been shown , that CsgD binds to conserved 11-bp sequences upstream of the csgB promoters , activating transcription of these genes .	426	Indeed , it has been suggested , although it has never been shown , that CsgD binds to conserved 11-bp sequences upstream of the csgB and adrA promoters , activating transcription of these genes ( 9 , 16 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	csgB	regulator	25437188	3	ver/dev	In vitro , unphosphorylated CsgD binds directly to the promoter region of csgB .	111	In vitro , unphosphorylated CsgD binds directly to the promoter region of csgB and transcriptionally activates curli synthesis [ 15,76 ] .	5	REGULATION OF THE RDAR PHENOTYPE IN S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	csgB	regulator	27260360	2	ver/dev	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgB , coding for curli fimbria production , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	315	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD and csgB , coding for curli fimbria production , and adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	csgB	regulator	29163440	9	ver/dev	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in absence of CsgD in both cya genetic backgrounds .	337	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm promoting factors , the csgB expression was monitored in presence and absence of CsgD in both wt and cya genetic backgrounds ( Figure 6B ) .	16	PRESENCE OF AMINO ACIDS REPRESSES CELLULOSE PRODUCTION AND PROMOTES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgB	regulator	29163440	9	ver/dev	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in absence of CsgD in both wt genetic backgrounds .	337	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm promoting factors , the csgB expression was monitored in presence and absence of CsgD in both wt and cya genetic backgrounds ( Figure 6B ) .	16	PRESENCE OF AMINO ACIDS REPRESSES CELLULOSE PRODUCTION AND PROMOTES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgB	regulator	29163440	9	ver/dev	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in presence of CsgD in both cya genetic backgrounds .	337	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm promoting factors , the csgB expression was monitored in presence and absence of CsgD in both wt and cya genetic backgrounds ( Figure 6B ) .	16	PRESENCE OF AMINO ACIDS REPRESSES CELLULOSE PRODUCTION AND PROMOTES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgB	regulator	29163440	9	ver/dev	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in presence of CsgD in both wt genetic backgrounds .	337	To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm promoting factors , the csgB expression was monitored in presence and absence of CsgD in both wt and cya genetic backgrounds ( Figure 6B ) .	16	PRESENCE OF AMINO ACIDS REPRESSES CELLULOSE PRODUCTION AND PROMOTES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MltC	gene	csgD	regulator	25437188	37	ver/dev	the mechanism _ resulting in regulation of csgD expression by MltC	378	Although the mechanism resulting in regulation of csgD expression and rdar morphotype development by MltE and MltC is not known , regulation of csgD expression is dependent on the enzymatic activity of the LTs .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MltC	gene	csgD	regulator	25437188	39	ver/dev	Therefore , the MltE MltC-dependent regulation of csgD expression occurs regulating biofilm formation , suggesting the existence of a novel signaling pathway .	384	Therefore , the MltE MltC-dependent regulation of csgD expression and rdar morphotype development occurs independently of major signaling pathways sensing cell wall disturbance and turnover , and regulating biofilm formation , suggesting the existence of a novel signaling pathway .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MltC	gene	csgD	regulator	25437188	39	ver/dev	Therefore , the MltE MltC-dependent regulation of csgD expression occurs independently of major signaling pathways sensing turnover , suggesting the existence of a novel signaling pathway .	384	Therefore , the MltE MltC-dependent regulation of csgD expression and rdar morphotype development occurs independently of major signaling pathways sensing cell wall disturbance and turnover , and regulating biofilm formation , suggesting the existence of a novel signaling pathway .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MltC	gene	csgD	regulator	25437188	39	ver/dev	Therefore , the MltE MltC-dependent regulation of csgD expression occurs independently of major signaling pathways sensing cell wall disturbance , suggesting the existence of a novel signaling pathway .	384	Therefore , the MltE MltC-dependent regulation of csgD expression and rdar morphotype development occurs independently of major signaling pathways sensing cell wall disturbance and turnover , and regulating biofilm formation , suggesting the existence of a novel signaling pathway .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	relA	activator	19091955	28	att	This phenotype is not associated with the PhoP/PhoQ system because transcriptional levels of PhoP-dependent but SlyA-independent genes , such as pcgL , are reduced 2-fold overall in a relA spoT mutant ( data not shown ) .	183	This phenotype is not associated with the PhoP/PhoQ system because transcriptional levels of PhoP-dependent but SlyA-independent genes , such as pcgL , are reduced 2-fold overall in a relA spoT mutant ( data not shown ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	relA	activator	19091955	4	att	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	38	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus	0	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	hupB	activator	21212121	12	att	Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .	348	Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .	11	HU AND THE RPOS REGULON	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hupB	activator	21212121	0	ver/dev	In contrast , inactivation of just the hupB gene correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures .	19	In contrast , inactivation of just the hupB gene resulted in increased fitness and correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hupB	activator	26039089	7	att	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	164	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
MntR	gene	mntH	repressor	17555437	1	ver/dev	In the presence of Mn , MntR represses the expression of mntH , through direct binding of specific sites within the promoter regions of these genes .	270	In the presence of Mn ( 2 + ) , MntR represses the expression of mntH and sitABCD , through direct binding of specific sites within the promoter regions of these genes .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	repressor	17555437	7	ver/dev	Hantke , K. Dual repression by Fe - Mn - MntR of the mntH gene , encoding an NRAMP-like Mn transporter in Escherichia coli .	473	Patzer , S.I. , and Hantke , K. ( 2001 ) Dual repression by Fe ( 2 + ) - Fur and Mn ( 2 + ) - MntR of the mntH gene , encoding an NRAMP-like Mn ( 2 + ) transporter in Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	repressor	17555437	7	ver/dev	Hantke , K. Dual repression by Fe - Fur - MntR of the mntH gene , encoding an NRAMP-like Mn transporter in Escherichia coli .	473	Patzer , S.I. , and Hantke , K. ( 2001 ) Dual repression by Fe ( 2 + ) - Fur and Mn ( 2 + ) - MntR of the mntH gene , encoding an NRAMP-like Mn ( 2 + ) transporter in Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	repressor	24596096	2	ver/dev	a different palindromic sequence _ termed MntR-box , thus implementing repression of mntH transcription	48	In E. coli and Salmo-nella , binding to Mn2 facilitates these MntR proteins to interact with a different palindromic sequence termed MntR-box , 5 - AAACATAGCAAAGGCTATGTTT-3 , thus implementing repression of mntH transcription ( 18 , 19 ) .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
MntR	gene	mntH	repressor	24596096	2	ver/dev	a different palindromic sequence _ termed MntR-box , thus implementing repression of mntH transcription	48	In E. coli and Salmo-nella , binding to Mn2 facilitates these MntR proteins to interact with a different palindromic sequence termed MntR-box , 5 - AAACATAGCAAAGGCTATGTTT-3 , thus implementing repression of mntH transcription ( 18 , 19 ) .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
MntR	gene	mntH	repressor	24596096	14	ver/dev	Hantke , K. Dual repression by Fe2 - Mn2 - MntR of the mntH gene , encoding an NRAMP-like Mn2 transporter in Escherichia coli .	509	Patzer , S. I. , and Hantke , K. ( 2001 ) Dual repression by Fe2 - Fur and Mn2 - MntR of the mntH gene , encoding an NRAMP-like Mn2 transporter in Escherichia coli .	11	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	repressor	24596096	14	ver/dev	Hantke , K. Dual repression by Fe2 - Fur - MntR of the mntH gene , encoding an NRAMP-like Mn2 transporter in Escherichia coli .	509	Patzer , S. I. , and Hantke , K. ( 2001 ) Dual repression by Fe2 - Fur and Mn2 - MntR of the mntH gene , encoding an NRAMP-like Mn2 transporter in Escherichia coli .	11	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	crl	activator	16707690	12	ver/dev	E. coli showed that RpoS production is increased by a crl mutation	305	This is consistent with previous results for E. coli which showed that RpoS production is increased by a crl mutation ( 8 , 35 ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	crl	activator	16707690	37	ver/dev	When present in HB101 , crl may increase an otherwise low level of RpoS activity	452	When present in HB101 , crl may increase an otherwise low level of RpoS activity , and the increase would then be sufficient for curli production ( 35 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	STM0834	regulator	15866924	4	ver/dev	Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM0834	regulator	15866924	4	ver/dev	Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM0834	regulator	15866924	4	ver/dev	Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM0834	regulator	15866924	4	ver/dev	Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM0834	regulator	15866924	4	ver/dev	Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM0834	regulator	15866924	4	ver/dev	Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM0834	regulator	15866924	6	ver/dev	This analysis demonstrated that neither STM0834 was regulated by PmrA .	159	This analysis demonstrated that neither STM0834 nor STM3635 was regulated by PmrA ( data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pagC	repressor	19202096	2	ver/dev	pagC are known to be repressed , respectively , by the active form of PhoP .	332	pagC and prgI are known to be activated and repressed , respectively , by the active form of PhoP , and were used as controls .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PmrA	gene	pmrA	repressor	19076233	9	ver/dev	Further support for PmrA pathways is the observation that inactivation of pmrA does not completely abolish the DrpoN-mediated PM resistance .	157	Further support for independent RpoN and PmrA pathways is the observation that inactivation of pmrA does not completely abolish the DrpoN-mediated PM resistance ( Fig. 1c ) .	15	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PmrA	gene	pmrA	repressor	23690578	37	ver/dev	We have now determined that the regulatory protein PmrA is an antivirulence factor because inactivation of the pmrA gene exacerbated Salmonella virulence in Fig. 1A .	149	We have now determined that the regulatory protein PmrA is an antivirulence factor because inactivation of the pmrA gene exacerbated Salmonella virulence in C3H/HeN mice ( Fig. 1A ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrA	repressor	23690578	37	ver/dev	We have now determined that the regulatory protein PmrA is an antivirulence factor because inactivation of the pmrA gene exacerbated Salmonella virulence in C3H/HeN mice .	149	We have now determined that the regulatory protein PmrA is an antivirulence factor because inactivation of the pmrA gene exacerbated Salmonella virulence in C3H/HeN mice ( Fig. 1A ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella;Mus sp.	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	ptsG	regulator	20965974	4	ver/dev	Hence , binding of IHF to the ptsG promoters is unspecific , which is in line with previous data reporting that IHF binds DNA with lower affinity also in sequence-independent manner .	336	Hence , binding of IHF to the lacZ and ptsG promoters is unspecific , which is in line with previous data reporting that IHF binds DNA with lower affinity also in sequence-independent manner ( 30 ) .	15	ACTIVITY OF THE P -DEPENDENT GLMY PROMOTER REQUIRES BINDING OF IHF	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoR	gene	phoB	activator	31346161	10	ver/dev	These data suggest that the interaction between PhoR is required for a full induction of the mRNA levels of the phoB genes inside macrophages .	294	These data suggest that the interaction between MgtC and PhoR is required for a full induction of the mRNA levels of the phoE and phoB genes inside macrophages .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	narG	regulator	29857034	19	ver/dev	-RRB- , narG -LRB- are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoA	repressor	18790861	2	ver/dev	increased ferrous iron uptake associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein	12	This FeoB induction resulted in increased ferrous iron uptake , which associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
TviA	gene	fliC	regulator	18034866	0	ver/dev	It has been shown recently that the TviA regulatory protein controls transcription of the flagellin gene fliC , thereby reducing TLR5-mediated IL-8 production in human intestinal epithelial cells by reducing flagellin secretion .	39	It has been shown recently that the TviA regulatory protein controls transcription of the flagellin gene fliC , thereby reducing TLR5-mediated IL-8 production in human intestinal epithelial cells by reducing flagellin secretion ( Winter et al. , 2007 ) .	3	INTRODUCTION	Homo sapiens	0	L3	OTHER	Analysis	OTHER	Other	Level 2
NsrR	gene	hcr	activator	23651595	12	ver/dev	Additional experiments , showed that NsrR-binding plays a major role in the induction of hcr operon .	608	Additional experiments , using electrophoretic mobility shift assays , showed that NsrR-binding plays a major role in the induction of the hcp -- hcr operon and that hcp is totally dependent upon anaerobiosis and the FNR protein ( Chismon , Browning , Farrant , & Busby , 2010 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	csgD	activator	25437188	31	ver/dev	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by RtsA .	339	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs ( see above ) , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator , RtsA [ 86,87,123 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	csgD	activator	25437188	31	ver/dev	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by RtsA .	339	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs ( see above ) , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator , RtsA [ 86,87,123 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HU	gene	ssrA	repressor	21212121	17	ver/dev	There is a much closer correspondence between the effects of IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU , as are the genes .	363	There is a much closer correspondence between the effects of HU and IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU or IHF , as are the genes coding for the secretion apparatus and the effector proteins .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HU	gene	ssrA	repressor	21212121	17	ver/dev	There is a much closer correspondence between the effects of HU among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU , as are the genes .	363	There is a much closer correspondence between the effects of HU and IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU or IHF , as are the genes coding for the secretion apparatus and the effector proteins .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilE	regulator	34048498	25	ver/dev	HilD can be reached with the positive regulation of the hilE expression by SirA	179	It is reasonable to suggest that when SirA counteracts the CsrA-mediated repression of hilD , higher levels of HilE would be required to negatively control the activity of HilD , which can be reached with the positive regulation of the hilE expression by SirA .	9	HILE REPRESSES HILD-MEDIATED EXPRESSION OF SPI-1, SPI-2 AND SPI-5 GENES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
MarR	TU	marRAB	regulator	15073288	2	ver/dev	MarR inhibits binding of MarR to the marRAB promoter	41	The mechanism of induction by phenolic compounds , specifically salicylate , is by the binding of salicylate to MarR , which inhibits binding of MarR to the marRAB promoter ( Martin & Rosner , 1995 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	regulator	19120970	11	ver/dev	Alekshun M.N. , Levy S.B. Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in-vitro .	400	Alekshun M.N. , Levy S.B. ( 1999 ) Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in vitro .	33	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	regulator	20237076	9	ver/dev	Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in-vitro .	384	Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in vitro .	29	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	regulator	22752112	25	ver/dev	Alekshun M , Levy S Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in-vitro .	315	Alekshun M , Levy S ( 1999 ) Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in vitro .	19	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	regulator	9068629	4	ver/dev	The similarity to E. coli of functional similarities of MarR to its E. coli counterpart all suggests that regulated control of marRAB expression in S. typhimurium is nearly identical to that of E. coli .	382	The similarity to E. coli of nucleotide sequences of the operator/promoter regions , Northern data on inducibility of the operon by SAL , and structural and functional similarities of MarR to its E. coli counterpart all suggests that regulated control of marRAB expression in S. typhimurium is nearly identical to that of E. coli .	5	DISCUSSION	Escherichia coli;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
MarR	TU	marRAB	regulator	9068629	4	ver/dev	The similarity to E. coli of structural similarities of MarR to its E. coli counterpart all suggests that regulated control of marRAB expression in S. typhimurium is nearly identical to that of E. coli .	382	The similarity to E. coli of nucleotide sequences of the operator/promoter regions , Northern data on inducibility of the operon by SAL , and structural and functional similarities of MarR to its E. coli counterpart all suggests that regulated control of marRAB expression in S. typhimurium is nearly identical to that of E. coli .	5	DISCUSSION	Escherichia coli;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sirA	regulator	19537165	9	ver/dev	However , the sirA knock-out does not lead to a complete loss in HilD levels since HilD is regulated by other factors .	270	However , the sirA knock-out does not lead to a complete loss in HilD levels since HilD is regulated by other factors such as HilE , EnvZ/OmpRr , etc. [ Baxter et al. , 2003 ] .	18	PARAMETER ESTIMATION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Sigma28	gene	flgA	activator	9765570	0	att	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaG	repressor	28704543	43	ver/dev	Together , these results show that SsrB simultaneously represses the expression of ssaG , respectively , inside Fig 8D .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaG	repressor	28704543	43	ver/dev	Together , these results show that SsrB simultaneously represses the expression of ssaG , respectively , inside macrophages .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	iagA	regulator	10899868	1	ver/dev	Under conditions of low-osmolarity , the transcription of iagA is negatively controlled by the RcsB regulator , acting in concert with the TviA protein .	322	Under conditions of low osmolarity , the transcription of iagA , invF , and sipB ( encoding proteins involved in cell invasion ) is negatively controlled by the RcsB regulator , acting in concert with the TviA protein , which is encoded by tviA within the viaB locus .	6	CVD 908-HTRA 9/10 A (90) 10 CVD 909B 3/8 B (38) 62 PBS 10/10 C (100) 0	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	iagA	regulator	19901065	1	ver/dev	The transcription of the iagA is negatively controlled by the RcsB regulator .	29	The transcription of the iagA , invF , and sipB genes is negatively controlled by the RcsB regulator ( 2 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DeoR	gene	tsx	repressor	16489221	0	ver/dev	Repression by DeoR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DeoR	gene	tsx	repressor	16489221	0	ver/dev	Repression by DeoR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	srfN	regulator	21711513	0	att	Osborne et al. [ 27 ] recently reported that srfN , an ancestral PhoP-regulated gene , acquired an SsrB-regula-tory module during Salmonella 's evolution to a pathogenic bacterium .	170	Osborne et al. [ 27 ] recently reported that srfN , an ancestral PhoP-regulated gene , acquired an SsrB-regula-tory module during Salmonella 's evolution to a pathogenic bacterium .	6	DISCUSSION	Salmonella;Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilE	regulator	29378886	35	ver/dev	Together , these data suggest that although there is some regulation of hilE transcription and translation , this regulation is not dramatic under normal conditions and/or the identified regulators have effects on the system of HilE .	277	Together , these data suggest that although there is some regulation of hilE transcription and translation , this regulation is not dramatic under normal conditions and/or the identified regulators have effects on the system that are independent of HilE .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Fis	gene	fis	regulator	17784910	4	ver/dev	Fis protein expression is controlled at the level of fis transcription .	135	Fis protein expression is controlled at the level of fis transcription ( Osuna et al. , 1995 ; Walker et al. , 1999 ) and by a post-transcriptional mechanism ( Owens et al. , 2004 ) .	8	TRANSCRIPTION OF THE FIS GENE IN STRAINS SL1344 AND CSH50	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	fis	regulator	17784910	28	ver/dev	The influence of low oxygen tension on expression of the Fis protein was shown to be a manifestation of its impact on the activity of the fis gene promoter .	518	The influence of low oxygen tension on expression of the Fis protein was shown to be a manifestation of its impact on the activity of the fis gene promoter .	14	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	fis	regulator	24885225	51	ver/dev	the fis expression in S. Typhi _ suggesting that Fis is also regulated by its level in S. enterica	205	In this work , we found that glucose induces the fis expression in S. Typhi , suggesting that Fis is also regulated by its level in S. enterica ( Figure 1E ) .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	fis	regulator	32900812	1	ver/dev	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within vice versa .	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain versa .	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within vice versa _ creating strain	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain versa _ creating strain	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within vice versa _ creating OX	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within vice versa _ creating the open reading frame exchange	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain versa _ creating OX	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	1	ver/dev	the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain versa _ creating the open reading frame exchange	7	In a parallel experiment , we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain , and vice versa , creating the open reading frame exchange ( OX ) strain .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	fis	regulator	32900812	13	ver/dev	We sought to investigate if , due to the pervasive influence of Fis , altering the location of the fis gene might produce significant changes to bacterial physiology .	239	We sought to investigate if , due to the pervasive influence of Fis , altering the location of the fis gene might produce significant changes to bacterial physiology .	4	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	3	ver/dev	HilD , regulates the expression of sinR .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sinR	regulator	27886269	11	ver/dev	that HilD directly controls the expression of the sinR genes	94	Thus , these data strongly support that HilD directly controls the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly , through a regulator found in S. Typhimurium but not in E. coli MC4100 , that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sinR	regulator	27886269	12	ver/dev	HilD binds to the regulatory regions of sinR .	110	HilD binds to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sinR	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of sinR is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sinR	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of sinR is direct , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sinR	regulator	27886269	16	ver/dev	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the sinR genes .	120	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sinR	regulator	27886269	17	ver/dev	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : sinR .	125	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes that are co-expressed with SPI-1 were identified : gtgE , phoH , sinR , SL1028 , lpxR , SL1896 , SL3812 , SL4247 and SL4433 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Escherichia coli	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of sinR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Salmonella;Salmonella	0.5	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	sinR	regulator	27886269	21	ver/dev	Thus , HilD directly regulates the expression of the sinR genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sinR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the sinR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sinR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the sinR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sinR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the sinR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sinR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the sinR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sinR	regulator	27886269	31	ver/dev	HilD binds to the regulatory region of sinR .	177	HilD binds to the regulatory region of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IscR	gene	torT	regulator	33751923	19	ver/dev	Carey et al. showed that the E. coli global regulator IscR binds the intergenic region between torT .	589	Carey et al. ( 2018 ) showed that the E. coli global regulator IscR binds the intergenic region between torT and torS , repressing their regulation in aerobic conditions ( Carey et al. 2018 ) .	20	TORSR	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	sseD	regulator	24272778	30	ver/dev	Thus , it is possible that AraC regulates transcription from the site within sseD under conditions .	329	Thus , it is possible that AraC regulates transcription from the site within sseD under conditions that derepress SPI2 .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	feoB	regulator	18790861	55	att	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	TU	umuDC	activator	21102598	0	ver/dev	the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes include umuDC	78	DNA damage created by quinolone antibiotics has been shown to be sufficient to stimulate umuC transcription and the SOS response .4,5 The initial response to DNA damage is the reduction in LexA protein levels and induction of LexA repressed genes , which include lexA , umuDC and dinP .2,3 ( In Escherichia .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsA	regulator	12519186	49	att	The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .	137	The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	regulator	15469511	0	att	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	14	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsA	regulator	15469511	4	att	These results indicate that constitutive expression and/or inhibition of RcsB-regulated genes inhibits phagocytosis , possibly resulting from capsule overproduction , and reduces bacterial replication within macrophages in a mechanism that requires genes in addition to rcsA and cps .	88	These results indicate that constitutive expression and/or inhibition of RcsB-regulated genes inhibits phagocytosis , possibly resulting from capsule overproduction , and reduces bacterial replication within macrophages in a mechanism that requires genes in addition to rcsA and cps .	7	THE RCSC11 MUTANT DISPLAYS LOWER PHAGOCYTOSIS BY AND SURVIVAL WITHIN MACROPHAGES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsA	regulator	29186528	5	ver/dev	the rcsA promoter is autoregulated by RcsB in the so named RcsAB box	172	We selected these regions since P1flhDC accounts for the RcsB box while a similar consensus sequence is observed in the rcsA promoter , which is autoregulated by RcsA and RcsB in the so named RcsAB box ( 4,40 ) ( Supplementary Figure S6B ) .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	regulator	29186528	6	ver/dev	However , binding of RcsB ∼ P to P1flhDC caused a higher band shift compared to o the rcsA promot .	174	However , binding of RcsB ∼ P to P1flhDC caused a higher band shift compared to the rcsA promoter , which could account for higher affinity to the former promoter .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsA	regulator	29186528	7	ver/dev	Since RcsA assists the binding of RcsB to the rcsA promoter , the absence of this protein would explain the weaker binding of RcsB alone to the rcsA promoter .	175	Since RcsA assists the binding of RcsB to the rcsA promoter ( 10 ) , the absence of this protein would explain the weaker binding of RcsB alone to the rcsA promoter .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsA	regulator	29186528	7	ver/dev	Since RcsA assists the binding of RcsB to the rcsA promoter , the absence of this protein would explain the weaker binding of RcsB alone to the rcsA promoter .	175	Since RcsA assists the binding of RcsB to the rcsA promoter ( 10 ) , the absence of this protein would explain the weaker binding of RcsB alone to the rcsA promoter .	16	THE CONFORMATION OF PHOSPHORYLATED RCSB IS COMPETENT TO INTERACT WITH DNA	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FlhD	TU	marRAB	repressor	21168230	3	ver/dev	sprB transcriptional regulator hilC invasion regulatory protein orgB needle complex export protein orgA needle complex assembly protein prgK needle complex inner membrane lipoprotein prgJ needle complex minor subunit prgH needle complex inner membrane protein hilD invasion protein regulatory protein iagB invasion protein precursor sptP tyrosine phosphatase ( associated with virulence ) sicP secretion chaperone sipA secreted effector protein sipB translocation machinery component sipC translocation machinery component sipD translocation machinery component sicA surface presentation of antigens secretory proteins invB secretory protein ( associated with virulence ) invA needle complex export protein invB secretion chaperone invC type III secretion system ATPase invE invasion protein invF invasion regulatory protein invH needle complex outer membrane lipoprotein sopE Invasion associate secreted protein pipC pathogenicity island-encoded protein C Flagellar genes fliT flagellar protein FliT fliF flagellar M-ring protein fliK flagellar hook-length control protein fliL flagellar biosynthesis protein fliM flagellar motor switch protein fliP flagellar biosynthesis protein flgB flagellar basal body rod protein flgE flagellar hook protein flgF cell-proximal portion of basal-body rod flgG flagellar basal-body rod protein flgH flagellar L-ring protein precursor flgI flagellar P-ring protein precursor flhC flagellar transcriptional activator flhD transcriptional activator FlhD fimA major type 1 subunit fimbrin ( pilin ) fimZ fimbrial protein Z , putative transcriptional regulator Chemotaxis cheM methyl-accepting chemotaxis protein II STM3138 putative methyl-accepting chemotaxis protein STM3216 putative methyl-accepting chemotaxis protein Efflux pump/Defense acrB RND family , acridine efflux pump acrA RND family , acridine efflux pump acrF RND family , multidrug transport protein , acriflavin resistance marR transcriptional repressor of marRAB operon , multiple antibiotic ybhS putative ABC superfamily ( membrane ) transport protei Molecular chaperone grpE molecular chaperone heat-shock protein	249	sprB transcriptional regulator hilC invasion regulatory protein orgB needle complex export protein orgA needle complex assembly protein prgK needle complex inner membrane lipoprotein prgJ needle complex minor subunit prgH needle complex inner membrane protein hilD invasion protein regulatory protein iagB invasion protein precursor sptP tyrosine phosphatase ( associated with virulence ) sicP secretion chaperone sipA secreted effector protein sipB translocation machinery component sipC translocation machinery component sipD translocation machinery component sicA surface presentation of antigens secretory proteins invB secretory protein ( associated with virulence ) invA needle complex export protein invB secretion chaperone invC type III secretion system ATPase invE invasion protein invF invasion regulatory protein invH needle complex outer membrane lipoprotein sopE Invasion associate secreted protein pipC pathogenicity island-encoded protein C Flagellar genes fliT flagellar protein FliT fliF flagellar M-ring protein fliK flagellar hook-length control protein fliL flagellar biosynthesis protein fliM flagellar motor switch protein fliP flagellar biosynthesis protein flgB flagellar basal body rod protein flgE flagellar hook protein flgF cell-proximal portion of basal-body rod flgG flagellar basal-body rod protein flgH flagellar L-ring protein precursor flgI flagellar P-ring protein precursor flhC flagellar transcriptional activator flhD transcriptional activator FlhD fimA major type 1 subunit fimbrin ( pilin ) fimZ fimbrial protein Z , putative transcriptional regulator Chemotaxis cheM methyl-accepting chemotaxis protein II STM3138 putative methyl-accepting chemotaxis protein STM3216 putative methyl-accepting chemotaxis protein Efflux pump/Defense acrB RND family , acridine efflux pump acrA RND family , acridine efflux pump acrF RND family , multidrug transport protein , acriflavin resistance marR transcriptional repressor of marRAB operon , multiple antibiotic ybhS putative ABC superfamily ( membrane ) transport protei Molecular chaperone grpE molecular chaperone heat shock protein	20	3.5. GENES INVOLVED IN DEFENSE MECHANISM INFLUENCED BY NARINGENIN	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HilE	gene	hilC	regulator	17993530	36	ver/dev	Deletion of either hilC in this experiment did not block regulation by either HilE .	258	Deletion of either hilC or rtsA in this experiment decreased expression of hilA but did not block regulation by either HilE or Fur .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FlhD	TU	flhDC	regulator	22291596	0	ver/dev	The class I flhDC operon is the master regulator , with FlhD .	538	The class I flhDC operon is the master regulator , with FlhD and FlhC forming a hetero-tetramer that is required for transcriptional activation of the class II genes , which encode the hook-basal body complexes and the alternative sigma factor FliA ( sigma28 ) .	25	EXPRESSION OF FLAGELLA GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	activator	24450479	35	att	However , full chiP induction in the presence of chitobiose or chitotriose requires the relief of both NagC-dependent transcriptional repression and ChiX-dependent translational repression .	162	However , full chiP induction in the presence of chitobiose or chitotriose requires the relief of both NagC-dependent transcriptional repression and ChiX-dependent translational repression .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	activator	24450479	28	ver/dev	GlcNAc6P inactivates NagC leading to full-scale induction of both the chiP	119	The subsequent metabolism of chitobiose by the enzymes of the chb operon , ChbFG ( Verma and Mahadevan , 2012 ) generates GlcNAc6P , which inactivates NagC leading to full-scale induction of both the chiP and chb operons .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	activator	24450479	28	ver/dev	GlcNAc6P inactivates NagC leading to full-scale induction of both the chiP	119	The subsequent metabolism of chitobiose by the enzymes of the chb operon , ChbFG ( Verma and Mahadevan , 2012 ) generates GlcNAc6P , which inactivates NagC leading to full-scale induction of both the chiP and chb operons .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	repressor	24450479	0	ver/dev	Here , we show that the chiP gene , like the chbBCARFG operon , is also downregulated at the transcriptional level by the NagC repressor .	17	Here , we show that the chiP gene , like the chbBCARFG operon , is also downregulated at the transcriptional level by the NagC repressor .	2	SUMMARY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	repressor	24450479	22	ver/dev	Inactivation of the NagC repressor causes chiP expression to increase no more than twofold to threefold in ΔchiX background .	101	Inactivation of the NagC repressor causes chiP expression to increase no more than twofold to threefold in ΔchiX background .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	repressor	24450479	27	ver/dev	The NagC repressor inhibits chiP transcription under uninduced conditions through binding to the chiP promoter .	117	The NagC repressor inhibits chiP transcription under uninduced conditions through binding to the chiP promoter .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	repressor	24450479	27	ver/dev	The NagC repressor inhibits chiP transcription under uninduced conditions through binding to the chiP promoter .	117	The NagC repressor inhibits chiP transcription under uninduced conditions through binding to the chiP promoter .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	repressor	24450479	34	ver/dev	However , in both organisms repression of chiP by NagC is inefficient resulting in a relatively high basal level of chiP transcription in the absence of chitobi-ose .	156	However , in both organisms repression of chiP by NagC is inefficient resulting in a relatively high basal level of chiP transcription in the absence of chitobi-ose ( Figueroa-Bossi et al. , 2009 ) .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	repressor	24450479	44	ver/dev	In uninduced the chb , chiP operons are repressed by NagC .	200	In the absence of chitosugars ( uninduced ) the chb , chiP and nag operons are repressed by NagC .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	repressor	24450479	44	ver/dev	In the absence-of-chitosugars the chb , chiP operons are repressed by NagC .	200	In the absence of chitosugars ( uninduced ) the chb , chiP and nag operons are repressed by NagC .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	repressor	24450479	48	ver/dev	Second , as the flux of chitobiose through the ChbBCA ChbFG enzymes relieves repression by NagC of both chiP operons .	221	Second , as the flux of chitobiose through the ChbBCA transporter and ChbFG enzymes increases , the level of GlcNAc6P , the inducer for NagC , increases and relieves repression by NagC of both chiP and chb operons .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	repressor	24450479	48	ver/dev	Second , as the flux of chitobiose through the ChbBCA transporter enzymes relieves repression by NagC of both chiP operons .	221	Second , as the flux of chitobiose through the ChbBCA transporter and ChbFG enzymes increases , the level of GlcNAc6P , the inducer for NagC , increases and relieves repression by NagC of both chiP and chb operons .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CadC	gene	marT	activator	20195364	0	ver/dev	An in silico analysis of sequences from S. Typhimurium SPI-3 suggested that the main factor responsible for the phenotypic changes could be marT , since its protein product exhibits similarity to the putative DNA binding domain of the CadC transcriptional activator of E. coli K-12 .	136	An in silico analysis of sequences from S. Typhimurium SPI-3 suggested that the main factor responsible for the phenotypic changes observed in the SPI-3 STm hybrid could be marT , since its protein product exhibits similarity to the putative DNA binding domain of the CadC transcriptional activator of E. coli K-12 , which has been associated with the acid stress response [ 2,12,23 ] .	13	THE S. TYPHI T3766 MUTANT STRAIN HAS A LOWER EARLY SURVIVAL RATE INSIDE HUMAN CELLS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yaiB	activator	24885225	56	ver/dev	RpoS stabilization where PhoPQ participates by serving as a transcriptional activator of yaiB gene in S. Typhimurium	214	One component of induction is RpoS stabilization , where PhoPQ participates by serving as a transcriptional activator of the iraP ( yaiB ) gene in S. Typhimurium .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	relA	activator	19091955	30	att	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	187	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	relA	activator	19091955	30	att	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	187	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	relA	activator	19091955	21	ver/dev	When induced at a similar level , SlyA tends to form more dimers in the wild-type strain than in a relA spoT mutant , suggesting that ppGpp probably induces a conformational change in SlyA structure that preferentially forms a dimer .	132	When induced at a similar level , SlyA tends to form more dimers in the wild-type strain than in a relA spoT mutant ( Fig. 3E ) , suggesting that ppGpp probably induces a conformational change in SlyA structure that preferentially forms a dimer .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus	0	L2	SPEC	Analysis	OTHER	New	Level 1
FliA	gene	tdcB	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	cobB	activator	26705535	0	ver/dev	Notably , CRP activates cobB .	85	Notably , the S. enterica catabolite repressor protein ( CRP ) activates expression pat and acs , but not cobB .	9	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	sifA	activator	21059643	7	ver/dev	Thus , in contrast to previous reports activation of sifA by OmpR is indirect .	163	Thus , in contrast to previous reports ( 40 ) activation of sifA by OmpR is indirect , working through SsrB .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagM	activator	25624475	3	att	We establish that this surface migration is dependent on the PhoP-activated MgtA-dependent pagM gene .	15	We establish that this surface migration is dependent on the PhoP-activated MgtA-dependent pagM gene .	3	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagM	activator	25624475	4	att	This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 's own F1Fo ATPase , and a small protein of unknown function , respectively .	20	This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 's own F1Fo ATPase , and a small protein of unknown function , respectively .	4	MAIN	Salmonella;unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	pagM	activator	25624475	8	att	The PhoP-activated mgtA , mgtC , and pagM genes are required for motility on 0.3 % agarose low Mg2 + media .	116	The PhoP-activated mgtA , mgtC , and pagM genes are required for motility on 0.3 % agarose low Mg2 + media .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	lpxO	regulator	29937757	0	ver/dev	genetic analyses indicate that this process is regulated by Fnr controlling the expression of lpxO .	17	Biochemical and genetic analyses indicate that this process is regulated by Fnr and ArcA controlling the expression of lpxO .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	lpxO	regulator	29937757	0	ver/dev	Biochemical analyses indicate that this process is regulated by Fnr controlling the expression of lpxO .	17	Biochemical and genetic analyses indicate that this process is regulated by Fnr and ArcA controlling the expression of lpxO .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	lpxO	regulator	29937757	3	ver/dev	The above results led us to hypothesize that lpxO expression is regulated by oxygen availability through the activity of transcription regulators ArcA and/or Fnr .	225	The above results led us to hypothesize that lpxO expression is regulated by oxygen availability through the activity of transcription regulators ArcA and/or Fnr .	18	LIPID A HYDROXYLATION IS MODULATED BY OXYGEN AVAILABILITY IN S. ENTERITIDIS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
FNR	gene	lpxO	regulator	29937757	4	ver/dev	Thus , the oxygen-dependent regulation of lpxO expression is lost when fnr is deleted , indicating that Fnr is a negative regulator of lpxO expression under anaerobic conditions .	232	Thus , the oxygen-dependent regulation of lpxO expression described for the wild-type strain is lost when fnr is deleted , indicating that Fnr is a negative regulator of lpxO expression under anaerobic conditions .	18	LIPID A HYDROXYLATION IS MODULATED BY OXYGEN AVAILABILITY IN S. ENTERITIDIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	lpxO	regulator	29937757	4	ver/dev	Thus , the oxygen-dependent regulation of lpxO expression is lost when fnr is deleted , indicating that Fnr is a negative regulator of lpxO expression under anaerobic conditions .	232	Thus , the oxygen-dependent regulation of lpxO expression described for the wild-type strain is lost when fnr is deleted , indicating that Fnr is a negative regulator of lpxO expression under anaerobic conditions .	18	LIPID A HYDROXYLATION IS MODULATED BY OXYGEN AVAILABILITY IN S. ENTERITIDIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	lpxO	regulator	29937757	5	ver/dev	Fnr Bind to the lpxO Promoter Region	241	Fnr and ArcA Bind to the lpxO Promoter Region	19	FNR AND ARCA BIND TO THE LPXO PROMOTER REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	lpxO	regulator	29937757	9	ver/dev	lpxO Expression Is Regulated by Fnr in Response to Oxygen Availability	255	lpxO Expression Is Regulated by Fnr and ArcA in Response to Oxygen Availability	19	FNR AND ARCA BIND TO THE LPXO PROMOTER REGION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	lpxO	regulator	29937757	10	ver/dev	These results indicate that Fnr regulate lpxO expression through direct binding to its promoter region .	262	These results indicate that Fnr and ArcA regulate lpxO expression through direct binding to its promoter region .	19	FNR AND ARCA BIND TO THE LPXO PROMOTER REGION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FNR	gene	lpxO	regulator	29937757	12	ver/dev	In addition , we also demonstrate that global regulators Fnr control the oxygen-dependent lipid-A hydroxylation by directly regulating the expression of lpxO .	282	In addition , we also demonstrate that global regulators Fnr and ArcA control the oxygen-dependent lipid A hydroxylation by directly regulating the expression of lpxO .	20	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FNR	gene	lpxO	regulator	29937757	15	ver/dev	Our results also showed that both Fnr are able to bind in-vitro to the promoter regions of lpxO , strongly suggesting a direct role for these regulators in the control of lpxO transcription .	304	Our results also showed that both Fnr and ArcA are able to bind in vitro to the promoter regions of lpxO ( Figure 5 ) , strongly suggesting a direct role for these regulators in the control of lpxO transcription .	20	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	lpxO	regulator	29937757	15	ver/dev	Our results also showed that both Fnr are able to bind in-vitro to the promoter regions of lpxO , strongly suggesting a direct role for these regulators in the control of lpxO transcription .	304	Our results also showed that both Fnr and ArcA are able to bind in vitro to the promoter regions of lpxO ( Figure 5 ) , strongly suggesting a direct role for these regulators in the control of lpxO transcription .	20	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	lpxO	regulator	29937757	18	ver/dev	a model in which Fnr control the expression of lpxO in S. Enteritidis to achieve a fine-tuning of lipid-A hydroxylation levels	337	Overall , our results support a model in which Fnr and ArcA control the expression of lpxO in S. Enteritidis to achieve a fine-tuning of lipid A hydroxylation levels .	20	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PocR	gene	tetA	regulator	16585772	5	ver/dev	the plasmid pPocR expresses PocR under control of the tetA promoter on pBR322 , into the mutant	145	Introduction of the plasmid pPocR ( Table 1 ) , which expresses PocR under control of the tetA promoter on pBR322 , into the mutant restored the repression ( Fig. 1 ) .	2	MAIN	unidentified plasmid;Hypostomus robinii	0.5	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	flhD	repressor	28439039	5	ver/dev	FimZ is known to negatively regulate flhD expression .	248	FimZ is known to negatively regulate flhD expression .	4	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
FimZ	gene	flhD	repressor	28439039	6	ver/dev	It is possible that the increase in FimZ in the ΔinvS background strain led to the decrease of flhD expression .	249	It is possible that the increase in FimZ in the ΔinvS background strain led to the decrease of flhD expression .	4	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	hilA	repressor	29857034	3	ver/dev	hilA are negatively regulated by SlyA	267	Presumptive genes involved in these pathways include sopD , sopE2 , and hilA , which belong to pathogenicity island-1 ( SPI-1 ) and are negatively regulated by SlyA .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	hilA	repressor	29857034	7	ver/dev	These results suggest that hilA is downregulated by SlyA .	281	These results suggest that hilA is downregulated by SlyA .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	hilA	repressor	29857034	25	ver/dev	These results suggest that SlyA negatively regulates hilA .	356	These results suggest that SlyA negatively regulates hilA .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	TU	flhDC	activator	30355489	14	att	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC ( Figure S3D ) .	143	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC ( Figure S3D ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	TU	flhDC	activator	30355489	7	att	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC ( Figure S3D ) .	115	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC ( Figure S3D ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	TU	flhDC	activator	30355489	3	ver/dev	flhDC is activated by SsrB	95	For example , SlyA is a repressor of flhDC that is activated by SsrB ; however SsrB was able to repress motility in a DslyA mutant equivalently to wild-type , thus ruling out contributions by SlyA ( Figure S3A ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	sopB	regulator	24947562	0	ver/dev	However , it is important to mention that sopB , is cooperatively regulated by lowered levels of HilD were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control .	232	However , it is important to mention that sopB , is cooperatively regulated by InvF and HilA [ 30 ] and lowered levels of all SPI-1-encoded transcriptional regulators ( HilA , HilC , HilD , and InvF ) were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control [ 24 ] .	19	4. DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sopB	regulator	31017982	6	att	A plasmid-borne sopB : : luxCDABE was additionally tested as a HilD-regulated gene outside of SPI-1 , showing peak expression of the mutants increased by > 2.6-fold and areas under the curve increased by at least 2.7-fold ( Fig 2B ) .	92	A plasmid-borne sopB : : luxCDABE was additionally tested as a HilD-regulated gene outside of SPI-1 , showing peak expression of the mutants increased by > 2.6-fold and areas under the curve increased by at least 2.7-fold ( Fig 2B ) .	7	ACTIVATING MUTATIONS OF HILD OCCUR IN ITS 5’ REGION	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sopB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in sopE229 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sopB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in sopE , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sopB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in sopF28 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sopB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in SPI-527 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
Fis	gene	gyrA	activator	12898222	14	ver/dev	Radiolabelled gyrA was incubated with increasing concentrations of Fis protein prior to digestion with DNase I .	183	Radiolabelled gyrA ( A ) or gyrB ( C ) promoter DNA was incubated with increasing concentrations of Fis protein prior to digestion with DNase I .	15	EXPRESSION OF THE FIS PROTEIN IN E. COLI AND S. ENTERICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrA	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over TopA levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	gyrA	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssaG	activator	20396961	1	att	The results of β-galactosidase assays and FACS analysis showed that , among the four PhoP-dependent genes tested , the expression of ssaG , which is located in Salmonella pathogenicity island 2 ( SPI2 ) , was reduced in the tdcA mutant , especially in the intracellular environment of macrophages .	13	The results of β-galactosidase assays and FACS analysis showed that , among the four PhoP-dependent genes tested , the expression of ssaG , which is located in Salmonella pathogenicity island 2 ( SPI2 ) , was reduced in the tdcA mutant , especially in the intracellular environment of macrophages .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssaB	activator	17630976	44	att	Expression of the ssaB gene is also OmpR-dependent , suggesting that OmpR might contribute to pH-dependent induction ( D. Walthers and L.J. Kenney , unpublished ) .	349	Expression of the ssaB gene is also OmpR-dependent , suggesting that OmpR might contribute to pH-dependent induction ( D. Walthers and L.J. Kenney , unpublished ) .	12	ACIDIC PH INDUCES SSRB-DEPENDENT SPI-2 GENE EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NagC	TU	glmUS	repressor	27628932	0	ver/dev	Plumbridge , the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon .	583	Plumbridge , J. Co-ordinated regulation of amino sugar biosynthesis and degradation : the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites .	17	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	pgtE	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of pgtE we performed EMSA with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged Fig 3B .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	pgtE	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of pgtE we performed EMSA with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	pgtE	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of pgtE we performed electrophoretic-mobility-shift assays with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged Fig 3B .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	pgtE	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of pgtE we performed electrophoretic-mobility-shift assays with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	emrR	regulator	30992361	11	ver/dev	In contrast to PhoP-activated slyA transcription , transcription of the emrR gene was not regulated by either SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains -LRB- Fig. 3A , top panel -RRB- .	114	In contrast to PhoP-activated slyA transcription ( 5 , 21 ) , transcription of the emrR gene was not regulated by either PhoP/PhoQ system or SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains ( Fig. 3A , top panel ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	prgK	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgK remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	prgK	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgK remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	prgK	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgK remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	spvABCD	activator	15790293	6	ver/dev	RpoS appears essential for SpvR-assisted induction of the spvABCD genes .	239	RpoS appears essential for SpvR-assisted induction of the spvABCD genes .	14	ALTERNATIVE R-FACTORS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
SoxS	gene	fpr	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates Mn-containing superoxide dismutase , fpr .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	fpr	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , fpr .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	fpr	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , fpr .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	fpr	activator	12886427	0	ver/dev	SoxS protein , activates sodA , fpr .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	yaeB	repressor	31487966	0	ver/dev	H-NS confirmed in this study can repress the expression of yaeB	17	Moreover , qRT-PCR data showed YaeB was induced by the acidic pH inside macrophages , and the acidic pH passed to YeaB through inhibiting global regulator histone-like nucleoid structuring ( H-NS ) which confirmed in this study can repress the expression of yaeB .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HNS	gene	yaeB	repressor	31487966	6	ver/dev	H-NS directly repressed yaeB gene expression .	182	H-NS directly repressed yaeB gene expression .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	yaeB	repressor	31487966	7	ver/dev	To investigate whether H-NS repression of Pst requires YaeB , we constructed the ∆ and then tested the expression We then investigated the environmental signals that induced yaeB expres .	201	To investigate whether H-NS repression of Pst requires YaeB , we constructed the ∆ hns ∆ yaeB double mutant strain and then tested the expression We then investigated the environmental signals that induced yaeB expression .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	SPEC	Other	OTHER	New	Level 1
HNS	gene	yaeB	repressor	31487966	8	ver/dev	the WT strain _ indicating that the deletion of yaeB in the hns mutant abolished the Pst induction , thus H-NS repression of Pst	204	Through qRT-PCR analysis , we tested whether acidic pH influenced the WT strain ( Figure 4C ) , indicating that the deletion of yaeB in the hns mutant abolished the Pst induction , thus H-NS repression of Pst required YaeB	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FabR	gene	fabR	regulator	27004424	8	ver/dev	FabR involvement in S. Typhimurium biofilm formation Mutant screening revealed a S. Typhimurium SL1344 fabR deletion mutant to show an impaired biofilm formation at 30 °C when grown in TSB 1/20 for 48 h. Different temperatures were tested because the regulation of biofilm formation in Salmon-ella is known to be strongly temperature dependent .	149	FabR involvement in S. Typhimurium biofilm formation Mutant screening revealed a S. Typhimurium SL1344 fabR deletion mutant ( CMPG5624 ) to show an impaired biofilm formation at 16 , 25 and 30 °C when grown in TSB 1/20 for 48 h. Different temperatures were tested because the regulation of biofilm formation in Salmon-ella is known to be strongly temperature dependent [ 4 ] .	11	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
FabR	gene	fabR	regulator	27004424	8	ver/dev	FabR involvement in S. Typhimurium biofilm formation Mutant screening revealed a S. Typhimurium SL1344 fabR deletion mutant to show an impaired biofilm formation at 25 °C when grown in TSB 1/20 for 48 h. Different temperatures were tested because the regulation of biofilm formation in Salmon-ella is known to be strongly temperature dependent .	149	FabR involvement in S. Typhimurium biofilm formation Mutant screening revealed a S. Typhimurium SL1344 fabR deletion mutant ( CMPG5624 ) to show an impaired biofilm formation at 16 , 25 and 30 °C when grown in TSB 1/20 for 48 h. Different temperatures were tested because the regulation of biofilm formation in Salmon-ella is known to be strongly temperature dependent [ 4 ] .	11	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
FabR	gene	fabR	regulator	27004424	8	ver/dev	FabR involvement in S. Typhimurium biofilm formation Mutant screening revealed a S. Typhimurium SL1344 fabR deletion mutant to show an impaired biofilm formation at 16 °C when grown in TSB 1/20 for 48 h. Different temperatures were tested because the regulation of biofilm formation in Salmon-ella is known to be strongly temperature dependent .	149	FabR involvement in S. Typhimurium biofilm formation Mutant screening revealed a S. Typhimurium SL1344 fabR deletion mutant ( CMPG5624 ) to show an impaired biofilm formation at 16 , 25 and 30 °C when grown in TSB 1/20 for 48 h. Different temperatures were tested because the regulation of biofilm formation in Salmon-ella is known to be strongly temperature dependent [ 4 ] .	11	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	hilA	activator	11755416	25	att	Little is known about the significance of HilC-dependent hilA expression versus HilD-dependent hilA expression to pathogenesis .	273	Little is known about the significance of HilC-dependent hilA expression versus HilD-dependent hilA expression to pathogenesis .	9	7. FUTURE DIRECTIONS IN REGULATION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	hilA	activator	12535071	17	ver/dev	A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA	73	A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	12535071	22	ver/dev	These data demonstrate that HilD can activate a subset of SPI1 genes in the absence of hilA .	81	These data demonstrate that HilD can activate a subset of SPI1 genes in the absence of hilA .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	hilA	activator	15661008	22	ver/dev	To understand how Lon negatively regulates the key regulator hilA , we have focused on two activators of HilD .	257	To understand how Lon negatively regulates the expression of SPI1 genes , including the key regulator hilA , we have focused on two activators of hilA , HilC and HilD .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	15661008	23	ver/dev	HilD can independently activate the hilA promoter .	267	HilC and HilD can independently bind and activate the hilA promoter ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	activator	15765064	14	ver/dev	However , evidence from our laboratory indicates that HilD is a required activator of hilA expression necessary for recruitment of RNA polymerase at the hilA promoter .	99	However , evidence from our laboratory indicates that HilD is a required activator of hilA expression necessary for contact and recruitment of RNA polymerase at the hilA promoter ( Boddicker et al. , 2002 ) .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	15765064	14	ver/dev	However , evidence from our laboratory indicates that HilD is a required activator of hilA expression necessary for contact of RNA polymerase at the hilA promoter .	99	However , evidence from our laboratory indicates that HilD is a required activator of hilA expression necessary for contact and recruitment of RNA polymerase at the hilA promoter ( Boddicker et al. , 2002 ) .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	15765064	30	ver/dev	This finding suggests that HilE functions as a repressor by binding to HilD to prevent its activation of the hilA promoter .	160	This finding suggests that HilE functions as a repressor by binding to HilD to prevent its activation of the hilA promoter .	7	NEGATIVE REGULATORS OF INVASION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	16045614	24	ver/dev	We wanted to determine if HilD could induce expression of hilA in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	hilA	activator	16045614	26	ver/dev	The data in Fig. 2 demonstrate that HilD are able to induce expression of hilA in the absence of the other regulators .	127	The data in Fig. 2 demonstrate that RtsA , HilC and HilD are able to induce expression of hilA in the absence of the other regulators .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	16045614	27	ver/dev	Production of HilC induced expression of hilA ~ 120-fold , while HilD induced expression of hilA 30 - to 40-fold , similar to previously reported values .	128	Production of HilC induced expression of hilA ~ 120-fold , while RtsA and HilD induced expression of hilA 30 - to 40-fold , similar to previously reported values ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Schechter et al. , 1999 ; Schechter and Lee , 2001 ; Ellermeier and Slauch , 2003 ) .	5	RESULTS	Terfezia pini	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	activator	16045614	34	ver/dev	RtsA , HilD each contribute to activating hilA in-vitro	144	RtsA, HilC and HilD each contribute to activating hilA in vitro	6	RTSA, HILC AND HILD EACH CONTRIBUTE TO ACTIVATING HILA IN VITRO	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	hilA	activator	16045614	69	ver/dev	We show that HilD can each independently activate expression of the hilA genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	activator	16045614	70	ver/dev	However , HilD normally act in concert to activate hilA .	466	However , HilD , HilC and RtsA normally act in concert to activate hilA .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	16045614	73	ver/dev	However , our most striking results show that even though HilD appears to be the best hilA activator of the three in-vitro , when working alone it can not induce hilA enough to stimulate invasion .	473	However , our most striking results show that even though HilD appears to be the best hilA activator of the three in vitro , when working alone it can not induce hilA enough to stimulate invasion .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	hilA	activator	16045614	96	ver/dev	Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilD .	762	Olekhnovich , I.N. , and Kadner , R.J. ( 2004 ) Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC and HilD .	27	REFERENCES	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	16045614	96	ver/dev	Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilD .	762	Olekhnovich , I.N. , and Kadner , R.J. ( 2004 ) Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC and HilD .	27	REFERENCES	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	16443238	2	ver/dev	HilD can activate expression of hilA .	39	Three homologous proteins , 8,13,14 HilC , HilD , and RtsA , which belong to the AraC/XylS family of transcription factors can activate expression of hilA and some of its target genes .	5	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilA	activator	16443238	13	ver/dev	As expected , activation of hilA promoter in the absence of the activators HilD and HilC was significantly reduced in inducing -LRB- high-osmolarity -RRB- conditions .	169	As expected , activation of hilA promoter in the absence of the activators HilD and HilC ( lines 5 -- 8 ) was lost or significantly reduced in inducing ( high osmolarity ) conditions .	10	SYNERGISTIC EFFECT OF H-NS AND HHA ON HILA PROMOTER	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilA	activator	16443238	13	ver/dev	As expected , activation of hilA promoter in the absence of the activators HilD and HilC was lost .	169	As expected , activation of hilA promoter in the absence of the activators HilD and HilC ( lines 5 -- 8 ) was lost or significantly reduced in inducing ( high osmolarity ) conditions .	10	SYNERGISTIC EFFECT OF H-NS AND HHA ON HILA PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	16443238	35	ver/dev	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .	625	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD .	50	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	16443238	35	ver/dev	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .	625	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD .	50	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	17060472	1	ver/dev	Since HilD activates hilA transcription , it was surprising that reduced transcription of the central regulator HilA was not detected by microarray analysis .	278	Since HilD activates hilA transcription , which in turn activates the transcription of the InvF transcriptional regulator ( 2 ) , it was surprising that reduced transcription of the central regulator HilA was not detected by microarray analysis .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	hilA	activator	17208038	28	att	All of the global regulators seem to be controlling hilA expression in a HilD-dependent manner .	153	All of the global regulators seem to be controlling hilA expression in a HilD-dependent manner .	11	REGULATION OF HILD	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	activator	17208038	9	ver/dev	These mixed dimers might account for the fact that HilD alone is not sufficient for activation of hilA in competition assays , because a DhilC DrtsA strain competes evenly with a DhilD DhilC DrtsA strain .	84	These mixed dimers might account for the fact that HilD alone is not sufficient for activation of hilA in competition assays , because a DhilC DrtsA strain competes evenly with a DhilD DhilC DrtsA strain [ 19 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
HilD	gene	hilA	activator	17208038	10	ver/dev	The mechanism by which HilD activate expression of hilA	85	The mechanism by which HilC , HilD and RtsA activate expression of hilA ( and possibly of each other ) apparently involves counteracting silencing by the nucleoid protein Hns [ 30,31 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	17675384	3	ver/dev	That means that at least hilA are induced by HilD .	43	That means that at least hilA and rtsA are induced by HilD , HilC , and RtsA proteins .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	17675384	9	ver/dev	To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilD-lac chromosomal fusions .	125	To test whether the RtsA , HilC , and HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac , hilC-lac , and hilD-lac chromosomal fusions ( 13 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	activator	17675384	9	ver/dev	To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilC-lac .	125	To test whether the RtsA , HilC , and HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac , hilC-lac , and hilD-lac chromosomal fusions ( 13 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	activator	17675384	9	ver/dev	To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac .	125	To test whether the RtsA , HilC , and HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac , hilC-lac , and hilD-lac chromosomal fusions ( 13 ) .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	activator	17675384	15	ver/dev	Under high-osmolarity conditions , HilD activate SPI1 genes indirectly through hilA .	288	Under high-osmolarity conditions , HilD , HilC , and RtsA activate SPI1 genes directly and indirectly through hilA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	17675384	15	ver/dev	Under high-osmolarity conditions , HilD activate SPI1 genes directly through hilA .	288	Under high-osmolarity conditions , HilD , HilC , and RtsA activate SPI1 genes directly and indirectly through hilA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	17675384	24	ver/dev	C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .	548	C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD .	19	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	17993530	1	att	Fur activates hilA transcription in a HilD-dependent manner .	12	Fur activates hilA transcription in a HilD-dependent manner .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	17993530	13	ver/dev	HilD are each capable of activating hilA transcription .	86	HilD , HilC , and RtsA are each capable of activating hilA transcription .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	17993530	23	ver/dev	Since Fur activation of hilA is clearly dependent upon HilD , we constructed hilD-lacZ-fusions in a hilD background .	210	Since Fur activation of hilA is clearly dependent upon HilD , we constructed hilD-lacZ fusions in a hilD background .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD is consistent with our model for SPI1 regulation ; transcription of hilA were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD is consistent with our model for SPI1 regulation ; transcription of rtsA were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD be present ; transcription of hilA were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD be present ; transcription of rtsA were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	activator	17993530	42	ver/dev	The BarA/SirA two-component system activates hilA by controlling HilD expression posttranscriptionally via activation of the small RNAs CsrB and CsrC .	321	The BarA/SirA two-component system activates hilA by controlling HilD expression posttranscriptionally via activation of the small RNAs CsrB and CsrC , which antagonize the CsrA RNA binding protein that presumably acts directly at the hilD mRNA ( 2 , 3 , 20 , 28 , 49 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	19074398	42	ver/dev	HilD induces expression of the hilA gene by derepressing the silencing effect of Hha on the hilA promoter	508	Based on these observations , we suggest that Lrp acts as an antagonist of HilD , which induces expression of the hilA gene by derepressing the silencing effect of H-NS and Hha on the hilA promoter .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	19074398	42	ver/dev	HilD induces expression of the hilA gene by derepressing the silencing effect of H-NS on the hilA promoter	508	Based on these observations , we suggest that Lrp acts as an antagonist of HilD , which induces expression of the hilA gene by derepressing the silencing effect of H-NS and Hha on the hilA promoter .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	19537165	3	ver/dev	Earlier work on mathematical modeling of regulation of expression of hilA by HilD was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .	44	Earlier work on mathematical modeling of regulation of expression of hilA by HilC , HilD and RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop [ Maithreye and Mande , 2007 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	20008574	1	ver/dev	Transcriptional activation by HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha .	36	Transcriptional activation by HilC and HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	21573071	2	ver/dev	It has been suggested that the negative regulatory effects of HilE are exerted by its direct interaction with HilD , such that HilDmediated activation of hilA is prevented .	40	It has been suggested that the negative regulatory effects of HilE are exerted by its direct interaction with HilD , such that HilDmediated activation of hilA is prevented [ 20 ] .	4	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	22291596	1	ver/dev	Both HilC and HilD activate expression of SPI-1 genes by binding upstream of the master regulatory gene hilA to induce its expression .	595	Both HilC and HilD activate expression of SPI-1 genes by binding upstream of the master regulatory gene hilA to induce its expression [ 48 ] .	27	EXPRESSION OF SPI-1 AND SPI-2 TYPE 3 SECRETION SYSTEM REGULATORY GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	23676436	1	ver/dev	HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; Schechter et al. ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	23676436	1	ver/dev	HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; 2001 ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	23676436	1	ver/dev	HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lee ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	23676436	1	ver/dev	HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	25135218	5	ver/dev	The AraC-like transcriptional regulator HilD , positively regulates the expression of the SPI-1 genes in a cascade fashion , mainly by directly inducing the expression of hilA .	21	The AraC-like transcriptional regulator HilD , encoded within SPI-1 , positively regulates the expression of the SPI-1 genes in a cascade fashion , mainly by directly inducing the expression of hilA , which encodes the master regulator of SPI-1 ( 2 , 5 , 23 -- 26 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	25135218	10	ver/dev	Several studies strongly support the idea that HilD induces the expression of hilA by counteracting the repression .	40	Several studies strongly support the idea that HilD induces the expression of hilA and rtsA by counteracting the repression exerted by H-NS on the promoters of these genes ( 23 , 24 , 27 , 48 , 49 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	hilA	activator	25375226	29	ver/dev	hilA expression is induced by three transcriptional activators , HilD .	402	hilA expression is induced by three transcriptional activators , HilC , HilD and RtsA [ 70 ] .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	25547794	4	ver/dev	HilD prevents the activation of hilA by HilD	61	Previous work by our research group has shown that HilE interacts with HilD , which prevents the activation of hilA by HilD ( 39 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	25991823	0	ver/dev	Transcription of hilA is directly activated by HilD .	24	Transcription of hilA is directly activated by HilC and HilD , both members of the AraC/XylS family of transcriptional regulators ( Schechter and Lee 2001 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	26300871	17	att	In agreement with our results indicating that CpxR represses the HilD-dependent expression of hilD and hilA , both the overexpression of CpxR and the absence of CpxA drastically reduced the production of SsrB-FLAG and SseB proteins ( Figures 1C , 3B ) , which are encoded in SPI-2 and whose expression is also dependent of HilD in the condition tested .	389	In agreement with our results indicating that CpxR represses the HilD-dependent expression of hilD and hilA , both the overexpression of CpxR and the absence of CpxA drastically reduced the production of SsrB-FLAG and SseB proteins ( Figures 1C , 3B ) , which are encoded in SPI-2 and whose expression is also dependent of HilD in the condition tested .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26300871	6	ver/dev	HilD positively regulates hilA	368	To start to define whether CpxR affects hilA directly or through HilD , which positively regulates hilA , we determined the effect of the overexpression of CpxR on the activity of a hilDcat transcriptional fusion in the WT S. Typhimurium strain .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	26300871	15	ver/dev	Previous studies indicate that HilD induces the expression of hilA by counteracting the repression hilA can be expressed independently of HilD .	377	Previous studies indicate that HilD induces the expression of hilA by counteracting the repression exerted by the nucleoid protein H-NS on the promoter of this gene ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2006 ) ; thus , in the absence of H-NS activity hilA can be expressed independently of HilD .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	5	ver/dev	lectively , these data indicated that expression of SPI-1 genes was Induction of the HilD-3 FLAG protein induced expression of reduced at 42 °C through decreased function of the HilD protein , the hilA-lacZ fusion by 13-fold following growth at 37 °C ; how - which resulted in reduced expression of d hi .	369	lectively , these data indicated that expression of SPI-1 genes was Induction of the HilD-3 FLAG protein induced expression of reduced at 42 °C through decreased function of the HilD protein , the hilA-lacZ fusion by 13-fold following growth at 37 °C ; how - which resulted in reduced expression of rtsA and hilA .	4	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	5	ver/dev	lectively , these data indicated that expression of SPI-1 genes was Induction of the HilD-3 FLAG protein induced expression of reduced at 42 °C through decreased function of the HilD protein , the hilA-lacZ fusion by 13-fold following growth at 37 °C ; how - which resulted in reduced expression of f rt .	369	lectively , these data indicated that expression of SPI-1 genes was Induction of the HilD-3 FLAG protein induced expression of reduced at 42 °C through decreased function of the HilD protein , the hilA-lacZ fusion by 13-fold following growth at 37 °C ; how - which resulted in reduced expression of rtsA and hilA .	4	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	6	ver/dev	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of r Rt .	370	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of HilC or RtsA .	4	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	6	ver/dev	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of r Rt .	370	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of HilC or RtsA .	4	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	6	ver/dev	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of f Hi .	370	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of HilC or RtsA .	4	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	6	ver/dev	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of f Hi .	370	In addition , ever , when cells were cultivated at 42 °C , induction of HilD - this implied that expression of SPI-1 genes at 42 °C could be re-3 FLAG resulted in modest ( only 2-fold ) activation of the hilA - stored through HilD-independent expression of HilC or RtsA .	4	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	26386070	7	ver/dev	This effect was specific for HilD since the other AraC/XylS type activators of hilA , was sufficient to activate SPI-1 expression at Fig. 6 .	385	This effect was specific for HilD since overexpression of either RtsA or HilC , the other AraC/XylS type activators of hilA , was sufficient to activate SPI-1 expression at 42 °C ( Fig. 6C ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	26386070	7	ver/dev	This effect was specific for HilD since the other AraC/XylS type activators of hilA , was sufficient to activate SPI-1 expression at 42 ° .	385	This effect was specific for HilD since overexpression of either RtsA or HilC , the other AraC/XylS type activators of hilA , was sufficient to activate SPI-1 expression at 42 °C ( Fig. 6C ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	26441883	30	ver/dev	HilD is the key activator of hilA transcription	425	In this context , HilD is the key activator of hilA transcription and various environmental signals are known to influence HilD production and activity , whereby RtsA and HilC function as amplifiers of the activating signal ( Ellermeier and Slauch , 2007 ) .	9	ATTACHMENT AND INVASION OF THE INTESTINAL EPITHELIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	27404739	1	ver/dev	HilD , activate directly the expression of hilA , independently of HilA .	131	Two additional regulators , HilC and HilD , activate directly the expression of hilA and the invF operon , independently of HilA ( Dieye et al. , 2007 ) .	6	SPI-1 RELATED GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	28329249	0	ver/dev	HilD , induces the expression of hilA .	25	HilD , a member of the AraC/XylS family of transcriptional regulators , induces the expression of hilA , encoding a transcriptional activator of the inv/spa , prg/org , and sic/sip operons [ 3 ] .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	28335027	10	ver/dev	H-NS repression of hilA counteracts transcriptional activation by HilD	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	28426789	9	ver/dev	Altogether , these results suggest that HilD plays a pivotal role in activating hilA expression under the experimental conditions .	206	Altogether , these results suggest that HilD plays a pivotal role in activating hilA expression under the experimental conditions used .	6	INVASION OF EPITHELIAL CELLS REQUIRES A BATTERY OF EFFECTOR PROTEINS ENCODED MAINLY BY GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via an unknown regulation of HilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	unidentified	1	L3	OTHER	Analysis	NEG	New	Level 1
HilD	gene	hilA	activator	28575106	4	ver/dev	It was found that LoiA positively regulates the expression of hilA -LRB- the master activator of SPI-1 -RRB- through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .	98	It was found that LoiA positively regulates the expression of hilA ( the master activator of SPI-1 ) through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	28575106	4	ver/dev	It was found that LoiA positively regulates the expression of hilA -LRB- the master activator of SPI-1 -RRB- through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .	98	It was found that LoiA positively regulates the expression of hilA ( the master activator of SPI-1 ) through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	28575106	4	ver/dev	It was found that LoiA positively regulates the expression of hilA -LRB- the master activator of SPI-1 -RRB- through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .	98	It was found that LoiA positively regulates the expression of hilA ( the master activator of SPI-1 ) through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	28575106	9	ver/dev	HilD in turn activates hilA expression	207	Collectively , these results demonstrate that LoiA directly binds to the hilD promoter to activate hilD expression ; and HilD in turn activates hilA expression , leading to the activation of	9	LOIA ACTIVATES EXPRESSION OF HILA GENE THROUGH ACTIVATING HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	28575106	12	ver/dev	Briefly , ArcB responds to low oxygen conditions when bacteria undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA-P activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .	275	Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum and undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA ( ArcA-P ) activates loiA gene expression indirectly through unknown regulator ( s ) ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA and other SPI-1 genes , and thus facilitates the invasion process .	13	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	hilA	activator	28575106	12	ver/dev	Briefly , ArcB responds to low oxygen conditions when bacteria undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .	275	Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum and undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA ( ArcA-P ) activates loiA gene expression indirectly through unknown regulator ( s ) ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA and other SPI-1 genes , and thus facilitates the invasion process .	13	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	hilA	activator	28575106	12	ver/dev	Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum ; phosphorylated ArcA-P activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .	275	Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum and undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA ( ArcA-P ) activates loiA gene expression indirectly through unknown regulator ( s ) ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA and other SPI-1 genes , and thus facilitates the invasion process .	13	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	New	Level 3
HilD	gene	hilA	activator	28575106	12	ver/dev	Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum ; phosphorylated ArcA activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .	275	Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum and undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA ( ArcA-P ) activates loiA gene expression indirectly through unknown regulator ( s ) ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA and other SPI-1 genes , and thus facilitates the invasion process .	13	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	New	Level 3
HilD	gene	hilA	activator	28704543	58	ver/dev	Mutations in hilA also affect activation by HilD .	657	Mutations in hilA affecting repression by SsrB also affect activation by HilD .	25	SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	29378886	1	ver/dev	Transcriptional activation of hilA is dependent upon three AraC-like proteins , HilD , .	45	Transcriptional activation of hilA is dependent upon three AraC-like proteins , HilD , HilC , and RtsA , which bind to the same sites upstream of activated promoters ( 11 , 12 ) .	3	KEYWORDS SALMONELLA, SPI1, HILD, HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	31182495	4	ver/dev	The hilA gene is transcriptionally activated by three AraC-like regulatory proteins , HilD , .	33	The hilA gene is transcriptionally activated by three AraC-like regulatory proteins , HilD , HilC , and RtsA , each of which can activate expression of the hilD , hilC , rtsA , and hilA genes , creating a complex feed-forward regulatory loop ( Fig. 1 ) ( 8 , 12 , 18 ) .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilD activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilD activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	31182495	53	ver/dev	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD are still required for full stimulation of the polymerase .	227	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD , HilC , and RtsA are still required for full stimulation of the polymerase .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of rtsA .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	activator	31182495	56	ver/dev	FIG 8 HilD activate hilA expression independently of H-NS .	246	FIG 8 HilD , HilC , and RtsA activate hilA expression independently of H-NS .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	31262841	0	ver/dev	Expression of hilA is activated by HilD , .	9	Expression of hilA is activated by HilD , HilC , and RtsA , which act in a complex feed-forward regulatory loop .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	31262841	2	ver/dev	HilD , activate transcription of hilA by binding the promoter .	39	Three AraC-like proteins , HilD , HilC , and RtsA , activate transcription of hilA by binding the promoter ( 15 ) .	3	KEYWORDS PHOPQ, SPI1, SALMONELLA, SRNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	32021316	2	ver/dev	HilD also induce the expression of hilD genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	32021316	2	ver/dev	HilD also induce the expression of hilC genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	32021316	2	ver/dev	HilC also induce the expression of hilD genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	32021316	2	ver/dev	HilC also induce the expression of hilC genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	32041797	4	ver/dev	Thus , HilD acts as a switch to initiate activation of hilA expression .	43	Thus , HilD acts as a switch to integrate environmental cues and initiate activation of hilC , rtsA , and hilA expression .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	activator	32041797	5	ver/dev	The AraC-like proteins HilD activate transcription of hilA , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	32571967	0	ver/dev	Transcription of hilA , is activated by three AraC-like regulators , HilD , .	8	Transcription of hilA , encoding the transcriptional activator of the SPI1 structural genes , is activated by three AraC-like regulators , HilD , HilC , and RtsA , that act in a complex feed-forward loop .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	32571967	2	ver/dev	The hilA gene is directly activated by three AraC-like regulators , HilD , .	36	The hilA gene is directly activated by three AraC-like regulators , HilD , HilC , and RtsA , which act in a feed-forward loop to activate expression of themselves , each other , and hilA ( Fig. 1 ) ( 2 ) .	3	KEYWORDS BAM, RCSCDB, SPI1, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	34202800	8	ver/dev	Moreover , HilD induces hilA expression by forming a feedback loop with the transcriptional activators , HilC and RtsA , belonging to the AraC/XylS family .	277	Moreover , HilD induces hilA expression by forming a feedback loop with the transcriptional activators , HilC and RtsA , belonging to the AraC/XylS family [ 58 ] .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	34424033	4	ver/dev	HilD directly activates hilA transcription	41	NS-mediated repression of the hilA promoter , downstream of hilD , is through its control of HilD , which directly activates hilA transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	activator	34424033	7	ver/dev	The hilA gene is activated by three AraC-like proteins : HilD , HilC and	101	The hilA gene is activated by three AraC-like proteins : HilD , HilC and	3	36 INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	activator	34424033	13	ver/dev	Although H-NS is apparently oligomerizing throughout the hilA promoter region , HilD protein largely activates	156	Although H-NS is apparently oligomerizing throughout the hilA promoter region , HilD protein largely activates	3	36 INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilA	activator	34424033	26	ver/dev	These mutants exhibited a severe growth defect similar to that of HilD over-expression , preventing us from hilD promoter region affects expression of HilD , as evidenced by activation of hilA transcription .	287	These mutants exhibited a severe growth defect similar to that of HilD over-expression ( Fig. 1 ; Mut6 ) , preventing us from hilD promoter region affects expression of HilD , as evidenced by activation of hilA transcription .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
MarA	gene	acrB	regulator	21982147	0	ver/dev	the two-step regulon activates PmrD , which in turn activates the global regulator of efflux pumps , the MarA operon , eventually leads to the activation of acrB	42	Failure of antibiotic therapy is also assured by the two-step regulon that activates PmrD , which in turn activates the global regulator of efflux pumps , the MarA operon , that eventually leads to the activation of acrB , the gene coding for the transporter component of the main efflux pump ( AcrAB ) of the organism [ 5 ] .	2	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	leuO	regulator	17908208	6	ver/dev	also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region	44	Furthermore , expression of LeuO has been found to affect the expression of several genes influenced by mutations in hns : LeuO relieved silencing of the bgl operon , the operon involved in the utilization of certain b-glucosides ( Ueguchi et al. , 1998 ) ; suppressed the effect of an hns mutation on cadC , which codes for the activator of the acid-inducible lysine decarboxylase ( Shi and Bennet , 1995 ) ; and also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene and the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region ( Chen et al. , 2001 ; 2003 ) .	3	B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	leuO	regulator	18156266	41	ver/dev	H-NS are involved in regulation of leuO .	349	LeuO and H-NS are involved in regulation of leuO and ompS1 ( 2 , 5 ) , in addition to bgl , cadC , dsrA , and rovA ( 27 , 45 , 50 , 55 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LrhA	TU	flhDC	regulator	24706743	4	ver/dev	LrhA is also a known regulator of flhDC .	130	LrhA is also a known regulator of flhDC that has been shown to bind within the flhDC promoter region to inhibit flhDC operon transcription ( 25 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LrhA	TU	flhDC	regulator	26441883	17	ver/dev	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-type regulator LrhA .	361	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / EcnR , the Spi-1-encoded regulator RtsB , the LysR-type regulator LrhA ( RovM in Yersinia ) , and SlyA ( RovA in Yersinia ) with the P1 and P5 promoters being the main regulatory targets ( Yanagihara et al. , 1999 ; Wang et al. , 2007 ; Singer et al. , 2013 ; Mouslim and Hughes , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	TU	flhDC	regulator	23443158	14	att	Group III is represented by OmrA/B , which by binding directly to flhDC and csgD mRNA [ 62,75 ] , can down-regulate both motility and the expression of CsgD-controlled curli fibres and cellulose .	169	Group III is represented by OmrA/B , which by binding directly to flhDC and csgD mRNA [ 62,75 ] , can down-regulate both motility and the expression of CsgD-controlled curli fibres and cellulose .	6	3. SRNAS CONTRIBUTE TO INVERSE REGULATION OF FLAGELLA AND BIOFILM COMPONENTS IN DIFFERENT REGULATORY PATTERNS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SirA	gene	flgA	regulator	11244064	13	ver/dev	SirA-dependent regulation of flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar .	286	SirA-dependent regulation of sopB and flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar containing kanamycin and X-Gal at 37 °C .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YdiV	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliT , YdiV .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrF	activator	12438352	20	att	Mutants in pmrE or pmrF , two PmrA-activated loci , lack Ara4N modification to lipid-A and demonstrate reduced virulence when administered orally to mice ( 19 ) .	273	Mutants in pmrE or pmrF , two PmrA-activated loci , lack Ara4N modification to lipid A and demonstrate reduced virulence when administered orally to mice ( 19 ) .	5	DISCUSSION	Mus sp.	0	L3	OTHER	Analysis	NEG	New	Level 1
PmrA	gene	pmrF	activator	12756767	0	ver/dev	Recently , it has been demonstrated that the PhoP-PhoQ mediated transcriptional activation of the pmrF operon occurs via the PhoP-promoted biosynthesis of a 85 amino-acid PmrA activator .	11	Recently , it has been demonstrated that the PhoP-PhoQ mediated transcriptional activation of the pmrF operon occurs via the PhoP-promoted biosynthesis of PmrD , a 85 amino-acid PmrA activator .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrF	activator	15205413	3	att	Consistent with this notion , the PmrA-activated ugd gene and pbg operon ( designated pmrF by Gunn et al. [ 13 ] and arn by Trent et al. [ 43 ] ) are necessary for both the biosynthesis and incorporation of aminoarabinose into lipid-A ( 13 ) and for polymyxin B resistance ( 12 , 13 ) .	19	Consistent with this notion , the PmrA-activated ugd gene and pbg operon ( designated pmrF by Gunn et al. [ 13 ] and arn by Trent et al. [ 43 ] ) are necessary for both the biosynthesis and incorporation of aminoarabinose into lipid A ( 13 ) and for polymyxin B resistance ( 12 , 13 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrF	activator	15681155	15	att	Additionally , previously identified PmrA-activated genes , such as pmrE and pmrF that affect Ara4N biosynthesis , have been shown to play a role in virulence of S. enterica serovar Typhimurium in mice [ 7,14 ] .	246	Additionally , previously identified PmrA-activated genes , such as pmrE and pmrF that affect Ara4N biosynthesis , have been shown to play a role in virulence of S. enterica serovar Typhimurium in mice [ 7,14 ] .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrF	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16777370	5	ver/dev	However , proteome analysis of the genes revealed that Fis was bound directly to those of ssrA .	41	However , DNA microarray and proteome analysis of the genes regulated by Fis revealed that Fis was involved in the regulation of SPI2 genes and bound directly to SPI2 promoters such as those of ssrA and ssaG [ 23,24 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16777370	5	ver/dev	However , DNA microarray of the genes revealed that Fis was bound directly to those of ssrA .	41	However , DNA microarray and proteome analysis of the genes regulated by Fis revealed that Fis was involved in the regulation of SPI2 genes and bound directly to SPI2 promoters such as those of ssrA and ssaG [ 23,24 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16777370	31	ver/dev	We also found a direct binding of Fis to a reduced expression of ssrA in the absence of Fis ( data not shown ) .	134	We also found a direct binding of Fis to the ssrA promoter region and a reduced expression of ssrA in the absence of Fis ( data not shown ) .	9	3. DISCUSSION	unidentified	1	L3	OTHER	Analysis	OTHER	New	Level 2
Fis	gene	ssrA	regulator	16777370	31	ver/dev	We also found a direct binding of Fis to the ssrA promoter region .	134	We also found a direct binding of Fis to the ssrA promoter region and a reduced expression of ssrA in the absence of Fis ( data not shown ) .	9	3. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	ssrA	regulator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in bacteria ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in LB medium ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16999831	6	ver/dev	The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in Bertani medium ; Fis has also been shown to bind to the ssrA promoter .	104	The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity and to be required for upregulation of other SPI-2 genes in bacteria growing in Luria -- Bertani ( LB ) medium ; Fis has also been shown to bind to the ssrA promoter ( Kelly et al. , 2004 ) .	9	FIS AND SSRA PROMOTER ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssrA	regulator	16999831	12	ver/dev	Fis levels influence the ssrA promoter	139	Fis levels influence DNA supercoiling and the ssrA promoter	12	FIS LEVELS INFLUENCE DNA SUPERCOILING AND THE SSRA PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	ssrA	regulator	16999831	18	ver/dev	A role for Fis in the positive regulation of SPI-2 genes is also supported by a dem-onstration -- DNA complexes at the promoter regions of the ssrA .	191	A role for Fis in the positive regulation of SPI-2 genes is also supported by DNA microarray analysis and a dem-onstration that Fis protein binds to and forms discrete protein -- DNA complexes at the promoter regions of the ssrA and the ssaG genes ( Kelly et al. , 2004 ) .	15	GFP FLUORESCENCE INTENSITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RhaS	gene	STM4054	regulator	32894213	0	ver/dev	STM4054 is thought to be coregulated with proteins of the rhamnose utilization pathway by the activator RhaS through promoter analysis by RegPrecise .	168	The SBP of STM3671 -- STM3673 is 88 % identical to the previously characterized E. coli 2,3-diketo-l-gulonate binding protein , YiaO [ 31 -- 33 ] , whilst STM4052 -- STM4054 is thought to be coregulated with proteins of the rhamnose utilization pathway by the activator RhaS ( STM4048 ) through promoter analysis by RegPrecise [ 34 ] .	10	RESULTS AND DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
SdiA	TU	PSLT026	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	stf	regulator	31661351	13	ver/dev	related genes _ regulated by StpA as stf genes	298	pef ORFs seem not to be the only fimbriae related genes regulated by StpA as std , saf , fim , bcf and stf genes are overexpressed in a stpA mutant after Salmonella growth until exponential phase [ 29 ] .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysB	regulator	18957594	11	att	Since swarming motility in both cysB and cysE is restored by the inclusion of cysteine in the swarm medium , a CysB-regulated gene outside of the cysteine biosynthetic genes is not the reason that these strains are incapable of swarming on standard swarm medium .	344	Since swarming motility in both cysB and cysE is restored by the inclusion of cysteine in the swarm medium , a CysB-regulated gene outside of the cysteine biosynthetic genes is not the reason that these strains are incapable of swarming on standard swarm medium .	10	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CysB	gene	cysB	regulator	19447191	13	auto	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	149	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	8	4.5. CYSB AND METR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysB	regulator	19447191	13	ver/dev	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	149	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	8	4.5. CYSB AND METR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysB	regulator	19447191	13	ver/dev	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	149	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	8	4.5. CYSB AND METR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysB	regulator	19447191	13	ver/dev	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	149	CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .	8	4.5. CYSB AND METR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysB	regulator	30538683	0	ver/dev	Previous literature has characterized binding of CysB to cysB ( encodes a LysR regulator ) .	52	Previous literature has characterized binding of CysB to the promoter regions of cysK [ encodes O-acetylserine ( thiol ) - lyase , EC 2.5.1.47 ] , cysJIH ( encode sulfite reductase , EC 1.8.7.1 ) , cysP ( encodes thiosulfatebinding protein ) , and to cysB ( encodes a LysR regulator ) ( Monroe et al. , 1990 ; Hryniewicz and Kredich , 1991 , 1994 ; Ostrowski and Kredich , 1991 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysB	regulator	30538683	14	ver/dev	Negative autoregulation of cysB in Salmonella typhimurium : in-vitro interactions of CysB protein with the cysB promoter .	510	Negative autoregulation of cysB in Salmonella typhimurium : in vitro interactions of CysB protein with the cysB promoter .	26	FUNDING	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	NEG	New	Level 1
HilA	gene	sopB	activator	23419780	7	ver/dev	HilA are transcription activators of effectors downregulates sopB .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	ryhB	activator	17208038	23	att	Another ` Fur-activated ' gene , sodB , is controlled at the level of translation by the small RNA ryhB , with the help of the RNA binding protein Hfq , in Escherichia coli [ 45 -- 48 ] .	131	Another ` Fur-activated ' gene , sodB , is controlled at the level of translation by the small RNA ryhB , with the help of the RNA binding protein Hfq , in Escherichia coli [ 45 -- 48 ] .	9	FUR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	lacZ	regulator	20965974	4	ver/dev	Hence , binding of IHF to the lacZ promoters is unspecific , which is in line with previous data reporting that IHF binds DNA with lower affinity also in sequence-independent manner .	336	Hence , binding of IHF to the lacZ and ptsG promoters is unspecific , which is in line with previous data reporting that IHF binds DNA with lower affinity also in sequence-independent manner ( 30 ) .	15	ACTIVITY OF THE P -DEPENDENT GLMY PROMOTER REQUIRES BINDING OF IHF	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	narU	repressor	31563538	1	ver/dev	Our results demonstrated that the upstream narU promoter , is repressed by the RcsB regulator .	63	Our results demonstrated that the upstream narU promoter , controlling the expression of nar-UZYWV , is repressed by the RcsB regulator when either glucose , trehalose , mannitol or mannose is used as the carbon source .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	tpx	activator	18156266	44	ver/dev	Interestingly , the results indicate that H-NS is a positive regulator of tpx ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	354	Interestingly , the results presented here indicate that H-NS is a positive regulator of tpx and STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	iacP	repressor	30682134	12	ver/dev	Although the level of iacP RNA was below the level of reliable detection , qRT-PCR showed that CsrA represses accumulation of iacP mRNA in LB .	208	Although the level of iacP RNA was below the level of reliable detection , qRT-PCR was able to detect its expression and showed that CsrA represses accumulation of iacP mRNA ( S2 Table , Fig 5B ) in LB .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	proV	activator	27564394	18	ver/dev	The proV promoter were used as positive control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	hilA	activator	25375226	30	ver/dev	In the absence of H-NS it is possible that silencing complexes generated by StpA StpAA77D , although more effective than StpAWT , were unable to impede HilD-mediated activation of hilA .	403	In the absence of H-NS it is possible that silencing complexes generated by StpA and M4T StpAA77D , although more effective than StpAWT , were unable to impede the combined HilC and HilD-mediated activation of hilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Fis	gene	ndk	regulator	15256548	13	ver/dev	The involvement of Fis in negative regulation of ndk was of interest .	651	The involvement of Fis in negative regulation of ndk was of interest given its similar role in the expression of the nupG and rbsC nucleoside transport genes , suggesting that Fis coordinates the expression of genes involved in pyrimidine metabolism .	14	GENES INVOLVED IN METABOLISM AND TRANSPORT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	flhD	activator	27564394	13	ver/dev	HilD activates flhD expression .	363	HilD activates flhD expression [ 114 ] .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PutA	gene	putA	regulator	8483946	0	ver/dev	However , the effect of oxygen seems to be indirect because the regulation by oxygen requires the PutA protein : putA mutants express the put operon at high constitutive levels regardless of the amount of oxygenation .	26	However , the effect of oxygen seems to be indirect because the regulation by oxygen requires the PutA protein : putA mutants express the put operon at high constitutive levels regardless of the amount of oxygenation ( 6 ) .	2	DEPARTMENT OF MICROBIOLOGY, UNIVERSITY OF ILLINOIS, 131 BURILL HALL, 407 SOUTH GOODWIN AVENUE, URBANA, IL 61801 COMMUNICATED BY JOHN R. ROTH, FEBRUARY 1, 1993 (RECEIVED FOR REVIEW JULY 16, 1992)	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PutA	gene	putA	regulator	8483946	1	ver/dev	The phenotypes of putA mutants indicate that the PutA protein mediates the regulation of the put operon by proline .	27	The phenotypes of putA mutants indicate that the PutA protein mediates the regulation of the put operon by proline .	2	DEPARTMENT OF MICROBIOLOGY, UNIVERSITY OF ILLINOIS, 131 BURILL HALL, 407 SOUTH GOODWIN AVENUE, URBANA, IL 61801 COMMUNICATED BY JOHN R. ROTH, FEBRUARY 1, 1993 (RECEIVED FOR REVIEW JULY 16, 1992)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	sipD	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	aslB	activator	22752112	15	ver/dev	the activation of aslB expression present homology with the transcription factors Lrp and AstB	265	In this context , overexpression of Rob in E. coli results in the activation of ybaO and aslB expression , which present homology with the transcription factors Lrp and AstB ( Bennik et al. 2000 ) .	17	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	2	ver/dev	In vitro analyses by DNase I footprinting show that LeuO binds the hilE promoter region .	25	In vitro analyses by slot blotting , electrophoretic mobility shift analysis and DNase I footprinting show that LeuO binds the hilE promoter region .	7	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	hilE	regulator	24354910	2	ver/dev	In vitro analyses by electrophoretic-mobility-shift analysis show that LeuO binds the hilE promoter region .	25	In vitro analyses by slot blotting , electrophoretic mobility shift analysis and DNase I footprinting show that LeuO binds the hilE promoter region .	7	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	hilE	regulator	24354910	2	ver/dev	In vitro analyses by slot blotting show that LeuO binds the hilE promoter region .	25	In vitro analyses by slot blotting , electrophoretic mobility shift analysis and DNase I footprinting show that LeuO binds the hilE promoter region .	7	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	hilE	regulator	24354910	28	ver/dev	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in Fig. 4 .	115	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P1 , P2 and P3 hilE promoters in an independent manner ( Fig. 4C ) .	10	LEUO ACTIVATES HILE TRANSCRIPTION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	28	ver/dev	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in an independent manne .	115	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P1 , P2 and P3 hilE promoters in an independent manner ( Fig. 4C ) .	10	LEUO ACTIVATES HILE TRANSCRIPTION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	28	ver/dev	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in Fig. 4 .	115	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P1 , P2 and P3 hilE promoters in an independent manner ( Fig. 4C ) .	10	LEUO ACTIVATES HILE TRANSCRIPTION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	28	ver/dev	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in an independent manne .	115	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P1 , P2 and P3 hilE promoters in an independent manner ( Fig. 4C ) .	10	LEUO ACTIVATES HILE TRANSCRIPTION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	28	ver/dev	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in Fig. 4 .	115	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P1 , P2 and P3 hilE promoters in an independent manner ( Fig. 4C ) .	10	LEUO ACTIVATES HILE TRANSCRIPTION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	28	ver/dev	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in an independent manne .	115	Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P1 , P2 and P3 hilE promoters in an independent manner ( Fig. 4C ) .	10	LEUO ACTIVATES HILE TRANSCRIPTION	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	regulator	24354910	29	ver/dev	Binding of LeuO to the hilE promoter region To test whether LeuO is able to bind the hilE promoter region , a slot blot binding assay was performed .	117	Binding of LeuO to the hilE promoter region To test whether LeuO is able to bind the hilE promoter region , a slot blot binding assay was performed .	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	hilE	regulator	24354910	29	ver/dev	Binding of LeuO to the hilE promoter region To test whether LeuO is able to bind the hilE promoter region , a slot blot binding assay was performed .	117	Binding of LeuO to the hilE promoter region To test whether LeuO is able to bind the hilE promoter region , a slot blot binding assay was performed .	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	hilE	regulator	24354910	31	ver/dev	Quantitative analysis of Fig. 6B indicated that , under the conditions of the assay , LeuO bound the hilE DNA fragment with an approximate Kd of 0.37 μM .	120	Quantitative analysis of binding ( Fig. 6B ) indicated that , under the conditions of the assay , LeuO bound the hilE DNA fragment with an approximate Kd of 0.37 μM .	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	hilE	regulator	24354910	31	ver/dev	Quantitative analysis of binding indicated that , under the conditions of the assay , LeuO bound the hilE DNA fragment with an approximate Kd of 0.37 μM .	120	Quantitative analysis of binding ( Fig. 6B ) indicated that , under the conditions of the assay , LeuO bound the hilE DNA fragment with an approximate Kd of 0.37 μM .	10	LEUO ACTIVATES HILE TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	STM2585	regulator	27564394	11	ver/dev	Furthermore , STM2585 are regulated by SlyA .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	lacZ	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	STM2138	regulator	24021902	5	ver/dev	an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein _ regulated by SlyA c srcA STM2138 SPI-2 effector chaperone	127	pipB2 STM2780 Type III secretion system effector protein , regulated by SlyA siiA STM4257 SPI-4 genes that encode an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein , regulated by SlyA c srcA STM2138 SPI-2 effector chaperone required for systemic infection in c mice sseK2 STM2137 Type III secretion system effector protein c sseL STM2287 Type III secretion system effector protein , functions as a c deubiquitinase in vivo , regulated by SlyA steB STM1629 Type III secretion system effector protein c steC STM1698 Type III secretion system effector protein c STM2239 SPI-12-encoded genes regulated by SsrB , enhance fitness in c vivo , STM2239 encodes a transcriptional regulator STM2340 STM3117 SPI-13-encoded genes with suggested function in c biosynthesis of the cell wall peptidoglycan layer STM3118 c STM3119	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	dps	activator	21563813	1	att	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	dps	activator	22275872	0	att	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	125	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	9	ADAPTATION OF S. ENTERICA TO LETHAL CONCENTRATIONS OF SODIUM DEOXYCHOLATE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dps	activator	22275872	2	att	Activation of the RpoS-dependent general stress response in the presence of sublethal concentrations of DOC was further analyzed by monitoring expression of RpoS-dependent genes other than dps and osmY .	150	Activation of the RpoS-dependent general stress response in the presence of sublethal concentrations of DOC was further analyzed by monitoring expression of RpoS-dependent genes other than dps and osmY .	10	VALIDATION OF MICROARRAY ANALYSIS USING LAC FUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dps	activator	22275872	7	att	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	326	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	10	VALIDATION OF MICROARRAY ANALYSIS USING LAC FUSIONS	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	dps	activator	25028458	1	ver/dev	Almiron et al. reported that expression of the dps gene is induced by the cessation of bacterial growth under S control of RpoS .	33	Almiron et al. ( 1992 ) reported that expression of the dps gene is induced by the cessation of bacterial growth under S control of RpoS , the s factor .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	dps	activator	25028458	45	ver/dev	Then , in the transition to stationary-phase growth , RpoS , contribute to increase dps transcription to up to 200 000 molecules per cell .	362	Then , in the transition to stationary phase growth , other regulators , such as Fur and RpoS , contribute to increase dps transcription to up to 200 000 molecules per cell ( Almiron et al. , 1992 ; Yoo et al. , 2007 ) .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	15126450	0	ver/dev	LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin	3	OmpR and LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	15126450	4	ver/dev	Thus , the LeuO regulators positively regulate ompS2 .	15	Thus , the OmpR and LeuO regulators positively regulate ompS2 .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	15126450	19	ver/dev	The experiments described above indicated that both the LeuO were involved in the positive regulation of ompS2 expression .	242	The experiments described above indicated that both the LeuO and the OmpR regulators were involved in the positive regulation of ompS2 expression .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS2	regulator	15126450	21	ver/dev	LeuO participates in the regulation of ompS2 .	249	LeuO participates in the regulation of ompS2 .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	15126450	27	ver/dev	LeuO bound to the 5 upstream regulatory region of ompS2 in two .	291	LeuO bound to the 5 upstream regulatory region of ompS2 in two defined boxes , LeuO ( I ) and LeuO ( II ) , at 0.03 M and higher ( Fig. 2 and 8 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	16428792	1	ver/dev	ompS2 is positively regulated by the LeuO regulator	13	In addition , ompS1 is negatively regulated by the HN-S nucleoid protein , and ompS2 is positively regulated by the LeuO regulator ( 10 , 11 , 26 , 27 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	16428792	3	ver/dev	The LD50 of the mutant with a deletion of the gene for LeuO , the positive regulator of ompS2 , is also shown .	100	The LD50 of the mutant with a deletion of the gene for LeuO , the positive regulator of ompS2 , is also shown .	5	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	16428792	6	ver/dev	In agreement with the role of LeuO as a positive regulator of ompS2 expression , it also appears to play a role in the initial stages of infection .	120	In agreement with the role of LeuO as a positive regulator of ompS2 expression , it also appears to play a role in the initial stages of infection ( Table 3 ) .	5	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
LeuO	gene	ompS2	regulator	17908208	15	ver/dev	LeuO as a positive regulator of ompS2 in S. Typhi .	58	LeuO as a positive regulator of ompS1 and ompS2 in S. Typhi .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	17908208	19	ver/dev	IMSSTN103 where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2	68	Expression of pRO310 and pFM413 is also shown in the original S. Typhi Tn-10 insertion mutant ( IMSSTN103 ) , where the transposon insertion promoted leuO expression and allowed us to identify LeuO as a positive regulator of ompS2 ( Fernández-Mora et al. , 2004 ) .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	17908208	19	ver/dev	the original S. Typhi Tn-10 insertion mutant where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2	68	Expression of pRO310 and pFM413 is also shown in the original S. Typhi Tn-10 insertion mutant ( IMSSTN103 ) , where the transposon insertion promoted leuO expression and allowed us to identify LeuO as a positive regulator of ompS2 ( Fernández-Mora et al. , 2004 ) .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	17908208	19	ver/dev	IMSSTN103 where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2	68	Expression of pRO310 and pFM413 is also shown in the original S. Typhi Tn-10 insertion mutant ( IMSSTN103 ) , where the transposon insertion promoted leuO expression and allowed us to identify LeuO as a positive regulator of ompS2 ( Fernández-Mora et al. , 2004 ) .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	ompS2	regulator	17908208	19	ver/dev	the original S. Typhi Tn-10 insertion mutant where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2	68	Expression of pRO310 and pFM413 is also shown in the original S. Typhi Tn-10 insertion mutant ( IMSSTN103 ) , where the transposon insertion promoted leuO expression and allowed us to identify LeuO as a positive regulator of ompS2 ( Fernández-Mora et al. , 2004 ) .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	17908208	79	ver/dev	The observation that both ompS2 were regulated by LeuO at different levels of induction opens the possibility that there is a regulon in S. enterica .	314	The observation that both ompS1 and ompS2 were regulated by LeuO at different levels of induction opens the possibility that there is a regulon in S. enterica , where various genes are expressed at different levels according to the concentration of LeuO in the bacterial cell .	13	DISCUSSION	Salmonella;Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS2	regulator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	18156266	21	ver/dev	A previous report showed that LeuO bound to the promoter region of ompS2 at 93 to 109 to the transcription start site .	272	A previous report showed that LeuO bound to the promoter region of ompS2 at 93 to 109 and 139 to 152 bp with respect to the transcription start site ( 12 ) .	5	FIG. 2	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	19447191	3	ver/dev	ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action	94	Curiously , ompS1 is negatively regulated by the HN-S nucleoid protein , and ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action .	6	4.2. LEUO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	19447191	3	ver/dev	ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action	94	Curiously , ompS1 is negatively regulated by the HN-S nucleoid protein , and ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action .	6	4.2. LEUO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	regulator	33854491	1	ver/dev	Even more , the expression of a transcriptional-fusion of the 5 ' intergenic region of ompS2 , upon induction of the LeuO regulator at various points in the growth curve , was essentially abolished in the ∆ CRISPR-cas as compared with the wild-type strain .	171	Even more , the expression of a transcriptional fusion of the 5 ' intergenic region of ompS2 ( pKK9/ompS2 -482 + 77 , Supplementary Table S1 ) , upon induction of the LeuO regulator at various points in the growth curve , was essentially abolished in the ∆ CRISPR-cas as compared with the wild-type strain ( Figure 3B ) .	18	CRISPR-CAS IS FUNDAMENTAL FOR THE SYNTHESIS OF MAJOR AND QUIESCENT OUTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	11036033	1	ver/dev	Like marRAB , acrAB are positively regulated by MarA .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	15073288	8	ver/dev	acrAB activation by bile is independent of MarA , RpoS	260	acrAB activation by bile is independent of MarA , Rob , PhoP -- PhoQ and RpoS	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	15073288	8	ver/dev	acrAB activation by bile is independent of MarA , PhoQ	260	acrAB activation by bile is independent of MarA , Rob , PhoP -- PhoQ and RpoS	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	15073288	8	ver/dev	acrAB activation by bile is independent of MarA , PhoP	260	acrAB activation by bile is independent of MarA , Rob , PhoP -- PhoQ and RpoS	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	15073288	8	ver/dev	acrAB activation by bile is independent of MarA , Rob	260	acrAB activation by bile is independent of MarA , Rob , PhoP -- PhoQ and RpoS	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	16842216	0	ver/dev	The global regulatory proteins MarA are primarily responsible for activation of acrAB transcription .	343	The global regulatory proteins MarA , SoxS and Rob are primarily responsible for activation of acrAB and tolC transcription .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	18577510	2	ver/dev	Other regulators of MarA did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
MarA	TU	acrAB	activator	18577510	10	ver/dev	Prouty et al. further reported that acrAB activation by bile is independent of MarA .	153	Prouty et al. ( 47 ) further reported that acrAB activation by bile is independent of MarA , Rob , PhoP/PhoQ , and RpoS .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	acrAB	activator	18984645	1	ver/dev	8 -- 13 _ shown that MarA , play a role in antimicrobial resistance by activating acrAB	21	Studies in Escherichia coli have 8 -- 13 shown that transcriptional activators , such as MarA , SoxS and Rob , play a role in antimicrobial resistance by activating transcription of efflux pumps , including acrAB and tolC .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	acrAB	activator	20237076	5	ver/dev	However , acrAB are also induced by stress signals in additional ways , it was suggested that S. enterica to salicylate activates MarA through binding to its repressor , MarR .	35	However , micF and acrAB are also induced by stress signals in additional ways that are not dependent on the marRAB system .17 Interestingly , antibiotics that serve as substrates of the AcrAB efflux pump are very weak inducers of the marRAB operon in E. coli and do not induce these genes in Salmonella .6,8 Based on that , it was suggested that exposure of E. coli or S. enterica to salicylate activates MarA through binding to its repressor , MarR .	5	INTRODUCTION	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	5	ver/dev	However , acrAB are also induced by stress signals in additional ways , it was suggested that exposure of E. coli activates MarA through binding to its repressor , MarR .	35	However , micF and acrAB are also induced by stress signals in additional ways that are not dependent on the marRAB system .17 Interestingly , antibiotics that serve as substrates of the AcrAB efflux pump are very weak inducers of the marRAB operon in E. coli and do not induce these genes in Salmonella .6,8 Based on that , it was suggested that exposure of E. coli or S. enterica to salicylate activates MarA through binding to its repressor , MarR .	5	INTRODUCTION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of acrAB by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of acrAB by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of acrAB by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of acrAB by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of acrAB by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of micF by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of micF by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of marA by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	20237076	7	ver/dev	These results , together with the results of the induction of marA by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	acrAB	activator	23453941	0	ver/dev	The MarA proteins can activate acrAB expression .	39	The MarA and SoxS proteins can activate acrAB expression .	1	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
MarA	TU	acrAB	activator	23493314	0	ver/dev	MarA is induced following acrAB	23	MarA is induced following salicylate treatment ,5 SoxS in response to superoxide and Rob following treatment with bile salts and dipyridyl .6 -- 8 Up-regulation of these transcription factors has been shown to increase the expression of several genes , including acrAB and tolC .5,9,10	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	activator	29018419	4	ver/dev	The MarA protein positively regulates transcription of acrAB	378	The MarA protein positively regulates transcription of acrAB , and it was therefore unexpected that the latter genes were not up-regulated after exposure to TC .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	acrAB	activator	31501286	30	att	This increase in FliC levels might be due to MarA-dependent activation of acrAB , which is capable of removing tetracycline ( 76 ) , or other downstream targets affecting flagellar expression in motility agar , where oxygen partial pressures are lower than in aerated liquid medium .	218	This increase in FliC levels might be due to MarA-dependent activation of acrAB , which is capable of removing tetracycline ( 76 ) , or other downstream targets affecting flagellar expression in motility agar , where oxygen partial pressures are lower than in aerated liquid medium .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
MarA	TU	acrAB	activator	31501286	30	ver/dev	This increase in FliC levels might be due to MarA-dependent activation of acrAB .	218	This increase in FliC levels might be due to MarA-dependent activation of acrAB , which is capable of removing tetracycline ( 76 ) , or other downstream targets affecting flagellar expression in motility agar , where oxygen partial pressures are lower than in aerated liquid medium .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	srfJ	regulator	29270156	3	ver/dev	Interestingly , a transcriptional lux fusion with 2357 bp upstream of srfJ is regulated by PhoP , recapitulating the regulation patterns .	285	Interestingly , a transcriptional lux fusion with 2357 bp upstream of srfJ containing both promoters and the intervening genes ( PiolE -- PsrfJ ) is regulated by IolR , PhoP , SsrB , and Rcs , recapitulating the regulation patterns observed with the isolated promoters ( Figures 2B , D ) .	25	DIFFERENTIAL REGULATION OF PIOLE AND PSRFJ	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	hlyE	regulator	30201777	18	att	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	194	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Escherichia coli	0.5	L3	OTHER	Other	NEG	Other	Level 1
DksA	gene	sitA	activator	27065993	1	att	To validate • NO - and DksA-dependent regulatory control in aspects of iron homeostasis , we used quantitative real-time PCR ( qPCR ) to measure the mRNA levels of feoB , sitA , and sufA in wild-type and 1dksA Salmonella treated ± dNO ( Figure 3 ) .	173	To validate • NO - and DksA-dependent regulatory control in aspects of iron homeostasis , we used quantitative real-time PCR ( qPCR ) to measure the mRNA levels of feoB , sitA , and sufA in wild-type and 1dksA Salmonella treated ± dNO ( Figure 3 ) .	12	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	galS	repressor	24450479	31	ver/dev	However , mutations in galS did not affect repression by NagC .	127	However , mutations in neither galR nor galS had any effect on chiP -- lacZ expression ( Fig. 4 ) and did not affect repression by NagC .	6	BINDING OF GALR AND GALS PROTEINS IN THE REGION UPSTREAM FROM THE E. COLI CHIP PROMOTER	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsgD	TU	csgBA	regulator	17650335	1	ver/dev	csgBA is positively regulated by the global regulator CsgD	47	The curli subunits CsgA and CsgB are encoded by csgBA , which is positively regulated by the global regulator CsgD [ 20 ] .	5	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgBA	regulator	20545866	4	ver/dev	First , we show that unphosphorylated CsgD binds to the promoter regions of its target genes csgBA and adrA and stimulates their transcription in-vitro .	49	First , we show that unphosphorylated CsgD binds to the promoter regions of its target genes csgBA and adrA and stimulates their transcription in vitro .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	TU	csgBA	regulator	20545866	5	ver/dev	CsgD binds directly to the csgBA	55	CsgD binds directly to the csgBA and adrA promoter regions	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	TU	csgBA	regulator	20545866	6	ver/dev	In S. Typhimurium the expression of csgBA is positively regulated by the transcriptional regulator CsgD .	56	In S. Typhimurium the expression of csgBA and adrA is positively regulated by the transcriptional regulator CsgD ( Hammar et al. , 1995 ; Romling et al. , 2000 ; Gerstel and Romling , 2003 ) .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgBA	regulator	20545866	7	ver/dev	In order to demonstrate the direct binding of CsgD to the csgBA promoter regions we performed EMSA with purified CsgD-His6 tagged protein ( Fig .	58	In order to demonstrate the direct binding of CsgD to the csgBA and adrA promoter regions we performed electrophoretic mobility shift assays ( EMSA ) with purified CsgD-His6 tagged protein ( Fig .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	TU	csgBA	regulator	20545866	7	ver/dev	In order to demonstrate the direct binding of CsgD to the csgBA promoter regions we performed electrophoretic-mobility-shift assays with purified CsgD-His6 tagged protein ( Fig .	58	In order to demonstrate the direct binding of CsgD to the csgBA and adrA promoter regions we performed electrophoretic mobility shift assays ( EMSA ) with purified CsgD-His6 tagged protein ( Fig .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	TU	csgBA	regulator	20545866	8	ver/dev	Since CsgD is highly integrated into the c-di-GMP signalling network , we investigated whether c-di-GMP affects the binding of CsgD-His6 to the csgBA .	63	Since CsgD is highly integrated into the c-di-GMP signalling network , we investigated whether c-di-GMP affects the binding of CsgD-His6 to the csgBA and adrA promoter region .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CsgD	TU	csgBA	regulator	20545866	24	ver/dev	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the csgBA promoter fragments , compared with Fig. 5A .	154	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA and the csgBA promoter fragments , compared with CsgD alone ( Fig. 5A ) .	8	EFFECTS OF ACP ON CSGD ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	TU	csgBA	regulator	20545866	24	ver/dev	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the csgBA promoter fragments , compared with CsgD alone .	154	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA and the csgBA promoter fragments , compared with CsgD alone ( Fig. 5A ) .	8	EFFECTS OF ACP ON CSGD ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	TU	csgBA	regulator	20545866	25	ver/dev	Since the binding of CsgD to the csgBA is altered in the presence of the phosphodonor AcP , we investigated whether CsgD can be phosphorylated in-vitro .	181	Since the binding of CsgD to the csgBA and the adrA promoter regions is altered in the presence of the phosphodonor AcP , we investigated whether CsgD can be phosphorylated in vitro .	8	EFFECTS OF ACP ON CSGD ACTIVITY	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CsgD	TU	csgBA	regulator	20545866	49	ver/dev	However , we discovered that c-di-GMP , is not required for binding of CsgD to the csgBA promoters .	294	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	9	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	TU	csgBA	regulator	20545866	49	ver/dev	However , we discovered that an integral part of the regulatory network , is not required for binding of CsgD to the csgBA promoters .	294	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	9	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	TU	csgBA	regulator	22336758	1	ver/dev	The rdar -LRB- red , dry and rough -RRB- morphotype formed by Salmonella enterica serovar typhimurium -LRB- from here on S. Typhimurium -RRB- and Escherichia coli species constitutes a multicellular biofilm behavior characterized by the expression of extracellular matrix components , proteinaceous curli fimbriae and the exopolysaccharide cellulose .1 A major contributor to rdar development is the response regulator CsgD which acts as a transcriptional activator of csgBA encoding curli fimbrial subunits and adrA encoding a di-guanylate cyclase stimulating cellulose biosynthesis .2,3 The second messenger c-di-GMP produced by AdrA and other di-guanylate cyclases is a key molecule in the switch between sessility and motility4 and facilitates csgD expression at the transcriptional and post-transcriptional level .5 Transcriptional control of csgD is complex and integrates various outside stimuli such as temperature , osmolarity and nutritional status through a variety of regulatory factors , e.g. , two-component systems and nucleoid binding proteins .6,7 The alternative sigma factor RpoS -LRB- δS -RRB- activates csgD expression in stationary-phase , a process which is aided by the auxiliary protein Crl .8 Therefore RpoS constitutes a crucial factor for multicellular behavior and rdar morphotype development in S. Typhimurium and E. coli .	31	The rdar ( red , dry and rough ) morphotype formed by Salmonella enterica serovar typhimurium ( from here on S. Typhimurium ) and Escherichia coli species constitutes a multicellular biofilm behavior characterized by the expression of extracellular matrix components , proteinaceous curli fimbriae and the exopolysaccharide cellulose .1 A major contributor to rdar development is the response regulator CsgD which acts as a transcriptional activator of csgBA encoding curli fimbrial subunits and adrA encoding a di-guanylate cyclase stimulating cellulose biosynthesis .2,3 The second messenger c-di-GMP produced by AdrA and other di-guanylate cyclases is a key molecule in the switch between sessility and motility4 and facilitates csgD expression at the transcriptional and post-transcriptional level .5 Transcriptional control of csgD is complex and integrates various outside stimuli such as temperature , osmolarity and nutritional status through a variety of regulatory factors , e.g. , two-component systems and nucleoid binding proteins .6,7 The alternative sigma factor RpoS ( δS ) activates csgD expression in stationary phase , a process which is aided by the auxiliary protein Crl .8 Therefore RpoS constitutes a crucial factor for multicellular behavior and rdar morphotype development in S. Typhimurium and E. coli .	1	INTRODUCTION	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	csgBA	regulator	28889298	0	ver/dev	Expression of csgBA , is directly controlled by the transcriptional regulator CsgD .	47	Expression of csgBA , encoding the subunits of curli , is directly controlled by the transcriptional regulator CsgD [ 23 , 24 ] and csgD expression is in turn influenced by c-di-GMP [ 13 ] .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgBA	regulator	29797083	0	ver/dev	CsgD directly binds to the csgBA upstream promoter region and positively regulates the expression of cellulose biosynthesis by activating expression of adrA , encoding a diguanylate cyclase .	59	CsgD directly binds to the csgBA upstream promoter region activating transcription and positively regulates the expression of cellulose biosynthesis by activating expression of adrA , encoding a diguanylate cyclase .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	phoQ	regulator	29118452	1	ver/dev	Interestingly , a strain of Salmonella was even more susceptible to the RNS-dependent cytotoxicity than the phoQ mutant , suggesting that in the absence of PhoPQ the alternative sigma factor RpoS assumes a critical role in the regulation of the antinitrosative defenses of Salmonella .	58	Interestingly , a strain of Salmonella lacking both phoQ and rpoS was even more susceptible to the RNS-dependent cytotoxicity than the phoQ mutant , suggesting that in the absence of PhoPQ the alternative sigma factor RpoS assumes a critical role in the regulation of the antinitrosative defenses of Salmonella .	2	MAIN	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hha	regulator	17675384	12	ver/dev	To evaluate the role of the activators HilD and HilC in the regulation of rtsA transcription , the single-copy rtsA-lac transcriptional-fusion was tested in the hilD hilC background in the presence and absence of hha mutations .	231	To evaluate the role of the activators HilD and HilC in the regulation of rtsA transcription , the single-copy rtsA-lac transcriptional fusion was tested in the hilD hilC background in the presence and absence of hha and hns mutations ( Fig. 8 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	10	att	Given that the absence of barA decreases RcsB-dependent gene transcription in the presence of functional RcsC and RcsD proteins , BarA is a physiological activator of RcsB .	122	Given that the absence of barA decreases RcsB-dependent gene transcription in the presence of functional RcsC and RcsD proteins , BarA is a physiological activator of RcsB .	11	MATERIAL AND METHODS.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	33	att	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	10	ver/dev	Given that the absence of barA decreases RcsB-dependent gene transcription in the presence of RcsD proteins , BarA is a physiological activator of RcsB .	122	Given that the absence of barA decreases RcsB-dependent gene transcription in the presence of functional RcsC and RcsD proteins , BarA is a physiological activator of RcsB .	11	MATERIAL AND METHODS.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	10	ver/dev	Given that the absence of barA decreases RcsB-dependent gene transcription in the presence of functional RcsC , BarA is a physiological activator of RcsB .	122	Given that the absence of barA decreases RcsB-dependent gene transcription in the presence of functional RcsC and RcsD proteins , BarA is a physiological activator of RcsB .	11	MATERIAL AND METHODS.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	33	ver/dev	This is because a csrB csrC mutant strain behaved the same way as barA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5B ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	33	ver/dev	This is because a csrB csrC mutant strain behaved the same way as barA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	barA	activator	32392214	40	ver/dev	Transposon Tn10dTc-generated mutagenesis identifies barA as an activator of RcsB .	561	Transposon Tn10dTc-generated mutagenesis identifies barA as an activator of RcsB .	37	SUPPORTING INFORMATION	Transposon Tn10	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	csgD	regulator	16313619	0	ver/dev	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	40	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	regulator	22336758	33	att	In addition , the possibility that ArcZ is required for RpoS-regulated expression of csgD irrespectively of RpoS levels can not be excluded .	353	In addition , the possibility that ArcZ is required for RpoS-regulated expression of csgD irrespectively of RpoS levels can not be excluded .	3	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	csgD	regulator	22336758	1	ver/dev	The rdar -LRB- red , dry and rough -RRB- morphotype formed by Salmonella enterica serovar typhimurium -LRB- from here on S. Typhimurium -RRB- and Escherichia coli species constitutes a multicellular biofilm behavior characterized by the expression of extracellular matrix components , proteinaceous curli fimbriae and the exopolysaccharide cellulose .1 A major contributor to rdar development is the response regulator CsgD which acts as a transcriptional activator of csgBA encoding curli fimbrial subunits and adrA encoding a di-guanylate cyclase stimulating cellulose biosynthesis .2,3 The second messenger c-di-GMP produced by AdrA and other di-guanylate cyclases is a key molecule in the switch between sessility and motility4 and facilitates csgD expression at the transcriptional and post-transcriptional level .5 Transcriptional control of csgD is complex and integrates various outside stimuli such as temperature , osmolarity and nutritional status through a variety of regulatory factors , e.g. , two-component systems and nucleoid binding proteins .6,7 The alternative sigma factor RpoS -LRB- δS -RRB- activates csgD expression in stationary-phase , a process which is aided by the auxiliary protein Crl .8 Therefore RpoS constitutes a crucial factor for multicellular behavior and rdar morphotype development in S. Typhimurium and E. coli .	31	The rdar ( red , dry and rough ) morphotype formed by Salmonella enterica serovar typhimurium ( from here on S. Typhimurium ) and Escherichia coli species constitutes a multicellular biofilm behavior characterized by the expression of extracellular matrix components , proteinaceous curli fimbriae and the exopolysaccharide cellulose .1 A major contributor to rdar development is the response regulator CsgD which acts as a transcriptional activator of csgBA encoding curli fimbrial subunits and adrA encoding a di-guanylate cyclase stimulating cellulose biosynthesis .2,3 The second messenger c-di-GMP produced by AdrA and other di-guanylate cyclases is a key molecule in the switch between sessility and motility4 and facilitates csgD expression at the transcriptional and post-transcriptional level .5 Transcriptional control of csgD is complex and integrates various outside stimuli such as temperature , osmolarity and nutritional status through a variety of regulatory factors , e.g. , two-component systems and nucleoid binding proteins .6,7 The alternative sigma factor RpoS ( δS ) activates csgD expression in stationary phase , a process which is aided by the auxiliary protein Crl .8 Therefore RpoS constitutes a crucial factor for multicellular behavior and rdar morphotype development in S. Typhimurium and E. coli .	1	INTRODUCTION	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	csgD	regulator	25437188	29	ver/dev	In addition , the RpoS-dependent sRNA SdsR controls csgD expression most likely via a transcriptional regulator .	327	In addition , the RpoS-dependent sRNA SdsR identified as a positive regulator of rdar phenotype development controls csgD expression most likely via a transcriptional regulator ( Figure 2 ) [ 104 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L2	SPEC	Other	OTHER	New	Level 1
RpoS	gene	csgD	regulator	28148244	0	ver/dev	RpoS regulate the transcription of csgD in S. typhimurium .	33	Global transcriptional regulators such as RpoS , OmpR , H-NS and IHF regulate the transcription of csgD in S. typhimurium [ 25 ] .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgD	regulator	29018430	1	ver/dev	RpoS can bind to the csgD promoter .	251	RpoS can bind to the csgD promoter and has an important impact on the transcription of csgD , which is required for the formation of biofilms and production of cellulose by regulating the aggregation and motility of cells ( Gerstel et al. , 2003 ; Jonas et al. , 2007 ) .	15	DEGS IDENTIFIED BY COMPARING BIOFILM-ASSOCIATED CELLS WITH PLANKTONIC	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RpoS	gene	csgD	regulator	32604994	0	ver/dev	Temperature-mediated regulation of csgD on agar was altered by intracellular levels of RpoS .	14	Temperature-mediated regulation of csgD on agar was altered by intracellular levels of RpoS and cyclic-di-GMP .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	regulator	33251260	15	ver/dev	The EMSA assays showed that RpoS could bind the csgD promoter DNA	354	The EMSA assays showed that RpoS could bind the csgD promoter DNA and S11923-3 RpoS had stronger ability to bind promoter DNA than S6702 RpoS ( Figure 4B ) .	18	DISCUSSION	nan	1	L1	OTHER	Other	OTHER	New	Level 1
CsrA	gene	rpoE	activator	21388802	2	ver/dev	CsrA activates rpoE expression .	151	CsrA activates spvR and rpoE expression and represses himD .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CadC	gene	cadA	activator	18487329	4	ver/dev	Figure 4A shows that CadC degradation is coupled to induction of cadA transcription .	152	Figure 4A shows that CadC degradation occurs strictly in response to acid stress and is coupled to induction of cadA transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CadC	gene	cadA	activator	18487329	6	ver/dev	These results indicate that the immediate induction of cadA mRNA following stress is correlated with rapid cleavage of CadC .	154	These results indicate that the immediate induction of cadA mRNA following stress is correlated with rapid cleavage of CadC .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	cadA	activator	18487329	9	ver/dev	CadC degradation is coupled to transcriptional induction of cadA .	190	CadC degradation is coupled to transcriptional induction of cadA .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CadC	gene	cadA	activator	18487329	11	ver/dev	Therefore , we reasoned that acid stress-induced proteolysis of CadC might be a posttranslational control mechanism for activating membrane-bound CadC because the induction of cadA transcription is accompanied by proteolysis of CadC .	210	Therefore , we reasoned that acid stress-induced proteolysis of CadC might be a posttranslational control mechanism for activating membrane-bound CadC because the induction of cadA transcription is accompanied by proteolysis of CadC ( Fig. 4 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	phoH	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the phoH genes , independently of InvF .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the phoH genes , independently of HilA .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	activator	27886269	7	ver/dev	HilD induces the expression of phoH , in the absence of other Salmonella-specific regulators .	82	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not that of SL1896 , in the absence of other Salmonella-specific regulators .	3	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	phoH	activator	27886269	21	ver/dev	Thus , HilD positively regulates the expression of the phoH genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	phoH	activator	27886269	22	ver/dev	HilD positively regulates phoH in S. Typhimurium .	132	HilD positively regulates gtgE , phoH , sinR , lpxR , SL1896 and SL4247 in S. Typhimurium .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	activator	27886269	23	ver/dev	HilD induces the expression of phoH , in E. coli MC4100 .	151	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not SL1896 , in E. coli MC4100 .	4	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rflM	regulator	30373755	8	att	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	sroC	activator	26293911	3	ver/dev	The sroC expression was quantified by qRT-PCR , revealing an induction of ∼ 6 times in WT cells at t late-log pha , indicating a positive effect of RpoS on SroC expression .	89	The sroC expression was quantified by qRT-PCR , revealing an induction of ∼ 6 times in WT cells at late-log phase that already was not retained in the rpoS mutant strain ( rpoS ) ( Fig. 1B ) , indicating a positive effect of RpoS on SroC expression .	13	EXPRESSION OF THE SRNA SROC IS INDUCED AT LATE-EXPONENTIAL AND STATIONARY PHASE OF GROWTH IN AN RPOS-DEPENDENT MANNER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcdA	gene	csgD	activator	25437188	18	ver/dev	As H-NS binding regions largely overlap , RcdA might activate the csgD promoter via an antisilencing mechanism by displacing the silencer H-NS .	208	As RcdA and H-NS binding regions largely overlap , RcdA might activate the csgD promoter via an antisilencing mechanism by displacing the silencer H-NS .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcdA	gene	csgD	activator	25437188	18	ver/dev	As RcdA binding regions largely overlap , RcdA might activate the csgD promoter via an antisilencing mechanism by displacing the silencer H-NS .	208	As RcdA and H-NS binding regions largely overlap , RcdA might activate the csgD promoter via an antisilencing mechanism by displacing the silencer H-NS .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PmrA	gene	ugd	activator	12519186	19	att	The wild-type strain produced an S1 product ( Fig. 4A ) that originates from the PmrA-dependent promoter because it is also produced when ugd transcription is induced in low Mg2 + ( Wosten and	59	The wild-type strain produced an S1 product ( Fig. 4A ) that originates from the PmrA-dependent promoter because it is also produced when ugd transcription is induced in low Mg2 + ( Wosten and	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	12519186	0	ver/dev	The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by via the PmrA -- PmrB by low Mg2 + in a process .	7	The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by Fe3 + via the PmrA -- PmrB two-component system and by low Mg2 + in a process that requires the PhoP -- PhoQ two-component system , the PhoP-activated PmrD protein and the PmrA -- PmrB system .	2	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	12519186	0	ver/dev	The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by via the PmrA -- PmrB two-component system + in a process .	7	The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by Fe3 + via the PmrA -- PmrB two-component system and by low Mg2 + in a process that requires the PhoP -- PhoQ two-component system , the PhoP-activated PmrD protein and the PmrA -- PmrB system .	2	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes promoted by various signals -- PmrA .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ugd	activator	12519186	37	ver/dev	Role of the PmrA binding sites for activation of ugd transcription promoted by different signals .	110	Role of the PhoP , PmrA and RcsB binding sites for activation of ugd transcription promoted by different signals .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ugd	activator	12519186	52	ver/dev	This indicates that the PhoP-mediated activation of ugd requires the PmrA -- the RcsC -- YojN -- RcsB systems .	144	This indicates that the PhoP-mediated activation of ugd requires the PmrA -- PmrB or the RcsC -- YojN -- RcsB systems .	7	THE HOST SIGNALS CONTROLLING UGD EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ugd	activator	12519186	52	ver/dev	This indicates that the PhoP-mediated activation of ugd requires the PmrA -- PmrB -- YojN -- RcsB systems .	144	This indicates that the PhoP-mediated activation of ugd requires the PmrA -- PmrB or the RcsC -- YojN -- RcsB systems .	7	THE HOST SIGNALS CONTROLLING UGD EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ugd	activator	15205413	0	att	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid-A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	7	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	ugd	activator	15205413	14	att	The synthesis of aminoarabinose is mediated by the PmrA-activated ugd gene and pbgP operon ( 43 ) , which are necessary for resistance to polymyxin B .	236	The synthesis of aminoarabinose is mediated by the PmrA-activated ugd gene and pbgP operon ( 43 ) , which are necessary for resistance to polymyxin B .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	15205413	3	att	Consistent with this notion , the PmrA-activated ugd gene and pbg operon ( designated pmrF by Gunn et al. [ 13 ] and arn by Trent et al. [ 43 ] ) are necessary for both the biosynthesis and incorporation of aminoarabinose into lipid-A ( 13 ) and for polymyxin B resistance ( 12 , 13 ) .	19	Consistent with this notion , the PmrA-activated ugd gene and pbg operon ( designated pmrF by Gunn et al. [ 13 ] and arn by Trent et al. [ 43 ] ) are necessary for both the biosynthesis and incorporation of aminoarabinose into lipid A ( 13 ) and for polymyxin B resistance ( 12 , 13 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	ugd	activator	15681155	7	att	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	191	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	11	3. RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PmrA	gene	ugd	activator	15681155	7	att	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	191	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	11	3. RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PmrA	gene	ugd	activator	20593264	1	att	Synthesis of Ara4N and addition to the lipid-A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .	173	Synthesis of Ara4N and addition to the lipid A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .	10	5.2.2 PMRA–PMRB REGULATORY SYSTEM	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
PmrA	gene	ugd	activator	22921935	2	att	To test this hypothesis , we determined the β2 galactosidase activity produced by strains harboring chromosomal lac transcriptional-fusions to the PmrA-activated pbgP operon and ugd gene .	106	To test this hypothesis , we determined the β2 galactosidase activity produced by strains harboring chromosomal lac transcriptional fusions to the PmrA-activated pbgP operon and ugd gene .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	ugd	activator	22921935	3	att	Deletion of the ugd gene in these mutant strains further enhanced mRNA levels of PmrA-activated genes ( Figures 5A and 5B ) .	130	Deletion of the ugd gene in these mutant strains further enhanced mRNA levels of PmrA-activated genes ( Figures 5A and 5B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ugd	activator	22921935	5	att	That the ugd mutant behaved like the wild-type strain at 20 min reflects that PmrA-dependent lipid-A modifications were undetectable ( Figure 6C ) , possibly because these modifications are added to newly synthesized LPS ( Raetz et al. , 2007 ) .	140	That the ugd mutant behaved like the wild-type strain at 20 min reflects that PmrA-dependent lipid A modifications were undetectable ( Figure 6C ) , possibly because these modifications are added to newly synthesized LPS ( Raetz et al. , 2007 ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ugd	activator	22921935	6	att	By 120 min , the PmrA-dependent lipid-A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	141	By 120 min , the PmrA-dependent lipid A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	22921935	8	att	This is because inactivation of lpxT hindered the generation of lipid-A singly substituted with pEtN or L-Ara4N ( Figure 3E ) , and it eliminated the increased Fe3 + association to the bacterial cell and transcription of PmrA-activated genes displayed by pmrR and ugd mutants ( Figures 4A , 4D-E and 5D-F ) .	171	This is because inactivation of lpxT hindered the generation of lipid A singly substituted with pEtN or L-Ara4N ( Figure 3E ) , and it eliminated the increased Fe3 + association to the bacterial cell and transcription of PmrA-activated genes displayed by pmrR and ugd mutants ( Figures 4A , 4D-E and 5D-F ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	23019341	0	att	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	16	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ugd	activator	23019341	0	ver/dev	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta .	16	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NtrC	gene	glnG	activator	32265871	1	ver/dev	However , the correlation of activation of NtrBC two-component system [ encoded by NtrB and glnG ( NtrC ) genes ] need to be further .	314	However , the correlation of activation of NtrBC two-component system [ encoded by glnL ( NtrB ) and glnG ( NtrC ) genes ] need to be further validated .	23	THE DELETION OF GLNA ACTIVATES TRANSCRIPTION OF NTRBC TWO-COMPONENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NtrC	gene	glnG	activator	32265871	1	ver/dev	However , the correlation of activation of NtrBC two-component system [ encoded by NtrB and glnG ( NtrC ) genes ] need to be further .	314	However , the correlation of activation of NtrBC two-component system [ encoded by glnL ( NtrB ) and glnG ( NtrC ) genes ] need to be further validated .	23	THE DELETION OF GLNA ACTIVATES TRANSCRIPTION OF NTRBC TWO-COMPONENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	TU	flgKL	regulator	20717675	1	ver/dev	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of r70 , while the class-3 promoter in operon flgKL is regulated by FliA .	192	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC and r70 , while the class-3 promoter in operon flgKL is regulated by FliA .	14	FLJB:Z66 EXPRESSION REQUIRES RPOE UNDER HYPEROSMOTIC STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	TU	flgKL	regulator	20717675	1	ver/dev	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of r70 , while the class-3 promoter in operon flgKL is regulated by FliA .	192	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC and r70 , while the class-3 promoter in operon flgKL is regulated by FliA .	14	FLJB:Z66 EXPRESSION REQUIRES RPOE UNDER HYPEROSMOTIC STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	TU	flgKL	regulator	20717675	1	ver/dev	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC , while the class-3 promoter in operon flgKL is regulated by FliA .	192	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC and r70 , while the class-3 promoter in operon flgKL is regulated by FliA .	14	FLJB:Z66 EXPRESSION REQUIRES RPOE UNDER HYPEROSMOTIC STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	TU	flgKL	regulator	20717675	1	ver/dev	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC , while the class-3 promoter in operon flgKL is regulated by FliA .	192	The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC and r70 , while the class-3 promoter in operon flgKL is regulated by FliA .	14	FLJB:Z66 EXPRESSION REQUIRES RPOE UNDER HYPEROSMOTIC STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
GlnG	gene	glnA	regulator	33751923	23	ver/dev	GlnG can act as both negative regulator of glnA .	655	GlnG can act as both positive and negative regulator of glnA , which encodes a glutamine synthetase .	26	GLNGL	nan	1	L2	OTHER	Other	OTHER	New	Level 1
GlnG	gene	glnA	regulator	33751923	23	ver/dev	GlnG can act as both positive regulator of glnA .	655	GlnG can act as both positive and negative regulator of glnA , which encodes a glutamine synthetase .	26	GLNGL	nan	1	L2	OTHER	Other	OTHER	New	Level 1
IscR	gene	hilD	repressor	27704705	1	ver/dev	IscR was also demonstrated to repress hilD and subsequently Spi1 gene expression , consistent with the observation that an IscR mutant is hyper invasive in epithelial cells .	24	IscR was also demonstrated to repress hilD and subsequently Spi1 gene expression , consistent with the observation that an IscR mutant is hyper invasive in epithelial cells .	6	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IscR	gene	hilD	repressor	27704705	17	ver/dev	2.4 IscR represses the expression of hilD gene	158	2.4 | IscR represses the expression of hilD gene and HilD targets	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IscR	gene	hilD	repressor	27704705	20	ver/dev	The iscR mutation led to a 5.5 fold increase in hilD mRNA level compared to the wild‐type strain , confirming that IscR acts as a repressor of hilD .	168	The iscR mutation led to a 5.5 fold increase in hilD mRNA level compared to the wild‐type strain , confirming that IscR acts as a repressor of hilD ( Figure 4e ) .	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IscR	gene	hilD	repressor	27704705	22	ver/dev	FIGURE 4 IscR represses hilD gene expression .	172	FIGURE 4 IscR represses hilD gene expression .	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	katN	activator	17293430	14	ver/dev	Therefore , even though decreased S abundance increased the magnitude of Crl activation of gene expression , it did not affect the differential responsiveness of the katN genes to Crl activation .	254	Therefore , even though decreased S abundance increased the magnitude of Crl activation of gene expression , it did not affect the differential responsiveness of the katE and katN genes to Crl activation .	5	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
MlrA	gene	csgD	regulator	11489123	0	ver/dev	MlrA represents a newly defined transcriptional regulator of csgD	61	MlrA represents a newly defined transcriptional regulator of csgD and agfD that is required for curli production and extracellular matrix formation by wild-type E. coli and S. typhimurium , and it is positively regulated by RpoS .	7	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
MlrA	gene	csgD	regulator	11489123	5	ver/dev	These results suggest that , as with RpoS , control of curli regulation by MlrA acts at the level of transcription of csgD .	172	These results suggest that , as with RpoS , control of curli regulation by MlrA acts at the level of transcription of csgD .	10	MLRA IS REQUIRED FOR CURLI PRODUCTION BY E. COLI X7122	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MlrA	gene	csgD	regulator	11489123	5	ver/dev	These results suggest that , as with RpoS , control of curli regulation by MlrA acts at the level of transcription of csgD .	172	These results suggest that , as with RpoS , control of curli regulation by MlrA acts at the level of transcription of csgD .	10	MLRA IS REQUIRED FOR CURLI PRODUCTION BY E. COLI X7122	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MlrA	gene	csgD	regulator	15458421	2	ver/dev	In addition , MlrA , controls csgD expression .	35	In addition , a recently defined transcriptional regulator , MlrA , controls csgD expression and is positively regulated by RpoS ( Brown et al. , 2001 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MlrA	gene	csgD	regulator	15458421	4	ver/dev	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene in S. typhimurium .	110	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene , aggregative morphology and extracellular matrix formation in E. coli and S. typhimurium ( Brown et al. , 2001 ) .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	csgD	regulator	15458421	4	ver/dev	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene in E. coli .	110	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene , aggregative morphology and extracellular matrix formation in E. coli and S. typhimurium ( Brown et al. , 2001 ) .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	csgD	regulator	23443158	15	ver/dev	Ogasawara , H. ; Yamamoto , K. ; Ishihama , A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	353	Ogasawara , H. ; Yamamoto , K. ; Ishihama , A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	9	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MlrA	gene	csgD	regulator	24735176	8	ver/dev	Under the influence of unknown environmental signals , MlrA induces the csgD expression .	411	Under the influence of unknown environmental signals , MlrA induces the csgD expression , which is the master regulator of the Salmonella ( and E. coli ) biofilm formation .	16	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	New	Level 3
MlrA	gene	csgD	regulator	25437188	13	ver/dev	The MerR-like regulator MlrA is another positive regulator of csgD expression .	203	The MerR-like regulator MlrA is another positive regulator of csgD expression [ 87 ] .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MlrA	gene	csgD	regulator	25437188	15	ver/dev	The direct regulation of csgD expression by MlrA in S. Typhimurium needs to be experimentally confirmed .	205	The direct regulation of csgD expression by MlrA in S. Typhimurium needs to be experimentally confirmed .	8	REGULATION OF CSGD TRANSCRIPTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	csgD	regulator	26293911	6	ver/dev	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	286	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	24	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MlrA	gene	csgD	regulator	29163440	7	ver/dev	that _ described in wt , indicating that MlrA is not required for the regulation of csgD by the composition of the culture media	195	Furthermore , the csgD expression pattern in MM and CFA in the mlrA mutant is similar to that described in wt , indicating that MlrA is not required for the regulation of csgD by the composition of the culture media .	14	TRANSCRIPTIONAL EXPRESSION OF GENES INVOLVED IN CURLI AND CELLULOSE SYNTHESIS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
MlrA	gene	csgD	regulator	29163440	7	ver/dev	that _ described in wt , indicating that MlrA is not required for the regulation of csgD by the composition of the culture media	195	Furthermore , the csgD expression pattern in MM and CFA in the mlrA mutant is similar to that described in wt , indicating that MlrA is not required for the regulation of csgD by the composition of the culture media .	14	TRANSCRIPTIONAL EXPRESSION OF GENES INVOLVED IN CURLI AND CELLULOSE SYNTHESIS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
MlrA	gene	csgD	regulator	31233504	12	ver/dev	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	778	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	46	44	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the lpxR genes , independently of InvF .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the lpxR genes , independently of HilA .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	activator	27886269	7	ver/dev	HilD induces the expression of lpxR , in the absence of other Salmonella-specific regulators .	82	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not that of SL1896 , in the absence of other Salmonella-specific regulators .	3	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	lpxR	activator	27886269	21	ver/dev	Thus , HilD positively regulates the expression of the lpxR genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	lpxR	activator	27886269	22	ver/dev	HilD positively regulates lpxR in S. Typhimurium .	132	HilD positively regulates gtgE , phoH , sinR , lpxR , SL1896 and SL4247 in S. Typhimurium .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	activator	27886269	23	ver/dev	HilD induces the expression of lpxR , in E. coli MC4100 .	151	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not SL1896 , in E. coli MC4100 .	4	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	regulator	27886269	3	ver/dev	HilD , regulates the expression of phoH .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	regulator	27886269	11	ver/dev	that HilD directly controls the expression of the phoH genes	94	Thus , these data strongly support that HilD directly controls the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly , through a regulator found in S. Typhimurium but not in E. coli MC4100 , that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	regulator	27886269	12	ver/dev	HilD binds to the regulatory regions of phoH .	110	HilD binds to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	phoH	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of phoH is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	phoH	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of phoH is direct , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	phoH	regulator	27886269	16	ver/dev	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the phoH genes .	120	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	phoH	regulator	27886269	17	ver/dev	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : phoH .	125	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes that are co-expressed with SPI-1 were identified : gtgE , phoH , sinR , SL1028 , lpxR , SL1896 , SL3812 , SL4247 and SL4433 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Escherichia coli	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of phoH .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Salmonella;Salmonella	0.5	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	phoH	regulator	27886269	21	ver/dev	Thus , HilD directly regulates the expression of the phoH genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	phoH	regulator	27886269	31	ver/dev	HilD binds to the regulatory region of phoH .	177	HilD binds to the regulatory region of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	ybeM	activator	33257526	15	att	In the case of ybeM , there are two predicted FliA-dependent promoters , and mutations were made in each individually ( p1 or p2 ) or both simultaneously ( p1 plus p2 ) .	125	In the case of ybeM , there are two predicted FliA-dependent promoters , and mutations were made in each individually ( p1 or p2 ) or both simultaneously ( p1 plus p2 ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FliA	gene	ybeM	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgB	activator	16707690	33	ver/dev	Experiments with purified CsgD are needed to determine whether CsgD can activate transcription by E S and/or E 70 at the csgB promoters .	433	Experiments with purified CsgD are needed to determine whether CsgD can activate transcription by E S and/or E 70 at the adrA and csgB promoters .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
LacI	gene	araC	regulator	19074398	19	ver/dev	LacI whose expression is under the control of the araC PBAD system	303	In the resulting strain 9449 , the expression of Lrp is regulated by LacI , whose expression is under the control of the araC PBAD system ( 57 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysE	regulator	18957594	11	att	Since swarming motility in both cysB and cysE is restored by the inclusion of cysteine in the swarm medium , a CysB-regulated gene outside of the cysteine biosynthetic genes is not the reason that these strains are incapable of swarming on standard swarm medium .	344	Since swarming motility in both cysB and cysE is restored by the inclusion of cysteine in the swarm medium , a CysB-regulated gene outside of the cysteine biosynthetic genes is not the reason that these strains are incapable of swarming on standard swarm medium .	10	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FimZ	gene	fimZ	regulator	17074910	25	auto	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	750	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	79	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
FimZ	gene	fimZ	regulator	21852351	0	auto	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	628	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	62	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
FimZ	gene	fimZ	regulator	22778099	0	auto	FimZ binds the Salmonella typhimu-rium fimA promoter region and may regulate its own expression with FimY .	527	FimZ binds the Salmonella typhimu-rium fimA promoter region and may regulate its own expression with FimY .	27	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
FimZ	gene	fimZ	regulator	25547794	39	auto	FimZ binds the Salmonella Typhimu-rium fimA promoter region and may regulate its own expression with FimY .	525	FimZ binds the Salmonella Typhimu-rium fimA promoter region and may regulate its own expression with FimY .	37	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
FimZ	gene	fimZ	regulator	29369799	2	auto	[ 40 ] K. Yeh , J.K. Tinker , S. Clegg , FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY , Microbiol .	351	[ 40 ] K. Yeh , J.K. Tinker , S. Clegg , FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY , Microbiol .	30	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
FimZ	gene	fimZ	regulator	31139165	15	auto	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	1246	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	18	TIME: 14:52 # 17	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
OmpR	gene	map	regulator	30524381	37	att	( C ) A heat map shows the expression profiles of the overlapping OmpR-regulated genes grouped based on differences in their fold change .	360	( C ) A heat map shows the expression profiles of the overlapping OmpR-regulated genes grouped based on differences in their fold change .	23	OMPR NUMBERS AND PH REGULATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	cas5	regulator	33854491	11	ver/dev	The results also support the complex genetic regulation of porins , since in the absence of cas5 , OmpR becomes undetectable , as does OmpC .	275	The results also support the complex genetic regulation of porins ( De la Cruz and Calva , 2010 ) , since in the absence of cas5 and cas2 , OmpR becomes undetectable ( Figure 4D ) , as does OmpC ( Figure 2C ) , demonstrating the specific role of these cas genes on ompR regulation to mediate OmpC synthesis .	19	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RtsA	gene	invF	activator	16045614	54	ver/dev	RtsA are each capable of partially activating invF	390	Transcription of invF is primarily regulated by HilA , but HilD , HilC and RtsA are each capable of partially activating invF ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Akbar et al. , 2003 ; Ellermeier and Slauch , 2003 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	18577510	1	ver/dev	RamA was required for indole induction of acrAB .	13	RamA was required for indole induction of acrAB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	18577510	4	ver/dev	Here we report on induction of acrAB in Salmonella via the specific regulator RamA in response to indole .	55	Here we report on induction of acrAB in Salmonella via the specific regulator RamA in response to indole , bile , and an E. coli conditioned medium .	2	MAIN	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
RamA	TU	acrAB	activator	18577510	8	ver/dev	The results indicate that the RamA regulator is required for indole induction of acrAB in Salmonella .	149	The results indicate that the RamA regulator is required for indole induction of acrAB in Salmonella .	2	MAIN	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	18577510	13	ver/dev	Indole activation of acrAB expression through the RamA regulator .	169	Indole activation of acrAB expression through the RamA regulator .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	activator	18577510	15	ver/dev	RamA Binds to the Upstream Regions of tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals .	187	RamA Binds to the Upstream Regions of acrA and tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals such as indole and bile .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	TU	acrAB	activator	18577510	15	ver/dev	RamA Binds to the Upstream Regions of acrA -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals .	187	RamA Binds to the Upstream Regions of acrA and tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals such as indole and bile .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	TU	acrAB	activator	18577510	15	ver/dev	RamA Binds to the Upstream Regions of tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to bile .	187	RamA Binds to the Upstream Regions of acrA and tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals such as indole and bile .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	TU	acrAB	activator	18577510	15	ver/dev	RamA Binds to the Upstream Regions of tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to indole .	187	RamA Binds to the Upstream Regions of acrA and tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals such as indole and bile .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	TU	acrAB	activator	18577510	15	ver/dev	RamA Binds to the Upstream Regions of acrA -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to bile .	187	RamA Binds to the Upstream Regions of acrA and tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals such as indole and bile .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	TU	acrAB	activator	18577510	15	ver/dev	RamA Binds to the Upstream Regions of acrA -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to indole .	187	RamA Binds to the Upstream Regions of acrA and tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals such as indole and bile .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	TU	acrAB	activator	18577510	21	ver/dev	RamA induction of acrAB by conditioned-medium of E. coli .	198	RamA induction of acrAB and tolC by conditioned medium of E. coli .	2	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	activator	18577510	35	ver/dev	We found that acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .	269	We found that acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .	3	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	18577510	35	ver/dev	We found that acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .	269	We found that acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .	3	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	18577510	36	ver/dev	However , our data indicate that bile induction of acrAB in Salmonella is completely dependent on RamA , not Rob .	278	However , our data indicate that bile induction of acrAB in Salmonella is completely dependent on RamA , not Rob .	3	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	18984645	8	att	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	315	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	17	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	19230852	11	ver/dev	The acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .	356	The acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB ( Fig. 4 ) [ 92 ] .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	19230852	11	ver/dev	The acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .	356	The acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB ( Fig. 4 ) [ 92 ] .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	19230852	12	ver/dev	However , our data indicate that bile induction of acrAB in Salmonella is completely dependent on RamA , not Rob .	361	However , our data indicate that bile induction of acrAB in Salmonella is completely dependent on RamA , not Rob .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	19230852	17	ver/dev	Our results suggest that RamAmediated acrAB expression is induced either via overexpression of activation of poorly-expressed RamA .	373	Our results suggest that RamAmediated acrAB expression is induced either via overexpression of a weakly active RamA protein or activation of poorly-expressed RamA ( Fig. 4 ) .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RamA	TU	acrAB	activator	19230852	17	ver/dev	Our results suggest that RamAmediated acrAB expression is induced either via overexpression of activation of poorly-expressed RamA .	373	Our results suggest that RamAmediated acrAB expression is induced either via overexpression of a weakly active RamA protein or activation of poorly-expressed RamA ( Fig. 4 ) .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RamA	TU	acrAB	activator	19230852	17	ver/dev	Our results suggest that RamAmediated acrAB expression is induced either via overexpression of a weakly active RamA protein .	373	Our results suggest that RamAmediated acrAB expression is induced either via overexpression of a weakly active RamA protein or activation of poorly-expressed RamA ( Fig. 4 ) .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RamA	TU	acrAB	activator	21148208	2	ver/dev	In Salmonella , RamA is involved in inducing acrAB in addition to the abovementioned regulators .	45	In Salmonella , RamA is involved in inducing acrAB in addition to the abovementioned regulators ( Bailey et al. ,2008 ; Schneiders et al. , 2003 ) .	2	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	21148208	8	ver/dev	The induction of acrAB in response to paraquat suggested that this induction mechanism might be mediated by the RamA regulator .	182	The induction of acrAB in response to paraquat suggested that this induction mechanism might be mediated by the RamA regulator .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	acrAB	activator	21148208	9	ver/dev	acrAB induction by paraquat was observed in the DramA strain , indicating that RamA was not required for this induction response .	184	acrAB induction by paraquat was observed in the DramA strain ( Fig. 4a ) , indicating that RamA was not required for this induction response .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RamA	TU	acrAB	activator	21148208	12	ver/dev	RamA directly induces acrAB .	210	RamA belongs to the AraC/XylS transcriptional activator family and directly induces acrAB .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	activator	21858134	1	ver/dev	In SI3 , RamA played predominant role in ciprofloxacin resistance via increasing the expression level of acrAB .	17	In SI3 , RamA played predominant role in ciprofloxacin resistance via increasing the expression level of acrAB .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	activator	23230062	0	ver/dev	Activation of the acrAB operon is achieved through the direct binding of RamA , to the operator regions of these genes .	27	Activation of the acrAB operon and tolC gene transcription is achieved through the direct binding of RamA , a positive regulator of the AraC/XylS family , to the operator regions of these genes [ 13 , 14 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	23493314	1	ver/dev	that acrAB induction by indole is dependent on RamA	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	23493314	1	ver/dev	that acrAB induction by indole is dependent on RamA	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	23493314	1	ver/dev	that acrAB induction by indole is dependent on RamA	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	24816212	0	ver/dev	The acrAB genes are transcriptionally activated by RamA .	10	The acrAB and tolC genes are transcriptionally activated by RamA , the gene for which is itself transcriptionally repressed by RamR .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	24816212	1	ver/dev	As expected , since RamA is PramA , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB ,18 bile DNA fragment	95	As expected , since RamA is the main the ramA promoter ( PramA ) , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB and tolC efflux genes ,18 bile DNA fragment amplified from the ramR-ramA intergenic region and	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	24816212	1	ver/dev	As expected , since RamA is the main the ramA promoter , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB ,18 bile DNA fragment	95	As expected , since RamA is the main the ramA promoter ( PramA ) , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB and tolC efflux genes ,18 bile DNA fragment amplified from the ramR-ramA intergenic region and	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	24816212	3	ver/dev	Regulation model for the bile-mediated activation of acrAB via RamA .	264	Regulation model for the bile-mediated activation of acrAB and tolC via RamA .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	activator	25128419	0	ver/dev	RamA plays a key role in increasing the expression level of the efflux pump by binding to the upstream promoter region of acrAB and to .	35	RamA plays a key role in increasing the expression level of the efflux pump by binding to the upstream promoter region of acrAB and tolC ( Nikaido et al. , 2008 ) , and can be regulated by the local repressor RamR .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	TU	acrAB	activator	34202800	4	ver/dev	RamA is the main activator of acrAB transcription	234	RamA is the main activator of acrAB and tolC transcription , and bile induces an over two-fold increase in acrB and tolC transcript levels .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	acrAB	activator	34202800	10	ver/dev	Nikaido et al. showed that induction of the acrAB via indole is regulated by the RamA .	283	Nikaido et al. [ 89 ] showed that induction of the acrAB via indole is regulated by the RamA .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	narZ	regulator	18790861	7	att	In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary-phase ( 4 ) .	33	In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary phase ( 4 ) .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	dam	repressor	12067346	27	ver/dev	In contrast , the presence of both dam mutations in the donor strain restored the repression of pSLT transfer to a level similar to that of an Lrp .	150	In contrast , the presence of both dam and lrp mutations in the donor strain restored the repression of pSLT transfer to a level similar to that of an Lrp - mutant ( Table 1 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lacZ	activator	27601571	8	ver/dev	However , we assayed transcription activation by HilD in Escherichia coli , by fusing regions upstream of candidate genes to the lacZ reporter gene ; failure to observe transcription activation by HilD in such experiments does not necessarily indicate that HilD does not regulate these genes , since factors specific to Salmo-nella may be required for their activation .	98	However , we assayed transcription activation by HilD in Escherichia coli , by fusing regions upstream of candidate genes to the lacZ reporter gene ; failure to observe transcription activation by HilD in such experiments does not necessarily indicate that HilD does not regulate these genes , since factors specific to Salmo-nella may be required for their activation .	3	RESULTS AND DISCUSSION	Escherichia coli;Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
HilD	gene	lacZ	activator	27601571	8	ver/dev	However , we assayed transcription activation by HilD in Escherichia coli , by fusing regions upstream of candidate genes to the lacZ reporter gene ; failure to observe transcription activation by HilD in such experiments does not necessarily indicate that HilD does not regulate these genes , since factors specific to Salmo-nella may be required for their activation .	98	However , we assayed transcription activation by HilD in Escherichia coli , by fusing regions upstream of candidate genes to the lacZ reporter gene ; failure to observe transcription activation by HilD in such experiments does not necessarily indicate that HilD does not regulate these genes , since factors specific to Salmo-nella may be required for their activation .	3	RESULTS AND DISCUSSION	Escherichia coli;Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
SdiA	gene	repA2	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	siiA	regulator	27601571	18	ver/dev	scription activation of protein-coding genes outside SPI-1 overlap Table S1 -RRB- , suggesting that failure to detect binding of InvF by regions _ bound by H-NS -LRB- HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites , , siiA , mcpC , epitope tags	210	scription activation of protein-coding genes outside SPI-1 overlap Table S1 ) , suggesting that failure to detect binding of InvF by regions that are likely bound by H-NS ( HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites associated with regulation of lpxR , STM14_5184 , siiA , mcpC , epitope tags .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	siiA	regulator	27601571	18	ver/dev	scription activation of protein-coding genes outside SPI-1 overlap Table S1 -RRB- , suggesting that failure to detect binding of InvF by regions _ bound by H-NS -LRB- HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites , , siiA , mcpC , epitope tags	210	scription activation of protein-coding genes outside SPI-1 overlap Table S1 ) , suggesting that failure to detect binding of InvF by regions that are likely bound by H-NS ( HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites associated with regulation of lpxR , STM14_5184 , siiA , mcpC , epitope tags .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	cas2	activator	30760616	1	att	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	148	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HilD	gene	lon	regulator	28329249	15	att	Therefore , we compared the transcription of HilD-regulated genes in eK297R and eWT in the lon deletion background , which excludes the effect of protein stability , and found that the messenger RNA levels of HilD-regulated genes in eK297R increased dramatically compared with these in eWT ( Figure 3D ) , indicating that K297R mimicking deacetylation can effectively activate HilD-regulated genes by increasing its DNA-binding affiffinity in the lon mutant background in-vivo .	166	Therefore , we compared the transcription of HilD-regulated genes in eK297R and eWT in the lon deletion background , which excludes the effect of protein stability , and found that the messenger RNA levels of HilD-regulated genes in eK297R increased dramatically compared with these in eWT ( Figure 3D ) , indicating that K297R mimicking deacetylation can effectively activate HilD-regulated genes by increasing its DNA-binding affiffinity in the lon mutant background in vivo .	13	K297 ACETYLATION MAINTAINING HILD STABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lon	regulator	28329249	15	att	Therefore , we compared the transcription of HilD-regulated genes in eK297R and eWT in the lon deletion background , which excludes the effect of protein stability , and found that the messenger RNA levels of HilD-regulated genes in eK297R increased dramatically compared with these in eWT ( Figure 3D ) , indicating that K297R mimicking deacetylation can effectively activate HilD-regulated genes by increasing its DNA-binding affiffinity in the lon mutant background in-vivo .	166	Therefore , we compared the transcription of HilD-regulated genes in eK297R and eWT in the lon deletion background , which excludes the effect of protein stability , and found that the messenger RNA levels of HilD-regulated genes in eK297R increased dramatically compared with these in eWT ( Figure 3D ) , indicating that K297R mimicking deacetylation can effectively activate HilD-regulated genes by increasing its DNA-binding affiffinity in the lon mutant background in vivo .	13	K297 ACETYLATION MAINTAINING HILD STABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	tviA	activator	30145252	3	ver/dev	In this study , we found that OxyR positively regulated the gene expression of Vi antigen in S. Typhi by directly binding to the promoter region of tviA .	41	In this study , we found that OxyR positively regulated the gene expression of Vi antigen in S. Typhi by directly binding to the promoter region of tviA .	3	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
OxyR	gene	tviA	activator	30145252	4	ver/dev	OxyR activates the promoter activity of tviA .	169	OxyR activates the promoter activity of tviA .	16	3.1. GLOBAL TRANSCRIPTIONAL PROFILING WITH OXYR DELETION UNDER OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	tviA	activator	30145252	5	ver/dev	OxyR activates the promoter activity of tviA	185	3.3. OxyR activates the promoter activity of tviA	17	3.3. OXYR ACTIVATES THE PROMOTER ACTIVITY OF TVIA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseA	activator	30682134	18	att	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	225	SlyA activates pagC and sseA expression in a PhoP-dependent manner [ 68,72,73 ] , and only in LB was their translation repressed by CsrA 3.5 - and 4.0-fold , respectively ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ydeI	activator	33106344	1	ver/dev	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of PydeI .	56	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of its promoter ( PydeI ) .	2	MAIN	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ydeI	activator	33106344	1	ver/dev	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of its promoter .	56	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of its promoter ( PydeI ) .	2	MAIN	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ydeI	activator	33106344	14	ver/dev	Additionally , GFP reporter assays also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	410	Additionally , our qRTPCR and GFP reporter assays also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	activator	33106344	14	ver/dev	Additionally , our qRTPCR also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	410	Additionally , our qRTPCR and GFP reporter assays also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM2297	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	hilE	regulator	25547794	10	ver/dev	We have previously shown that hilE is regulated by the transcriptional activator FimZ .	107	We have previously shown that hilE is regulated by the transcriptional activator FimZ ( 50 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FimZ	gene	hilE	regulator	27564394	0	ver/dev	The hilE gene is transcriptionally activated by the regulator of fimbrial gene expression , FimZ .	152	The hilE gene is transcriptionally activated by the regulator of fimbrial gene expression , FimZ [ 29 ] , and HilE interacts with the HilD protein to repress hilA transcription [ 52 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	mgtA	activator	22431636	0	att	A mutation in the mgtA leader that favors the `` high Mg2 + '' conformation of the riboswitch promoted Rho-dependent transcription termination in-vivo and in-vitro and enhanced the ability of the RNA to stimulate Rho 's ATPase activity in-vitro .	9	A mutation in the mgtA leader that favors the `` high Mg2 + '' conformation of the riboswitch promoted Rho-dependent transcription termination in vivo and in vitro and enhanced the ability of the RNA to stimulate Rho 's ATPase activity in vitro .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
Rho	gene	mgtA	activator	22431636	10	att	We sought to identify sequences within the mgtA leader RNA that are required for Rho-dependent transcription termination .	109	We sought to identify sequences within the mgtA leader RNA that are required for Rho-dependent transcription termination .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	mgtA	activator	22431636	11	att	The R1 mutation hinders Rho-dependent termination by preventing the mgtA leader RNA from establishing a productive interaction with Rho because it decreased the ability of the C145G RNA to stimulate Rho 's ATPase activity 2.5 - to threefold in-vitro , to values that were even lower than those promoted by the wild-type mgtA leader RNA ( Fig. 2D ) .	120	The R1 mutation hinders Rho-dependent termination by preventing the mgtA leader RNA from establishing a productive interaction with Rho because it decreased the ability of the C145G RNA to stimulate Rho 's ATPase activity 2.5 - to threefold in vitro , to values that were even lower than those promoted by the wild-type mgtA leader RNA ( Fig. 2D ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
Rho	gene	mgtA	activator	22431636	12	att	The effect of the R1 mutation is not specific to a leader that is genetically `` locked '' into the high Mg2 + conformation because mutation of the R1 region in an otherwise wildtype mgtA leader overcame the repressive effect of growth in high Mg2 + on transcription through the leader in-vivo ( Fig. 1B ) , inhibited Rho-dependent termination in-vitro ( Fig. 2C ) , and reduced the ability of the mgtA leader RNA to stimulate Rho 's ATPase activity in-vitro ( Fig. 2D ) .	121	The effect of the R1 mutation is not specific to a leader that is genetically `` locked '' into the high Mg2 + conformation because mutation of the R1 region in an otherwise wildtype mgtA leader overcame the repressive effect of growth in high Mg2 + on transcription through the leader in vivo ( Fig. 1B ) , inhibited Rho-dependent termination in vitro ( Fig. 2C ) , and reduced the ability of the mgtA leader RNA to stimulate Rho 's ATPase activity in vitro ( Fig. 2D ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	OTHER	Other	NEG	Other	Level 1
Rho	gene	mgtA	activator	22431636	12	att	The effect of the R1 mutation is not specific to a leader that is genetically `` locked '' into the high Mg2 + conformation because mutation of the R1 region in an otherwise wildtype mgtA leader overcame the repressive effect of growth in high Mg2 + on transcription through the leader in-vivo ( Fig. 1B ) , inhibited Rho-dependent termination in-vitro ( Fig. 2C ) , and reduced the ability of the mgtA leader RNA to stimulate Rho 's ATPase activity in-vitro ( Fig. 2D ) .	121	The effect of the R1 mutation is not specific to a leader that is genetically `` locked '' into the high Mg2 + conformation because mutation of the R1 region in an otherwise wildtype mgtA leader overcame the repressive effect of growth in high Mg2 + on transcription through the leader in vivo ( Fig. 1B ) , inhibited Rho-dependent termination in vitro ( Fig. 2C ) , and reduced the ability of the mgtA leader RNA to stimulate Rho 's ATPase activity in vitro ( Fig. 2D ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	OTHER	Other	NEG	Other	Level 1
Rho	gene	mgtA	activator	22431636	2	att	A Rho-dependent terminator in the Salmonella mgtA leader prevents transcription into the mgtA coding region during-growth at high Mg2 + .	57	A Rho-dependent terminator in the Salmonella mgtA leader prevents transcription into the mgtA coding region during growth at high Mg2 + .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	mgtA	activator	22431636	4	att	High Mg2 + enhanced Rho-dependent termination in the mgtA leader in-vitro because termination was more efficient at 3.5 mM than at 0.35 mM Mg2 + ( Fig. 2 B and C ) .	72	High Mg2 + enhanced Rho-dependent termination in the mgtA leader in vitro because termination was more efficient at 3.5 mM than at 0.35 mM Mg2 + ( Fig. 2 B and C ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	mgtA	activator	22431636	5	att	The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 + did not enhance termination ( and actually decreased it ) at the well-characterized Rho-dependent terminator λtR1 ( Fig .	73	The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 + did not enhance termination ( and actually decreased it ) at the well-characterized Rho-dependent terminator λtR1 ( Fig .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Rho	gene	mgtA	activator	22431636	5	att	The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 + did not enhance termination ( and actually decreased it ) at the well-characterized Rho-dependent terminator λtR1 ( Fig .	73	The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 + did not enhance termination ( and actually decreased it ) at the well-characterized Rho-dependent terminator λtR1 ( Fig .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Rho	gene	mgtA	activator	22431636	6	att	Taken together , our data establish that the mgtA leader contains a Rho-dependent terminator that prevents transcription elongation into the mgtA coding region during-growth in high Mg2 + .	81	Taken together , our data establish that the mgtA leader contains a Rho-dependent terminator that prevents transcription elongation into the mgtA coding region during growth in high Mg2 + .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Rho	gene	mgtA	activator	22431636	6	att	Taken together , our data establish that the mgtA leader contains a Rho-dependent terminator that prevents transcription elongation into the mgtA coding region during-growth in high Mg2 + .	81	Taken together , our data establish that the mgtA leader contains a Rho-dependent terminator that prevents transcription elongation into the mgtA coding region during growth in high Mg2 + .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Rho	gene	mgtA	activator	22431636	7	att	Mg2 + stimulates Rho-dependent transcription termination in the mgtA leader by promoting an RNA conformation that enhances Rho 's catalytic activity .	83	Mg2 + stimulates Rho-dependent transcription termination in the mgtA leader by promoting an RNA conformation that enhances Rho 's catalytic activity .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	mgtA	activator	22431636	8	att	Thus , the RNA structure promoted in high Mg2 + may stimulate Rho-dependent termination by facilitating interaction of Rho with the mgtA leader RNA .	98	Thus , the RNA structure promoted in high Mg2 + may stimulate Rho-dependent termination by facilitating interaction of Rho with the mgtA leader RNA .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
Rho	gene	mgtA	activator	22431636	9	att	Taken together , our data suggest that high Mg2 + stimulates Rho-dependent termination in the mgtA leader by promoting a conformation in the leader mRNA that favors interaction with Rho .	107	Taken together , our data suggest that high Mg2 + stimulates Rho-dependent termination in the mgtA leader by promoting a conformation in the leader mRNA that favors interaction with Rho .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Rho	gene	mgtA	activator	22431636	5	ver/dev	The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 .	73	The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 + did not enhance termination ( and actually decreased it ) at the well-characterized Rho-dependent terminator λtR1 ( Fig .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	mgtA	activator	24596096	5	att	Also , a regulatory mechanism that controls transcription termination is involved in the mgtA Mg2 riboswitch function via a Rho-dependent terminator ( 30 ) as an open reading frame encoding a 17-residue leader peptide that is translated within the 5 - leader region ( LR ) 2 ( 31 , 32 ) .	66	Also , a regulatory mechanism that controls transcription termination is involved in the mgtA Mg2 riboswitch function via a Rho-dependent terminator ( 30 ) as an open reading frame encoding a 17-residue leader peptide that is translated within the 5 - leader region ( LR ) 2 ( 31 , 32 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	mgtA	activator	27849575	1	att	Transcription of mgtA is regulated at two steps : activation of the promoter by PhoP , which is phosphorylated by PhoQ in response to low [ Mg2 + ] and other periplasmic signals ( inset 1 ) ( 4 ) , and translation of mgtL ( encoded by nucleotides 71 -- 124 ) ( 12 ) , which governs folding of the 5 ′ LR mRNA and Rho-dependent termination .	62	Transcription of mgtA is regulated at two steps : activation of the promoter by PhoP , which is phosphorylated by PhoQ in response to low [ Mg2 + ] and other periplasmic signals ( inset 1 ) ( 4 ) , and translation of mgtL ( encoded by nucleotides 71 -- 124 ) ( 12 ) , which governs folding of the 5 ′ LR mRNA and Rho-dependent termination .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	mgtA	activator	27849575	3	att	The PhoQP two-component system was suggested to activate transcription of mgtA at low extracellular Mg2 + concentrations ( 6 , 9 ) , and the mgtA 5 ′ LR mRNA has been proposed to function as an Mg2 + - sensing riboswitch that regulates read-through or Rho-dependent transcription termination at a site upstream of the mgtA structural gene in response to intracellular Mg2 + ( 11 , 15 ) .	151	The PhoQP two-component system was suggested to activate transcription of mgtA at low extracellular Mg2 + concentrations ( 6 , 9 ) , and the mgtA 5 ′ LR mRNA has been proposed to function as an Mg2 + - sensing riboswitch that regulates read-through or Rho-dependent transcription termination at a site upstream of the mgtA structural gene in response to intracellular Mg2 + ( 11 , 15 ) .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	mgtA	activator	27849575	3	att	The PhoQP two-component system was suggested to activate transcription of mgtA at low extracellular Mg2 + concentrations ( 6 , 9 ) , and the mgtA 5 ′ LR mRNA has been proposed to function as an Mg2 + - sensing riboswitch that regulates read-through or Rho-dependent transcription termination at a site upstream of the mgtA structural gene in response to intracellular Mg2 + ( 11 , 15 ) .	151	The PhoQP two-component system was suggested to activate transcription of mgtA at low extracellular Mg2 + concentrations ( 6 , 9 ) , and the mgtA 5 ′ LR mRNA has been proposed to function as an Mg2 + - sensing riboswitch that regulates read-through or Rho-dependent transcription termination at a site upstream of the mgtA structural gene in response to intracellular Mg2 + ( 11 , 15 ) .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Crl	gene	katE	repressor	17293430	23	ver/dev	In addition , katE is not resistant to Crl activation per se because it responded to Crl activation when S levels were decreased by the rpoSLT2 mutation .	356	In addition , katE is not resistant to Crl activation per se because it responded to Crl activation when S levels were decreased by the rpoSLT2 mutation ( Fig. 4 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
MarA	gene	asmA	activator	19346309	1	ver/dev	A tentative hypothesis is that asmA mutations might activate a MarA-regulated efflux pump hitherto unknown to transport bile-salts .	327	A tentative hypothesis is that asmA mutations might activate a MarA-regulated efflux pump hitherto unknown to transport bile salts .	5	DISCUSSION	unidentified	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hns	activator	11673423	0	ver/dev	The E. coli proU P1 promoter was also cryptic in these cases activation of in-vivo expression was achieved either by an hns null mutatio ( affecting the nucleoid protein H-NS ) at 30 °C .	7	The E. coli proU P1 promoter was also cryptic in constructs that carried 1.2 kb of downstream proU sequence , and in these cases activation of in vivo expression was achieved either by a rho mutation during growth at 10 °C or by an hns null mutation ( affecting the nucleoid protein H-NS ) at 30 °C .	0	Unknown	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	activator	12228306	0	att	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) and YMZ16 ( clyA hns ) ( solid bars ) carrying different constructs .	322	H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) and YMZ16 ( clyA hns ) ( solid bars ) carrying different constructs .	5	SEROVAR PARATYPHI A S3068/99 CLYASPA	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
IgaA	gene	dsbA	repressor	32571967	9	ver/dev	One is that the repressor of Rcs , IgaA , becomes dysfunctional in the dsbA background .	202	One enticing hypothesis is that the repressor of Rcs , IgaA , which contains four conserved periplasmic cysteines ( 73 ) , becomes dysfunctional in the dsbA background .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ssaG	repressor	23690578	7	ver/dev	PmrA Represses Transcription of the SPI-2 ssaG Gene .	42	PmrA Represses Transcription of the SPI-2 ssaG Gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssaG	repressor	23690578	9	ver/dev	PmrA decreases expression of the SPI-2 ssaG gene .	60	PmrA decreases expression of the SPI-2 ssaG gene .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssaG	repressor	23690578	12	ver/dev	PmrA Represses ssaG Transcription Indirectly , by Hindering Expression of the ssaG Activator SsrB .	73	PmrA Represses ssaG Transcription Indirectly , by Hindering Expression of the ssaG Activator SsrB .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssaG	repressor	23690578	13	ver/dev	In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator or by furthering expression of an ssaG repressor .	74	In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator ( s ) or by furthering expression of an ssaG repressor ( s ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L1	SPEC	Other	NEG	New	Level 1
PmrA	gene	ssaG	repressor	23690578	13	ver/dev	In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator or by furthering expression of an ssaG repressor .	74	In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator ( s ) or by furthering expression of an ssaG repressor ( s ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L1	SPEC	Other	NEG	New	Level 1
PmrA	gene	ssaG	repressor	23690578	16	ver/dev	PmrA decreases expression of the SPI-2 ssaG gene .	80	PmrA decreases expression of the SPI-2 ssaG gene .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssaG	repressor	23690578	32	ver/dev	Binding of PmrA to the ssrB promoter is required for PmrA-mediated repression of the SPI-2 ssaG gene .	119	Binding of PmrA to the ssrB promoter is required for PmrA-mediated repression of the SPI-2 ssaG gene .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dam	activator	18805972	2	att	Some of the DNA sequences found in the std promoter region are also compatible with the existence of an RpoS-dependent promoter ( 50 ) ; however , this possibility was judged unlikely since a previous study showed that std is expressed in dam derivatives of LT2 ( 3 ) , a serovar Typhimurium strain known to be lacking RpoS ( 52 ) .	179	Some of the DNA sequences found in the std promoter region are also compatible with the existence of an RpoS-dependent promoter ( 50 ) ; however , this possibility was judged unlikely since a previous study showed that std is expressed in dam derivatives of LT2 ( 3 ) , a serovar Typhimurium strain known to be lacking RpoS ( 52 ) .	4	RESULTS	Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L1	SPEC	Fact	OTHER	Other	Level 1
CpxR	gene	clpX	activator	26300871	34	ver/dev	CpxR , induces the transcription of clpX .	480	FIGURE 7 | RpoH , but not CpxR , induces the transcription of lon , clpX , and clpP .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	clpX	activator	26300871	35	ver/dev	Our results show that CpxR , induces the transcription of the clpX encoding the ClpXP protease .	491	Our results show that RpoH , but not CpxR , induces the transcription of lon , as well as of the clpX and clpP neighbor genes encoding the ClpXP protease .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sigE	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in sopE229 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sigE	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in sopE , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sigE	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in sopF28 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	sigE	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in SPI-527 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
SirC	gene	hilA	activator	11755416	31	ver/dev	Two reports have shown that prgH expression , can be upregulated by artificially expressing high levels of SirC , SprA even in the absence of hilA .	558	Two reports have shown that invF expression , but not prgH expression , can be upregulated by artificially expressing high levels of HilC ( SirC , SprA ) even in the absence of hilA ( figure 1B , blue arrow ) [ 50 , 51 ] .	16	REFERENCES	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SirC	gene	hilA	activator	11755416	31	ver/dev	Two reports have shown that invF expression , can be upregulated by artificially expressing high levels of SirC , SprA even in the absence of hilA .	558	Two reports have shown that invF expression , but not prgH expression , can be upregulated by artificially expressing high levels of HilC ( SirC , SprA ) even in the absence of hilA ( figure 1B , blue arrow ) [ 50 , 51 ] .	16	REFERENCES	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
OmpR	gene	sifB	activator	12949164	5	ver/dev	These results suggest that the induction of sifB expression by acidic pH inside the vacuole is mediated by both B and OmpR -- EnvZ .	466	These results suggest that the induction of sifB expression by acidic pH inside the vacuole is mediated by both SsrA -- B and OmpR -- EnvZ .	11	SSRA–B AND OMPR–ENVZ ARE BOTH REQUIRED TO MEDIATE THE EFFECT OF ACIDIC PH ON SPI-2 TTSS GENE EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	sifB	activator	12949164	5	ver/dev	These results suggest that the induction of sifB expression by acidic pH inside the vacuole is mediated by both SsrA and OmpR -- EnvZ .	466	These results suggest that the induction of sifB expression by acidic pH inside the vacuole is mediated by both SsrA -- B and OmpR -- EnvZ .	11	SSRA–B AND OMPR–ENVZ ARE BOTH REQUIRED TO MEDIATE THE EFFECT OF ACIDIC PH ON SPI-2 TTSS GENE EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	hmpA	activator	27065993	3	att	Absent from positively regulated , • NO - and DksA-dependent transcripts was hmpA which encodes flavohaemoglobin , a prominent • NO detoxifying protein ( Poole and Hughes , 2000 ) .	209	Absent from positively regulated , • NO - and DksA-dependent transcripts was hmpA which encodes flavohaemoglobin , a prominent • NO detoxifying protein ( Poole and Hughes , 2000 ) .	13	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	prgH	repressor	11083793	1	ver/dev	Our previous data showed that prgH was repressed by environmental bile independent of PhoP .	79	Our previous data showed that prgH was repressed by environmental bile independent of PhoP ( 30 ) .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	prgH	repressor	11083793	2	ver/dev	Our previous data showed that prgH was repressed by environmental bile independent of PhoP .	124	Our previous data showed that prgH was repressed by environmental bile independent of PhoP ( 30 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	prgH	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	ygbA	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
NsrR	gene	ygbA	regulator	23651595	18	att	These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .	625	These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	ygbA	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CpxR	gene	acrB	activator	30107570	0	ver/dev	CpxR overexpression increases the susceptibility of acrB double-deleted Salmonella enterica serovar Typhimurium to colistin	2	CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	acrB	activator	32620947	21	ver/dev	CpxR overexpression increases the susceptibility of acrB double-deleted Salmonella enterica serovar Typhimurium to colistin .	341	CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin .	21	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	acrB	activator	33300449	0	ver/dev	CpxR overexpression increases the susceptibility of acrB double-deleted Salmonella enterica serovar Typhimurium to colistin .	489	CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin .	54	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tdcA	regulator	20396961	0	att	To understand the function of TdcA in pathogenesis , we performed two-dimensional gel electrophoresis and found that flagellar and PhoP-regulated proteins were affected by the tdcA mutation .	12	To understand the function of TdcA in pathogenesis , we performed two-dimensional gel electrophoresis and found that flagellar and PhoP-regulated proteins were affected by the tdcA mutation .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tdcA	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimY	gene	fimY	regulator	12227641	0	ver/dev	Although fimY gene of Salmonella typhimurium is involved in regulating the amino-acid sequence of FimY shares very little homology with other known prokaryotic proteins in the GenBank database .	15	Although fimY gene of Salmonella typhimurium is involved in regulating type 1 fimbrial expression , the amino acid sequence of FimY shares very little homology with other known prokaryotic proteins in the GenBank database .	0	Unknown	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	lacZ	regulator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at LSP according to ChIP-chip data : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	lacZ	regulator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at LSP according to the microarray : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	lacZ	regulator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP according to ChIP-chip data : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	lacZ	regulator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP according to the microarray : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	spvR	regulator	12898222	10	ver/dev	Fis binds to a 280-bp spvR gene fragment .	167	Fis binds to a 493-bp DNA fragment encompassing the gyrA promoter ( A ) , but not to a 280-bp spvR gene fragment ( B ) .	14	EXPRESSION OF GYRA IN A FIS KNOCK-OUT MUTANT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	spvR	regulator	15256548	5	att	A DNA sequence from the promoter of the spvR gene , known not to be Fis-regulated ( our unpublished data ; see also supplementary data Tables S1 and S2 at http://mic.sgmjournals.org ) , was used as a negative control .	361	A DNA sequence from the promoter of the spvR gene , known not to be Fis-regulated ( our unpublished data ; see also supplementary data Tables S1 and S2 at http://mic.sgmjournals.org ) , was used as a negative control .	12	FIS BINDING TO FLAGELLAR AND SPI-2 PROMOTERS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
NsrR	gene	hmp	repressor	20829289	0	ver/dev	In Salmonella , five transcription factors have been implicated : hmp transcription is repressed by NsrR .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
NsrR	gene	hmp	repressor	20829289	0	ver/dev	In E. coli , five transcription factors have been implicated : hmp transcription is repressed by NsrR .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
FliA	gene	fliC	regulator	12791144	7	ver/dev	flgE Hook protein ( first module ) flgG Cell-distal portion of basal body rod flgK Hook -- filament junction protein 1 ( second module ) flgL Hook -- filament junction protein flgM Anti-FliA ( antisigma ) factor ; also known as RflB protein flgN Believed to be export chaperone for FlgK and FlgL fliA Sigma F ( sigma-28 ) factor of RNA polymerase , transcription of late genes fliC Flagellin , filament structural protein ( second module ) fliD Filament-capping protein ; enables filament assembly fliT Possible export chaperone for FliD fliZ Putative regulator of FliA fljA Repressor of fliC fljB Phase 2 flagellin ( filament structural protein ) motA Proton conductor component of motor motB Enables flagellar motor rotation Aerotaxis/chemotaxis aer Aerotaxis sensor receptor , senses cellular redox state or proton motive force cheA Sensory kinase , transduces signal between chemosignal receptors and CheB and cheB Methyl esterase cheW Purine-binding chemotaxis protein ; regulation cheY Chemotaxis regulator , transmits chemoreceptor signals to flagellar motor cheZ Chemotactic response ; CheY protein phosphatase tsr Methyl-accepting chemotaxis protein I , serine sensor receptor	129	flgE Hook protein ( first module ) flgG Cell-distal portion of basal body rod flgK Hook -- filament junction protein 1 ( second module ) flgL Hook -- filament junction protein flgM Anti-FliA ( antisigma ) factor ; also known as RflB protein flgN Believed to be export chaperone for FlgK and FlgL fliA Sigma F ( sigma 28 ) factor of RNA polymerase , transcription of late genes fliC Flagellin , filament structural protein ( second module ) fliD Filament-capping protein ; enables filament assembly fliT Possible export chaperone for FliD fliZ Putative regulator of FliA fljA Repressor of fliC fljB Phase 2 flagellin ( filament structural protein ) motA Proton conductor component of motor motB Enables flagellar motor rotation Aerotaxis/chemotaxis aer Aerotaxis sensor receptor , senses cellular redox state or proton motive force cheA Sensory kinase , transduces signal between chemosignal receptors and CheB and cheB Methyl esterase cheW Purine-binding chemotaxis protein ; regulation cheY Chemotaxis regulator , transmits chemoreceptor signals to flagellar motor cheZ Chemotactic response ; CheY protein phosphatase tsr Methyl-accepting chemotaxis protein I , serine sensor receptor	6	REGULATION OF INVASION GENES BY CSRA	Calophysus macropterus	0	L1	SPEC	Fact	OTHER	Other	Level 1
FliA	gene	fliC	regulator	17725646	3	ver/dev	Upon completion of the basal body , the anti-sigma factor FlgM is secreted , allowing the alternative sigma factor FliA to initiate transcription of genes under control of fliC .	186	Upon completion of the basal body , the anti-sigma factor FlgM is secreted , allowing the alternative sigma factor FliA to initiate transcription of genes under control of class III promoter , such as fliC .	7	THE TVIA-DEPENDENT DECREASE IN IL-8 EXPRESSION IS INDEPENDENT OF THE INVASION-ASSOCIATED TYPE III SECRETION SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	fliC	regulator	8631681	1	att	In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	6	In this investigation , we observed that ( i ) the in vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	OTHER	Other	OTHER	Other	Level 1
RcsB	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , mutation of the putative RcsB binding site in the ugd promoter abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , Fig. 2B abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , yojN genes abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , rcsC genes abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , rcsB genes abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	15126450	31	ver/dev	On the other hand , LeuO has only been found for ompS2 , although there is the distinct possibility that there is such a regulator for ompS1 .	310	On the other hand , a positive regulator such as LeuO has only been found for ompS2 , although there is the distinct possibility that there is such a regulator for ompS1 .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS1	regulator	17908208	1	ver/dev	The expression of ompS1 was positively regulated by LeuO .	13	The expression of ompS1 was positively regulated by LeuO , a LysR-type quiescent regulator that has been involved in pathogenesis .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	17908208	8	ver/dev	We report here that LeuO are the main negative regulators of ompS1 expression in Salmonella .	48	We report here that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	3	B	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	17908208	8	ver/dev	We report here that LeuO are the main positive regulators of ompS1 expression in Salmonella .	48	We report here that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	3	B	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	17908208	13	ver/dev	To test whether LeuO regulated the ompS1 gene , LeuO was expressed in S. Typhi wild type from plasmid pFMTrcleuO-50	54	To test whether LeuO regulated the ompS1 gene , LeuO was expressed in S. Typhi wild type from plasmid pFMTrcleuO-50 induced with a gradient of IPTG concentrations ( 0 -- 100 mM ) , and the effect was determined on the expression of S. Typhi ompS1 -- lacZ ( pRO310 ) and ompS2 -- lacZ ( pFM413 ) gene reporter fusions ( Oropeza et al. , 1999 ; Fernández-Mora et al. , 2004 ) ( Fig. 1A ) .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	ompS1	regulator	17908208	14	ver/dev	Interestingly , the pRO310 ompS1 was also positively regulated by LeuO .	55	Interestingly , the pRO310 ompS1 -- lacZ fusion was also positively regulated by LeuO , but at higher concentrations of IPTG than previously reported for ompS2 .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	17908208	15	ver/dev	LeuO as a positive regulator of ompS1 in S. Typhi .	58	LeuO as a positive regulator of ompS1 and ompS2 in S. Typhi .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	20	ver/dev	Hence , LeuO regulated positively the ompS1 gene .	72	Hence , LeuO regulated positively the ompS1 gene .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	17908208	43	ver/dev	that LeuO bound upstream from the ompS1 regulatory region , overlapping with one binding site of StpA , but not interacting with the promoter region and promoting a change in the local DNA architecture	176	These data showed that the binding of H-NS and StpA was located at two sites and that LeuO bound upstream from the ompS1 regulatory region , overlapping with one binding site of H-NS and StpA , but not interacting with the promoter region and promoting a change in the local DNA architecture .	11	F	nan	1	L3	OTHER	Other	NEG	New	Level 1
LeuO	gene	ompS1	regulator	17908208	43	ver/dev	that LeuO bound upstream from the ompS1 regulatory region , overlapping with one binding site of H-NS , but not interacting with the promoter region and promoting a change in the local DNA architecture	176	These data showed that the binding of H-NS and StpA was located at two sites and that LeuO bound upstream from the ompS1 regulatory region , overlapping with one binding site of H-NS and StpA , but not interacting with the promoter region and promoting a change in the local DNA architecture .	11	F	nan	1	L3	OTHER	Other	NEG	New	Level 1
LeuO	gene	ompS1	regulator	17908208	79	ver/dev	The observation that both ompS1 were regulated by LeuO at different levels of induction opens the possibility that there is a regulon in S. enterica .	314	The observation that both ompS1 and ompS2 were regulated by LeuO at different levels of induction opens the possibility that there is a regulon in S. enterica , where various genes are expressed at different levels according to the concentration of LeuO in the bacterial cell .	13	DISCUSSION	Salmonella;Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS1	regulator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	18156266	3	ver/dev	LeuO regulates the ompS1 , ompS2 , dsrA , and rovA genes .	24	LeuO regulates the bgl and cadAB operons , as well as the ompS1 , ompS2 , dsrA , and rovA genes ( 5 , 12 , 27 , 45 , 50 , 55 ) , and has been shown to be part of a promoter relay mechanism that explains the coordinate expression of the ilvIH-leuO-leuABCD gene cluster ( 9 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	18156266	41	ver/dev	LeuO are involved in regulation of ompS1 .	349	LeuO and H-NS are involved in regulation of leuO and ompS1 ( 2 , 5 ) , in addition to bgl , cadC , dsrA , and rovA ( 27 , 45 , 50 , 55 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	19406898	4	ver/dev	LeuO regulate ompS1 expression	66	This region was of interest for further research in this work , because it is located in the vicinity of the binding sites of two main transcription factors , LeuO and H-NS , which regulate ompS1 expression ( De la Cruz et al. , 2007 ) .	9	DIMINISHED AND RESTORED OMPS1 DNA CURVATURE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	19406898	11	ver/dev	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was expressed LeuO at different concentrations of IPTG .	112	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-wt , pRO310-mt and pRO310-re fusions in the presence of cloned and expressed LeuO at different concentrations of IPTG ( Fig. 4 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	19406898	11	ver/dev	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-re fusions in the presence of cloned .	112	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-wt , pRO310-mt and pRO310-re fusions in the presence of cloned and expressed LeuO at different concentrations of IPTG ( Fig. 4 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	19406898	11	ver/dev	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-mt fusions in the presence of cloned .	112	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-wt , pRO310-mt and pRO310-re fusions in the presence of cloned and expressed LeuO at different concentrations of IPTG ( Fig. 4 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	19406898	11	ver/dev	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-wt fusions in the presence of cloned .	112	Hence , the effect of curvature on LeuO-mediated regulation of ompS1 was examined by evaluating the expression of the pRO310-wt , pRO310-mt and pRO310-re fusions in the presence of cloned and expressed LeuO at different concentrations of IPTG ( Fig. 4 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	19406898	20	ver/dev	Effect of DNA curvature on the binding of LeuO to ompS1 .	184	Effect of DNA curvature on the binding of H-NS , StpA and LeuO to ompS1 .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	regulator	19447191	4	ver/dev	Moreover it has been reported that LeuO are the main negative regulators of ompS1 expression in Salmonella .	96	Moreover it has been reported that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	6	4.2. LEUO	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS1	regulator	19447191	4	ver/dev	Moreover it has been reported that LeuO are the main positive regulators of ompS1 expression in Salmonella .	96	Moreover it has been reported that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	6	4.2. LEUO	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	STM3611	regulator	26441883	21	ver/dev	In Salmonella , CsrA is known to control the expression of STM3611 .	378	In Salmonella , CsrA is known to control the expression of the specific phosphodiesterase YhjH ( STM3611 ) , governing the synthesis of ( 3 ′ -5 ′ ) - cyclic-diguanosine monophosphate ( c-di-GMP ) , which reciprocally regulates flagella function and production of biofilm matrix components ( Jonas et al. , 2010 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
SsrB	gene	invF	repressor	28704543	6	ver/dev	Together , these results demonstrate that SsrB represses the transcription of invF .	126	Together , these results demonstrate that SsrB represses the transcription of the SPI-1 regulatory genes hilD , hilA and invF .	7	SSRB REPRESSES THE SPI-1 REGULATORY CASCADE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	invF	repressor	28704543	8	ver/dev	To determine whether SsrB indirectly represses the expression of invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by EMSAs .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	invF	repressor	28704543	8	ver/dev	To determine whether SsrB indirectly represses the expression of invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility-shift assays .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	invF	repressor	28704543	8	ver/dev	To determine whether SsrB directly represses the expression of invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by EMSAs .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	invF	repressor	28704543	8	ver/dev	To determine whether SsrB directly represses the expression of invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility-shift assays .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrB muta , whereas the expression of the hns-lux control fusion was similar in d ( S8 F , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrB muta , whereas the expression of the hns-lux control fusion was similar in d ( S8 F , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrB muta , whereas the expression of the hns-lux control fusion was similar in d d these two mutan , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrB muta , whereas the expression of the hns-lux control fusion was similar in d d these two mutan , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a Δssr , whereas the expression of the hns-lux control fusion was similar in d ( S8 F , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a Δssr , whereas the expression of the hns-lux control fusion was similar in d ( S8 F , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a Δssr , whereas the expression of the hns-lux control fusion was similar in d d these two mutan , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	42	ver/dev	As expected , the de-repression of the invF-lux intracellular expression was also evident in a Δssr , whereas the expression of the hns-lux control fusion was similar in d d these two mutan , which indicates that both d SsrB response regulat are required for intracellular repression of invF and that no other SPI-2-encoded factors are requir .	258	As expected , the de-repression of the invF-lux intracellular expression was also evident in a ΔssrA and a ΔssrB mutant , whereas the expression of the hns-lux control fusion was similar in the WT strain and these two mutants ( S8 Fig ) , which indicates that both the SsrA sensor kinase and SsrB response regulator are required for intracellular repression of invF and that no other SPI-2-encoded factors are required .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	invF	repressor	28704543	43	ver/dev	Together , these results show that SsrB simultaneously represses the expression of invF , respectively , inside Fig 8D .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	invF	repressor	28704543	43	ver/dev	Together , these results show that SsrB simultaneously represses the expression of invF , respectively , inside macrophages .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	invF	repressor	28704543	63	ver/dev	SsrB repress the expression of invF inside macrophages .	699	SsrA and SsrB repress the expression of invF inside macrophages .	25	SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	fimAICDHF	repressor	31661351	3	ver/dev	This demonstrates a considerably stronger repression of PefA protein expression by H-NS than by the combined action of the 5ʹUTR of the fimAICDHF mRNA and CsrB/CsrC .	122	This demonstrates a considerably stronger repression of PefA protein expression by H-NS than by the combined action of the 5ʹUTR of the fimAICDHF mRNA and CsrB/CsrC .	7	H-NS STRONGLY REPRESSES PEF FIMBRIAE EXPRESSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	araD	regulator	24272778	14	att	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	201	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
AraC	gene	araD	regulator	24272778	6	att	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	88	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	2	MAIN	Escherichia coli;Iris germanica;Escherichia coli;Iris germanica;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	csgD	regulator	14643403	11	ver/dev	Binding of H-NS to the intergenic region caused moderate activation of the regulated csgD promoter .	170	Binding of H-NS to the intergenic region caused moderate activation of the regulated csgD promoter .	18	6.3. HISTONE-LIKE NUCLEOID STRUCTURING PROTEIN (H-NS)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	26880544	0	att	In the absence of SsrA , unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD ( agfD ) , the master biofilm regulator by disrupting the silenced , H-NS-bound promoter .	11	In the absence of SsrA , unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD ( agfD ) , the master biofilm regulator by disrupting the silenced , H-NS-bound promoter .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	26880544	35	att	Similar binding behavior with D56A SsrB and SsrBc at the H-NS-bound csgD regulatory region was also	294	Similar binding behavior with D56A SsrB and SsrBc at the H-NS-bound csgD regulatory region was also	12	SSRB BINDS AN H-NS STIFFENED NUCLEOPROTEIN FILAMENT AT CSGD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	regulator	26880544	50	att	SsrB D56A and SsrBc condense H-NS-bound csgD DNA .	356	SsrB D56A and SsrBc condense H-NS-bound csgD DNA .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	26880544	0	ver/dev	factors _ required for biofilm formation specifically by activating csgD , the master biofilm regulator by disrupting the silenced , H-NS-bound promoter	11	In the absence of SsrA , unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD ( agfD ) , the master biofilm regulator by disrupting the silenced , H-NS-bound promoter .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	26880544	5	ver/dev	We further showed that H-NS was a negative regulator of csgD .	70	We further showed that H-NS was a negative regulator of csgD .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	regulator	26880544	15	ver/dev	H-NS differentially regulate csgD expression	215	SsrB and H-NS differentially regulate csgD expression	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	26880544	16	ver/dev	Furthermore , H-NS , was also known to regulate the expression of csgD in S. Typhimurium .	218	Furthermore , H-NS , a known repressor of SPI-2 genes ( Walthers et al. , 2007 ) , was also known to regulate the expression of csgD in E. coli and S. Typhimurium ( Ogasawara et al. , 2010 ; Gerstel et al. , 2003 ) .	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	gene	csgD	regulator	26880544	16	ver/dev	Furthermore , H-NS , was also known to regulate the expression of csgD in E. coli .	218	Furthermore , H-NS , a known repressor of SPI-2 genes ( Walthers et al. , 2007 ) , was also known to regulate the expression of csgD in E. coli and S. Typhimurium ( Ogasawara et al. , 2010 ; Gerstel et al. , 2003 ) .	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	gene	csgD	regulator	26880544	47	ver/dev	SsrB condenses H-NS bound csgD DNA .	345	SsrB condenses H-NS bound csgD DNA .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	26880544	55	ver/dev	It is worth mentioning here that in our AFM images , it was apparent that H-NS was still bound to some regions of the csgD promoter when SsrB condensed the DNA .	372	It is worth mentioning here that in our AFM images , it was apparent that H-NS was still bound to some regions of the csgD promoter when SsrB condensed the DNA ( Figure 6A ( ii ) ) .	16	THE IMPORTANCE OF ANTI-SILENCING IN GENE REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	regulator	28148244	0	ver/dev	H-NS regulate the transcription of csgD in S. typhimurium .	33	Global transcriptional regulators such as RpoS , OmpR , H-NS and IHF regulate the transcription of csgD in S. typhimurium [ 25 ] .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	regulator	31827464	0	ver/dev	The transcription of csgD is regulated by H-NS proteins in response to metabolic stress .	56	The transcription of csgD is regulated by ompR , integration host factor ( IHF ) , and histone-like nucleoid structuring ( H-NS ) proteins in response to environmental cues and metabolic stress .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	regulator	31827464	0	ver/dev	The transcription of csgD is regulated by H-NS proteins in response to environmental cues .	56	The transcription of csgD is regulated by ompR , integration host factor ( IHF ) , and histone-like nucleoid structuring ( H-NS ) proteins in response to environmental cues and metabolic stress .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	regulator	33751923	9	ver/dev	the nucleoid-associated protein H-NS _ alleviating its repressive effect on the csgD promoter , the master regulator of biofilm genes ,	404	In this state , it disconnects the nucleoid-associated protein H-NS , alleviating its repressive effect on the csgD promoter , the master regulator of biofilm genes , driving biofilm formation and establishment of a carrier state ( Lo $ ber et al. 2006 ; Desai et al. 2016 ) .	10	SSRAB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	11036033	3	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	366	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	18	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	14742546	5	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	365	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	16	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	15336432	6	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress	256	[ 12 ] Ma , D. , Alberti , M. , Lynch , C. , Nikaido , H. and Hearst , J.E. ( 1996 ) The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	16201927	3	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	279	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	28	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	18083849	2	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	632	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	20	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	18407759	1	ver/dev	Expression of acrAB-tolC is regulated by AcrR .	254	Expression of acrAB-tolC is regulated by the global regulator , MarA , which is a positive regulator ( Alekshun and Levy , 1999 ) and by AcrR ( decreased expression in 2a ) , which is a repressor specific for the acrAB operon ( Ma et al. , 1996 ) .	19	EFFLUX SYSTEMS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	TU	acrAB	regulator	18407759	4	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	584	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	18577510	2	ver/dev	Other regulators of AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
AcrR	TU	acrAB	regulator	19120970	10	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	268	Ma D. , Alberti M. , Lynch C. , Nikaido H. , Hearst J.E. ( 1996 ) The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	23	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	19230852	20	ver/dev	D. Ma , M. Alberti , C. Lynch , H. Nikaido , J.E. Hearst , The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals , Mol .	571	[ 54 ] D. Ma , M. Alberti , C. Lynch , H. Nikaido , J.E. Hearst , The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals , Mol .	33	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	19778917	0	ver/dev	Furthermore , a local repres-6 -- 10 sor , AcrR , has been identified to play a role in the regulation of acrAB genes .	25	Furthermore , a local repres-6 -- 10 sor , AcrR , has been identified to play a role in the regulation of acrAB genes .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	TU	acrAB	regulator	19778917	2	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	249	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	13	DIS 2005; 41 SUPPL 2: 120–6.	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	21148208	26	ver/dev	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	352	The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .	38	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	regulator	28631419	1	ver/dev	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor by the AraC/XylS-like regulators RamA , MarA , SoxS and	25	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor encoded nearby , and by the AraC/XylS-like regulators RamA , MarA , SoxS and	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	TU	acrAB	regulator	28631419	1	ver/dev	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor encoded nearby	25	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor encoded nearby , and by the AraC/XylS-like regulators RamA , MarA , SoxS and	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CspE	gene	yciF	regulator	30992363	1	ver/dev	Northern blotting experiments with rifampicin disclosed that the regulation of yciF expression is , most likely , due to the RNA-stabilizing activity of CspE .	14	Northern blotting experiments with rifampicin disclosed that the regulation of yciF expression is , most likely , due to the RNA-stabilizing activity of CspE .	1	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CspE	gene	yciF	regulator	30992363	2	ver/dev	Importantly , electrophoretic-mobility-shift assays indicated that purified CspE , directly binds yciF mRNA .	15	Importantly , electrophoretic mobility shift assays indicated that purified CspE , but not the F30V variant , directly binds yciF mRNA .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CspE	gene	yciF	regulator	30992363	7	ver/dev	It is unlikely that CspE regulates the transcription of yciF .	149	It is unlikely that CspE regulates the transcription of yciF .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CspE	gene	yciF	regulator	30992363	11	ver/dev	We further validated the direct binding of CspE to yciF mRNA .	189	We further validated the direct binding of CspE to yciF mRNA using the in vitro-transcribed full-length mRNA as a substrate in EMSA .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CspE	gene	yciF	regulator	30992363	12	ver/dev	These data demonstrated that CspE directly binds to the yciF mRNA through the Phe-30 residue in RNP2 .	192	These data demonstrated that CspE directly binds to the yciF mRNA through the Phe-30 residue in RNP2 that plays an important role , effectuating its nucleic acid binding property .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CspE	gene	yciF	regulator	30992363	15	ver/dev	CspE binds to yciF mRNA	211	S. Typhimurium -- encoded CspE binds to yciF mRNA , and the Phe-30 residue is essential for this role .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CspE	gene	yciF	regulator	30992363	23	ver/dev	Using EMSA with the full-length yciF mRNA , we were able to show a direct , robust binding of CspE to the mRNA .	300	Using EMSA with the full-length yciF mRNA , we were able to show a direct , cooperative , and robust binding of CspE to the mRNA mediated by the Phe-30 residue ( Fig. 4C ) .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CspE	gene	yciF	regulator	30992363	23	ver/dev	Using EMSA with the full-length yciF mRNA , we were able to show a direct , cooperative binding of CspE to the mRNA .	300	Using EMSA with the full-length yciF mRNA , we were able to show a direct , cooperative , and robust binding of CspE to the mRNA mediated by the Phe-30 residue ( Fig. 4C ) .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CpxR	gene	acrB	repressor	32468234	11	ver/dev	This may imply that regulators are working via reciprocal regulation where CpxR is downregulating acrB expression via MarA .	147	This may imply that regulators are working via reciprocal regulation where CpxR is downregulating acrB expression via SoxS and MarA ( Fig. 2 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	acrB	repressor	32468234	11	ver/dev	This may imply that regulators are working via reciprocal regulation where CpxR is downregulating acrB expression via SoxS .	147	This may imply that regulators are working via reciprocal regulation where CpxR is downregulating acrB expression via SoxS and MarA ( Fig. 2 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	acrB	repressor	34202800	17	ver/dev	Moreover , the lower activity of decrease in acrB expression was observed , which suggest that CpxR can decrease acrB expression via MarA regulation .	372	Moreover , the lower activity of the SoxS and MarA regulators and decrease in acrB expression was observed , which suggest that CpxR can decrease acrB expression via SoxS and MarA regulation [ 11 ] .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	acrB	repressor	34202800	17	ver/dev	Moreover , the lower activity of decrease in acrB expression was observed , which suggest that CpxR can decrease acrB expression via SoxS regulation .	372	Moreover , the lower activity of the SoxS and MarA regulators and decrease in acrB expression was observed , which suggest that CpxR can decrease acrB expression via SoxS and MarA regulation [ 11 ] .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	acrB	repressor	34202800	17	ver/dev	Moreover , the lower activity of the MarA regulators was observed , which suggest that CpxR can decrease acrB expression via MarA regulation .	372	Moreover , the lower activity of the SoxS and MarA regulators and decrease in acrB expression was observed , which suggest that CpxR can decrease acrB expression via SoxS and MarA regulation [ 11 ] .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	acrB	repressor	34202800	17	ver/dev	Moreover , the lower activity of the SoxS regulators was observed , which suggest that CpxR can decrease acrB expression via SoxS regulation .	372	Moreover , the lower activity of the SoxS and MarA regulators and decrease in acrB expression was observed , which suggest that CpxR can decrease acrB expression via SoxS and MarA regulation [ 11 ] .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rpoS	regulator	33638994	32	ver/dev	Moreover , the rpoS positive transcription depends primarily on RprA which transcriptional activation is controlled by RcsB .	541	Moreover , the rpoS positive transcription depends primarily on small RNAs such as RprA ( 67 ) which transcriptional activation is controlled by RcsB .	27	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ydhJ	regulator	29857034	15	ver/dev	For genes , we found two genes , ydhJ are negatively regulated by SlyA .	312	For genes involved in multidrug resistance , we found two genes , ydhJ and ydhI ( STM14_1740 ; STM14_1741 ) , which are transcribe divergent to slyA and are negatively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	yibD	activator	15681155	18	att	These loci represent PmrA-activated genes , like those identified in this study , that are regulated by PmrA at the transcriptional level and that do contain ( yibD ) or do not contain ( dgoRKAT ) the consensus binding site ( within a 200 bp region upstream of the translational start ) binding of PmrA to dgop1 , PmrA was incubated with dgop1 and specific or non-specific cold ( unlabeled ) competitors .	265	These loci represent PmrA-activated genes , like those identified in this study , that are regulated by PmrA at the transcriptional level and that do contain ( yibD ) or do not contain ( dgoRKAT ) the consensus binding site ( within a 200 bp region upstream of the translational start ) binding of PmrA to dgop1 , PmrA was incubated with dgop1 and specific or non-specific cold ( unlabeled ) competitors .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PmrA	gene	yibD	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	mutS	regulator	9765570	10	ver/dev	Negative regulation of mutS RpoS global regulators of Escherichia coli K-12 .	940	Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12 .	46	REFERENCES	Escherichia coli	0	L3	OTHER	Other	NEG	New	Level 1
RpoS	gene	mutS	regulator	9765570	10	ver/dev	Negative regulation of mutS RpoS global regulators of Escherichia coli K-12 .	940	Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12 .	46	REFERENCES	Escherichia coli	0	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	map	regulator	15703297	0	att	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5-7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8-10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in-vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	12	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5–7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8–10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Shigella flexneri;Yersinia pestis;Pectobacterium carotovorum;Neisseria meningitidis;Photorhabdus luminescens;Escherichia coli;Escherichia coli	0.5	L3	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	lacZ	activator	29324231	6	ver/dev	the addition of IPTG _ indicating that stimulation of the expression of lacZ reporter is likely due to the loss of H-NS activity	150	The increased pltB expression observed in these mutants did not require the addition of IPTG , indicating that stimulation of the expression of the pltB : lacZ reporter is likely due to the loss of H-NS activity .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgB	regulator	11254626	1	att	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	208	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	6	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgB	regulator	15130116	9	ver/dev	Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates other genes of srgB .	223	Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates accessory factors that may contribute to intestinal survival or colonization ( rck , pefI , srgA ) and other genes of unknown function ( srgB -- E ) .	5	THE SALMONELLA SDIA SYSTEM	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgB	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	STM3156	activator	22356617	6	att	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	358	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	dnaK	repressor	23385142	3	ver/dev	The heat-shock protein DnaK has been shown to inhibit RpoS proteolysis , with a significant decrease in RpoS stability in dnaK mutants .	39	The heat-shock protein DnaK has been shown to inhibit RpoS proteolysis , with a significant decrease in RpoS stability in dnaK mutants ( Rockabrand et al. , 1998 ) .	4	1. INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SsrB	gene	spiR	activator	33045730	7	ver/dev	S. Typhimurium acquired the spiR genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in purple , enables activation of virulence .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilD	regulator	12535071	88	ver/dev	HilC do not seem to regulate expression of hilD .	251	HilD and HilC do not seem to regulate expression of hilD or prgH ( Olekhnovich and Kadner , 2002 ) ( Figs 1 and 2B ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Other	NEG	New	Level 1
HilC	gene	hilD	regulator	15661008	15	ver/dev	These results indicate that Lon is involved in the autoregulation of hilD transcription by modulating amounts of HilC .	181	These results indicate that Lon is involved in the autoregulation of hilC and hilD transcription by modulating amounts of HilC and HilD .	7	LEVEL OF HILC AND HILD TRANSCRIPTION IN WILD-TYPE AND LON-DISRUPTED MUTANT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilD	regulator	17208038	32	ver/dev	Thus , HilC are also apparently indirectly regulating hilD , contributing to the feedforward loop .	163	Thus , HilC and RtsA are also apparently indirectly regulating hilD , contributing to the feedforward loop .	11	REGULATION OF HILD	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilC	gene	hilD	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilD by HilC .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilD	regulator	17993530	29	ver/dev	Again , when hilD was deleted in these strains , Fur regulation of hilD was abrogated , while overproduction of HilC still induced hilD expression .	221	Again , when hilD was deleted in these strains , Fur regulation of hilD was abrogated , while overproduction of HilC still induced hilD expression .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	regulator	17993530	30	ver/dev	When the hilD translational fusion was placed under control of the lacUV5 promoter , overproduction of HilC had no effect .	222	When the hilD translational fusion was placed under control of the lacUV5 promoter , overproduction of Fur or HilC had no effect .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilC	gene	hilD	regulator	22479568	0	ver/dev	HilC can activate expression of hilD of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilD	regulator	27341691	4	ver/dev	The regulation of hilD is complex ; hilD is also regulated by the transcriptional regulators HilC and RtsA .	148	The regulation of hilD is complex ; hilD regulates itself but is also regulated by the transcriptional regulators HilC and RtsA , which constitute a feed-forward circuit to control the downstream SPI1 regulator HilA ( Ellermeier et al. , 2005 ; Ellermeier and Slauch , 2007 ) .	7	PAT POST-TRANSCRIPTIONALLY REGULATES HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	regulator	27341691	4	ver/dev	The regulation of hilD is complex ; hilD is also regulated by the transcriptional regulators HilC and RtsA .	148	The regulation of hilD is complex ; hilD regulates itself but is also regulated by the transcriptional regulators HilC and RtsA , which constitute a feed-forward circuit to control the downstream SPI1 regulator HilA ( Ellermeier et al. , 2005 ; Ellermeier and Slauch , 2007 ) .	7	PAT POST-TRANSCRIPTIONALLY REGULATES HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	regulator	27341691	4	ver/dev	The regulation of hilD is complex ; hilD is also regulated by the transcriptional regulators HilC and RtsA .	148	The regulation of hilD is complex ; hilD regulates itself but is also regulated by the transcriptional regulators HilC and RtsA , which constitute a feed-forward circuit to control the downstream SPI1 regulator HilA ( Ellermeier et al. , 2005 ; Ellermeier and Slauch , 2007 ) .	7	PAT POST-TRANSCRIPTIONALLY REGULATES HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
TviA	TU	flhDC	repressor	20808848	2	ver/dev	Under conditions of low-osmolarity , TviA is represses flhDC transcription , thereby negatively regulating flagella biosynthesis .	54	Under conditions of low osmolarity , TviA is expressed and represses flhDC transcription , thereby negatively regulating flagella biosynthesis [ 8,11 ] .	7	TVIA ALTERS EXPRESSION OF S. TYPHIMURIUM FLHC AND MOTILITY IN RESPONSE TO OSMOLARITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
TviA	TU	flhDC	repressor	22479568	13	ver/dev	TviA affects flagellar genes by repressing the transcription of flhDC .	229	TviA affects flagellar genes by repressing the transcription of flhDC .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	TU	flhDC	repressor	24643532	1	ver/dev	TviA exerts its effect on flagellar gene regulation in conjunction with RcsB by repressing transcription of the flagellar master regulators flhDC .	179	TviA exerts its effect on flagellar gene regulation in conjunction with RcsB by repressing transcription of the flagellar master regulators flhDC , which control the expression of flagellar genes ( 15 , 16 ) .	4	8	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	TU	flhDC	repressor	24992093	3	ver/dev	Expression of TviA results in diminished flagellin secretion due to downregulation of the flagellar regulon by repressing transcription of the flhDC genes .	123	Expression of TviA results in diminished motility and flagellin secretion due to downregulation of the flagellar regulon by repressing transcription of the flhDC genes [ 42,44 ] .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	TU	flhDC	repressor	24992093	3	ver/dev	Expression of TviA results in diminished motility secretion due to downregulation of the flagellar regulon by repressing transcription of the flhDC genes .	123	Expression of TviA results in diminished motility and flagellin secretion due to downregulation of the flagellar regulon by repressing transcription of the flhDC genes [ 42,44 ] .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	TU	flhDC	repressor	24992093	7	ver/dev	Gene expression profiling experiments suggest that TviA affects transcription of T3SS-1 genes through the following signaling cascade : By repressing transcription of flhDC , TviA downregulates expression of FliZ .	155	Gene expression profiling experiments suggest that TviA affects transcription of T3SS-1 genes through the following signaling cascade [ 42 ] : By repressing transcription of flhDC , TviA downregulates expression of FliZ .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
TviA	TU	flhDC	repressor	32021316	0	ver/dev	TviA can repress flagellar regulator flhDC -LRB- which finally activated promotors -RRB- ,54 .	85	TviA can repress flagellar regulator flhDC , the master regulator ( which finally activated promotors ) ,54 and alter the expression of T3SS and Vi in response to osmolarity .	11	VI ANTIGEN (CAPSULE)	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RamA	gene	ramA	activator	18984645	8	att	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	315	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	17	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	18984645	8	ver/dev	bile-mediated 52 regulation of AcrAB in Salmonella is also that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium	315	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	17	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	19778917	1	ver/dev	the ramA promoter region led to activation of RamA in a single	198	A similar observation was made by Zheng et al. , who detected 14 a 9 bp deletion in the ramA promoter region that led to activation of RamA in a single Salmonella Typhimurium strain .	9	TETRACYCLINE RESISTANCE GENE IN SALMONELLA PARATYPHI B 5	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	ramA	activator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	activator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	activator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be amplified by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	Phaeoacremonium santali	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be amplified by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be relayed by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	Phaeoacremonium santali	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be relayed by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be amplified by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	Phaeoacremonium santali	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be amplified by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be amplified by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	Phaeoacremonium santali	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be amplified by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be relayed by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	Phaeoacremonium santali	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be relayed by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be relayed by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	Phaeoacremonium santali	0	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	activator	24816212	7	ver/dev	At the transcriptional level , the induction of ramA expression may be relayed by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .	273	At the transcriptional level , the induction of ramA expression may be relayed and amplified by StyR-3 , a 144 bp non-coding RNA ( ncRNA ) likely processed from ′ the 5 untranslated region ( 5 ′ - UTR ) of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At the protein level , Ricci et al. 28 revealed a higher order of RamA regulation mediated by the Lon protease , the direct proteolytic action of which on RamA remains , however , to be demonstrated .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	csgBA	activator	11489123	14	ver/dev	Normark , S s - dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in-vivo by s in the absence of 70 the nucleoid-associated protein H-NS .	391	Arnqvist , A. , Olsén , A. , and Normark , S. ( 1994 ) s - dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in vivo by s in the absence of 70 the nucleoid-associated protein H-NS .	26	REFERENCES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	TU	csgBA	activator	11489123	14	ver/dev	Arnqvist , A. , Olsén , A. s - dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in-vivo by s in the absence of 70 the nucleoid-associated protein H-NS .	391	Arnqvist , A. , Olsén , A. , and Normark , S. ( 1994 ) s - dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in vivo by s in the absence of 70 the nucleoid-associated protein H-NS .	26	REFERENCES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	TU	csgBA	activator	23230292	1	ver/dev	Sigma S-dependent growthphase induction of the csgBA promoter in Escherichia coli can be achieved in-vivo by sigma-70 in the absence of the nucleoid-associated protein H-NS .	713	Sigma S-dependent growthphase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS .	50	REFERENCES	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	sopB	activator	20221735	3	ver/dev	Among the SPI-5 genes , primer-extension analysis revealed that sopB were induced at entry into the stationary-phase under standard growt conditions independently of RpoS .	314	Among the SPI-5 genes , which include pipA ~ D and sopB ( Wood et al. , 1998 ) , primer extension analysis revealed that sopB and pipC were induced at entry into the stationary phase under standard growt conditions independently of RpoS .	9	DISCUSSION	synthetic construct	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	yciG	regulator	11260470	6	att	The 210 and 235 regions of the putative RpoS-regulated promoter of yciG ( yciGp1 ) are underlined .	259	The 210 and 235 regions of the putative RpoS-regulated promoter of yciG ( yciGp1 ) are underlined .	9	IDENTIFICATION OF A PUTATIVE RPOS-DEPENDENT PROMOTER UPSTREAM OF THE YCIGFEKATN OPERON	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HilC	gene	lacZ	activator	12535071	56	att	To better define the sequences required for HilD - and HilC-dependent activation of invF , we cloned 919 bp from upstream of the invF ORF in front of a lacZ reporter gene in the pRW50 vector ( Lodge et al. , 1992 ) .	147	To better define the sequences required for HilD - and HilC-dependent activation of invF , we cloned 919 bp from upstream of the invF ORF in front of a lacZ reporter gene in the pRW50 vector ( Lodge et al. , 1992 ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	sufC	regulator	26026834	0	ver/dev	sufC was not regulated by either RpoS alone	55	In a screen for genes coregulated by RpoE and RpoS in S. Typhi under hyperosmotic stress , we found obvious decreased expression of sufC , which was not regulated by either RpoE or RpoS alone [ 10 ] .	7	2.2. SUFC MAY PROMOTE S. TYPHI SURVIVAL IN MACROPHAGES	nan	1	L3	OTHER	Other	NEG	Other	Level 1
DksA	gene	ilvD	activator	29487237	3	ver/dev	Our data suggest that ppGpp acts in concert with DksA for activation of the ilvD promoters , an observation .	289	Our data suggest that ppGpp acts in concert with DksA for activation of the ivbL and ilvD promoters , an observation that is consistent with the auxotrophies of dksA and relA spoT mutants for leucine and valine ( 56 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	araC	activator	19103774	0	att	PphoPQ107 : : TT araC PBAD phoPQ and 9108 with the PphoPQ107 : : TT araC PBAD phoPQ and Pcrp527 : : TT araC PBAD crp mutations when streaked on X-P plates without and with 0.2 % arabinose reveal acid phosphatase activity due to expression of the PhoP-activated phoN gene only when grown in the presence of arabinose ( Fig. 2c ) .	130	PphoPQ107 : : TT araC PBAD phoPQ and 9108 with the PphoPQ107 : : TT araC PBAD phoPQ and Pcrp527 : : TT araC PBAD crp mutations when streaked on X-P plates without and with 0.2 % arabinose reveal acid phosphatase activity due to expression of the PhoP-activated phoN gene only when grown in the presence of arabinose ( Fig. 2c ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoR	gene	mgtC	regulator	31346161	8	att	We speculated that such an increase in the mRNA levels of the PhoB / PhoR-controlled genes during infection might be due to the presence of the MgtC protein because the mgtC gene is one of the most highly expressed genes inside macrophages18 , and also because MgtC activates PhoR autophosphorylation to promote PhoB-dependent gene expression ( Figs. 1 and 4 ) .	289	We speculated that such an increase in the mRNA levels of the PhoB / PhoR-controlled genes during infection might be due to the presence of the MgtC protein because the mgtC gene is one of the most highly expressed genes inside macrophages18 , and also because MgtC activates PhoR autophosphorylation to promote PhoB-dependent gene expression ( Figs. 1 and 4 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	csgD	activator	27206164	24	att	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	csgD	activator	27206164	10	ver/dev	The biofilm master regulatory gene csgD is activated by unphosphorylated RcsB .	66	The biofilm master regulatory gene csgD is activated by unphosphorylated RcsB , but repressed upon RcsB phosphorylation ( Latasa et al. , 2012 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	fljB	regulator	24031550	0	ver/dev	underlying the expressional regulation of fljB , gene deletion mutants of FlhDC were constructed in this study .	8	underlying the expressional regulation of fljB : z66 , gene deletion mutants of the regulators FliA , FlhDC , and OmpR were constructed in this study .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	fljB	regulator	24031550	6	ver/dev	To investigate whether fljB is regulated by FlhDC	245	To investigate whether fljB : z66 is regulated by FlhDC and FliA	5	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilC	gene	sopB	regulator	24947562	0	ver/dev	However , it is important to mention that sopB , is cooperatively regulated by lowered levels of HilC were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control .	232	However , it is important to mention that sopB , is cooperatively regulated by InvF and HilA [ 30 ] and lowered levels of all SPI-1-encoded transcriptional regulators ( HilA , HilC , HilD , and InvF ) were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control [ 24 ] .	19	4. DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR-P	gene	spiC	activator	12753201	0	ver/dev	In the present work , we demonstrate that OmpR-P functions as an activator at the spiC -- ssrA / B locus .	9	In the present work , we demonstrate that phospho-OmpR ( OmpR-P ) functions as an activator at the spiC -- ssrA / B locus .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR-P	gene	spiC	activator	15491370	8	ver/dev	OmpR-P also activates spiC , although it has not been established whether this is a indirect effect -LRB- denoted by a dashed arrow -RRB- .	87	OmpR-P also activates spiC , although it has not been established whether this is a direct or indirect effect ( denoted by a dashed arrow ) .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
OmpR-P	gene	spiC	activator	15491370	8	ver/dev	OmpR-P also activates spiC , although it has not been established whether this is a direct effect -LRB- denoted by a dashed arrow -RRB- .	87	OmpR-P also activates spiC , although it has not been established whether this is a direct or indirect effect ( denoted by a dashed arrow ) .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	invE	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	cat	repressor	28704543	12	ver/dev	the hilD-cat-364 +88 fusion showed repression by SsrB	147	To determine whether SsrB represses hilD through these two putative SsrB-binding sites , three different cat transcriptional fusions were constructed , each with distinct 5 ' and 3 ' deletions of the hilD-cat-364 +88 fusion that showed repression by SsrB ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	ssaG	activator	23690578	29	att	Iron regulates expression of the SPI-2 ssaG gene in a PmrA-dependent manner .	103	Iron regulates expression of the SPI-2 ssaG gene in a PmrA-dependent manner .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	virK	activator	15225317	5	att	Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .	35	Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .	3	2 ND POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	virK	activator	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- virK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	virK	activator	21511762	0	att	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	217	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	4	METHODS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	virK	activator	23782700	0	att	Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. Typhimurium strain that harbors a reporter transcriptional lacZ fusion to virK , a previously characterized PhoP-activated gene ( 12 , 34 ) .	161	Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. Typhimurium strain that harbors a reporter transcriptional lacZ fusion to virK , a previously characterized PhoP-activated gene ( 12 , 34 ) .	3	EXPERIMENTAL PROCEDURES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	23782700	2	att	A , - galactosidase activity from lacZ-transcriptional-fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	168	A , - galactosidase activity from lacZ transcriptional fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	virK	activator	23782700	3	att	Additionally , as shown in Fig. 3A , PhoP-activated genes other than virK were down-regulated by linoleic acid ( C18 :2 ) , confirming the specific action of the LCUFAs on the PhoP-regulon .	193	Additionally , as shown in Fig. 3A , PhoP-activated genes other than virK were down-regulated by linoleic acid ( C18 :2 ) , confirming the specific action of the LCUFAs on the PhoP-regulon .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	virK	activator	24185747	0	att	Methods -- The TLC plates were covered by a staining solution containing agar , Luria-Bertani medium , 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside ( X-gal ) , kanamycin and a S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to an archetypal PhoP-activated gene virK .	15	Methods -- The TLC plates were covered by a staining solution containing agar , Luria-Bertani medium , 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside ( X-gal ) , kanamycin and a S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to an archetypal PhoP-activated gene virK .	2	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	24185747	1	att	( a ) Bioautography carried out with the S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to a PhoP-activated gene virK .	54	( a ) Bioautography carried out with the S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to a PhoP-activated gene virK .	7	PLANT MATERIAL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	24185747	2	att	After development the solvent was removed and the plate was revealed by bioautography with a S. Typhimurium strain that harbours a reporter transcriptional lacZ-fusion to a PhoP-activated gene virK as described in the Methods section .	59	After development the solvent was removed and the plate was revealed by bioautography with a S. Typhimurium strain that harbours a reporter transcriptional lacZ-fusion to a PhoP-activated gene virK as described in the Methods section .	7	PLANT MATERIAL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	virK	activator	24185747	3	att	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB-medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	87	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	12	STAINING SOLUTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Chryseobacterium gallinarum	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	24185747	4	att	Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to an archetypal PhoP-activated gene virK .	102	Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to an archetypal PhoP-activated gene virK .	13	RESULTS AND DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	24185747	3	ver/dev	of the S. typhimurium str in that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK or to a gene activated by the O	87	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	12	STAINING SOLUTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	virK	activator	31611347	0	att	In a first round of screening , isogenic Salmonella Typhimurium MS14028 strains carrying transcriptional lacZ-fusions to virK , a representative PhoP-activated gene , were grown in lysogeny broth ( LB ) supplemented with a 50 M concentration of each compound .	63	In a first round of screening , isogenic Salmonella Typhimurium MS14028 strains carrying transcriptional lacZ fusions to virK , a representative PhoP-activated gene , were grown in lysogeny broth ( LB ) supplemented with a 50 M concentration of each compound .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	31611347	1	att	We set 35 % inhibition of virK reporter activity levels as the threshold for compound progression and performed a second round of selection that included a second PhoP-dependent reporter ( pagC-lacZ ) and a PhoP/PhoQ-unrelated transcriptional reporter ( tppB-lacZ ) , whose expression is regulated by the EnvZ/OmpR TCS ( 28 , 29 ) , to exclude compounds that might cause indiscriminate inhibition of HKs ( Data Set S1 ) .	66	We set 35 % inhibition of virK reporter activity levels as the threshold for compound progression and performed a second round of selection that included a second PhoP-dependent reporter ( pagC-lacZ ) and a PhoP/PhoQ-unrelated transcriptional reporter ( tppB-lacZ ) , whose expression is regulated by the EnvZ/OmpR TCS ( 28 , 29 ) , to exclude compounds that might cause indiscriminate inhibition of HKs ( Data Set S1 ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	virK	activator	31611347	3	att	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ-transcriptional-fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	94	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ transcriptional fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	31611347	4	att	The inhibition action was calculated on the basis of the - galactosidase activity from lacZ-transcriptional-fusions to two different PhoP-activated genes ( virK and pagC ) and one PhoP-unrelated control reporter gene ( tppB ) .	129	The inhibition action was calculated on the basis of the - galactosidase activity from lacZ transcriptional fusions to two different PhoP-activated genes ( virK and pagC ) and one PhoP-unrelated control reporter gene ( tppB ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	activator	31611347	5	att	S4A , we determined that GI261520A downregulated the expression of the representative PhoP-activated virK gene in - galactosidase activity assays performed in the S. Typhimurium STM23 , S. Enteritidis Pt4 , and S. Dublin Sdu5 strain backgrounds ( linoleic acid , a known PhoP/PhoQ inhibitor , was used as control [ 27 ] ) .	205	S4A , we determined that GI261520A downregulated the expression of the representative PhoP-activated virK gene in - galactosidase activity assays performed in the S. Typhimurium STM23 , S. Enteritidis Pt4 , and S. Dublin Sdu5 strain backgrounds ( linoleic acid , a known PhoP/PhoQ inhibitor , was used as control [ 27 ] ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	ugtL	activator	19843227	18	att	Our data show that ugtL is StpA-dependent , as are other genes involved in LPS modification including pagC and pagP .	107	Our data show that ugtL is StpA-dependent , as are other genes involved in LPS modification including pagC and pagP .	8	STPA REPRESSES GENES REQUIRED FOR CELL ENVELOPE MODIFICATION AND RESISTANCE TO CATIONIC PEPTIDES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	ivbL	activator	29487237	3	ver/dev	Our data suggest that ppGpp acts in concert with DksA for activation of the ivbL promoters , an observation .	289	Our data suggest that ppGpp acts in concert with DksA for activation of the ivbL and ilvD promoters , an observation that is consistent with the auxotrophies of dksA and relA spoT mutants for leucine and valine ( 56 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	ftnA	activator	17302823	0	att	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	ftnA	activator	17302823	1	att	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Other	OTHER	Other	Level 1
Fur	gene	ftnA	activator	17302823	0	ver/dev	Thus , ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	ftnA	activator	17302823	1	ver/dev	Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
Fur	gene	ftnA	activator	17302823	1	ver/dev	Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the Δemr strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , botto panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	phoP	activator	30992361	12	ver/dev	the wild-type strains -LRB- Fig. 3A , middl panels ruled out the possibility that EmrR could stimulate phoP transcriptio	115	Also , the slyA and phoP mRNA levels were similar in the wild-type and ΔemrR strains ( Fig. 3A , middle and bottom panels ) , which ruled out the possibility that EmrR could stimulate slyA and phoPQ transcription .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	fimA	activator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of fimA genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	fimA	activator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of fimA genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
YdcI	gene	gltA	regulator	30038032	4	ver/dev	Previously in E. coli , YdcI was shown to regulate the expression of gltA carbon flux to the TCA cycle .	310	Previously in E. coli , YdcI was shown to regulate the expression of gltA and control carbon flux to the TCA cycle ( 25 ) .	7	REPRESSION OF THE ETHANOLAMINE UTILIZATION OPERON BY ARCA—	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsB	gene	flgM	regulator	27601571	16	ver/dev	We also observed negative regulation of flgM by RtsB .	180	We also observed negative regulation of flgM and yddX by RtsB ( Fig. 2 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilC	gene	hilA	repressor	10844688	18	ver/dev	If a condition exists in which hilA is repressed while invF expression is induced through HilC , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilC	gene	hilA	repressor	20008574	1	ver/dev	Transcriptional activation by HilC relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha .	36	Transcriptional activation by HilC and HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	repressor	21168230	6	ver/dev	In addition , a role of HilC mediated repression of hilA was not investigated .	417	In addition , a role of HilC mediated repression of hilA was not investigated .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilC	gene	hilA	repressor	25991823	1	ver/dev	HilC relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha .	25	HilC and HilD relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) and can activate expression of the invF and sicA/sip transcriptional units independently of HilA ( Rakeman et al. 1999 ; Akbar et al. 2003 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	repressor	28335027	10	ver/dev	H-NS repression of hilA counteracts transcriptional activation by HilC	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	repressor	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of rtsA .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	repressor	31428589	15	ver/dev	a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression through the degradation of HilC .	202	Lon protease , a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression and intracellular survival after the invasion of epithelial cells through the degradation of HilC and HilD ( Boddicker and Jones , 2004 ; Takaya et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	repressor	31428589	15	ver/dev	Lon protease , is important for the downregulation of hilA expression through the degradation of HilC .	202	Lon protease , a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression and intracellular survival after the invasion of epithelial cells through the degradation of HilC and HilD ( Boddicker and Jones , 2004 ; Takaya et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	repressor	33593291	12	ver/dev	Nonetheless , we tested whether HilC are necessary for repression of hilA expression by yeast extract in a ΔhilE mutant .	103	Nonetheless , we tested whether HilC or RtsA are necessary for repression of hilA expression by acetate and yeast extract in a ΔhilE mutant .	6	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilC	gene	hilA	repressor	33593291	12	ver/dev	Nonetheless , we tested whether HilC are necessary for repression of hilA expression by acetate extract in a ΔhilE mutant .	103	Nonetheless , we tested whether HilC or RtsA are necessary for repression of hilA expression by acetate and yeast extract in a ΔhilE mutant .	6	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	STM2585	regulator	27564394	11	ver/dev	Furthermore , STM2585 are regulated by the master regulators of the SsrB regulon .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM2585	regulator	27564394	11	ver/dev	Furthermore , STM2585 are regulated by the master regulators of the SsrB regulon .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	cat	regulator	30718301	74	ver/dev	pBR322 derivative containing a promoterless chloramphenicol acetyltransferase ( cat ) gene , Apr pKK232-8 derivative containing a ssrAB-cat transcriptional-fusion from nucleotides 302 to 478 pKK232-8 derivative containing a ssrAB-cat transcriptional-fusion from nucleotides 302 to 10 pKK232-8 derivative containing a ssaG-cat transcriptional-fusion from nucleotides 303 to 361 pKK232-8 derivative containing a pagK-cat transcriptional-fusion from nucleotides 880 to 251 p15A derivative low-copy-number cloning vector , lac promoter , Kanr pMPM-K3 derivative expressing SlyA from the lac promoter pMPM-K3 derivative expressing SsrB from the lac promoter pMPM-K3 derivative expressing PhoP from the lac promoter p15A derivative low-copy-number cloning vector , arabinose-inducible promoter , Tcr pMPM-T6 derivative expressing promoter WT H-NS from the arabinose-inducible pMPM-T6 derivative expressing H-NSG113D from the arabinose-inducible promoter Vector for expression of recombinant proteins , lac promoter , Apr pQE30 derivative expressing His-HA-SlyA from the lac promoter , Apr pBADMycHisC derivative expressing H-NS FH from an ara promoter , Apr pINT-ts derivative expressing red recombinase under the control of an arabinose-inducible promoter , pANTs derivative template plasmid containing the kanamycin cassette for Red recombination , Apr Plasmid expressing FLP recombinase from a temperature-inducible promoter , Apr	232	pBR322 derivative containing a promoterless chloramphenicol acetyltransferase ( cat ) gene , Apr pKK232-8 derivative containing a ssrAB-cat transcriptional fusion from nucleotides 302 to 478 pKK232-8 derivative containing a ssrAB-cat transcriptional fusion from nucleotides 302 to 10 pKK232-8 derivative containing a ssaG-cat transcriptional fusion from nucleotides 303 to 361 pKK232-8 derivative containing a pagK-cat transcriptional fusion from nucleotides 880 to 251 p15A derivative low-copy-number cloning vector , lac promoter , Kanr pMPM-K3 derivative expressing SlyA from the lac promoter pMPM-K3 derivative expressing SsrB from the lac promoter pMPM-K3 derivative expressing PhoP from the lac promoter p15A derivative low-copy-number cloning vector , arabinose-inducible promoter , Tcr pMPM-T6 derivative expressing promoter WT H-NS from the arabinose-inducible pMPM-T6 derivative expressing H-NSG113D from the arabinose-inducible promoter Vector for expression of recombinant proteins , lac promoter , Apr pQE30 derivative expressing His-HA-SlyA from the lac promoter , Apr pBADMycHisC derivative expressing H-NS FH from an ara promoter , Apr pINT-ts derivative expressing red recombinase under the control of an arabinose-inducible promoter , pANTs derivative template plasmid containing the kanamycin cassette for Red recombination , Apr Plasmid expressing FLP recombinase from a temperature-inducible promoter , Apr	6	STRAIN FOR EXPRESSION OF RECOMBINANT PROTEINS LABORATORY STRAIN	Felis catus;Felis catus;Felis catus;Felis catus;Felis catus;unidentified cloning vector;unidentified cloning vector;unidentified plasmid;unidentified plasmid	0.5	L3	OTHER	Other	OTHER	New	Level 2
TviA	gene	hilA	regulator	24992093	8	ver/dev	The regulatory protein FliZ is an activator of hilA , thus placing T3SS-1 gene expression under negative control of TviA ( Fig .	156	The regulatory protein FliZ is an activator of hilA [ 48 -- 50 ] , the master regulator of T3SS-1 genes [ 51,52 ] , thus placing T3SS-1 gene expression under negative control of TviA ( Fig .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	dctA	activator	19843227	42	att	( ii ) Regulation of CRP-cAMP-dependent genes ( e.g. glpF , dctA , mglA ) is restricted to the late exponential phase .	302	( ii ) Regulation of CRP-cAMP-dependent genes ( e.g. glpF , dctA , mglA ) is restricted to the late exponential phase .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	polB	activator	24272778	46	ver/dev	polB are positively regulated by AraC due to partial read-through of Rho-independent terminators .	423	ygeA and polB are positively regulated by AraC and arabinose due to partial read-through of Rho-independent terminators ( Fig. 2 , 4 , and 5 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MprA	gene	hlyE	activator	11882648	3	ver/dev	E. coli MprA proteins activate expression of hlyE , thereby conferring a hemolytic phenotype on E. coli .	35	Overproduction of S. typhimurium SlyA , Actinobacillus pleuropneumoniae FNR ( HlyX ) , or E. coli MprA proteins activate expression of hlyE , thereby conferring a hemolytic phenotype on E. coli ( 8 -- 11 ) .	2	MAIN	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hmp	activator	17024490	5	ver/dev	RpoS , known to aVect hmp expression , apparently are not involved in the hmpEc induction by NO .	43	Other regulators such as RpoS and IHF , known to aVect hmp expression , apparently are not involved in the hmpEc induction by NO ( Memb-rillo-Hernández et al. 1996 , 1997a ) .	4	INTRODUCTION	nan	1	L2	OTHER	Fact	NEG	Other	Level 1
FlhDC	gene	STM1344	regulator	25437188	45	ver/dev	STM1344 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .	552	STM1344 ( YdiV ) and Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis [ 168,174 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	STM1344	regulator	25437188	45	ver/dev	STM1344 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .	552	STM1344 ( YdiV ) and Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis [ 168,174 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	STM1344	regulator	25437188	49	ver/dev	Besides positive regulation of FlhDC , CsrA indirectly inhibits the expression of several GGDEF and/or EAL domain proteins STM1344 .	559	Besides positive regulation of FlhDC , CsrA directly or indirectly inhibits the expression of several GGDEF and/or EAL domain proteins involved in motility repression including the DGCs STM4551 and STM1987 and the degenerated EAL proteins STM1344 and STM1697 .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	NEG	New	Level 1
FlhDC	gene	STM1344	regulator	25437188	49	ver/dev	Besides positive regulation of FlhDC , CsrA directly inhibits the expression of several GGDEF and/or EAL domain proteins STM1344 .	559	Besides positive regulation of FlhDC , CsrA directly or indirectly inhibits the expression of several GGDEF and/or EAL domain proteins involved in motility repression including the DGCs STM4551 and STM1987 and the degenerated EAL proteins STM1344 and STM1697 .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	recA	activator	10852882	2	ver/dev	In E. coli , recA null mutants are unable to stimulate the LexA cleavage reaction .	330	In E. coli , recA null mutants are unable to stimulate the LexA cleavage reaction and are unable to establish the SOS response .	7	DISCUSSION	Escherichia coli	0	L2	OTHER	Other	NEG	Other	Level 1
LexA	gene	recA	activator	16713610	1	att	To further determine whether this induction was LexA-dependent , a lexA ( Ind ) S. enterica derivative was constructed ( Table 2 ) , and its recA expression after bacteriophage infection was also analyzed .	64	To further determine whether this induction was LexA-dependent , a lexA ( Ind ) S. enterica derivative was constructed ( Table 2 ) , and its recA expression after bacteriophage infection was also analyzed .	4	RESULTS AND DISCUSSION	Salmonella;Salmonella;Bacteriophage sp.	0.5	L3	SPEC	Analysis	OTHER	Other	Level 1
Hha	gene	hilA	regulator	15765064	27	ver/dev	Importantly , Hha has been shown to bind to the hilA promoter .	149	Importantly , Hha has been shown to bind to the hilA promoter ( Fahlen et al. , 2001 ) .	7	NEGATIVE REGULATORS OF INVASION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Hha	gene	hilA	regulator	16949866	7	ver/dev	The hilA promoter is directly controlled by Hha .	53	The hilA promoter is a target site for numerous evolutionarily conserved `` housekeeping '' regulators , and is directly controlled by BarA/SirA , Hha , RtsAB , and Fis ( Baxter et al. , 2003 ; Fahlen et al. , 2001 ; Olekhnovich and Kadner , 2006 ; Teplitski et al. , 2003 ) .	5	CORRESPONDING AUTHOR. TEL.: +1 352 392 1951X254; FAX: +1 352 392 3902.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Hha	gene	hilA	regulator	17675384	16	ver/dev	Nevertheless , Hha was able to bind to the S. enterica hilA promoter with high affinity .	292	Nevertheless , Hha was able to bind to the E. coli ler promoter and the S. enterica hilA promoter with high affinity ( 16 , 36 , 45 ) .	5	DISCUSSION	Salmonella;Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
Hha	gene	hilA	regulator	21680637	56	ver/dev	In spite of the fact that several reports have shown that Hha influences hilA expression , information is not yet available .	311	In spite of the fact that several reports have shown that Hha , H-NS or an H-NS/Hha complex influences hilA expression ( Fahlen et al. , 2001 ; Olekhnovich & Kadner , 2006 ; Schechter et al. , 2003 ) , information integrating the role of H-NS/Hha-mediated hilA modulation in the bacterial response to different environmental inputs is not yet available .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
Hha	gene	hilA	regulator	23515315	1	ver/dev	Hha mutants with a diminished positively charged surface can no longer regulate hilA .	15	Hha mutants with a diminished positively charged surface maintain the ability to interact with H-NS but can no longer regulate hilA .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	New	Level 1
IHF	gene	ssrA	repressor	21212121	17	ver/dev	There is a much closer correspondence between the effects of IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either IHF , as are the genes .	363	There is a much closer correspondence between the effects of HU and IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU or IHF , as are the genes coding for the secretion apparatus and the effector proteins .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	ssrA	repressor	21212121	17	ver/dev	There is a much closer correspondence between the effects of HU among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either IHF , as are the genes .	363	There is a much closer correspondence between the effects of HU and IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU or IHF , as are the genes coding for the secretion apparatus and the effector proteins .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	11755416	4	ver/dev	pH coordinately affect the transcription of hilA in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .	155	Osmolarity , oxygen and pH coordinately affect the transcription of hilA and changes in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	regulator	11755416	4	ver/dev	oxygen coordinately affect the transcription of hilA in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .	155	Osmolarity , oxygen and pH coordinately affect the transcription of hilA and changes in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	regulator	11755416	4	ver/dev	Osmolarity coordinately affect the transcription of hilA in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .	155	Osmolarity , oxygen and pH coordinately affect the transcription of hilA and changes in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	regulator	12396235	0	ver/dev	Although a great deal is known about the complex regulation of hilA gene expression , very little is known about the HilA protein .	16	Although a great deal is known about the complex regulation of hilA gene expression , very little is known about the HilA protein .	2	MAIN	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilA	gene	hilA	regulator	12453229	5	ver/dev	Genes in SPI-5 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .	62	Genes in SPI-4 and SPI-5 are controlled by HilA , a transcriptional regulator encoded within SPI-1 , and by SirA , a regulator of hilA ( Ahmer et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	12453229	5	ver/dev	Genes in SPI-4 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .	62	Genes in SPI-4 and SPI-5 are controlled by HilA , a transcriptional regulator encoded within SPI-1 , and by SirA , a regulator of hilA ( Ahmer et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	16647227	0	ver/dev	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in internal organs in poultry , animals were infected with 10 CFU of its parent strain at day of hatch .	13	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut and internal organs in poultry , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis and its parent strain at day of hatch .	2	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	16647227	0	ver/dev	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in internal organs in poultry , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis .	13	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut and internal organs in poultry , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis and its parent strain at day of hatch .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	16647227	0	ver/dev	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut , animals were infected with 10 CFU of its parent strain at day of hatch .	13	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut and internal organs in poultry , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis and its parent strain at day of hatch .	2	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	16647227	0	ver/dev	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis .	13	HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut and internal organs in poultry , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis and its parent strain at day of hatch .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	20002188	3	ver/dev	Although the effect of INP0403 on hilA expression was not statistically significant , it remains feasible that it produces a biologically significant effect on T3S even though transcription of few genes under the control of HilA was significantly modulated .	177	Although the effect of INP0403 on hilA expression was not statistically significant , it remains feasible that it produces a biologically significant effect on T3S even though transcription of few genes under the control of HilA was significantly modulated .	20	EFFECT OF INP0403 ON TRANSCRIPTION OF KNOWN T3SS-1 REGULATORS	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
HilA	gene	hilA	regulator	22694285	0	ver/dev	Surprisingly , no correlation was found between the expression of SPI-1 genes hilA for a certain strain , although this can be due to the fact that expression of the effector protein SopB is only partly regulated by HilA .	426	Surprisingly , no correlation was found between the expression of SPI-1 genes hilA and sopB for a certain strain , although this can be due to the fact that expression of the effector protein SopB is only partly regulated by HilA [ 22 ] .	16	DISCUSSION	nan	1	L2	OTHER	Other	NEG	Other	Level 1
HilA	gene	hilA	regulator	23370732	0	ver/dev	As HilA is an important transcriptional regulator of SPI-1 , Bohez et al. discovered that Salmonella with hilA mutant is the promising vaccines due to its remarkable role in reducing colonization .	128	As HilA is an important transcriptional regulator of SPI-1 , Bohez et al. [ 4 ] discovered that Salmonella with hilA mutant is the promising vaccines due to its remarkable role in reducing invasion and colonization .	7	VACCINES OF SPI-1 MUTANTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	23370732	0	ver/dev	As HilA is an important transcriptional regulator of SPI-1 , Bohez et al. discovered that Salmonella with hilA mutant is the promising vaccines due to its remarkable role in reducing invasion .	128	As HilA is an important transcriptional regulator of SPI-1 , Bohez et al. [ 4 ] discovered that Salmonella with hilA mutant is the promising vaccines due to its remarkable role in reducing invasion and colonization .	7	VACCINES OF SPI-1 MUTANTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	27601571	29	ver/dev	However , RNA-seq data from a hilA strain with/without transient overexpression of HilA were consistent with regulation of transcripts within SPI-1 .	260	However , RNA-seq data from a hilA strain with/without transient overexpression of HilA were consistent with regulation of transcripts within SPI-1 ( see Table S1 in the supplemental material ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilA	gene	hilA	regulator	28426789	4	att	Our data show that Gre factors are involved in the transcriptional expression of both hilA and HilA-regulated genes .	194	Our data show that Gre factors are involved in the transcriptional expression of both hilA and HilA-regulated genes .	6	INVASION OF EPITHELIAL CELLS REQUIRES A BATTERY OF EFFECTOR PROTEINS ENCODED MAINLY BY GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	28575106	5	att	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	167	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	8	THE GENE LOIA IS THE VIRULENCE DETERMINANT IN SPI-14	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	29857034	43	att	We can infer that this negative regulation is a consequence of SlyA binding to the hilA promoter region ( Fig. 4C ) , which affects the expression of all HilA-regulated genes in a downstream cascade .	465	We can infer that this negative regulation is a consequence of SlyA binding to the hilA promoter region ( Fig. 4C ) , which affects the expression of all HilA-regulated genes in a downstream cascade .	29	4. DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	hilA	regulator	30223195	0	ver/dev	The protein HilA is an activator of Salmonella the regulator of hilA is Fur .	260	The protein HilA is an activator of Salmonella Pathogenicity Island 1 ( SPI1 ) and the regulator of hilA is Fur , which is required for virulence in S. Typhimurium and activation of hilA and the hilA-dependent genes invF and sipC ( Troxell et al. , 2011 ) .	26	3.3.5. TRANSPORTER AND REGULATION-RELATED PROTEINS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	31428589	1	ver/dev	The feed-forward regulatory loop of HilC -- RtsA -- HilD is the most important core part of the regulatory networks to control the transcription of hilA , while HilA is the central regulator of SPI-1 .	150	The feed-forward regulatory loop of HilC -- RtsA -- HilD is the most important core part of the regulatory networks to control the transcription of hilA , while HilA is the central regulator of SPI-1 ( Ellermeier et al. , 2005 ; Dieye et al. , 2007 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	31428589	13	ver/dev	Because environmental changes , influence because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the .	189	Because environmental changes , such as osmolarity , pH , and oxygen tension , influence the expression of hilA and because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the coordinated environmental regulatory effects of invasion genes ( Bajaj et al. , 1996 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	31428589	13	ver/dev	Because oxygen tension , influence because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the .	189	Because environmental changes , such as osmolarity , pH , and oxygen tension , influence the expression of hilA and because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the coordinated environmental regulatory effects of invasion genes ( Bajaj et al. , 1996 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	31428589	13	ver/dev	Because pH , influence because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the .	189	Because environmental changes , such as osmolarity , pH , and oxygen tension , influence the expression of hilA and because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the coordinated environmental regulatory effects of invasion genes ( Bajaj et al. , 1996 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	regulator	31428589	13	ver/dev	Because osmolarity , influence because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the .	189	Because environmental changes , such as osmolarity , pH , and oxygen tension , influence the expression of hilA and because constitutive expression of hilA substantially frees invasion genes from the control of these environmental signals , it has been supposed that HilA plays a central role in the coordinated environmental regulatory effects of invasion genes ( Bajaj et al. , 1996 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	yggX	activator	18835989	1	ver/dev	As previously reported , yggX mutant strains have increased expression of the SoxR reporter fpr .	115	As previously reported , yggX mutant strains have increased expression of the SoxR reporter fpr , which is exacerbated by a gshA mutation ( 37 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxR	gene	yggX	activator	18835989	2	ver/dev	These data indicated that the induction of the SoxR regulon in a yggX mutant strain was not due to the hydroxyl radical .	117	These data indicated that the induction of the SoxR regulon in a yggX mutant strain was not due to the hydroxyl radical resulting from iron-mediated Fenton chemistry and showed that not all phenotypes of a yggX mutant are the consequence of increased labile iron .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	ssaG	activator	23690578	8	att	Thus , we investigated expression of the SsrB-activated ssaG gene , which is the first gene of a large operon ( from ssaG to ssaU ) and encodes a component of the Spi/Ssa T3SS ( 22 ) .	51	Thus , we investigated expression of the SsrB-activated ssaG gene , which is the first gene of a large operon ( from ssaG to ssaU ) and encodes a component of the Spi/Ssa T3SS ( 22 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaG .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaG .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaG .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaG .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaG .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaG .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	28704543	43	ver/dev	Together , these results show that SsrB simultaneously induces the expression of ssaG , respectively , inside Fig 8D .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaG	activator	28704543	43	ver/dev	Together , these results show that SsrB simultaneously induces the expression of ssaG , respectively , inside macrophages .	259	Together , these results show that SsrB simultaneously represses and induces the expression of invF and ssaG , respectively , inside macrophages ( Fig 8D ) .	9	SSRB SIMULTANEOUSLY REPRESSES SPI-1 AND ACTIVATES SPI-2 INSIDE RAW264.7 MOUSE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaG	activator	30602583	1	att	In this reporter , GFP expression is driven by the promoter of the SsrB-activated gene ssaG ( 42 ) , and thus , GFP intensity serves as a proxy for SPI-2 activity .	278	In this reporter , GFP expression is driven by the promoter of the SsrB-activated gene ssaG ( 42 ) , and thus , GFP intensity serves as a proxy for SPI-2 activity .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaG	activator	33045730	76	att	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	333	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrA	activator	26880544	1	ver/dev	Under low osmolality , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrA	activator	26880544	1	ver/dev	Under acidic pH , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrA	activator	34202800	20	ver/dev	As a result , PhoP activate transcription of ssrA genes .	390	As a result , OmpR and PhoP activate transcription of ssrA and ssrB genes , leading to the formation of SsrA and SsrB .	11	3.3.4. THE ENVZ/OMPR SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrD	activator	15569938	0	att	The highly divergent PmrD protein is responsible for this phenotype as replacement of the E. coli pmrD gene by its Salmonella counterpart resulted in an E. coli strain that transcribed PmrA-activated genes and displayed poly-myxin B resistance under the same conditions as Salmonella .	12	The highly divergent PmrD protein is responsible for this phenotype as replacement of the E. coli pmrD gene by its Salmonella counterpart resulted in an E. coli strain that transcribed PmrA-activated genes and displayed poly-myxin B resistance under the same conditions as Salmonella .	1	ABSTRACT	Escherichia coli;Salmonella;Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	activator	15569938	13	att	This behavior is due to the highly divergent PmrD protein ( Figs. 6 and 7 ) , because replacement of the E. coli pmrD gene by the Salmonella pmrD gene endowed E. coli with the ability to transcribe the PmrA-activated pbgP gene and to exhibit resistance to polymyxin B in response to the low Mg2 signal ( Fig. 3 ) .	182	This behavior is due to the highly divergent PmrD protein ( Figs. 6 and 7 ) , because replacement of the E. coli pmrD gene by the Salmonella pmrD gene endowed E. coli with the ability to transcribe the PmrA-activated pbgP gene and to exhibit resistance to polymyxin B in response to the low Mg2 signal ( Fig. 3 ) .	5	DISCUSSION	Escherichia coli;Salmonella;Escherichia coli	0.5	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrD	activator	15569938	7	att	The Salmonella pmrD gene enables E. coli to promote transcription of the PmrA-activated pbgP gene and to be resistant to polymyxin B after 2 growth in low Mg .	138	The Salmonella pmrD gene enables E. coli to promote transcription of the PmrA-activated pbgP gene and to be resistant to polymyxin B after 2 growth in low Mg .	4	RESULTS	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	activator	15703297	13	att	Transcription of the pmrD gene is induced in low Mg2 in a PhoP-dependent fashion and repressed in the presence of Fe3 in a PmrA-dependent manner .	139	Transcription of the pmrD gene is induced in low Mg2 in a PhoP-dependent fashion and repressed in the presence of Fe3 in a PmrA-dependent manner .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	activator	18792679	19	att	4-76 These PmrA-dependent changes increases bacterial resistance to serum '' to the antibiotic polymyxin B3S .42,49.7 S. 78.79 and to Fe3 +.78 When Salmonella experiences low Mg '' , the PhoP protein binds to the pmrD promoter and stimulates pmrD transcription.v The purified PmrD protein binds specifically to the phosphorylated form ofthe PmrA protein ( PmrA-P ) and protects it from dephosphorylation by the sensor PmrB .72 Because PmrA-P exhibits higher affinity for its target promoters than unphosphorylated PmrA , transcription ofPmrA-activated genes is stimulated and that ofPmrA-repressed genes are inhibited .	231	4-76 These PmrA-dependent changes increases bacterial resistance to serum '' to the antibiotic polymyxin B3S .42,49.7 S. 78.79 and to Fe3 +.78 When Salmonella experiences low Mg '' , the PhoP protein binds to the pmrD promoter and stimulates pmrD transcription.v The purified PmrD protein binds specifically to the phosphorylated form ofthe PmrA protein ( PmrA-P ) and protects it from dephosphorylation by the sensor PmrB .72 Because PmrA-P exhibits higher affinity for its target promoters than unphosphorylated PmrA , transcription ofPmrA-activated genes is stimulated and that ofPmrA-repressed genes are inhibited .	9	PHOP AS A CO-ACTIVATOR PROTEIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	tolC	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , have been associated with tolC expression levels .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	tolC	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , MarA , have been associated with tolC expression levels .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	tolC	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , SoxS , have been associated with tolC expression levels .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	tolC	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , RamA , have been associated with tolC expression levels .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sipC	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	gatZ	regulator	27956522	11	ver/dev	These data showed that cAMP-CRP binds to the promoters of gatZ , .	180	These data showed that cAMP-CRP binds to the promoters of gatY , gatZ , and gatR , confirming that the expression of galactitol degradation is subject to catabolite repression .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrA	regulator	15205413	16	att	We have now established that both of these PmrA-controlled modifications are required for polymyxin B resistance , as a pbgP pmrC1 double mutant is as susceptible to polymyxin B as a pmrA null mutant ( Fig. 3B ) and has a lipid-A profile that is identical to that of a pmrA null mutant , lacking both aminoarabinose and phosphoethanolamine ( Fig. 4 ) .	253	We have now established that both of these PmrA-controlled modifications are required for polymyxin B resistance , as a pbgP pmrC1 double mutant is as susceptible to polymyxin B as a pmrA null mutant ( Fig. 3B ) and has a lipid A profile that is identical to that of a pmrA null mutant , lacking both aminoarabinose and phosphoethanolamine ( Fig. 4 ) .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrA	regulator	15205413	2	att	A pbgP pmrC double mutant resembled a pmrA mutant both in its lipid-A profile and in its susceptibility to polymyxin B , indicating that the PmrA-dependent modification of lipid-A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance .	11	A pbgP pmrC double mutant resembled a pmrA mutant both in its lipid A profile and in its susceptibility to polymyxin B , indicating that the PmrA-dependent modification of lipid A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrA	regulator	15569938	1	att	This result is surprising because : ( i ) E. coli encodes homologues of the PhoP PhoQ and PmrA PmrB systems , the PmrD protein , as well as the PmrA-regulated genes mediating the LPS modifications required for polymyxin B resistance ( 24 ) ; ( ii ) its PhoP PhoQ system also responds to Mg2 ( 25 ) ; and ( iii ) mutations in its pmrA gene produce strains with the same phenotypes as Salmo-nella pmrA mutants ( 8 , 12 ) .	29	This result is surprising because : ( i ) E. coli encodes homologues of the PhoP PhoQ and PmrA PmrB systems , the PmrD protein , as well as the PmrA-regulated genes mediating the LPS modifications required for polymyxin B resistance ( 24 ) ; ( ii ) its PhoP PhoQ system also responds to Mg2 ( 25 ) ; and ( iii ) mutations in its pmrA gene produce strains with the same phenotypes as Salmo-nella pmrA mutants ( 8 , 12 ) .	2	PHOP PHOQ PMRA PMRB PMRD	Escherichia coli;Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	katE	repressor	20713450	15	ver/dev	The katE promoter , was hardly repressed by H-NS and was insensitive to YncC , in agreement with in-vivo data -LRB- not shown -RRB- .	411	The katE promoter , used as a control , was hardly repressed by H-NS and was insensitive to YncC ( Fig. 7 , lanes 17 -- 24 ) , in agreement with in vivo data ( not shown ) .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	regulator	28575106	14	ver/dev	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in-vitro SPI-1-inducing conditions .	306	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in vitro SPI-1-inducing conditions ( low O2 and high salt ) [ 46,55 ] .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	regulator	28575106	14	ver/dev	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in-vitro high salt .	306	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in vitro SPI-1-inducing conditions ( low O2 and high salt ) [ 46,55 ] .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	regulator	28575106	14	ver/dev	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in-vitro low O2 .	306	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in vitro SPI-1-inducing conditions ( low O2 and high salt ) [ 46,55 ] .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoN	regulator	14563863	16	ver/dev	PhoP binds to the promoter region of phoN .	155	PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL , and pmrC genes but not to the promoter region of phoN , pagC , or mgtC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoN	regulator	14742517	3	ver/dev	in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoN	regulator	14742517	3	ver/dev	in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoN	regulator	14742517	3	ver/dev	Interestingly we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoN	regulator	14742517	3	ver/dev	Interestingly we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoN	regulator	19348639	0	ver/dev	phoN are known to be regulated by PhoP ,56	254	The SPI-2 cluster is closely associated with three virulence-related genes ( pagJ , pagK , and phoN ) , which are known to be regulated by two virulenceassociated regulators , SlyA and PhoP ,56 that also regulate a number of SPI-2 genes .	14	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	phoN	regulator	20396961	7	att	Considering that some PhoP-regulated genes such as pag loci and phoN , which encodes a nonspecific acid phosphatase , are maximally induced under starvation conditions ( Behlau and Miller , 1995 ; Kier et al. , 1997 ) , it is reasonable to conclude that induced synthesis of the tdc genes inside macrophages affects the expression of a subset of PhoP-dependent genes such as SPI2 .	329	Considering that some PhoP-regulated genes such as pag loci and phoN , which encodes a nonspecific acid phosphatase , are maximally induced under starvation conditions ( Behlau and Miller , 1995 ; Kier et al. , 1997 ) , it is reasonable to conclude that induced synthesis of the tdc genes inside macrophages affects the expression of a subset of PhoP-dependent genes such as SPI2 .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoN	regulator	25182488	15	ver/dev	As seen in Fig. 7B , PhoP was able to bind to the phoN promoter .	258	As seen in Fig. 7B , PhoP was able to bind to the promoters of slrP and slyB but not to the phoN promoter .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	phoN	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	slyA	regulator	18270203	47	att	We investigated the possibility that PhoP may be unable to associate with H-NS-bound promoters in the absence of SlyA by comparing the in-vivo promoter occupancy by the PhoP protein in isogenic wild-type and slyA strains .	236	We investigated the possibility that PhoP may be unable to associate with H-NS-bound promoters in the absence of SlyA by comparing the in vivo promoter occupancy by the PhoP protein in isogenic wild-type and slyA strains .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	slyA	regulator	19091955	24	ver/dev	As suggested by our previous study , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the slyA mutants in low-Mg2 conditions .	150	As suggested by our previous study ( 14 ) , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS , which antagonizes the functions of SlyA and PhoP ; thus the mRNA level is reduced greatly in the phoP or slyA mutants in PhoP-activating ( low-Mg2 ) conditions but remains high in PhoP-repressing ( high-Mg2 ) conditions in the hns mutant ( Fig. 4B ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	slyA	regulator	19091955	24	ver/dev	As suggested by our previous study , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the slyA mutants in PhoP-activating conditions .	150	As suggested by our previous study ( 14 ) , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS , which antagonizes the functions of SlyA and PhoP ; thus the mRNA level is reduced greatly in the phoP or slyA mutants in PhoP-activating ( low-Mg2 ) conditions but remains high in PhoP-repressing ( high-Mg2 ) conditions in the hns mutant ( Fig. 4B ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	slyA	regulator	19229334	11	ver/dev	Thus , one explanation for the transcription we observe following overexpression of slyA may be that both SlyA and SsrB counteract binding of both H-NS and YdgD/Hha in this A+T rich SPI-2 region .	519	Thus , one explanation for the transcription we observe following overexpression of ssrB or slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins including both H-NS and YdgD/Hha in this A+T rich SPI-2 region [ 70 ] .	15	WHAT ARE THE SIGNALS BEING SENSED DURING SYSTEMIC INFECTION AND HOW ARE THEY INTEGRATED TO EXPRESS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	slyA	activator	21388802	3	ver/dev	OmpR activates slyA expression .	160	OmpR activates slyA , phoP and ssrB expression and represses rpoS .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DeoR	gene	tsx	regulator	32849316	3	ver/dev	The expression of the tsx gene is controlled by two differentially regulated promoters ; one of these promoters is down-regulated by the DeoR repressor .	263	The expression of the tsx gene is controlled by two differentially regulated promoters ; one of these promoters is down-regulated by the DeoR repressor ( Bremer et al. , 1988 ; Bucarey et al. , 2006 ) .	20	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DeoR	gene	tsx	regulator	32849316	3	ver/dev	The expression of the tsx gene is controlled by two differentially regulated promoters ; one of these promoters is down-regulated by the DeoR repressor .	263	The expression of the tsx gene is controlled by two differentially regulated promoters ; one of these promoters is down-regulated by the DeoR repressor ( Bremer et al. , 1988 ; Bucarey et al. , 2006 ) .	20	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilD	regulator	17208038	17	ver/dev	It is probable that CsrA binds to the hilD mRNA to .	111	It is probable that CsrA binds to the hilD mRNA to either prevent translation or to promote mRNA degradation .	8	BARA/SIRA	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	hilD	regulator	20008574	18	ver/dev	However , with the potential exception of CsrA , post-transcriptional regulators of hilD seem to affect either HilD protein activity .	295	However , with the potential exception of FliZ ( Kage et al. 2008 ) and CsrA ( Altier et al. 2000 ; Ellermeier and Slauch 2007 ) , post-transcriptional regulators of hilD seem to affect either the HilD protein level ( Takaya et al. 2005 ; Matsui et al. 2008 ) or HilD protein activity ( Baxter et al. 2003 ; Ellermeier and Slauch 2008 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
CsrA	gene	hilD	regulator	20008574	18	ver/dev	However , with the potential exception of CsrA , post-transcriptional regulators of hilD seem to affect either the HilD protein level .	295	However , with the potential exception of FliZ ( Kage et al. 2008 ) and CsrA ( Altier et al. 2000 ; Ellermeier and Slauch 2007 ) , post-transcriptional regulators of hilD seem to affect either the HilD protein level ( Takaya et al. 2005 ; Matsui et al. 2008 ) or HilD protein activity ( Baxter et al. 2003 ; Ellermeier and Slauch 2008 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
CsrA	gene	hilD	regulator	22291968	3	ver/dev	CsrA binds to a region in hilD mRNA , likely preventing accelerating mRNA decay .	50	CsrA binds to a region in hilD mRNA that overlaps with the ribosome-binding sequence , likely preventing translation and accelerating mRNA decay [ 30 ] .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	New	Level 1
CsrA	gene	hilD	regulator	22291968	3	ver/dev	CsrA binds to a region in hilD mRNA , likely preventing translation .	50	CsrA binds to a region in hilD mRNA that overlaps with the ribosome-binding sequence , likely preventing translation and accelerating mRNA decay [ 30 ] .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	New	Level 1
CsrA	gene	hilD	regulator	23676436	19	ver/dev	This CsrA-mediated repression of hilD is caused by binding of CsrA to Dalgarno sequence of hilD mRNA .	409	This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine -- Dalgarno sequence of hilD mRNA ( Martınez et al. , 2011 ) .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilD	regulator	23676436	19	ver/dev	This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine .	409	This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine -- Dalgarno sequence of hilD mRNA ( Martınez et al. , 2011 ) .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilD	regulator	24682814	0	ver/dev	Regulation of hilD expression at the mRNA level has also been proposed : overproduction of the RNA binding protein CsrA represses	32	Regulation of hilD expression at the mRNA level has also been proposed : overproduction of the RNA binding protein CsrA represses	3	MAIN	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilD	regulator	24682814	1	ver/dev	CsrA has been shown to bind a hilD mRNA region .	42	SPI-1 expression ( 14,15 ) , and CsrA has been shown to bind a hilD mRNA region that overlaps with the ribosome binding sequence , likely preventing translation and accelerating mRNA decay ( 15 ) .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	hilD	regulator	28426789	15	ver/dev	CsrA post-transcriptionally regulates hilD .	360	CsrA post-transcriptionally regulates hilD [ 41 ] .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilD	regulator	30682134	20	ver/dev	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the regulator of SPI-2 encoded effectors , slyA in LB .	227	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM and repressing the regulator of SPI-2 encoded effectors , slyA in LB .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	hilD	regulator	30682134	20	ver/dev	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM encoded effectors , slyA in LB .	227	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM and repressing the regulator of SPI-2 encoded effectors , slyA in LB .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	Salmonella;unidentified plasmid	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	hilD	regulator	31017982	0	ver/dev	CsrA binds to the 5 ' end of the hilD mRNA , sequestering the ribosome-binding site and start codon , and thus is proposed to prevent HilD translation .	58	CsrA binds to the 5 ' end of the hilD mRNA , sequestering the ribosome-binding site and start codon , and thus is proposed to prevent HilD translation [ 18 ] .	4	INTRODUCTION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilD	regulator	31017982	17	ver/dev	Conformation of the hilD mRNA alters message stability through binding of SL1 to CsrA .	178	Conformation of the hilD mRNA alters message stability through binding of SL1 to CsrA .	10	ALTERNATIVE TRANSCRIPT SECONDARY STRUCTURE ALTERS INVASION GENE EXPRESSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsrA	gene	hilD	regulator	31017982	22	ver/dev	Indeed , both T53C hilD mutants , with their reduced binding of CsrA to SL1 significantly increased the proportion of the invasion-competent population to 35 , respectively .	211	Indeed , both the A25G and T53C hilD mutants , with their reduced binding of CsrA to SL1 , and the csrAΔ50 truncation mutant significantly increased the proportion of the invasion-competent population to 43 % , 28 % and 35 % , respectively .	11	AMPLIFICATION OF HILD OVERCOMES THE THRESHOLD FOR INVASION GENE INDUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsrA	gene	hilD	regulator	31017982	22	ver/dev	Indeed , both T53C hilD mutants , with their reduced binding of CsrA to SL1 significantly increased the proportion of the invasion-competent population to 28 , respectively .	211	Indeed , both the A25G and T53C hilD mutants , with their reduced binding of CsrA to SL1 , and the csrAΔ50 truncation mutant significantly increased the proportion of the invasion-competent population to 43 % , 28 % and 35 % , respectively .	11	AMPLIFICATION OF HILD OVERCOMES THE THRESHOLD FOR INVASION GENE INDUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsrA	gene	hilD	regulator	31017982	22	ver/dev	Indeed , both T53C hilD mutants , with their reduced binding of CsrA to SL1 significantly increased the proportion of the invasion-competent population to 43 , respectively .	211	Indeed , both the A25G and T53C hilD mutants , with their reduced binding of CsrA to SL1 , and the csrAΔ50 truncation mutant significantly increased the proportion of the invasion-competent population to 43 % , 28 % and 35 % , respectively .	11	AMPLIFICATION OF HILD OVERCOMES THE THRESHOLD FOR INVASION GENE INDUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsrA	gene	hilD	regulator	31488053	3	ver/dev	CsrA binds to hilD mRNA	200	The BarA/SirA two-component system posttranscriptionally regulates HilD expression through the action of CsrA , which binds to hilD mRNA and inhibits translation [ 39 ] .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilD	regulator	33751923	14	ver/dev	BarA-SirA positively regulate the expression of SPI-1 genes mainly b antagonising repression ; CsrA binds to the 50 end of hilD mRNA .	484	BarA-SirA positively regulate the expression of SPI-1 genes mainly b antagonising repression mediated by CsrA on the hilD mRNA ; CsrA binds to the 50 end of hilD mRNA and occupies the regulatory regions required for translation , presumably preventing the production of the HilD protein ( Martınez et al. 2011 ; Salvail and Groisman 2020 ) .	14	BARA-SIRA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
KdgR	gene	kdgK	regulator	26682862	1	ver/dev	kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	kdgK	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SirA	gene	phoP	activator	29555922	14	ver/dev	SirA , induced the activity of the grhD1-cat fusion in the ∆ phoP ∆ hilD mu .	137	Expression of PhoP or HilD , but not SirA , induced the activity of the grhD1-cat fusion in the ∆ phoP ∆ hilD mutant ( Fig. 5C ) .	3	RESULTS	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	oafA	activator	10844662	8	ver/dev	It is tempting to speculate that SsrB activates oafA within macrophages , via the inversion system , to trigger a protective LPS conformational change .	226	It is tempting to speculate that SsrB activates oafA within macrophages , via the inversion system , to trigger a protective LPS conformational change that is vulnerable to the immune system when extracellular .	15	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hyaB	regulator	9882690	3	ver/dev	Consistent with the situation for E. coli hya , anaerobic control of S. typhimurium hyaB did not require Fnr	143	Consistent with the situation for E. coli hya ( 7 ) , anaerobic control of S. typhimurium hyaB did not require Fnr	4	MAIN	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	NEG	New	Level 1
RamA	gene	tolC	activator	18577510	21	ver/dev	RamA induction of tolC by conditioned-medium of E. coli .	198	RamA induction of acrAB and tolC by conditioned medium of E. coli .	2	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	tolC	activator	23230062	0	ver/dev	Activation of tolC gene transcription is achieved through the direct binding of RamA , to the operator regions of these genes .	27	Activation of the acrAB operon and tolC gene transcription is achieved through the direct binding of RamA , a positive regulator of the AraC/XylS family , to the operator regions of these genes [ 13 , 14 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	tolC	activator	24816212	0	ver/dev	The tolC genes are transcriptionally activated by RamA .	10	The acrAB and tolC genes are transcriptionally activated by RamA , the gene for which is itself transcriptionally repressed by RamR .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	tolC	activator	24816212	1	ver/dev	As expected , since RamA is PramA , we first conducted EMSAs with a 97 bp transcriptional activator of tolC efflux genes ,18 bile DNA fragment	95	As expected , since RamA is the main the ramA promoter ( PramA ) , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB and tolC efflux genes ,18 bile DNA fragment amplified from the ramR-ramA intergenic region and	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	tolC	activator	24816212	1	ver/dev	As expected , since RamA is the main the ramA promoter , we first conducted EMSAs with a 97 bp transcriptional activator of tolC efflux genes ,18 bile DNA fragment	95	As expected , since RamA is the main the ramA promoter ( PramA ) , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB and tolC efflux genes ,18 bile DNA fragment amplified from the ramR-ramA intergenic region and	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	tolC	activator	24816212	3	ver/dev	Regulation model for the bile-mediated activation of tolC via RamA .	264	Regulation model for the bile-mediated activation of acrAB and tolC via RamA .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	tolC	activator	34202800	4	ver/dev	RamA is the main activator of tolC transcription	234	RamA is the main activator of acrAB and tolC transcription , and bile induces an over two-fold increase in acrB and tolC transcript levels .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	tolC	activator	34202800	6	ver/dev	RamA , , are involved in activating tolC expression .	254	Three homologous transcriptional activators , RamA , SoxS , and MarA , controlled by RamR , SoxR , and MarR , are involved in activating acrB and tolC expression [ 68 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyB	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyB	activator	18248433	1	att	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyB	activator	18792679	1	att	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	113	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	5	DIRECT TRANSCRIPTIONAL CONTROL BYTHE PHOP PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyB	activator	21563813	0	att	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnB .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnB .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrH .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP1 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrH .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP1 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnC .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnC .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrF .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP2 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrF .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	21563813	0	ver/dev	slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP2 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyB	activator	23504014	16	att	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	277	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	slyB	activator	23504014	19	att	Two additional PhoP-activated genes , slyB and phoN , were used as positive and negative controls , respectively , since previous experiments have shown direct interaction of PhoP with the promoter of slyB but not with the promoter of phoN ( 50 ) .	296	Two additional PhoP-activated genes , slyB and phoN , were used as positive and negative controls , respectively , since previous experiments have shown direct interaction of PhoP with the promoter of slyB but not with the promoter of phoN ( 50 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	slyB	activator	25182488	12	att	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	250	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilC	repressor	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	ygaE	regulator	24592164	0	ver/dev	ygaE _ coregulated by RpoS	161	We speculated that ygaE , coregulated by RpoE and RpoS , is required for survival under extreme stresses of S. Typhi .	7	3.1. YGAE REPRESSES THE EXPRESSION OF GAB OPERON UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	slyB	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
InvF	gene	siiA	activator	23419780	7	ver/dev	InvF are transcription activators of effectors downregulates siiA .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CspA	gene	cspD	activator	24056458	0	ver/dev	this effect was reflected by induction of cspD and proteins ( CspA ) in response to preadaptation to cold-stress	146	Cold stress genes and proteins regulate membrane fluidity and resume protein synthesis ( 18 ) , and this effect was reflected by induction of cold stress genes ( cspB and cspD ) and proteins ( CspA , CspE , and CspC ) in response to preadaptation to cold stress .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	sodB	repressor	31479952	3	ver/dev	FNR negatively regulates sodA + , sodB +	59	Accordingly , it was demonstrated that FNR negatively regulates genes such as sodA + , sodB + , cycD + C + and metE + and thereby FnrS functions to adjust gene expression for adaptation to anaerobic growth ( Boysen et al. , 2010 ; Durand and Storz , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	sodB	repressor	31479952	3	ver/dev	FNR negatively regulates genes + , sodB +	59	Accordingly , it was demonstrated that FNR negatively regulates genes such as sodA + , sodB + , cycD + C + and metE + and thereby FnrS functions to adjust gene expression for adaptation to anaerobic growth ( Boysen et al. , 2010 ; Durand and Storz , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	ssrB	regulator	21984608	1	ver/dev	HilD binds directly to the regulatory regions of the coding regions of ssrB .	141	HilD binds directly to the regulatory regions of the ssrAB operon ( the coding regions of ssrA and ssrB ) and counteracts the repression exerted by the negative regulator , H-NS , or ompR ( a factor required for the activation of SPI-2 genes ) .	6	SALMONELLA RELIES ON T3SS2 TO SURVIVE AND REPLICATE INTRACELLULARLY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	ssrB	regulator	31262841	1	ver/dev	PinT also indirectly represses expression of a posttranslational regulator of HilD , and directly represses translation of ssrB , encoding the primary regulator of the SPI2 T3SS .	15	PinT also indirectly represses expression of FliZ , a posttranslational regulator of HilD , and directly represses translation of ssrB , encoding the primary regulator of the SPI2 T3SS .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	ssrB	regulator	31262841	1	ver/dev	PinT also indirectly represses expression of a posttranslational regulator of HilD , and directly represses translation of ssrB , encoding the primary regulator of the SPI2 T3SS .	15	PinT also indirectly represses expression of FliZ , a posttranslational regulator of HilD , and directly represses translation of ssrB , encoding the primary regulator of the SPI2 T3SS .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	recA	regulator	12399494	13	ver/dev	LexA _ regulated because their induction is prevented by a recA mutation	431	They were inferred to be LexA ( SOS ) regulated because their induction is prevented by a recA mutation and induced by overexpression of LexA ( 48 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	recA	regulator	20457791	0	ver/dev	Transcription of the Salmonella enterica recA gene is negatively controlled by the LexA protein , the repressor of the SOS response .	7	Transcription of the Salmonella enterica recA gene is negatively controlled by the LexA protein , the repressor of the SOS response .	1	ABSTRACT	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	fur	repressor	27242152	0	ver/dev	However , in the presence of H2O2 , transcription of fur is also activated by OxyR in E. coli , resulting in repression of target mRNAs for iron-uptake proteins .	136	However , in the presence of H2O2 , transcription of fur is also activated by OxyR in E. coli ( Zheng et al. , 1999 ) , resulting in repression of target mRNAs for iron-uptake proteins .	11	3.3. POSSIBLE MODEL OF RYHB(S)-MEDIATED REGULATION IN SALMONELLA	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompX	repressor	18156266	11	ver/dev	The proteomic data revealed that LeuO represses the expression of ompX .	240	The proteomic data mentioned above also revealed that LeuO represses the expression of tpx , ompX , and STY1978 .	5	FIG. 2	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	ptsN	repressor	33853321	3	ver/dev	In agreement with the notion that EIIANtr are in the same pathway , a lack of CRP resulted in a decrease of ptsN expression .	118	In agreement with the notion that CRP and EIIANtr are in the same pathway , a lack of CRP resulted in a decrease of ptsN expression ( Figures 2C and 3A ) .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	ptsN	repressor	33853321	3	ver/dev	In agreement with the notion that CRP are in the same pathway , a lack of CRP resulted in a decrease of ptsN expression .	118	In agreement with the notion that CRP and EIIANtr are in the same pathway , a lack of CRP resulted in a decrease of ptsN expression ( Figures 2C and 3A ) .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	stpA	activator	19406898	10	ver/dev	The maximum level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG from the same as that stpA background .	111	The maximum level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG from pFMTrcleuO-50 , the same as that attained in a double hns stpA background ( De la Cruz et al. , 2007 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	marR	regulator	9068629	0	ver/dev	marR controls the production of MarA in response to environmental signals .	6	marR encodes a repressor of marRAB transcription and controls the production of MarA in response to environmental signals .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	speF	repressor	30524381	1	ver/dev	In E. coli , OmpR represses speF , the ornithine decarboxylation system .	69	In E. coli , OmpR represses speF , the ornithine decarboxylation system , which has a higher pH optimum of 7 ( Vivijs et al. , 2016 ) compared to the glutamate and arginine decarboxylation systems ( pH optima 4 and 5 , respectively ) ( Bearson et al. , 2009 ) .	4	NTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaB	activator	15491370	9	ver/dev	SsrB , in turn , activates ssaB .	88	SsrB , in turn , activates ssrB , ssrA and spiC ( ssaB ) as well as additional genes , including srfH .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaB	activator	17630976	16	att	Removal of the SsrB binding site eliminates SsrB-dependent activation at ssaB	158	Removal of the SsrB binding site eliminates SsrB-dependent activation at ssaB	7	REMOVAL OF THE SSRB BINDING SITE ELIMINATES SSRB-DEPENDENT ACTIVATION AT SSAB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaB	activator	17630976	19	att	Thus , it is clear that the SsrB binding site at the ssaB promoter is required for SsrB-dependent activation of transcription .	165	Thus , it is clear that the SsrB binding site at the ssaB promoter is required for SsrB-dependent activation of transcription .	7	REMOVAL OF THE SSRB BINDING SITE ELIMINATES SSRB-DEPENDENT ACTIVATION AT SSAB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	17630976	21	att	The SsrB binding site at ssaB is required for SsrB-dependent activation of gene expression .	204	The SsrB binding site at ssaB is required for SsrB-dependent activation of gene expression .	8	ACTIVATION OF SPI-2 GENES IN VITRO REQUIRES SSRB AND ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	17630976	16	ver/dev	Removal of the SsrB binding site eliminates SsrB-dependent activation at ssaB	158	Removal of the SsrB binding site eliminates SsrB-dependent activation at ssaB	7	REMOVAL OF THE SSRB BINDING SITE ELIMINATES SSRB-DEPENDENT ACTIVATION AT SSAB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaB	activator	17630976	19	ver/dev	Thus , it is clear that the SsrB binding site at the ssaB promoter is required for SsrB-dependent activation of transcription .	165	Thus , it is clear that the SsrB binding site at the ssaB promoter is required for SsrB-dependent activation of transcription .	7	REMOVAL OF THE SSRB BINDING SITE ELIMINATES SSRB-DEPENDENT ACTIVATION AT SSAB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	17630976	21	ver/dev	The SsrB binding site at ssaB is required for SsrB-dependent activation of gene expression .	204	The SsrB binding site at ssaB is required for SsrB-dependent activation of gene expression .	8	ACTIVATION OF SPI-2 GENES IN VITRO REQUIRES SSRB AND ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaB .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaB .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaB .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaB .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : ssaB .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaB	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : ssaB .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagK	regulator	19348639	0	ver/dev	pagK are known to be regulated by SlyA	254	The SPI-2 cluster is closely associated with three virulence-related genes ( pagJ , pagK , and phoN ) , which are known to be regulated by two virulenceassociated regulators , SlyA and PhoP ,56 that also regulate a number of SPI-2 genes .	14	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
DksA	gene	dksA	activator	22311927	0	att	Given the inhibitory effects of NO on amino-acid biosynthetic pathways and the DksA-dependent regulation of the transcription of amino-acid synthesis and transport , we tested whether the addition of amino-acids had any effect on the marked susceptibility of dksA mutant Salmonella strains to chemically generated NO .	127	Given the inhibitory effects of NO on amino acid biosynthetic pathways and the DksA-dependent regulation of the transcription of amino acid synthesis and transport , we tested whether the addition of amino acids had any effect on the marked susceptibility of dksA mutant Salmonella strains to chemically generated NO .	4	RESULTS	Salmonella	1	L3	SPEC	Other	OTHER	Other	Level 1
Lrp	TU	ilvIH	repressor	11591661	1	ver/dev	The expression of ilvIH gene products is inhibited by leucine , apparently due to a requirement for Lrp for activation of ilvIH transcription .	49	The expression of AHAS III ( ilvIH gene products ) is inhibited by leucine , apparently due to a requirement for the leucine-responsive regulatory protein ( Lrp ) for activation of ilvIH transcription .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Lrp	TU	ilvIH	repressor	11591661	1	ver/dev	The expression of AHAS III is inhibited by leucine , apparently due to a requirement for Lrp for activation of ilvIH transcription .	49	The expression of AHAS III ( ilvIH gene products ) is inhibited by leucine , apparently due to a requirement for the leucine-responsive regulatory protein ( Lrp ) for activation of ilvIH transcription .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SoxS	gene	rob	repressor	22752112	6	ver/dev	Furthermore , we demonstrate that SoxS mediate repression of rob by binding to its promoter region .	69	Furthermore , we demonstrate that MarA and SoxS mediate repression of rob by binding to its promoter region .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SoxS	gene	rob	repressor	22752112	9	ver/dev	rob is negatively regulated by SoxS	200	rob is negatively regulated by MarA and SoxS	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	rob	repressor	22752112	10	ver/dev	This confirms our previous results that repression of rob in the must have been due to overexpression of SoxS .	218	This confirms our previous results that repression of rob in the complemented strains in the presence of arabinose must have been due to overexpression of MarA or SoxS .	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	rob	repressor	22752112	11	ver/dev	The results above suggest that SoxS could mediate together a repression of rob in response to NaOCl .	220	The results above suggest that MarA and SoxS could mediate together a repression of rob in response to NaOCl .	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SoxS	gene	rob	repressor	22752112	12	ver/dev	NaOCl _ supporting our hypothesis of a repression of rob by both SoxS	230	NaOCl ( 0.86 ± 0.01-fold change , Fig. 3d ) , supporting our hypothesis of a repression of rob by both MarA and SoxS .	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
SoxS	gene	rob	repressor	22752112	21	ver/dev	other studies _ performed in E. coli where rob was shown to be negatively regulated by both SoxS by a direct interaction with its promoter region	304	Our results are in agreement with other studies performed in E. coli where rob was shown to be negatively regulated by both MarA and SoxS by a direct interaction with its promoter region ( Schneiders and Levy 2006 ; Michán et al. 2002 ) .	17	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	spvC	regulator	14633100	0	att	virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .	15	virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .	1	ABSTRACT	Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	spvC	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	spvC	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	TU	ssrAB	regulator	25135218	78	ver/dev	Thus , it is possible that RtsA can regulate the expression of ssrAB .	224	Thus , it is possible that the feed forward loop constituted by HilD , HilC , and RtsA can regulate the expression of ssrAB .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1703	activator	17322315	8	ver/dev	These data indicate that in STM4264 mutants , CsgD expression is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1703	activator	17322315	8	ver/dev	These data indicate that in STM4264 mutants , the rdar morphotype is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1703	activator	17322315	8	ver/dev	These data indicate that in STM1703 , STM1827 , STM3611 , CsgD expression is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1703	activator	17322315	8	ver/dev	These data indicate that in STM1703 , STM1827 , STM3611 , the rdar morphotype is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1703	activator	17322315	19	ver/dev	In order to demonstrate that upregulation of the rdar morphotype in the STM1703 mutants is mediated by CsgD , csgD was knocked out in the STM1703 mutants .	223	In order to demonstrate that upregulation of the rdar morphotype in the STM1703 and STM4264 mutants is mediated by CsgD , csgD was knocked out in the STM1703 and STM4264 mutants .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
QseB	gene	invF	regulator	28062286	3	ver/dev	QseB regulation of S. Typhi invasion of SPI-1 gene invF .	180	QseB regulation of S. Typhi invasion of epithelial cells and SPI-1 gene invF .	15	4. DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	flhDC	regulator	30373755	8	att	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	31501286	9	ver/dev	Interestingly , the repressive effects of SoxS on motility are due to both posttranscriptional regulation of flhDC expression .	144	Interestingly , the repressive effects of SoxS on motility are due to both transcriptional and posttranscriptional regulation of flhDC expression .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	31501286	9	ver/dev	Interestingly , the repressive effects of SoxS on motility are due to both transcriptional regulation of flhDC expression .	144	Interestingly , the repressive effects of SoxS on motility are due to both transcriptional and posttranscriptional regulation of flhDC expression .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	31501286	18	ver/dev	For this reason , we hypothesized that SoxS may bind to flhDC as well .	193	For this reason , we hypothesized that MarA , SoxS , and RamA may bind to flhDC as well .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxS	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test SoxS , we replaced class I in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test SoxS , we replaced the native flhDC promoter in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	31501286	39	ver/dev	the mechanism _ underlying SoxS-dependent posttranscriptional regulation of flhDC	283	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	31501286	47	ver/dev	SoxS , however , primarily controls flhDC expression through a posttranscriptional pathway , resulting in decreased translation of flhDC .	448	SoxS , however , primarily controls flhDC expression through a posttranscriptional pathway , resulting in decreased translation of flhDC .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	flhDC	regulator	34202800	12	ver/dev	Interestingly , the repressive influence of SoxS on mobility is a result of both post-transcriptional regulation of flhDC .	299	Interestingly , the repressive influence of SoxS on mobility is a result of both transcriptional and post-transcriptional regulation of flhDC [ 58,110 ] .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	34202800	12	ver/dev	Interestingly , the repressive influence of SoxS on mobility is a result of both post-transcriptional regulation of flhDC .	299	Interestingly , the repressive influence of SoxS on mobility is a result of both transcriptional and post-transcriptional regulation of flhDC [ 58,110 ] .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	regulator	34202800	12	ver/dev	Interestingly , the repressive influence of SoxS on mobility is a result of both transcriptional of flhDC .	299	Interestingly , the repressive influence of SoxS on mobility is a result of both transcriptional and post-transcriptional regulation of flhDC [ 58,110 ] .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM4417	gene	srfJ	regulator	27999939	0	ver/dev	A more recent study by Cordero-Alba et al. revealed that or STM4417 in S. Typhimurium played a role in regulating srfJ negatively , a Salmonella T3SS effector for SPI-2 and associated iolR with virulence .	236	A more recent study by Cordero-Alba et al. [ 15 ] revealed that iolR ( STM14_5307 or STM4417 ) in S. Typhimurium played a role in regulating srfJ negatively , a Salmonella T3SS effector for SPI-2 and associated iolR with virulence .	13	STM14_5307 MUTANT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
AraC	gene	sicA	activator	10692170	8	att	AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA .	207	AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA .	8	INVF AND SICA ARE SUFFICIENT TO ACTIVATE TRANSCRIPTION OF SICA- AND SIGD±LACZYA IN E:COLI CC118LPIR.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
UvrY	gene	csrB	regulator	16045614	11	ver/dev	The transcription of csrB is regulated by UvrY .	59	The transcription of csrB and csrC is regulated by UvrY ( SirA ) ( Suzuki et al. , 2002 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
UvrY	gene	csrB	regulator	16949866	32	ver/dev	UvrY of E. coli both control the csr system by directly binding the csrB gene .	458	SirA of Salmonella and UvrY of E. coli both control the csr system by directly binding and activating the csrB gene ( Pernestig et al. , 2001 ; Teplitski et al. , 2003 ) .	19	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	ssaG	regulator	16777370	0	ver/dev	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium	3	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	2	ver/dev	footprinting analysis showed Fis bound to four distinct sites of the ssaG promoter region with different affinities .	13	Gel-shift and footprinting analysis showed Fis bound to four distinct sites of the ssaG promoter region with different affinities .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	2	ver/dev	Gel-shift analysis showed Fis bound to four distinct sites of the ssaG promoter region with different affinities .	13	Gel-shift and footprinting analysis showed Fis bound to four distinct sites of the ssaG promoter region with different affinities .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	5	ver/dev	However , proteome analysis of the genes revealed that Fis was bound directly to those of ssaG .	41	However , DNA microarray and proteome analysis of the genes regulated by Fis revealed that Fis was involved in the regulation of SPI2 genes and bound directly to SPI2 promoters such as those of ssrA and ssaG [ 23,24 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	5	ver/dev	However , DNA microarray of the genes revealed that Fis was bound directly to those of ssaG .	41	However , DNA microarray and proteome analysis of the genes regulated by Fis revealed that Fis was involved in the regulation of SPI2 genes and bound directly to SPI2 promoters such as those of ssrA and ssaG [ 23,24 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	8	ver/dev	In the present work , the effects of Fis on the expression of the ssaG gene , known to be induced by about 400-fold in the intracellular environment , were analyzed to understand the role of Fis in the regulation of the virulence genes of Salmonella in detail .	55	In the present work , the effects of Fis on the expression of the ssaG gene , known to be induced by about 400-fold in the intracellular environment [ 8 ] , were analyzed to understand the role of Fis in the regulation of the virulence genes of Salmonella in detail .	3	1. INTRODUCTION	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Fis	gene	ssaG	regulator	16777370	12	ver/dev	Fis binds to ssaG promoter region	65	2.2. Fis binds to ssaG promoter region	6	2.2. FIS BINDS TO SSAG PROMOTER REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	ssaG	regulator	16777370	13	ver/dev	Because previous work has established that Fis protein bound to the promoter region of ssaG , we performed a DNase I footprinting assay .	66	Because previous work has established that Fis protein bound to the promoter region of ssaG [ 24 ] , we performed a DNase I footprinting assay using the ssaG promoter DNA region from 386 to +33 to find Fis-binding sites ( Fig. 2 ) .	6	2.2. FIS BINDS TO SSAG PROMOTER REGION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	27	ver/dev	Johnson reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary-phase as was observed in the case of ssaG in our study .	112	Xu and Johnson [ 30 ] reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary phase as was observed in the case of ssaG in our study .	9	3. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	27	ver/dev	Xu reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary-phase as was observed in the case of ssaG in our study .	112	Xu and Johnson [ 30 ] reported that a second promoter of proP gene was strongly activated by direct binding of Fis when cells entered the stationary phase as was observed in the case of ssaG in our study .	9	3. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16777370	32	ver/dev	These observations imply that Fis may exert positive effect on the ssaG expression via two ways , that is , through the direct binding of ssaG promoter region .	135	These observations imply that Fis may exert positive effect on the ssaG expression via two ways , that is , through the direct binding of ssaG promoter region and the modulation of SsrA/B regulatory system of SPI2 .	9	3. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	ssaG	regulator	16999831	18	ver/dev	A role for Fis in the positive regulation of SPI-2 genes is also supported by a dem-onstration -- DNA complexes at the promoter regions of the ssaG genes .	191	A role for Fis in the positive regulation of SPI-2 genes is also supported by DNA microarray analysis and a dem-onstration that Fis protein binds to and forms discrete protein -- DNA complexes at the promoter regions of the ssrA and the ssaG genes ( Kelly et al. , 2004 ) .	15	GFP FLUORESCENCE INTENSITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	16999831	25	ver/dev	Ryu , S. Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	443	Lim , S. , Kim , B. , Choi , H.S. , Lee , Y. , and Ryu , S. ( 2006 ) Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	42	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	17630976	56	ver/dev	Ryu , S. Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	573	Lim , S. , Kim , B. , Choi , H.S. , Lee , Y. , and Ryu , S. ( 2006 ) Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	33	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	20221735	6	ver/dev	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	571	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	22	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	20396961	8	ver/dev	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	455	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	24	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	21134969	13	ver/dev	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhi-murium .	738	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhi-murium .	36	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	ssaG	regulator	26441883	35	ver/dev	Fis binds directly to the promoter regions of ssaG	474	Fis binds directly to the promoter regions of spiR and ssaG ( Kelly et al. , 2004 ; Lim et al. , 2006 ) and its expression correlates with Spi-2 gene expression inside macrophages ( O Croinin et al. , 2006 ) .	10	REGULATORY CIRCUITS CONTROLLING LATER STAGES OF INFECTION AND DEFENSE SYSTEMS AGAINST THE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	ssaG	regulator	26441883	45	ver/dev	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	1131	Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .	65	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM3611	activator	24127899	3	ver/dev	YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 .	47	YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 ( YhjH ) , which is part of the flagellar regulon ( Simm et al. , 2009 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	STM3611	activator	24127899	27	ver/dev	FlhD4C2 suppresses CsgD expression through activation of STM3611 expression by the class 2 sigma factor FliA .	258	FlhD4C2 suppresses rdar biofilm formation and CsgD expression through activation of STM3611 expression by the class 2 sigma factor FliA ( Jonas et al. , 2010 ) .	11	FUNCTIONAL FLAGELLA AND CHEMOTAXIS ARE REQUIRED FOR INVASION OF HT-29 CELLS BY S. TYPHIMURIUM UMR1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	tolC	regulator	11036033	1	ver/dev	Like marRAB , tolC are positively regulated by MarA .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilA	activator	11123690	6	ver/dev	These results indicate that Fis is essential for full activation of hilA : .	67	These results indicate that Fis is essential for full activation of hilA : : Tn5lacZY expression from both plasmid and chromosomally located reporters .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	hilA	activator	11123690	8	ver/dev	Fis is required for full induction of chromosomal S. typhimurium hilA : : Tn5lacZY expression .	94	Fis is required for full induction of chromosomal S. typhimurium hilA : : Tn5lacZY expression .	7	A S. TYPHIMURIUM FIS MUTANT DOES NOT EXPRESS SEVERAL SECRETED PROTEINS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilA	activator	11123690	17	ver/dev	Using a genetic approach , Fis was shown to be necessary for the induction of hilA expression , genes .	151	Using a genetic approach , Fis was shown to be necessary for the induction of hilA and invF expression , genes that encode two positive regulators of several SPI-1 genes .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	hilA	activator	14553938	0	ver/dev	Positive regulation of SPI-1 genes by Fis was expected considering the fact that hilA , is upregulated by Fis .	142	Positive regulation of SPI-1 genes by Fis was expected considering the fact that hilA , a transcriptional regulator of SPI-1 , is upregulated by Fis [ 16 ] .	12	3.3. FIS IS INVOLVED IN SPI EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilA	activator	16443238	1	ver/dev	Expression of hilA is increased by the Factor for Inversion Stimulation , Fis .	38	Expression of hilA is increased by the pleiotropic activator proteins OmpR , PhoPQ , and the Factor for Inversion Stimulation , Fis .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilA	activator	16443238	1	ver/dev	Expression of hilA is increased by PhoPQ for Inversion Stimulation , Fis .	38	Expression of hilA is increased by the pleiotropic activator proteins OmpR , PhoPQ , and the Factor for Inversion Stimulation , Fis .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	ssaH	repressor	19126220	0	ver/dev	HilA represses the promoter of ssaH	32	These include HilA that binds and represses the promoter of ssaH [ 24 ] , and HilD that binds and activates the promoter of the ssrAB operon [ 25 ] .	3	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	tpx	regulator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	tpx	regulator	18156266	31	ver/dev	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code during biofilm formation .	323	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme that is induced under several pH conditions ( 51 ) , in the exponential growth phase , and during biofilm formation ( 22 ) .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	tpx	regulator	18156266	31	ver/dev	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code in the exponential-growth-phase .	323	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme that is induced under several pH conditions ( 51 ) , in the exponential growth phase , and during biofilm formation ( 22 ) .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	tpx	regulator	18156266	31	ver/dev	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme .	323	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme that is induced under several pH conditions ( 51 ) , in the exponential growth phase , and during biofilm formation ( 22 ) .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	xylA	regulator	24272778	18	att	isrB was originally annotated as a AraC-regulated gene ( 36 ) , nor did we detect binding of AraC up - small RNA but has more recently been shown to encode a small stream of xylA .	225	isrB was originally annotated as a AraC-regulated gene ( 36 ) , nor did we detect binding of AraC up - small RNA but has more recently been shown to encode a small stream of xylA .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	xylA	regulator	24272778	36	att	With the exception of xylA , the last AraC-regulated gene to be identified was araJ , more than 30 years ago ( 27 ) .	375	With the exception of xylA , the last AraC-regulated gene to be identified was araJ , more than 30 years ago ( 27 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sprB	activator	27601571	22	ver/dev	InvF , sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - .	222	InvF , sopB ( sigD ) , sicA , and sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - ( 14 , 46 ) ( note that sopE is not present in the strain we used but that a close homologue , sopE2 , is present ) .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sprB	activator	27601571	22	ver/dev	InvF , sigD , sicA , , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - .	222	InvF , sopB ( sigD ) , sicA , and sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - ( 14 , 46 ) ( note that sopE is not present in the strain we used but that a close homologue , sopE2 , is present ) .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sprB	activator	27601571	22	ver/dev	InvF , sopB , sicA , , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - .	222	InvF , sopB ( sigD ) , sicA , and sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - ( 14 , 46 ) ( note that sopE is not present in the strain we used but that a close homologue , sopE2 , is present ) .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sprB	activator	31484980	0	ver/dev	Our data show that HilD induces expression of sprB by directly counteracting H-nS-mediated repression on the promoter region upstream of this gene .	10	Our data show that HilD induces expression of sprB by directly counteracting H-nS-mediated repression on the promoter region upstream of this gene .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sprB	activator	31484980	5	ver/dev	Our results show that HilD directly induces expression of sprB by antagonizing repression .	42	Our results show that HilD directly induces expression of sprB by antagonizing repression mediated by H-NS .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sprB	activator	31484980	20	ver/dev	The results suggest that HilD positively regulates the expression of sprB .	121	The results described above strongly suggest that HilD positively regulates the expression of sprB .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	sprB	activator	31484980	23	ver/dev	d the activity of this fusion in the ∆ hilD mu _ t , indicating that HilD induces expression of sprB by also acting on the regulatory region upstream of this	126	As shown in Fig. 6A , activity of the sprB-cat fusion was 2-fold reduced in the ∆ hilD mutant , compared with its activity in the WT strain ; furthermore , expression of HilD from the pK6-HilD plasmid increased 3-fold the activity of this fusion in the ∆ hilD mutant , indicating that HilD induces expression of sprB by also acting on the regulatory region upstream of this gene .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sprB	activator	31484980	25	ver/dev	the activity of sprB-cat in Fig. 6B _ supporting that HilD induces expression of sprB directly	151	Expression of HilD from pK6-HilD induced 3-fold the activity of sprB-cat in the E. coli strain ( Fig. 6B ) , supporting that HilD induces expression of sprB directly .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sprB	activator	31484980	25	ver/dev	the activity of sprB-cat in the E. coli strain _ supporting that HilD induces expression of sprB directly	151	Expression of HilD from pK6-HilD induced 3-fold the activity of sprB-cat in the E. coli strain ( Fig. 6B ) , supporting that HilD induces expression of sprB directly .	3	RESULTS	Felis catus;Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sprB	activator	31484980	28	ver/dev	To know whether HilD induces expression of sprB by a similar way , we analyzed if inactivation of H-NS leads to HilD-independent expression of this gene .	157	To know whether HilD induces expression of sprB by a similar way , we analyzed if inactivation of H-NS leads to HilD-independent expression of this gene .	3	RESULTS	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
HilD	gene	sprB	activator	31484980	34	ver/dev	HilD positively controls expression of sprB .	169	HilD positively controls expression of sprB .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sprB	activator	31484980	37	ver/dev	Altogether , these results demonstrate that HilD induces expression of sprB by antagonizing H-NS-mediated repression on this gene .	182	Altogether , these results demonstrate that HilD induces expression of sprB by antagonizing H-NS-mediated repression on this gene .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sprB	activator	31484980	51	ver/dev	Our results demonstrate that HilD positively controls expression of sprB by acting on the regulatory region upstream of this gene .	240	Our results demonstrate that HilD positively controls expression of sprB by acting on the regulatory region upstream of this gene .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sprB	activator	31484980	53	ver/dev	We show that HilD induces expression of sprB by directly displacing the repressor H-NS from the regulatory region a mechanism that HilD follows to induce expression of other target genes36 ,37,41 -- 43 .	242	We show that HilD induces expression of sprB by directly displacing the repressor H-NS from the regulatory region upstream of this gene ; a mechanism that HilD follows to induce expression of other target genes36 ,37,41 -- 43 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	sprB	activator	31484980	53	ver/dev	We show that HilD induces expression of sprB by directly displacing the repressor H-NS from the regulatory region upstream of this gene ,37,41 -- 43 .	242	We show that HilD induces expression of sprB by directly displacing the repressor H-NS from the regulatory region upstream of this gene ; a mechanism that HilD follows to induce expression of other target genes36 ,37,41 -- 43 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	spvR	activator	21388802	0	ver/dev	SPI2 Description Crp activates spvR expression .	141	SPI2 Description Crp activates spvR and ompR expression .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	spvR	activator	21388802	7	ver/dev	spvR transcription is activated by CRP .	209	spvR transcription is activated by Hnr , CRP , RpoE , HimD and CsrA and is repressed by PhoP .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	3	ver/dev	six putative Lrp binding sites _ suggesting direct binding of Lrp to the tcfA promoter	124	Promoter sequence analysis of the intergenic region , upstream to tcfA in S. Infantis identified six putative Lrp binding sites , all containing the consensus sequence GN ( 2-3 ) TTT recognized by Lrp36 ( Fig. 5C ) , suggesting direct binding of Lrp to the tcfA promoter .	6	TCF CONTAINS INTERCHANGING ALLELES OF THE FIMBRIA ADHESIN TCFD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	tcfA	regulator	28922626	3	ver/dev	six putative Lrp binding sites _ suggesting direct binding of Lrp to the tcfA promoter	124	Promoter sequence analysis of the intergenic region , upstream to tcfA in S. Infantis identified six putative Lrp binding sites , all containing the consensus sequence GN ( 2-3 ) TTT recognized by Lrp36 ( Fig. 5C ) , suggesting direct binding of Lrp to the tcfA promoter .	6	TCF CONTAINS INTERCHANGING ALLELES OF THE FIMBRIA ADHESIN TCFD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	tcfA	regulator	28922626	3	ver/dev	all _ suggesting direct binding of Lrp to the tcfA promoter	124	Promoter sequence analysis of the intergenic region , upstream to tcfA in S. Infantis identified six putative Lrp binding sites , all containing the consensus sequence GN ( 2-3 ) TTT recognized by Lrp36 ( Fig. 5C ) , suggesting direct binding of Lrp to the tcfA promoter .	6	TCF CONTAINS INTERCHANGING ALLELES OF THE FIMBRIA ADHESIN TCFD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	tcfA	regulator	28922626	3	ver/dev	all _ suggesting direct binding of Lrp to the tcfA promoter	124	Promoter sequence analysis of the intergenic region , upstream to tcfA in S. Infantis identified six putative Lrp binding sites , all containing the consensus sequence GN ( 2-3 ) TTT recognized by Lrp36 ( Fig. 5C ) , suggesting direct binding of Lrp to the tcfA promoter .	6	TCF CONTAINS INTERCHANGING ALLELES OF THE FIMBRIA ADHESIN TCFD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
NsrR	gene	trpD	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
OmpR-P	gene	ssrB	repressor	12753201	48	ver/dev	An increase in OmpR-P levels would enable OmpR-P to bind to lower affinity sites , repressing ssrB .	248	An increase in OmpR-P levels would enable OmpR-P to bind to lower affinity sites , repressing ssrA and ssrB .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	phoB	regulator	16339942	29	ver/dev	Bacillus subtilis PhoP binds to the phoB tandem promoter exclusively within the phosphate-starvation-inducible promoter .	504	Bacillus subtilis PhoP binds to the phoB tandem promoter exclusively within the phosphate starvation-inducible promoter .	31	REFERENCES	Bacillus subtilis	0	L3	OTHER	Other	OTHER	New	Level 2
KdgR	gene	kduI	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	kduI	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	kduI	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RflM	TU	flhDC	repressor	27206164	0	ver/dev	In this study , we elucidated the molecular mechanism of RflM-dependent repression of flhDC .	23	In this study , we elucidated the molecular mechanism of RflM-dependent repression of flhDC .	3	SUMMARY	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RflM	TU	flhDC	repressor	27206164	15	ver/dev	RflM functions by repression of flhDC transcription .	78	RflM functions by repression of flhDC transcription .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RflM	TU	flhDC	repressor	27206164	20	ver/dev	To test a putative link between RflM in repression of flhDC , we performed an unbiased genetic screen using random transposon mutagenesis .	90	To test a putative link between RflM and RcsB in repression of flhDC , we performed an unbiased genetic screen using random transposon mutagenesis .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RflM	TU	flhDC	repressor	27206164	21	ver/dev	The transposon mutagenesis thus provided further evidence for a functional link between RflM in repression of flhDC .	101	The transposon mutagenesis thus provided further evidence for a functional link between RcsB and RflM in repression of flhDC .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RflM	TU	flhDC	repressor	27206164	28	ver/dev	Coordinated repression of flhDC transcription by RflM .	170	Coordinated repression of flhDC transcription by RcsB and RflM .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RflM	TU	flhDC	repressor	27206164	29	ver/dev	A. Schematic regulatory model of repression of the flagellar master regulator flhDC by coordinated action of RflM .	171	A. Schematic regulatory model of repression of the flagellar master regulator flhDC by coordinated action of RcsB and RflM .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RflM	TU	flhDC	repressor	27206164	35	ver/dev	expression of flhC-lac _ providing further evidence for a cooperative action of RflM in repression of flhDC	201	S6C , increasing levels of rflM decreased expression of flhC-lac , providing further evidence for a cooperative action of RflM and RcsB in repression of flhDC .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
RflM	TU	flhDC	repressor	27206164	41	ver/dev	To test if the HTH DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of binding to the flhDC promoter , we analyzed the function of a RflM mutant .	224	To test if the helix-turn-helix ( HTH ) DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC and binding to the flhDC promoter , we analyzed the function of a RflM mutant lacking its HTH domain .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	repressor	27206164	41	ver/dev	To test if the HTH DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC to the flhDC promoter , we analyzed the function of a RflM mutant .	224	To test if the helix-turn-helix ( HTH ) DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC and binding to the flhDC promoter , we analyzed the function of a RflM mutant lacking its HTH domain .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	repressor	27206164	41	ver/dev	To test if the helix-turn-helix DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of binding to the flhDC promoter , we analyzed the function of a RflM mutant .	224	To test if the helix-turn-helix ( HTH ) DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC and binding to the flhDC promoter , we analyzed the function of a RflM mutant lacking its HTH domain .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	Cantareus apertus;Cornu aspersum;Cantareus apertus;Cornu aspersum	0	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	repressor	27206164	41	ver/dev	To test if the helix-turn-helix DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC to the flhDC promoter , we analyzed the function of a RflM mutant .	224	To test if the helix-turn-helix ( HTH ) DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC and binding to the flhDC promoter , we analyzed the function of a RflM mutant lacking its HTH domain .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	Cantareus apertus;Cornu aspersum;Cantareus apertus;Cornu aspersum	0	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	repressor	27206164	42	ver/dev	DNA-binding domain of RflM is indispensable to mediate repression of flhDC by the RcsB-RflM complex .	231	DNA-binding domain of RflM is indispensable to mediate repression of flhDC by the RcsB-RflM complex .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	repressor	27206164	55	ver/dev	RflM , however , did not repress flhDC transcription in the absence of RcsB protein .	285	RflM , however , did not repress flhDC transcription in the absence of RcsB protein .	11	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
RflM	TU	flhDC	repressor	27206164	63	ver/dev	the P1flhDC promoter _ resulting in high affinity binding of a RcsB-RflM heterodimer and repression of flhDC operon transcription	316	RflM would then be able to subsequently direct an existing pool of unphosphorylated RcsB to its target DNA downstream of the P1flhDC promoter resulting in high affinity binding of a RcsB-RflM heterodimer and repression of flhDC operon transcription .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RflM	TU	flhDC	repressor	31501286	4	ver/dev	RcsB-mediated repression of flhDC is coordinated by the FlhD4C2-controlled regulator RflM ( also known as EcnR ) .	35	RcsB-mediated repression of flhDC is coordinated by the FlhD4C2-controlled regulator RflM ( also known as EcnR ) ( 26 , 27 ) .	3	MAIN	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
RflM	TU	flhDC	repressor	33090999	2	ver/dev	The production of RflM leads to repression of flhDC expression .	143	The production of RflM leads to repression of flhDC expression .	8	SUB-SYSTEM MODEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hha	activator	15256548	15	ver/dev	These included the cold-shock-responsive hns gene previously shown to be activated by the hha gene and -LRB- like H-NS -RRB- regulates several virulence genes in response to temperature .	667	These included the cold-shock-responsive hns gene previously shown to be activated by Fis ( Dersch et al. , 1994 ; Falconi et al. , 1996 ) , the hha gene whose product can form heteromeric complexes with H-NS and ( like H-NS ) regulates several virulence genes in response to temperature ( Madrid et al. , 2002 ; Nieto et al. , 2002 ) , and the stpA gene that encodes a paralogue of H-NS and can also form heteromers with it ( Deighan et al. , 2003 ; Free et al. , 2001 ; Johansson et al. , 2001 ; Williams et al. , 1996 ) .	15	STRESS RESPONSE GENES AND GLOBAL REGULATORS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	sbmC	activator	21102598	2	ver/dev	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is LexA .	92	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS and LexA mediated .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	sbmC	activator	21102598	2	ver/dev	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is LexA .	92	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS and LexA mediated .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	sbmC	activator	21102598	2	ver/dev	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS .	92	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS and LexA mediated .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	sbmC	activator	21102598	2	ver/dev	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS .	92	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS and LexA mediated .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Hha	gene	pefB	regulator	31661351	17	ver/dev	While the precise mechanism of pef fimbriae regulation by Hha remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefB since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs .	344	While the precise mechanism of pef fimbriae regulation by Hha and YdgT remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefB and pefA since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs [ 24 ] .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Cbl	gene	metE	activator	16547066	0	att	strain NRC-1 carrying a block in de novo corrin ring bio-synthesis and a chromosomal in-frame deletion of ORF Vng1577 ( Vng1577-1 cbiP1 ) , grew when the medium was supplemented with Cby or Cbi , indicating that the putative a All S. enterica strains used in these studies carry a null allele of the metE gene ( 16 ) , making growth of the cell dependent on the activity of the Cbl-dependent methionine synthase ( MetH ) enzyme ( 9 , 10 , 24 ) .	44	strain NRC-1 carrying a block in de novo corrin ring bio-synthesis and a chromosomal in-frame deletion of ORF Vng1577 ( Vng1577-1 cbiP1 ) , grew when the medium was supplemented with Cby or Cbi , indicating that the putative a All S. enterica strains used in these studies carry a null allele of the metE gene ( 16 ) , making growth of the cell dependent on the activity of the Cbl-dependent methionine synthase ( MetH ) enzyme ( 9 , 10 , 24 ) .	2	MAIN	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	narH	activator	29857034	19	ver/dev	narH are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1987	activator	17322315	2	ver/dev	In a starvation medium , the GGDEF domain protein STM1987 activated cellulose biosynthesis independent of CsgD .	42	In a starvation medium , which does not support the growth of Salmonella serovar Typhimurium , the GGDEF domain protein STM1987 activated cellulose biosynthesis independent of CsgD ( 10 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1987	activator	33468583	1	att	The DGC AdrA induces cellulose production in lysogeny broth ( LB ) medium without salt at 28 °C ( biofilm-inducing conditions ) in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD ( 29 , 33 ) .	66	The DGC AdrA induces cellulose production in lysogeny broth ( LB ) medium without salt at 28 °C ( biofilm-inducing conditions ) in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD ( 29 , 33 ) .	3	KEYWORDS CELLULOSE, DIGUANYLATE CYCLASE, STM1987, INVASIVE SALMONELLA, CSGD INDEPENDENT, VIRULENCE, CELLULOSE, CYCLIC-DI-GMP, MACROPHAGE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsgD	gene	STM1987	activator	33468583	0	ver/dev	STM1987 is proposed to stimulate production of cellulose independent of the master biofilm regulator CsgD .	13	STM1987 catalyzes the formation of bis - ( 39,59 ) - cyclic dimeric GMP ( c-di-GMP ) and is proposed to stimulate production of cellulose independent of the master biofilm regulator CsgD .	1	ABSTRACT	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1987	activator	33468583	1	ver/dev	The DGC AdrA induces cellulose production in LB medium without salt at biofilm-inducing condition in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD .	66	The DGC AdrA induces cellulose production in lysogeny broth ( LB ) medium without salt at 28 °C ( biofilm-inducing conditions ) in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD ( 29 , 33 ) .	3	KEYWORDS CELLULOSE, DIGUANYLATE CYCLASE, STM1987, INVASIVE SALMONELLA, CSGD INDEPENDENT, VIRULENCE, CELLULOSE, CYCLIC-DI-GMP, MACROPHAGE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsgD	gene	STM1987	activator	33468583	1	ver/dev	The DGC AdrA induces cellulose production in LB medium without salt at 28 ° in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD .	66	The DGC AdrA induces cellulose production in lysogeny broth ( LB ) medium without salt at 28 °C ( biofilm-inducing conditions ) in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD ( 29 , 33 ) .	3	KEYWORDS CELLULOSE, DIGUANYLATE CYCLASE, STM1987, INVASIVE SALMONELLA, CSGD INDEPENDENT, VIRULENCE, CELLULOSE, CYCLIC-DI-GMP, MACROPHAGE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsgD	gene	STM1987	activator	33468583	1	ver/dev	The DGC AdrA induces cellulose production in lysogeny broth medium without salt at biofilm-inducing condition in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD .	66	The DGC AdrA induces cellulose production in lysogeny broth ( LB ) medium without salt at 28 °C ( biofilm-inducing conditions ) in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD ( 29 , 33 ) .	3	KEYWORDS CELLULOSE, DIGUANYLATE CYCLASE, STM1987, INVASIVE SALMONELLA, CSGD INDEPENDENT, VIRULENCE, CELLULOSE, CYCLIC-DI-GMP, MACROPHAGE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CsgD	gene	STM1987	activator	33468583	1	ver/dev	The DGC AdrA induces cellulose production in lysogeny broth medium without salt at 28 ° in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD .	66	The DGC AdrA induces cellulose production in lysogeny broth ( LB ) medium without salt at 28 °C ( biofilm-inducing conditions ) in a CsgD-dependent manner , while STM1987 can induce cellulose production at 37 °C in nutrient-deficient medium , independent of CsgD ( 29 , 33 ) .	3	KEYWORDS CELLULOSE, DIGUANYLATE CYCLASE, STM1987, INVASIVE SALMONELLA, CSGD INDEPENDENT, VIRULENCE, CELLULOSE, CYCLIC-DI-GMP, MACROPHAGE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SsrB	gene	flhD	activator	30355489	12	att	( B ) Expression of PflhDCSBG does not show SsrB-dependent repression of STM flhD , measured by RT-qPCR .	133	( B ) Expression of PflhDCSBG does not show SsrB-dependent repression of STM flhD , measured by RT-qPCR .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
Fur	gene	fhuF	repressor	18790861	19	att	Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB-medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .	155	Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	dam	activator	33475482	0	ver/dev	HdfR acts as an activator of std expression in a dam .	39	HdfR is repressed by H-NS and acts as an activator of std expression in a dam or seqA mutant strain [ 8 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	dam	activator	33475482	4	ver/dev	This suggested that the crp mutation did not impact on the dam mutation in the std promoter as HdfR was still brought a major activation of std .	189	This suggested that the crp mutation did not impact on the dam mutation in the std promoter as HdfR was still produced and brought a major activation of std .	10	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HdfR	gene	dam	activator	33475482	4	ver/dev	This suggested that the crp mutation did not impact on the dam mutation in the std promoter as HdfR was still produced a major activation of std .	189	This suggested that the crp mutation did not impact on the dam mutation in the std promoter as HdfR was still produced and brought a major activation of std .	10	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	treR	repressor	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	repressor	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	repressor	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	repressor	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	repressor	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	repressor	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagK	activator	12775700	0	att	The genes pagJ and pagK are PhoP-activated genes and are nearly identical to each other ( 14 ) .	402	The genes pagJ and pagK are PhoP-activated genes and are nearly identical to each other ( 14 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagK	activator	23782700	2	att	A , - galactosidase activity from lacZ-transcriptional-fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	168	A , - galactosidase activity from lacZ transcriptional fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagK	activator	31611347	3	att	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ-transcriptional-fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	94	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ transcriptional fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	yqaE	activator	26307765	2	ver/dev	For example , the yqaE gene is activated by CpxR .	426	For example , the yqaE gene is activated by CpxR ( 22 ) and RprA , which may constitute another FFL featuring both transcriptional and posttranscriptional control .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NarL	gene	ytfE	activator	23651595	17	ver/dev	it has been suggested that ytfE becomes activated by NarL upon exposure to nitrite	621	Expression of ytfE is repressed by NsrR and it has been suggested that ytfE becomes activated by NarL upon exposure to nitrate and nitrite ( Constantinidou et al. , 2006 ; Filenko et al. , 2007 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Overton et al. , 2008 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NarL	gene	ytfE	activator	23651595	17	ver/dev	it has been suggested that ytfE becomes activated by NarL upon exposure to nitrate	621	Expression of ytfE is repressed by NsrR and it has been suggested that ytfE becomes activated by NarL upon exposure to nitrate and nitrite ( Constantinidou et al. , 2006 ; Filenko et al. , 2007 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Overton et al. , 2008 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yliH	activator	18176541	0	ver/dev	the molecular mechanism _ underlying the stationary-phase induction of yliH under LB with vigorous aeration , by analyzing its promoter activity in various mutant backgrounds,-lacking stationary-phase σ , RpoS , or stringent signal-molecules ppGpp , ∆ relA ∆	6	We set out to establish the molecular mechanism underlying the stationary phase induction of yliH under the standard culture condition , LB with vigorous aeration , by analyzing its promoter activity in various mutant backgrounds,-lacking stationary phase σ , RpoS , or stringent signal molecules ppGpp , ∆ relA ∆ spoT .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	yliH	activator	18176541	0	ver/dev	the molecular mechanism _ underlying the stationary-phase induction of yliH under the standard culture condition , by analyzing its promoter activity in various mutant backgrounds,-lacking stationary-phase σ , RpoS , or stringent signal-molecules ppGpp , ∆ relA ∆	6	We set out to establish the molecular mechanism underlying the stationary phase induction of yliH under the standard culture condition , LB with vigorous aeration , by analyzing its promoter activity in various mutant backgrounds,-lacking stationary phase σ , RpoS , or stringent signal molecules ppGpp , ∆ relA ∆ spoT .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	ihfA	regulator	21680637	50	ver/dev	The effect of ihfA mutant alleles on hilA expression in cells growing in LB-medium suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	278	The effect of ihfA or ihB mutant alleles on hilA expression in cells growing in LB medium and entering the stationary phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants , as well as the gel-shift data presented above suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
IHF	gene	ihfA	regulator	21680637	50	ver/dev	The effect of ihfA mutant alleles on hilA expression in cells entering the stationary-phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	278	The effect of ihfA or ihB mutant alleles on hilA expression in cells growing in LB medium and entering the stationary phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants , as well as the gel-shift data presented above suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
IHF	gene	ihfA	regulator	21680637	50	ver/dev	The effect of ihfA mutant alleles on hilA expression in cells entering the gel-shift data suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	278	The effect of ihfA or ihB mutant alleles on hilA expression in cells growing in LB medium and entering the stationary phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants , as well as the gel-shift data presented above suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	dinB	activator	20421601	2	att	Among these RpoS-induced genes the dinB gene encoding the trans-lesion DNA polymerase Pol IV can be found ( Layton and Foster 2003 ) .	34	Among these RpoS-induced genes the dinB gene encoding the trans-lesion DNA polymerase Pol IV can be found ( Layton and Foster 2003 ) .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	ssrA	activator	17259627	41	ver/dev	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators SsrB .	367	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators OmpR and SsrB .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HNS	gene	ssrA	activator	17259627	41	ver/dev	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators OmpR .	367	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators OmpR and SsrB .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	STM3595	activator	30992361	10	att	In contrast , EmrR did not exert an effect on transcription merely dependent on the PhoP/PhoQ system because transcription of two PhoP-activated genes , pcgL and STM3595 ( 36 ) , remained at similar levels in wild-type and ΔemrR strains ( Fig .	91	In contrast , EmrR did not exert an effect on transcription merely dependent on the PhoP/PhoQ system because transcription of two PhoP-activated genes , pcgL and STM3595 ( 36 ) , remained at similar levels in wild-type and ΔemrR strains ( Fig .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	STM3595	activator	30992361	14	att	On the other hand , dopamine could not act on the PhoP/PhoQ system because the PhoP-activated transcription of the pcgL and STM3595 genes remained unchanged under the conditions with 2 mM dopamine or without dopamine ( Fig .	123	On the other hand , dopamine could not act on the PhoP/PhoQ system because the PhoP-activated transcription of the pcgL and STM3595 genes remained unchanged under the conditions with 2 mM dopamine or without dopamine ( Fig .	3	RESULTS	nan	1	L1	OTHER	Other	NEG	New	Level 1
CspC	gene	rpoS	regulator	32159509	11	ver/dev	Phadtare S , Inouye M. Role of CspC in regulation of expression of rpoS , the stress response proteins in Escherichia coli .	380	Phadtare S , Inouye M. Role of CspC and CspE in regulation of expression of rpoS and UspA , the stress response proteins in Escherichia coli .	29	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	pepE	activator	11932449	3	att	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , as well as the basal expression of the cAMP-regulated S. typhimurium pepE gene ( Conlin et al. , 1994 ) , encoding an - aspartyl α dipeptidase , was analysed .	231	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , as well as the basal expression of the cAMP-regulated S. typhimurium pepE gene ( Conlin et al. , 1994 ) , encoding an - aspartyl α dipeptidase , was analysed .	6	EXPRESSION OF CAMP-REGULATED GENES IN S. TYPHIMURIUM FUR CELLS	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	dctA	activator	33593945	2	att	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary-phase ) .	135	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary phase ) .	3	KEYWORDS DCTA, ESCHERICHIA COLI, IRAP, RPOS, SALMONELLA, DICARBOXYLATES, GENE REGULATION, METABOLISM, SUCCINATE, VIRULENCE REGULATION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dctA	activator	33593945	2	att	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary-phase ) .	135	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary phase ) .	3	KEYWORDS DCTA, ESCHERICHIA COLI, IRAP, RPOS, SALMONELLA, DICARBOXYLATES, GENE REGULATION, METABOLISM, SUCCINATE, VIRULENCE REGULATION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dctA	activator	33593945	0	ver/dev	that activation of RpoS results in the repression of dctA , encoding the primary dicarboxylate importer	9	We demonstrate that activation of RpoS results in the repression of dctA , encoding the primary dicarboxylate importer , and that constitutive expression of dctA induces growth .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	dctA	activator	33593945	3	ver/dev	We hypothesized that activation of the RpoS regulon may repress the expression of the dctA gene .	136	We hypothesized that activation of the RpoS regulon may repress the expression of the dctA gene and thereby restrict Salmonella from taking up dicarboxylates such as succinate for consumption in response to stresses encountered within the host .	3	KEYWORDS DCTA, ESCHERICHIA COLI, IRAP, RPOS, SALMONELLA, DICARBOXYLATES, GENE REGULATION, METABOLISM, SUCCINATE, VIRULENCE REGULATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	rpoE	repressor	25713562	12	ver/dev	It is likely the effects of σE on SPI-2 transcription is mediated by SsrB because Sly , can complement the decrease of SPI-2 expression as a result of rpoE deletion .	294	It is likely the effects of σE on SPI-2 transcription is mediated by SsrB because overexpression of SsrB , but not SlyA , can complement the decrease of SPI-2 expression as a result of rpoE deletion ( Yoon et al. , 2009 ) .	13	DISCUSSION E	Strawberry lethal yellows phytoplasma	0	L2	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	rpoE	repressor	25713562	12	ver/dev	It is likely the effects of σE on SPI-2 transcription is mediated by SsrB because overexpression of Ssr , can complement the decrease of SPI-2 expression as a result of rpoE deletion .	294	It is likely the effects of σE on SPI-2 transcription is mediated by SsrB because overexpression of SsrB , but not SlyA , can complement the decrease of SPI-2 expression as a result of rpoE deletion ( Yoon et al. , 2009 ) .	13	DISCUSSION E	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CreB	gene	creB	activator	33563986	7	ver/dev	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of creB vrpB double mutant was significantly outcompeted by the vrpB mutant in spleen of the infected mice , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	240	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of the vrpB mutant ( Supplementary Fig. 6k ) and creB vrpB double mutant was significantly outcompeted by the vrpB mutant in liver and spleen of the infected mice ( Supplementary Fig. 6l ) , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	3	RESULTS	Mus sp.	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CreB	gene	creB	activator	33563986	7	ver/dev	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of creB vrpB double mutant was significantly outcompeted by the vrpB mutant in liver of the infected mice , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	240	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of the vrpB mutant ( Supplementary Fig. 6k ) and creB vrpB double mutant was significantly outcompeted by the vrpB mutant in liver and spleen of the infected mice ( Supplementary Fig. 6l ) , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	3	RESULTS	Mus sp.	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CreB	gene	creB	activator	33563986	7	ver/dev	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of the vrpB mutant double mutant was significantly outcompeted by the vrpB mutant in spleen of the infected mice , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	240	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of the vrpB mutant ( Supplementary Fig. 6k ) and creB vrpB double mutant was significantly outcompeted by the vrpB mutant in liver and spleen of the infected mice ( Supplementary Fig. 6l ) , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	3	RESULTS	Mus sp.	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CreB	gene	creB	activator	33563986	7	ver/dev	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of the vrpB mutant double mutant was significantly outcompeted by the vrpB mutant in liver of the infected mice , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	240	The replication of the creB vrpB double mutant in PMs was significantly decreased compared to that of the vrpB mutant ( Supplementary Fig. 6k ) and creB vrpB double mutant was significantly outcompeted by the vrpB mutant in liver and spleen of the infected mice ( Supplementary Fig. 6l ) , indicating that the contribution of CreB to STM virulence is partially dependent on VrpB .	3	RESULTS	Mus sp.	0	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	rstA	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HilA	gene	lpxR	regulator	27886269	3	ver/dev	HilA , regulates the expression of lpxR .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tdcA	activator	20396961	1	att	The results of β-galactosidase assays and FACS analysis showed that , among the four PhoP-dependent genes tested , the expression of ssaG , which is located in Salmonella pathogenicity island 2 ( SPI2 ) , was reduced in the tdcA mutant , especially in the intracellular environment of macrophages .	13	The results of β-galactosidase assays and FACS analysis showed that , among the four PhoP-dependent genes tested , the expression of ssaG , which is located in Salmonella pathogenicity island 2 ( SPI2 ) , was reduced in the tdcA mutant , especially in the intracellular environment of macrophages .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tdcA	activator	20396961	3	att	The negative effect of the tdcA mutation on SPI2 expression is evident inside macrophages Of the proteins differentially expressed in the tdcA mutant strain ( Fig. 4 and Table 3 ) , TktA , AtpA , and MalE have been previously identified as a PhoP-dependent regulon in E. coli and S. Typhimurium ( Monsieurs et al. , 2005 ) .	207	The negative effect of the tdcA mutation on SPI2 expression is evident inside macrophages Of the proteins differentially expressed in the tdcA mutant strain ( Fig. 4 and Table 3 ) , TktA , AtpA , and MalE have been previously identified as a PhoP-dependent regulon in E. coli and S. Typhimurium ( Monsieurs et al. , 2005 ) .	11	RESULTS	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	tdcA	activator	20396961	5	att	To test the possibility that the effect of the tdcA mutation was increased under inducing conditions for PhoP-activated genes , Salmonella cultures were shifted from N minimal-medium containing a repressing Mg concentration ( 2 mM ) to that contain-2 + ing an activating Mg concentrations ( 50 μM ) ( Fig. 5B ) .	223	To test the possibility that the effect of the tdcA mutation was increased under inducing conditions for PhoP-activated genes , Salmonella cultures were shifted from N minimal medium containing a repressing Mg concentration ( 2 mM ) to that contain-2 + ing an activating Mg concentrations ( 50 μM ) ( Fig. 5B ) .	11	RESULTS	Salmonella	1	L1	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	tdcA	activator	20396961	6	att	The four PhoP-dependent genes tested were not strongly downregulated by the tdcA mutation in cultures , whereas the gene encoding the SPI2-associated apparatus protein SsaG , which was induced by about 400-fold in the intracellular environment ( Valdivia and Falkow , 1997 ) , showed significantly reduced expression in the tdcA mutant strains inside macrophages ( Figs. 5F and 6 ) .	296	The four PhoP-dependent genes tested were not strongly downregulated by the tdcA mutation in cultures , whereas the gene encoding the SPI2-associated apparatus protein SsaG , which was induced by about 400-fold in the intracellular environment ( Valdivia and Falkow , 1997 ) , showed significantly reduced expression in the tdcA mutant strains inside macrophages ( Figs. 5F and 6 ) .	12	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	sefA	activator	25217722	0	ver/dev	It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sefA	activator	25217722	0	ver/dev	It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	sifB	activator	31484980	50	ver/dev	binding analyses indicate that SprB positively controls expression of ugtL genes more28 , all these genes located outside SPI-1 , including the sifB .	238	Global expression and binding analyses indicate that SprB positively controls expression of yobH , slrP , ugtL and 20 genes more28 , all these genes located outside SPI-1 , including the sifB , yhgE , yibP , SL1344_3112 , SL1344_0336 and SL1344_0337 genes that have been associated to virulence56 ,68 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	sifB	activator	31484980	50	ver/dev	binding analyses indicate that SprB positively controls expression of slrP genes more28 , all these genes located outside SPI-1 , including the sifB .	238	Global expression and binding analyses indicate that SprB positively controls expression of yobH , slrP , ugtL and 20 genes more28 , all these genes located outside SPI-1 , including the sifB , yhgE , yibP , SL1344_3112 , SL1344_0336 and SL1344_0337 genes that have been associated to virulence56 ,68 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	sifB	activator	31484980	50	ver/dev	binding analyses indicate that SprB positively controls expression of yobH genes more28 , all these genes located outside SPI-1 , including the sifB .	238	Global expression and binding analyses indicate that SprB positively controls expression of yobH , slrP , ugtL and 20 genes more28 , all these genes located outside SPI-1 , including the sifB , yhgE , yibP , SL1344_3112 , SL1344_0336 and SL1344_0337 genes that have been associated to virulence56 ,68 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	sifB	activator	31484980	50	ver/dev	Global expression indicate that SprB positively controls expression of ugtL genes more28 , all these genes located outside SPI-1 , including the sifB .	238	Global expression and binding analyses indicate that SprB positively controls expression of yobH , slrP , ugtL and 20 genes more28 , all these genes located outside SPI-1 , including the sifB , yhgE , yibP , SL1344_3112 , SL1344_0336 and SL1344_0337 genes that have been associated to virulence56 ,68 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SprB	gene	sifB	activator	31484980	50	ver/dev	Global expression indicate that SprB positively controls expression of slrP genes more28 , all these genes located outside SPI-1 , including the sifB .	238	Global expression and binding analyses indicate that SprB positively controls expression of yobH , slrP , ugtL and 20 genes more28 , all these genes located outside SPI-1 , including the sifB , yhgE , yibP , SL1344_3112 , SL1344_0336 and SL1344_0337 genes that have been associated to virulence56 ,68 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SprB	gene	sifB	activator	31484980	50	ver/dev	Global expression indicate that SprB positively controls expression of yobH genes more28 , all these genes located outside SPI-1 , including the sifB .	238	Global expression and binding analyses indicate that SprB positively controls expression of yobH , slrP , ugtL and 20 genes more28 , all these genes located outside SPI-1 , including the sifB , yhgE , yibP , SL1344_3112 , SL1344_0336 and SL1344_0337 genes that have been associated to virulence56 ,68 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilE	gene	sopA	regulator	21949647	5	ver/dev	IsrM can potentially negatively regulate SopA protein level at the translation level through its direct binding of the sopA mRNA and positively at the transcriptional level simultaneously through its down-regulation of the negative regulator HilE .	404	IsrM can potentially negatively regulate SopA protein level at the translation level through its direct binding of the sopA mRNA and positively at the transcriptional level simultaneously through its down-regulation of the negative regulator HilE .	14	DIFFERENTIAL EXPRESSION OF SPI-1 PROTEINS REGULATED BY SRNA	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	rhuM	activator	26561851	1	att	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	159	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	7	THE PRIMARY TRANSCRIPTOME OF INTRA-MACROPHAGE S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	araE	regulator	24272778	14	att	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	201	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
AraC	gene	araE	regulator	24272778	6	att	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	88	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	2	MAIN	Escherichia coli;Iris germanica;Escherichia coli;Iris germanica;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	araE	regulator	24272778	21	ver/dev	To determine whether either ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeM .	251	To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	araE	regulator	24272778	21	ver/dev	To determine whether either ydeN is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN .	251	To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgA	regulator	11254626	1	att	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	208	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	6	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgA	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csrA	activator	23676436	17	att	This is consistent with a recent E. coli study which revealed that the P1 and P3 promoters of csrA transcription are RpoS-dependent ( Yakhnin et al. , 2011 ) .	398	This is consistent with a recent E. coli study which revealed that the P1 and P3 promoters of csrA transcription are RpoS-dependent ( Yakhnin et al. , 2011 ) .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	csrA	activator	25123657	25	ver/dev	As previously reported , the RpoS level was increased both in the csrA mutants at 37 °	218	As previously reported [ 13 ] , the RpoS level was increased both in the clpP and csrA mutants at 37 °C , and further it increased when transferred to 15 °C for 3 h ( Figure 3B ) .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
BaeR	gene	baeR	regulator	30448437	6	ver/dev	Results of our previous study also suggest that the expression of stm3031 is affected by the regulatory gene baeR of the BaeSR TCS in S. Typhimurium .11 To investigate whether such effect is mediated by regulator binding , the binding of BaeR to the stm3030 promoter was examined by EMSA .	194	Results of our previous study also suggest that the expression of stm3031 is affected by the regulatory gene baeR of the BaeSR TCS in S. Typhimurium .11 To investigate whether such effect is mediated by regulator binding , the binding of BaeR to the stm3030 promoter was examined by EMSA .	17	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Investigation	OTHER	Other	Level 1
FNR	TU	acrEF	regulator	21829527	4	ver/dev	As acrEF has been reported to be regulated by FNR in E. coli we investigated the level of fnr expression in our mutants	101	As acrEF has been reported to be regulated by FNR in E. coli [ 26 ] we investigated the level of fnr expression in our mutants but the level of expression was not significantly different between the mutants and wild-type .	15	TR 1% 32 8 2 0.12 0.06	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	lacZ	regulator	25972862	0	ver/dev	SsrB Independent Regulation of sseK1 by PhoQ/PhoP We took advantage of the chromosomal sseK1 : : lacZ fusion to look for genetic factors .	319	SsrB Independent Regulation of sseK1 by PhoQ/PhoP We took advantage of the chromosomal sseK1 : : lacZ fusion to look for genetic factors controlling sseK1 expression .	21	SYNTHESIS AND TRANSLOCATION INTO MAMMALIAN CELLS OF SSEK1 UNDER SPI1 AND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma54	gene	rpoN	regulator	19076233	10	att	Also , in Gram-positive bacteria , inactivation of rpoN or the s54-controlled PTS permeases has been reported to increase resistance to membrane-permeabilizing peptides of the subclass IIa bacteriocins .	163	Also , in Gram-positive bacteria , inactivation of rpoN or the s54-controlled PTS permeases has been reported to increase resistance to membrane-permeabilizing peptides of the subclass IIa bacteriocins .	15	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	spvR	repressor	23936152	12	ver/dev	the spvR inducer is normally repressed by H-NS	438	It is possible that stabilization of the StpA dimer by the StpA ( E42Del ) mutation allows StpA to increase spvgene expression by changing the DNA curvature at the spv locus thus allowing expression of the spvR inducer that is normally repressed by H-NS .	25	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	spvR	repressor	23936152	12	ver/dev	the spvR inducer is normally repressed by H-NS	438	It is possible that stabilization of the StpA dimer by the StpA ( E42Del ) mutation allows StpA to increase spvgene expression by changing the DNA curvature at the spv locus thus allowing expression of the spvR inducer that is normally repressed by H-NS .	25	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FadR	TU	fabHDG	activator	30325297	3	ver/dev	Transcription of the Escherichia coli fatty acid synthesis operon fabHDG is directly activated by FadR .	506	Transcription of the Escherichia coli fatty acid synthesis operon fabHDG is directly activated by FadR and inhibited by ppGpp .	27	9. JONES TH, VAIL KM, MCMULLEN LM. FILAMENT FORMATION BY FOOD- BORNE BACTERIA UNDER SUBLETHAL STRESS. INT J FOOD MICROBIOL 2013; 165:97–110.	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	regulator	21625519	68	att	We showed that this distinction resulted from a single amino-acid variation at position 169 , containing phenylalanine in place of valine ( Fig. 5D ) , that was important for the expression of sseL as well as for other PhoP-regulated genes ( Fig. 5 and Fig. 6 ) .	229	We showed that this distinction resulted from a single amino acid variation at position 169 , containing phenylalanine in place of valine ( Fig. 5D ) , that was important for the expression of sseL as well as for other PhoP-regulated genes ( Fig. 5 and Fig. 6 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	regulator	21625519	6	ver/dev	We show that PhoP directly controls sseL expression in a feed-forward regulatory loop .	58	We demonstrate a regulatory integration of a horizontally acquired virulence gene into the ancestral PhoPQ networks and show that PhoP directly controls sseL expression in a feed-forward regulatory loop .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	regulator	21625519	11	ver/dev	To elucidate the involvement of PhoP in the regulation of sseL , a reporter-gene fusion between a promoterless b-galacto-sidase was constructed using the vector pMC1403 .	66	To elucidate the involvement of PhoP in the regulation of sseL , a reporter-gene fusion between sseL and a promoterless b-galacto-sidase was constructed using the vector pMC1403 [ 30 ] .	5	RESULTS	Vector pMC1403	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	regulator	21625519	11	ver/dev	To elucidate the involvement of PhoP in the regulation of sseL , a reporter-gene fusion between sseL was constructed using the vector pMC1403 .	66	To elucidate the involvement of PhoP in the regulation of sseL , a reporter-gene fusion between sseL and a promoterless b-galacto-sidase was constructed using the vector pMC1403 [ 30 ] .	5	RESULTS	Vector pMC1403	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	regulator	21625519	13	ver/dev	Subsequently , we were interested in assessing the relative contribution of PhoP to the integrated regulation of sseL .	69	Subsequently , we were interested in assessing the relative contribution of PhoP and SsrB to the integrated regulation of sseL .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	regulator	21625519	30	ver/dev	PhoP binds directly to the promoter region of sseL	124	PhoP binds directly to the promoter region of sseL	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	regulator	21625519	32	ver/dev	To investigate the possibility of direct binding of PhoP to the promoter region of sseL , we conducted EMSA using a S. Typhimurium N-terminally His-tagged PhoP protein ( His -	126	To investigate the possibility of direct binding of PhoP to the promoter region of sseL , we conducted an electrophoretic mobility shift assay ( EMSA ) using a S. Typhimurium N-terminally His-tagged PhoP protein ( His -	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	sseL	regulator	21625519	32	ver/dev	To investigate the possibility of direct binding of PhoP to the promoter region of sseL , we conducted an electrophoretic-mobility-shift assay using a S. Typhimurium N-terminally His-tagged PhoP protein ( His -	126	To investigate the possibility of direct binding of PhoP to the promoter region of sseL , we conducted an electrophoretic mobility shift assay ( EMSA ) using a S. Typhimurium N-terminally His-tagged PhoP protein ( His -	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	sseL	regulator	21625519	51	ver/dev	Several lines of evidences indicated the ability of PhoP to promote expression of sseL in an SsrB-independent fashion : reduced expression of sseL : : lacZ was demonstrated in a phoP ssrB double mutant strain compared to direct in-vitro binding of His-PhoP to the promoter region of sseL in a gel mobility-shift assay .	184	Several lines of evidences indicated the ability of PhoP to promote expression of sseL in an SsrB-independent fashion : ( i ) reduced expression of sseL : : lacZ was demonstrated in a phoP ssrB double mutant strain compared to the ssrB background in S. Typhimur-ium ( Fig. 2A ) ; ( ii ) diminution in the abundance of sseL transcripts in the phoP ssrB background in relation to the ssrB strain ( Fig. 2B ) ; ( iii ) a PhoP-mediated induction of sseL : : lacZ in a S. bongori SsrB-free heterologous host ( Fig. 5 ) ; ( iv ) the presence of two putative PhoP boxes in the promoter region of sseL ( Fig. 3 ) ; and ( v ) direct in-vitro binding of His-PhoP to the promoter region of sseL in a gel mobility shift assay ( Fig. 4 ) .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	map	regulator	11237608	2	ver/dev	the class overcomes negative regulation by FlgM by reducing the af ® nity of the anti-sigma factor for s28 , since they map to the FlgM binding domains in region 3 and	306	Though the complete set of s28 * mutants was not examined in vitro , we think it likely that most of the substitutions would belong to the class which overcomes negative regulation by FlgM by reducing the af ® nity of the anti-sigma factor for s28 , since they map to the FlgM binding domains in region 3 and 4 .	8	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	mcpC	activator	33441540	16	ver/dev	In addition , mcpC reporter expression in strain was increased only in the presence of the HilD-binding site .	106	In addition , mcpC reporter expression in the hilD + strain was increased only in the presence of the HilD-binding site ( compare WT and HilD + strains in Fig. 2c , d ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	mcpC	activator	33441540	16	ver/dev	In addition , mcpC reporter expression in the hilD was increased only in the presence of the HilD-binding site .	106	In addition , mcpC reporter expression in the hilD + strain was increased only in the presence of the HilD-binding site ( compare WT and HilD + strains in Fig. 2c , d ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	bfd	regulator	27564394	16	att	This sRNA is encoded in an intergenic region and is transcribed divergently from the bfd gene , which encodes a Fur-regulated bacterioferritin-associated ferredoxin protein .	463	This sRNA is encoded in an intergenic region and is transcribed divergently from the bfd gene , which encodes a Fur-regulated bacterioferritin-associated ferredoxin protein .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	tdcA	activator	30682134	43	ver/dev	In LB , CsrA activated the translation of genes for tdcA metabolism -LRB- S2 Table -RRB- .	297	In LB , CsrA activated the translation of genes for fucose ( fucR ) , 1,2-propanediol ( pocR ) , and threonine/serine ( tdcA ) metabolism ( S2 Table ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	prgH	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgH remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	prgH	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgH remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	prgH	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgH remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hfq	repressor	24018968	8	ver/dev	The hfq mutation decreased HilD production compared with the wild-type at 4 h p.i. , cells h under shaking culture conditions .	193	The hfq mutation decreased HilD production compared with the wild-type at 4 h p.i. , cells grown for 4 and 12 h under shaking culture conditions .	15	HFQ AND ARCA CAN AFFECT HILD PROMOTER ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yhjH	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pgtE	repressor	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LsrR	gene	srgE	regulator	30286813	0	ver/dev	In Salmonella Typhimurium , srgE are regulated by the transcription factor LsrR .	254	In Salmonella Typhimurium , sdiA and srgE are regulated by the transcription factor LsrR .	13	DISCUSSION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	mig-14	regulator	17259627	8	att	In several SlyA-regulated genes , DNA sequences ( TTTAGTTTTTGTCTTAA , located in the ugtL promoter ; TTTGGAATGTAA , located in the pagC promoter ; and TTAGCTGTTAA , located in the mig-14 promoter ) have been identified as SlyA-specific binding sites by DNase-I-protection assay ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	60	In several SlyA-regulated genes , DNA sequences ( TTTAGTTTTTGTCTTAA , located in the ugtL promoter ; TTTGGAATGTAA , located in the pagC promoter ; and TTAGCTGTTAA , located in the mig-14 promoter ) have been identified as SlyA-specific binding sites by DNase I protection assay ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	mig-14	regulator	17379730	5	ver/dev	SlyA is also involved in the regulation of mig-14	362	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA , which is also involved in the regulation of virulence genes such as mig-14 , sopD2 and virK ( Brumell et al. , 2003 ; Ho et al. , 2002 ; Navarre et al. , 2005 ) .	14	GIFSY-1 AND GIFSY-2 PROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	mig-14	regulator	18221392	3	ver/dev	The mig-14 genes appear to be regulated by both SlyA , by a mechanism .	67	The mig-14 and pagC genes appear to be regulated by both SlyA and PhoP , by a mechanism that is not yet understood ( Navarre et al. , 2005 ) .	9	SALMONELLA VIRULENCE GENES ARE SPECIFICALLY EXPRESSED IN VIVO DURING INFECTION OF C. ELEGANS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssaG	regulator	17630976	0	att	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	14	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	2	SUMMARY	synthetic construct	0	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	ssaG	regulator	29930310	16	att	Transcription of the SsrB-regulated ssaG gene was also upregulated ( p < 0.001 ) in ssrADsc Salmonella compared to isogenic wild-type bacteria ( Fig. 4F ) .	121	Transcription of the SsrB-regulated ssaG gene was also upregulated ( p < 0.001 ) in ssrADsc Salmonella compared to isogenic wild-type bacteria ( Fig. 4F ) .	3	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagD	activator	19091955	16	ver/dev	Fig. 2B _ suggesting that a single SlyA box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagD	activator	19091955	16	ver/dev	low-Mg conditions _ suggesting that a single SlyA box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagD	activator	19091955	16	ver/dev	Fig. 2B _ suggesting that a single SlyA box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagD	activator	19091955	16	ver/dev	low-Mg conditions _ suggesting that a single SlyA box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagD	activator	19091955	16	ver/dev	Fig. 2B _ suggesting that a single SlyA box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagD	activator	19091955	16	ver/dev	low-Mg conditions _ suggesting that a single SlyA box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagD	activator	19091955	19	ver/dev	Transcriptional activation of pagD is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in Fig. 3C .	100	Transcriptional activation of pagD and pagC is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in the relA spoT mutant harboring pYS1109 ( Fig. 3C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Iris germanica	0	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagD	activator	19091955	19	ver/dev	Transcriptional activation of pagD is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in the relA spoT mutant harboring pYS1109 .	100	Transcriptional activation of pagD and pagC is a result of SlyA binding to the intergenic region in this condition , because a ChIP analysis shows that enrichment of the intergenic DNA by SlyA-FLAG reached levels similar to that in the wild-type strain in the relA spoT mutant harboring pYS1109 ( Fig. 3C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Iris germanica;Leiostomus xanthurus	0	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagD	activator	30992361	15	ver/dev	As a matter of fact , our previous study revealed that SlyA , at a high level , could stimulate deficient transcription of both pagD genes .	130	As a matter of fact , our previous study revealed that SlyA , at a high level that could not be attained physiologically in a wild-type cell , could stimulate deficient transcription of both pagC and pagD genes caused by an absence of the positive signal , i.e. , alarmine-guanosine pentaphosphate ( 23 ) .	3	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
CytR	gene	tsx	activator	16489221	0	ver/dev	Repression by CytR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CytR	gene	tsx	activator	16489221	0	ver/dev	Repression by CytR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	cas2	regulator	33854491	11	ver/dev	The results also support the complex genetic regulation of porins , since in the absence of cas2 , OmpR becomes undetectable , as does OmpC .	275	The results also support the complex genetic regulation of porins ( De la Cruz and Calva , 2010 ) , since in the absence of cas5 and cas2 , OmpR becomes undetectable ( Figure 4D ) , as does OmpC ( Figure 2C ) , demonstrating the specific role of these cas genes on ompR regulation to mediate OmpC synthesis .	19	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	eptA	regulator	34202800	22	ver/dev	the eptA expression is regulated by PmrA	407	A decrease in the pH of the medium is associated with activation of the eptA and arnBCADTEF-ugd expression , which is regulated by PmrA [ 122,137 ] .	12	3.3.5. THE PMRAB SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	gnd	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	gnd	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	gnd	regulator	12438352	21	att	gnd is the final gene in the rfb locus involved in LPS biosynthesis ( 34 ) and is located upstream of pmrE , a PmrA-regulated gene shown to be necessary for PM resistance and wild-type virulence ( 17 ) .	296	gnd is the final gene in the rfb locus involved in LPS biosynthesis ( 34 ) and is located upstream of pmrE , a PmrA-regulated gene shown to be necessary for PM resistance and wild-type virulence ( 17 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LexA	gene	tum	repressor	12399494	0	att	All three phage genomes included a homologue of the tum gene of coliphage 186 , which encodes a LexA-repressed cI antirepressor .	10	All three phage genomes included a homologue of the tum gene of coliphage 186 , which encodes a LexA-repressed cI antirepressor .	1	ABSTRACT	Escherichia virus 186	0	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	tum	repressor	12399494	1	att	The tum homologue of Fels-2 was responsible for lexA lethality and had a LexA-repressed promoter .	11	The tum homologue of Fels-2 was responsible for lexA lethality and had a LexA-repressed promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	tum	repressor	12399494	11	att	Control region of Fels-2 tum gene includes a LexA-repressed promoter .	424	Control region of Fels-2 tum gene includes a LexA-repressed promoter .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	tum	repressor	12399494	2	ver/dev	LexA protein represses the phage tum	19	In contrast , lysogens of coliphage 186 can be maintained only in the presence of LexA protein , which represses the phage tum ( antirepressor ) gene ( 27 , 44 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3611	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM3611	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM3611	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM3611	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM3611	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM1827 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	STM3611	regulator	24127899	26	ver/dev	Indirect regulation of biofilm formation by STM1697 The EAL domain protein STM3611 , a c-di-GMP phosphodiesterase , is one of the negative regulators of CsgD expression ( Simm et al. ,	256	Indirect regulation of biofilm formation by STM1697 The EAL domain protein STM3611 , a c-di-GMP phosphodiesterase , is one of the negative regulators of rdar morphotype formation and CsgD expression ( Simm et al. ,	11	FUNCTIONAL FLAGELLA AND CHEMOTAXIS ARE REQUIRED FOR INVASION OF HT-29 CELLS BY S. TYPHIMURIUM UMR1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	crp	repressor	18399940	1	ver/dev	To confirm CRP control , CyaR RNA levels were determined in Salmonella strains inactivated for crp in early stationary-phase .	235	To confirm the putative cAMP -- CRP control , CyaR RNA levels were determined in Salmonella strains inactivated for crp or cya ( Roof and Roth , 1992 ) in early stationary phase .	6	CYAR EXPRESSION IS STRICTLY CRP-DEPENDENT	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - CAMP in both Escherichia coli suggested that the synthesis of cAMP is inhibited by CRP .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - CAMP in both Escherichia coli suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - CAMP in both Salmonella typhimurium suggested that the synthesis of cAMP is inhibited by CRP .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - CAMP in both Salmonella typhimurium suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate in both Escherichia coli suggested that the synthesis of cAMP is inhibited by CRP .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate in both Escherichia coli suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate in both Salmonella typhimurium suggested that the synthesis of cAMP is inhibited by CRP .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	2168849	0	ver/dev	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate in both Salmonella typhimurium suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein .	14	THE observation that crp mutantsoverproduce adenosine 3 ' ,5 ' - cyclic monophosphate ( CAMP ) in both Salmonella typhimurium ( RAPHAELaInd SAIER 1976 ) and Escherichia coli ( POTTERC , HALMERS-LAR SON and YAMAZAKI1974 ; WAYNEand ROSEN1974 ) suggested that the synthesis of cAMP is inhibited by CAMP-CRP receptor protein ( CRP ) .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	27407104	7	ver/dev	Hence , combined repression of crp mRNAs by SdsR endorses down-regulation of the CRP regulon .	386	Hence , combined repression of crp and stpA mRNAs by SdsR fosters the expression of Sdependent genes and endorses down-regulation of the CRP regulon .	21	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	crp	repressor	32954419	0	ver/dev	a crp background may be indicative of repression by CRP	134	In contrast , the size of the ON HolA and OpvABON subpopulations increased in a crp background , which may be indicative of repression by CRP .	15	ROLE OF DAM METHYLATION IN TRANSCRIPTIONAL CONTROL OF UNDER- METHYLATED LOCI	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	32954419	0	ver/dev	a crp background may be indicative of repression by CRP	134	In contrast , the size of the ON HolA and OpvABON subpopulations increased in a crp background , which may be indicative of repression by CRP .	15	ROLE OF DAM METHYLATION IN TRANSCRIPTIONAL CONTROL OF UNDER- METHYLATED LOCI	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	32954419	1	ver/dev	a crp background may be indicative of repression by CRP	189	In contrast , the size of the ON HolA and OpvABON subpopulations increased in a crp background , which may be indicative of repression by CRP .	16	IDENTIFICATION OF REGULATORS INVOLVED IN TRANSCRIPTIONAL CONTROL	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	repressor	32954419	1	ver/dev	a crp background may be indicative of repression by CRP	189	In contrast , the size of the ON HolA and OpvABON subpopulations increased in a crp background , which may be indicative of repression by CRP .	16	IDENTIFICATION OF REGULATORS INVOLVED IN TRANSCRIPTIONAL CONTROL	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilD	activator	15661008	26	ver/dev	In the present study , the expression from lac fusion was retained after disruption in hilD in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilD	activator	15661008	26	ver/dev	In the present study , the expression from the hilA was retained after disruption in hilD in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilD	activator	16045614	1	ver/dev	that RtsA are each capable of independently inducing expression of the hilD genes	14	We demonstrate that HilC , HilD and RtsA are each capable of independently inducing expression of the hilC , hilD and rtsA genes , and that each can independently activate hilA .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilD	activator	16045614	20	ver/dev	We demonstrate that RtsA are each capable of inducing expression of hilD .	82	We demonstrate that HilC , HilD and RtsA are each capable of inducing expression of hilC , hilD and rtsA .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilD	activator	16045614	21	ver/dev	RtsA can independently induce expression of hilD	85	HilC , HilD and RtsA can independently induce expression of hilC , hilD and rtsA	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilD	activator	16045614	23	ver/dev	We had previously demonstrated that RtsA increased expression of hilD .	88	We had previously demonstrated that RtsA increased expression of hilC and hilD ( Ellermeier and Slauch , 2003 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilD	activator	16045614	24	ver/dev	We wanted to determine if RtsA could induce expression of hilD in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
RtsA	gene	hilD	activator	16045614	28	ver/dev	RtsA also induced expression of hilD .	131	RtsA , HilC and HilD also induced expression of hilC , hilD and rtsA ( Fig. 2 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilD	activator	16045614	29	ver/dev	RtsA induced expression of hilD ~ 10 - to 12-fold .	133	RtsA , HilC and HilD induced expression of hilC approximately threeto fourfold and hilD ~ 10 - to 12-fold .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilD	activator	16045614	30	ver/dev	These data show that RtsA are each capable of independently inducing expression of hilD , consistent with our model that RtsA constitute a feed forward regulatory loop .	134	These data show that HilC , HilD and RtsA are each capable of independently inducing expression of hilC , hilD and rtsA , consistent with our model that HilC , HilD and RtsA constitute a feed forward regulatory loop ( Fig. 1 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilD	activator	16045614	69	ver/dev	We show that RtsA can each independently activate expression of the hilD genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilD	activator	17208038	31	ver/dev	RtsA are clearly able to induce hilD transcription .	159	HilC , HilD and RtsA , when overproduced are clearly able to induce hilD transcription .	11	REGULATION OF HILD	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RtsA	gene	hilD	activator	17993530	6	ver/dev	RtsA are all also capable of activating expression of hilD independent of each other and comprise a complex feed forward regulatory loop .	39	HilC , HilD , and RtsA are all also capable of activating expression of hilC , hilD , and rtsA independent of each other and comprise a complex feed forward regulatory loop that controls hilA expression ( Fig. 1 ) ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilD	activator	22291968	6	ver/dev	Because RtsA is known to activate hilD transcription , we concluded that increased hilD : : lac930 expression was due to overproduction of RtsA .	173	Because RtsA is known to activate hilD transcription [ 35 ] , we concluded that increased hilD : : lac930 expression was due to overproduction of RtsA .	15	ETHICS STATEMENT	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
RtsA	gene	hilD	activator	22479568	0	ver/dev	RtsA can activate expression of hilD of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilD	activator	26039089	8	ver/dev	RtsA is a major regulator of both hilD expression of a feed-forward loop for activation of SPI1 expression .	181	RtsA is a major regulator of both hilA and hilD expression and forms part of a feed-forward loop for activation of SPI1 expression [ 53 ] .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilD	activator	27601571	4	ver/dev	Indeed , this is the case for activation of hilD by HilD/HilC / RtsA .	72	Indeed , this is the case for activation of hilD , hilC , rtsA , and hilA by HilD/HilC / RtsA ( 29 , 30 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilD	activator	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilD	activator	32041797	5	ver/dev	RtsA activate transcription of hilD , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	rpoS	regulator	30524381	48	ver/dev	if they are mediated through OmpR regulation of an intermediating regulator , as we observed with the OmpR repression of the stationary-phase sigma factor rpoS	394	The challenge will be to determine whether these are direct effects or if they are mediated through OmpR regulation of an intermediating regulator , as we observed with the OmpR repression of the stationary phase sigma factor rpoS ( Chakraborty et al. , 2017 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	TU	ssrAB	activator	29930310	21	ver/dev	A ΔrelA ΔspoT Salmonella strain does not express s ssrAB mRNA or SsrB prote is fundamental to transcriptional activation of ssrAB .	187	A ΔrelA ΔspoT Salmonella strain does not express ssrAB mRNA or SsrB protein , indicating ( p ) ppGpp is fundamental to transcriptional activation of ssrAB .	4	DISCUSSION	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
SirA	gene	hilA	repressor	33593291	13	ver/dev	These results suggest that repression of hilA expression by yeast extract in a ΔhilE mutant does not involve the BarA / SirA two-component system	115	These results suggest that repression of hilA expression by acetate and yeast extract in a ΔhilE mutant does not involve the BarA / SirA two-component system	6	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
SirA	gene	hilA	repressor	33593291	13	ver/dev	These results suggest that repression of hilA expression by acetate extract in a ΔhilE mutant does not involve the BarA / SirA two-component system	115	These results suggest that repression of hilA expression by acetate and yeast extract in a ΔhilE mutant does not involve the BarA / SirA two-component system	6	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
OmpR	gene	spiR	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
OmpR	gene	spiR	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
OmpR	gene	spiR	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by ofthe sensor SpiR at a posttranscriptionallevel .64 The PhoP protein appears to control translation of the spiR message ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	spiR	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by ofthe sensor SpiR at a posttranscriptionallevel .64 The PhoP protein appears to control translation of the spiR message ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	spiR	regulator	33045730	4	ver/dev	Transcription of spiR genes is regulated by OmpR .	29	Transcription of the horizontally acquired ssrB and spiR genes is regulated by several ancestral regulators , including SlyA ( 20 ) , OmpR ( 6 ) , and PhoP ( 7 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	TU	flhDC	repressor	30252837	3	ver/dev	A fliC : : lacZ fusion was repressed by StdEF in the presence of FlhDC only , suggesting that StdEF-mediated repression of flhDC transcription may be transmitted to downstream genes in the flagellar regulon .	206	A fliC : : lacZ fusion was repressed by StdEF in the presence of FlhDC only ( Fig 4 , panel D ) , suggesting that StdEF-mediated repression of flhDC transcription may be transmitted to downstream genes in the flagellar regulon .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	TU	flhDC	repressor	30252837	3	ver/dev	A fliC : : lacZ fusion was repressed by StdEF in the presence of FlhDC only , suggesting that StdEF-mediated repression of flhDC transcription may be transmitted to downstream genes in the flagellar regulon .	206	A fliC : : lacZ fusion was repressed by StdEF in the presence of FlhDC only ( Fig 4 , panel D ) , suggesting that StdEF-mediated repression of flhDC transcription may be transmitted to downstream genes in the flagellar regulon .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	TU	flhDC	repressor	30373755	0	ver/dev	We determined that relative to the wild type , the expression of the flagellin protein FliC is lower in the mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator .	12	We determined that relative to the wild type , the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CysB	gene	cysJIH	activator	2105304	12	ver/dev	Stimulation of CysB protein binding to a cysJIH promoter fragment by N-acetyl-L-serine .	168	Stimulation of CysB protein binding to a cysJIH promoter fragment by N-acetyl-L-serine .	6	GLUTATHIONE NONE 0.36 4.8	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	25637663	0	att	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative-stress	3	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative stress	0	Unknown	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	25637663	2	att	Moreover , the cysJIH operon exhibited a CysB-dependent upregulation in presence of these two antimicrobials compounds .	16	Moreover , the cysJIH operon exhibited a CysB-dependent upregulation in presence of these two antimicrobials compounds .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	25637663	4	att	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	39	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	6	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CysB	gene	cysJIH	activator	25637663	0	ver/dev	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds	3	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative stress	0	Unknown	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	25637663	7	ver/dev	cysJIH expression is upregulated by CysB in response to ione	111	3.3. cysJIH expression is upregulated by CysB in response to ceftriaxone or menadione	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	activator	25637663	7	ver/dev	cysJIH expression is upregulated by CysB in response to iaxone or m	111	3.3. cysJIH expression is upregulated by CysB in response to ceftriaxone or menadione	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CysB	gene	cysJIH	activator	27530757	3	att	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative-stress .	312	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative stress .	17	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	27530757	3	ver/dev	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds .	312	CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative stress .	17	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	33348574	1	att	[ CrossRef ] Alvarez , R. ; Neumann , G. ; Fravega , J. ; Díaz , F. ; Tejías , C. ; Fuentes , J.A. ; Paredes-Sabja , D. ; Calderón , I.L. ; Gil , F. Biochemical and Biophysical Research Communications CysB-dependent upregulation of the Salmonella typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative-stress .	465	[ CrossRef ] Alvarez , R. ; Neumann , G. ; Fravega , J. ; Díaz , F. ; Tejías , C. ; Fuentes , J.A. ; Paredes-Sabja , D. ; Calderón , I.L. ; Gil , F. Biochemical and Biophysical Research Communications CysB-dependent upregulation of the Salmonella typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative stress .	14	5. 6. 7.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	activator	33348574	1	ver/dev	[ CrossRef ] nd Biophysical Research Communications CysB-dependent upregulation of the Salmonella typhimurium cysJIH operon in respo to to antimicrobial compou .	465	[ CrossRef ] Alvarez , R. ; Neumann , G. ; Fravega , J. ; Díaz , F. ; Tejías , C. ; Fuentes , J.A. ; Paredes-Sabja , D. ; Calderón , I.L. ; Gil , F. Biochemical and Biophysical Research Communications CysB-dependent upregulation of the Salmonella typhimurium cysJIH operon in response to antimicrobial compounds that induce oxidative stress .	14	5. 6. 7.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
IHF	gene	hilA	repressor	21680637	49	ver/dev	IHF alleviates H-NS-mediated repression of hilA transcription	277	IHF alleviates H-NS-mediated repression of hilA transcription	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	gene	rfaG	regulator	26267246	8	ver/dev	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to Fig 5C , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting mRNA translation .	115	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to the WT ( Fig 5C ) , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting FlhDC stability or mRNA translation .	8	CHARACTERIZATION OF MUTANTS WITH AN ALTERED MOTILITY PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	rfaG	regulator	26267246	8	ver/dev	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to the WT , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting mRNA translation .	115	FlhC protein levels were reduced in a rfaG deletion mutant in contrast to the WT ( Fig 5C ) , indicating that RfaG is involved in regulation of flagellar class II gene expression by posttranscriptionally affecting FlhDC stability or mRNA translation .	8	CHARACTERIZATION OF MUTANTS WITH AN ALTERED MOTILITY PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	rck	activator	18791004	0	ver/dev	In response to AHLs , SdiA activates two Salmonella-specific loci , the rck operon	48	In response to AHLs , SdiA activates two Salmonella-specific loci , srgE ( sdiA-regulated gene E ) and the rck ( resistance to complement kill-ing ) operon , but the exact function of SdiA in Salmonella remains unclear ( 1 , 62 ) .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	20121449	0	ver/dev	In response to AHL under laboratory conditions , Salmonella SdiA activates the expression of the rck operon .	47	In response to AHL under laboratory conditions , Salmonella SdiA activates the expression of the chromosomally encoded srgE gene and the rck operon , which is borne on the S. enterica sv .	2	J. T. NOEL,1 J. JOY,2 J. N. SMITH,3 M. FATICA,2 K. R. SCHNEIDER,2 B. M. M. AHMER,3 AND M. TEPLITSKI1 1SOIL AND WATER SCIENCE DEPARTMENT AND 2DEPARTMENT OF FOOD SCIENCE AND HUMAN NUTRITION, UNIVERSITY OF FLORIDA-IFAS, GAINESVILLE 32610, U.S.A.; 3DEPARTMENT OF MICROBIOLOGY, OHIO STATE UNIVERSITY, COLUMBUS 43210, U.S.A.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	20368731	1	ver/dev	In Salmonella , rck is induced by SdiA .	415	In Salmonella , rck is not expressed in vitro in standard culture conditions , but is induced by quorum sensing and especially by SdiA [ 24 ] .	13	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	rck	activator	22149171	11	ver/dev	SdiA activates two operons in Salmonella in rck on the pSLT virulence-associated plasmid .	57	SdiA activates two operons in Salmonella in response to AHL binding , rck on the pSLT virulence-associated plasmid and srgE on the chromosome ( Ahmer et al. 1998 ; Smith and Ahmer 2003 ) .	5	INTRODUCTION	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	22610437	0	ver/dev	SdiA upregulates two loci in S. Typhimu-rium , the rck operon , located on the Salmonella virulence plasmid , and srgE -LRB- sdiA-regulated gene -RRB- , a horizontally acquired gene located on the chromosome .	54	SdiA upregulates two loci in S. Typhimu-rium , the rck ( resistance to complement killing ) operon , located on the Salmonella virulence plasmid , and srgE ( sdiA-regulated gene ) , a horizontally acquired gene located on the chromosome ( 1 , 21 , 32 ) .	13	6 22	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	24126528	0	ver/dev	In response to AHLs , SdiA increases the expression of the rck operon .	33	In response to AHLs , SdiA increases the expression of the rck operon and a gene named srgE that encodes a putative T3SS effector of unknown function ( 43 -- 45 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	24126528	2	ver/dev	SdiA increases the expression of the rck operon .	244	SdiA increases the expression of the rck operon and a putative T3SS effector of unknown function , SrgE .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	25080967	27	ver/dev	In this study , we first confirmed that the transcriptional regulation of rck by SdiA resulted in an increase of Rck protein expression .	257	In this study , we first confirmed that the transcriptional regulation of rck by SdiA described earlier ( Ahmer et al. , 1998 ; Smith and Ahmer , 2003 ) resulted in an increase of Rck protein expression .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	rck	activator	25966179	1	ver/dev	SdiA positively regulates two loci in the rck operon .	173	SdiA positively regulates two loci in Salmonella Typhimurium , the rck operon and the srgABC operon , both of which were found in a virulence plasmid .	11	QUORUM SENSING IN SALMONELLA ENTERITIDIS PT4 578	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	32849316	0	ver/dev	in Salmonella Typhimurium , SdiA positively regulates the expression of the rck operon	56	For instance , in Salmonella Typhimurium , SdiA positively regulates the expression of the rck ( resistance to complement killing ) operon , which codes for pefI , srgD , srgA , srgB , rck , and srgC genes , and it is found in the virulence plasmid pSLT ( Ahmer et al. , 1998 ; Soares and Ahmer , 2011 ; Sabag-Daigle et al. , 2012 ) .	4	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	33257526	16	ver/dev	In the presence of AHLs , SdiA activates rck .	132	In the presence of AHLs , SdiA activates the transcription of several genes , including rck , which encodes an outer membrane invasin ( 17 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	rck	activator	33257526	19	ver/dev	This result supports the established function of SdiA as an AHL-responsive transcriptional activator of rck .	140	This result supports the established function of SdiA as an AHL-responsive transcriptional activator of rck .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
NsrR	gene	hmpA	activator	21833325	1	ver/dev	In addition , hmpA expression is upregulated under iron-limiting conditions through NsrR , but independently of Fur .	259	In addition , hmpA expression is upregulated under iron-limiting conditions through NsrR , but independently of Fur ( Bang et al. , 2006 ) .	12	INDUCIBLE DETOXIFICATION OF RNS ENZYMATIC DETOXIFICATION OF NO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	hmpA	activator	24021902	1	att	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	78	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	ompR	regulator	12068808	26	ver/dev	HN-S is a negative regulator of ompR expression A previous report demonstrated that CRP affected ompR expression .	183	HN-S is a negative regulator of ompR expression A previous report using E. coli demonstrated that cAMP and CRP affected ompR expression ( Huang et al. , 1992 ) .	10	OMPR FOOTPRINT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	ompR	regulator	12080060	26	ver/dev	HN-S is a negative regulator of ompR expression A previous report demonstrated that CRP affected ompR expression .	183	HN-S is a negative regulator of ompR expression A previous report using E. coli demonstrated that cAMP and CRP affected ompR expression ( Huang et al. , 1992 ) .	10	OMPR FOOTPRINT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseB	activator	19202096	3	att	pagC and sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	335	pagC and sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	basR	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	lacZ	regulator	16713610	3	att	Among kanamycin-resistant tranductants , the presence of the lexA ( Ind ) mutation was confirmed through β-galactosidase assay after introduction of the pGE108 plasmid ( Table 2 ) which contains a LexA-regulated cea ∷ lacZ fusion ( Salles et al. , 1987 ) .	197	Among kanamycin-resistant tranductants , the presence of the lexA ( Ind ) mutation was confirmed through β-galactosidase assay after introduction of the pGE108 plasmid ( Table 2 ) which contains a LexA-regulated cea ∷ lacZ fusion ( Salles et al. , 1987 ) .	7	CONSTRUCTION OF S. ENTERICA MUTANTS	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LexA	gene	lacZ	regulator	24659766	8	ver/dev	The LexA-based genetic system detects in-vivo protein dimerization in E. coli SU101 , in which the reporter fusion sulA : : lacZ is controlled by the LexA dimer -LRB- dimerization is essential for operator recognition -RRB- .	148	The LexA-based genetic system detects in vivo protein dimerization in E. coli SU101 , in which the reporter fusion sulA : : lacZ is controlled by the LexA dimer ( dimerization is essential for operator recognition ) ( 50 ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PutA	gene	dctA	activator	33593945	6	ver/dev	Our finding that the polyfunctional proline metabolic enzyme PutA is essential for the proline-mediated induction of growth-on-succinate leaves open the question of whether the inducing cue is due to changes in the ability of PutA to bind DNA -LRB- perhaps PutA directly represses dctA in Salmonella -RRB- .	216	Our finding that the polyfunctional proline metabolic enzyme PutA is essential for the proline-mediated induction of growth on succinate leaves open the question of whether the inducing cue is due to changes in the ability of PutA to bind DNA ( perhaps PutA directly represses dctA in Salmonella ) , alterations in cellular energetics via the production of either reduced quinones or NADH , or increases in the concentrations of cellular glutamate ( although we note that addition of glutamate does not have the same effect as proline ) .	4	DISCUSSION	Salmonella	1	L2	SPEC	Other	OTHER	Other	Level 1
CRP	gene	sdiA	activator	22149171	1	ver/dev	The major activator of sdiA expression is CRP	8	The major activator of sdiA expression is cAMP-receptor protein ( CRP ) , and we define the CRP operator in the sdiA promoter using promoter and crp mutants .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sdiA	activator	22149171	15	ver/dev	Thus , the CRP binding site was converted to the CRP consensus sequence , resulting in increased sdiA expression .	248	Thus , the CRP binding site was converted to the CRP consensus sequence , resulting in increased sdiA expression .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	sdiA	activator	22149171	16	ver/dev	To test whether CRP was indeed activating sdiA , the mutant promoters were tested in a CRP mutant -LRB- crp -- -RRB- .	249	To test whether CRP was indeed activating sdiA , the wildtype and mutant promoters were tested in a CRP mutant ( crp -- ) .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	sdiA	activator	22149171	16	ver/dev	To test whether CRP was indeed activating sdiA , the wildtype promoters were tested in a CRP mutant -LRB- crp -- -RRB- .	249	To test whether CRP was indeed activating sdiA , the wildtype and mutant promoters were tested in a CRP mutant ( crp -- ) .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	sdiA	activator	22149171	19	ver/dev	CRP activates sdiA expression	254	CRP activates sdiA expression , and its activation is responsible for the majority of sdiA expression in exponential and early stationary phases of growth .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	sdiA	activator	22149171	20	ver/dev	cAMP-receptor-protein is an activator of sdiA	255	cAMP receptor protein is an activator of sdiA	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sdiA	activator	22149171	22	ver/dev	cAMP-receptor-protein is an activator of sdiA	259	cAMP receptor protein is an activator of sdiA	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sdiA	activator	22149171	43	ver/dev	Thus , a portion of increased sdiA expression could be due to increased CRP activity .	324	Thus , a portion of increased sdiA expression observed in DrcsD could be due to increased CRP activity .	17	THE RCS PHOSPHORELAY NEGATIVELY REGULATES SDIA	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	sdiA	activator	22149171	58	ver/dev	In this study , we show that CRP are the minor activators of sdiA , respectively .	377	In this study , we show that CRP and LeuO are the major and minor activators of sdiA , respectively .	21	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CRP	gene	sdiA	activator	22149171	58	ver/dev	In this study , we show that CRP are the major activators of sdiA , respectively .	377	In this study , we show that CRP and LeuO are the major and minor activators of sdiA , respectively .	21	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CRP	gene	sdiA	activator	22149171	60	ver/dev	CRP , is the main activator of sdiA expression .	388	CRP , a global regulator in bacteria , is the main activator of sdiA expression ( Saier et al. 1996 ) .	21	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	tpx	repressor	18156266	0	ver/dev	Expression of STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx in an hns background , suggesting that this global regulatory protein has a positive effect .	12	Expression of ompS1 , assT , and STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx and STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	tpx	repressor	18156266	0	ver/dev	Expression of assT was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx in an hns background , suggesting that this global regulatory protein has a positive effect .	12	Expression of ompS1 , assT , and STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx and STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	tpx	repressor	18156266	0	ver/dev	Expression of ompS1 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx in an hns background , suggesting that this global regulatory protein has a positive effect .	12	Expression of ompS1 , assT , and STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx and STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	tpx	repressor	18156266	44	ver/dev	Interestingly , the results indicate that H-NS is a positive regulator of tpx ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	354	Interestingly , the results presented here indicate that H-NS is a positive regulator of tpx and STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	tpx	repressor	18156266	45	ver/dev	global microarray analysis indicated that H-NS represses tpx expression .	357	global microarray analysis indicated that H-NS represses tpx expression .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	STM3611	regulator	25437188	48	ver/dev	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC via FliA .	556	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC , STM1344 and STM1697 via FliA ( Figure 2 ) .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	tolB	activator	12519186	15	ver/dev	To examine whether the effect of the tolB mutation resulted in induction of the RcsB regulon , we examined cps expression in tolB isogenic strains .	51	To examine whether the effect of the tolB mutation was specific to the ugd gene or resulted in induction of the RcsB regulon , we examined cps expression in tolB isogenic strains .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	SPEC	Investigation	OTHER	New	Level 1
CpxR	gene	cpxA	repressor	26300871	33	ver/dev	However , our data also show that both deletion of cpxA of CpxR slightly repress the expression of the SPI-1 genes in the absence of the Lon protease , suggesting an additional minor Lon-independent mechanism for the repression of the SPI-1 genes by CpxR-P .	477	However , our data also show that both deletion of cpxA and overexpression of CpxR slightly repress the expression of the SPI-1 genes in the absence of the Lon protease , suggesting an additional minor Lon-independent mechanism for the repression of the SPI-1 genes by CpxR-P .	18	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YdcI	gene	fumA	repressor	30038032	8	ver/dev	The transcription of fumA genes was most repressed by YdcI .	318	The transcription of acnB , icdA , sdhC , and fumA genes was most repressed by YdcI ( about 50 -- 100 fold higher in the ydcI strain ) .	7	REPRESSION OF THE ETHANOLAMINE UTILIZATION OPERON BY ARCA—	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PspC	gene	ompA	regulator	18458067	0	ver/dev	We evaluated the utilities of these vectors by fusing PspC , to the signal sequences of - bla SS , ompA , and phoA and the signal sequence under the control of the Ptrc promoter .	12	We evaluated the utilities of these vectors by fusing two different antigens , the - helix domains of pneumococcal surface protein A ( PspA ) and pneumococcal surface protein C ( PspC ) , to the signal sequences of - lactamase ( bla SS ) , ompA , and phoA and the signal sequence and C-terminal peptide of - lactamase ( bla SS CT ) on Asd plasmids under the control of the Ptrc promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PspC	gene	ompA	regulator	18458067	0	ver/dev	We evaluated the utilities of these vectors by fusing PspC , to the signal sequences of - lactamase , ompA , and phoA and the signal sequence under the control of the Ptrc promoter .	12	We evaluated the utilities of these vectors by fusing two different antigens , the - helix domains of pneumococcal surface protein A ( PspA ) and pneumococcal surface protein C ( PspC ) , to the signal sequences of - lactamase ( bla SS ) , ompA , and phoA and the signal sequence and C-terminal peptide of - lactamase ( bla SS CT ) on Asd plasmids under the control of the Ptrc promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	degP	regulator	23651595	5	ver/dev	As well as being regulated by RpoE , degP , is also CpxR .	276	As well as being regulated by RpoE , degP , is also CpxR regulated ( Danese , Snyder , Cosma , Davis , & Silhavy , 1995 ; Snyder et al. , 1995 ) .	16	2.3. ENVELOPE STRESS AND TWO COMPONENT SYSTEMS 2.3.1. THE CPX PATHWAY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	21984608	1	ver/dev	HilD binds directly to the regulatory regions of the ssrAB operon .	141	HilD binds directly to the regulatory regions of the ssrAB operon ( the coding regions of ssrA and ssrB ) and counteracts the repression exerted by the negative regulator , H-NS , or ompR ( a factor required for the activation of SPI-2 genes ) .	6	SALMONELLA RELIES ON T3SS2 TO SURVIVE AND REPLICATE INTRACELLULARLY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	23295139	0	ver/dev	HilD binds to the regulatory region of ssrAB , promoting OmpR binding .	229	HilD binds to the regulatory region of ssrAB , thereby counteracting H-NS mediated repression and promoting OmpR binding [ 40 ] .	9	REGULATION OF T3SS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	23295139	0	ver/dev	HilD binds to the regulatory region of ssrAB , thereby counteracting H-NS mediated repression .	229	HilD binds to the regulatory region of ssrAB , thereby counteracting H-NS mediated repression and promoting OmpR binding [ 40 ] .	9	REGULATION OF T3SS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	24728092	0	ver/dev	For instance , HilD is required for activating the regulatory region of the ssrAB operon , a key regulator of SPI-2 genes .	302	For instance , HilD is required for activating the regulatory region of the ssrAB operon , a key regulator of SPI-2 genes [ 4,23 ] .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	3	ver/dev	Furthermore , electrophoretic-mobility-shift assays showed that both HilD bind to the ssrAB region containing the repressing sequences .	10	Furthermore , electrophoretic mobility shift assays showed that both HilD and H-NS bind to the ssrAB region containing the repressing sequences .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	25135218	17	ver/dev	the mechanism by which HilD regulate the expression of ssrAB for the first time that HilD is able to displace H-NS from one of its target genes	47	Our results elucidate the mechanism by which HilD and H-NS regulate the expression of ssrAB and show for the first time that HilD is able to displace H-NS from one of its target genes .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	TU	ssrAB	regulator	25135218	18	ver/dev	cis elements required for the regulation of ssrAB by HilD .	79	cis elements required for the regulation of ssrAB by HilD .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	21	ver/dev	132.24 _ required for the regulation of ssrAB by HilD carrying different 5 = or 3 = deletions was constructed	85	To further identify sequences within the 302 / 478 region loaded from https://journals.asm.org/journal/jb on 19 October 2021 by 132.24 required for the regulation of ssrAB by HilD , a series of ssrAB-cat fusions carrying different 5 = or 3 = deletions was constructed ( Fig. 1 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	35	ver/dev	Our data from the expression analysis showed that HilD regulate the expression of ssrAB mainly by acting on the 55 / 119 / 336 regions , respectively .	134	Our data from the expression analysis showed that HilD and H-NS regulate the expression of ssrAB mainly by acting on the 55 / 240 and 119 / 336 regions , respectively .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	35	ver/dev	Our data from the expression analysis showed that HilD regulate the expression of ssrAB mainly by acting on the 55 / 240 / 336 regions , respectively .	134	Our data from the expression analysis showed that HilD and H-NS regulate the expression of ssrAB mainly by acting on the 55 / 240 and 119 / 336 regions , respectively .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	36	ver/dev	To further dissect ated regulation of ssrAB , we analyzed the interaction of HilD to different segments of EMSAs .	135	To further dissect the cis sequences required for the HilD/H-NS-medi - ated regulation of ssrAB , we analyzed the interaction of HilD and H-NS to different segments of the 302 / 478 region by electro-phoretic mobility shift assays ( EMSAs ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	25135218	36	ver/dev	To further dissect ated regulation of ssrAB , we analyzed the interaction of HilD to different segments of the 302 / 478 region by electro-phoretic mobility-shift assays .	135	To further dissect the cis sequences required for the HilD/H-NS-medi - ated regulation of ssrAB , we analyzed the interaction of HilD and H-NS to different segments of the 302 / 478 region by electro-phoretic mobility shift assays ( EMSAs ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	25135218	48	ver/dev	In this study , we elucidated the mechanism by which HilD regulate the expression of ssrAB .	162	In this study , we elucidated the mechanism by which HilD and H-NS regulate the expression of ssrAB and thus the SPI-2 genes ( Fig. 7 ) .	5	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	50	ver/dev	FIG 5 HilD bind to the same regions of ssrAB .	165	FIG 5 HilD and H-NS bind to the same regions of ssrAB .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	25135218	62	ver/dev	HilD binds to close to most of the sites of ssrAB .	202	HilD binds to sites overlapping or close to most of the sites bound by H-NS and thus displaces H-NS from most of its binding sites , which disrupts the H-NS nucleoprotein complex , thus leading to the expression of ssrAB .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	25135218	63	ver/dev	The regions _ required for the regulation of ssrAB by HilD	203	The regions required for the regulation of ssrAB by HilD and H-NS , defined in this study by expression and binding assays , are shown .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	25135218	86	ver/dev	To determine how HilD to regulate the expression of ssrAB in response to different growth-conditions is a matter of future studies .	238	To determine how HilD , OmpR , and SlyA coordinate to regulate the expression of ssrAB in response to different growth conditions is a matter of our current and future studies .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	25135218	86	ver/dev	To determine how HilD to regulate the expression of ssrAB in response to different growth-conditions is a matter of our current .	238	To determine how HilD , OmpR , and SlyA coordinate to regulate the expression of ssrAB in response to different growth conditions is a matter of our current and future studies .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	27886269	28	ver/dev	HilD cooperate to directly control the expression of ssrAB in our unpublished results .	170	HilD and SlyA cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions ( our unpublished results ) , which could also apply for lpxR .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	27886269	28	ver/dev	HilD cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions .	170	HilD and SlyA cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions ( our unpublished results ) , which could also apply for lpxR .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	29034217	4	ver/dev	reciprocally , SPI-1-encoded HilD upregulates SPI-2 gene expression by directly binding the ssrAB operon	299	For example , SPI-2-encoded SsrB downregulates SPI-1 genes by repressing HilA and HilD ( Pérez-Morales et al. , 2017 ) , and reciprocally , SPI-1-encoded HilD upregulates SPI-2 gene expression by directly binding the ssrAB operon ( Bustamante et al. , 2008 ) .	6	H-NS: THE MASTER SILENCER OF HORIZONTAL TRANSFER EVENTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	regulator	29555922	0	ver/dev	Interestingly , HilD is involved in the expression of the ssrAB operon encoding the SsrA/B two-component system , the central positive regulator for the SPI-2 genes .	41	Interestingly , HilD is involved in the expression of the ssrAB operon encoding the SsrA/B two-component system , the central positive regulator for the SPI-2 genes , but only when Salmonella is grown in LB23 ,44 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	regulator	30718301	69	ver/dev	FIG 8 Model for the regulation of ssrAB by HilD .	211	FIG 8 Model for the regulation of ssrAB by SlyA , HilD , OmpR , and H-NS .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilC	activator	16045614	1	ver/dev	that HilC are each capable of independently inducing expression of the hilC genes	14	We demonstrate that HilC , HilD and RtsA are each capable of independently inducing expression of the hilC , hilD and rtsA genes , and that each can independently activate hilA .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilC	activator	16045614	20	ver/dev	We demonstrate that HilC are each capable of inducing expression of hilC .	82	We demonstrate that HilC , HilD and RtsA are each capable of inducing expression of hilC , hilD and rtsA .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilC	activator	16045614	21	ver/dev	HilC can independently induce expression of hilC	85	HilC , HilD and RtsA can independently induce expression of hilC , hilD and rtsA	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilC	activator	16045614	24	ver/dev	We wanted to determine if HilC could induce expression of hilC in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
HilC	gene	hilC	activator	16045614	28	ver/dev	HilC also induced expression of hilC .	131	RtsA , HilC and HilD also induced expression of hilC , hilD and rtsA ( Fig. 2 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilC	activator	16045614	29	ver/dev	HilC induced expression of hilC approximately threeto fourfold 12-fold .	133	RtsA , HilC and HilD induced expression of hilC approximately threeto fourfold and hilD ~ 10 - to 12-fold .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilC	activator	16045614	30	ver/dev	These data show that HilC are each capable of independently inducing expression of hilC , consistent with our model that HilC constitute a feed forward regulatory loop .	134	These data show that HilC , HilD and RtsA are each capable of independently inducing expression of hilC , hilD and rtsA , consistent with our model that HilC , HilD and RtsA constitute a feed forward regulatory loop ( Fig. 1 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilC	activator	16045614	69	ver/dev	We show that HilC can each independently activate expression of the hilC genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilC	activator	17993530	6	ver/dev	HilC are all also capable of activating expression of hilC independent of each other and comprise a complex feed forward regulatory loop .	39	HilC , HilD , and RtsA are all also capable of activating expression of hilC , hilD , and rtsA independent of each other and comprise a complex feed forward regulatory loop that controls hilA expression ( Fig. 1 ) ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilC	activator	22479568	0	ver/dev	HilC can activate expression of hilC of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilC	activator	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilC	activator	32041797	5	ver/dev	HilC activate transcription of hilC , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagK	regulator	19348639	0	ver/dev	pagK are known to be regulated by PhoP ,56	254	The SPI-2 cluster is closely associated with three virulence-related genes ( pagJ , pagK , and phoN ) , which are known to be regulated by two virulenceassociated regulators , SlyA and PhoP ,56 that also regulate a number of SPI-2 genes .	14	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	pagK	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	fliC	repressor	18350168	3	att	According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .	295	According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	fliC	repressor	18350168	5	att	Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .	335	Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .	19	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	TU	flhDC	activator	16763111	6	ver/dev	For example , the apparent activation of flagellar genes by H-NS most likely occurs by a repressor of the flagellar regulators flhDC .	91	For example , the apparent activation of flagellar genes by H-NS most likely occurs by means of H-NS -- mediated repression of hdfR , a repressor of the flagellar regulators flhDC ( 1 ) .	4	6 FEBRUARY 2006; ACCEPTED 30 MAY 2006 10.1126/SCIENCE.1125878	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HNS	TU	flhDC	activator	26267246	0	ver/dev	H-NS indirectly activates flhDC transcription by repressing HdfR .	63	The his-tone-like nucleoid-structuring protein ( H-NS ) indirectly activates flhDC transcription by repressing a negative regulator , HdfR [ 20 ] .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	flhDC	activator	26267246	0	ver/dev	H-NS indirectly activates flhDC transcription by repressing a negative regulator .	63	The his-tone-like nucleoid-structuring protein ( H-NS ) indirectly activates flhDC transcription by repressing a negative regulator , HdfR [ 20 ] .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	hcr	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	STM1697	regulator	24127899	26	ver/dev	Indirect regulation of biofilm formation by STM1697 The EAL domain protein STM3611 , a c-di-GMP phosphodiesterase , is one of the negative regulators of CsgD expression ( Simm et al. ,	256	Indirect regulation of biofilm formation by STM1697 The EAL domain protein STM3611 , a c-di-GMP phosphodiesterase , is one of the negative regulators of rdar morphotype formation and CsgD expression ( Simm et al. ,	11	FUNCTIONAL FLAGELLA AND CHEMOTAXIS ARE REQUIRED FOR INVASION OF HT-29 CELLS BY S. TYPHIMURIUM UMR1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12068808	8	att	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner ( Thomas and Booth , 1992 ; Foster et al. , 1994 ; Heyde et al. , 2000 ; Sato et al. , 2000 ) .	71	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner ( Thomas and Booth , 1992 ; Foster et al. , 1994 ; Heyde et al. , 2000 ; Sato et al. , 2000 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12068808	8	ver/dev	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner .	71	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner ( Thomas and Booth , 1992 ; Foster et al. , 1994 ; Heyde et al. , 2000 ; Sato et al. , 2000 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12068808	11	ver/dev	This resulting low level of OmpR was adequate to enable the acid induction of ompC in Fig. 3C .	93	This resulting low level of OmpR was not sufficient for the induction of acid tolerance ( Fig. 3B , top , second bar set ) but was adequate to enable the acid induction of ompC in log phase cells ( Fig. 3C ) .	7	OMPR AUTOREGULATES ITS OWN EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12068808	11	ver/dev	This resulting low level of OmpR was adequate to enable the acid induction of ompC in log phase cells .	93	This resulting low level of OmpR was not sufficient for the induction of acid tolerance ( Fig. 3B , top , second bar set ) but was adequate to enable the acid induction of ompC in log phase cells ( Fig. 3C ) .	7	OMPR AUTOREGULATES ITS OWN EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12080060	8	att	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner ( Thomas and Booth , 1992 ; Foster et al. , 1994 ; Heyde et al. , 2000 ; Sato et al. , 2000 ) .	71	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner ( Thomas and Booth , 1992 ; Foster et al. , 1994 ; Heyde et al. , 2000 ; Sato et al. , 2000 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12080060	8	ver/dev	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner .	71	Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner ( Thomas and Booth , 1992 ; Foster et al. , 1994 ; Heyde et al. , 2000 ; Sato et al. , 2000 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12080060	11	ver/dev	This resulting low level of OmpR was adequate to enable the acid induction of ompC in Fig. 3C .	93	This resulting low level of OmpR was not sufficient for the induction of acid tolerance ( Fig. 3B , top , second bar set ) but was adequate to enable the acid induction of ompC in log phase cells ( Fig. 3C ) .	7	OMPR AUTOREGULATES ITS OWN EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	12080060	11	ver/dev	This resulting low level of OmpR was adequate to enable the acid induction of ompC in log phase cells .	93	This resulting low level of OmpR was not sufficient for the induction of acid tolerance ( Fig. 3B , top , second bar set ) but was adequate to enable the acid induction of ompC in log phase cells ( Fig. 3C ) .	7	OMPR AUTOREGULATES ITS OWN EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompC	activator	16023758	9	att	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC and ompF [ 69 ] suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	176	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC and ompF [ 69 ] suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	11	2.4. OMPR/ENVZ AND THE ACID STRESS RESPONSE	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	ompC	activator	16023758	9	ver/dev	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	176	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC and ompF [ 69 ] suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	11	2.4. OMPR/ENVZ AND THE ACID STRESS RESPONSE	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	ompC	activator	16905537	9	att	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	197	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ompC	activator	22179129	6	ver/dev	Forst S , Delgado J , Rampersaud A et al In vivo phosphorylation of OmpR , the transcription activator of the ompC genes in Escherichia coli .	216	Forst S , Delgado J , Rampersaud A et al ( 1990 ) In vivo phosphorylation of OmpR , the transcription activator of the ompF and ompC genes in Escherichia coli .	18	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompC	activator	25566242	25	att	Chatfield SN , Dorman CJ , Hayward C , Dougan G. Role of OmpR-dependent genes in Salmonella typhimurium virulence : mutants deficient in both ompC and ompF are attenuated in-vivo .	593	Chatfield SN , Dorman CJ , Hayward C , Dougan G. Role of OmpR-dependent genes in Salmonella typhimurium virulence : mutants deficient in both ompC and ompF are attenuated in vivo .	72	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
ArgR	gene	argI	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with tRNA hydroxylase S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
HNS	gene	csiD	activator	14996792	54	ver/dev	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both csiD genes in E. coli is stimulated by H-NS .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
InvF	gene	sipA	activator	12535071	24	ver/dev	InvF production indirectly increases transcription of the sipA genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	12535071	24	ver/dev	InvF production directly increases transcription of the sipA genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	12535071	24	ver/dev	InvF production indirectly increases transcription of the sipA genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	12535071	24	ver/dev	InvF production directly increases transcription of the sipA genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	21168230	1	att	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	208	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipA and located outside -LRB- sopE -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipA and located outside -LRB- sopD -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipA	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipA and located outside -LRB- sopB -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	micF	repressor	19843227	5	ver/dev	In contrast , H-NS positively regulates OmpF levels by transcriptionally repressing micF .	50	In contrast , H-NS positively regulates OmpF levels by transcriptionally repressing micF ( Deighan et al. , 2000 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	ssaG	regulator	27886269	8	ver/dev	the ssaG genes are controlled by HilD indirectly , respectively	85	As controls , the expression of cat transcriptional fusions of the hilA and ssaG genes , which are controlled by HilD directly and indirectly , respectively , were also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	ssaG	regulator	27886269	8	ver/dev	the ssaG genes are controlled by HilD directly , respectively	85	As controls , the expression of cat transcriptional fusions of the hilA and ssaG genes , which are controlled by HilD directly and indirectly , respectively , were also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	hfq	activator	29417203	6	ver/dev	In addition , hfq transcription was also induced by OmpR , while Hfq inhibited OmpR expression as a feedback .	96	In addition , hfq transcription was also induced by OmpR , while Hfq inhibited OmpR expression as a feedback .	13	AUTOREGULATION AND RECIPROCAL REGULATION OF OMPR AND HFQ	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	15145463	0	ver/dev	Interestingly , the same region upstream of the pagC translational start has been implicated in binding of the transcriptional regulatory protein SlyA ( J. Gunn and	167	Interestingly , the same region upstream of the pagC translational start has been implicated in binding of the transcriptional regulatory protein SlyA ( J. Gunn and	11	3. RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	17259627	8	att	In several SlyA-regulated genes , DNA sequences ( TTTAGTTTTTGTCTTAA , located in the ugtL promoter ; TTTGGAATGTAA , located in the pagC promoter ; and TTAGCTGTTAA , located in the mig-14 promoter ) have been identified as SlyA-specific binding sites by DNase-I-protection assay ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	60	In several SlyA-regulated genes , DNA sequences ( TTTAGTTTTTGTCTTAA , located in the ugtL promoter ; TTTGGAATGTAA , located in the pagC promoter ; and TTAGCTGTTAA , located in the mig-14 promoter ) have been identified as SlyA-specific binding sites by DNase I protection assay ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	17259627	37	ver/dev	However , SlyA has also been shown to have binding sites downstream of the transcriptional start site in the pagC promoters .	348	However , SlyA has also been shown to have binding sites downstream of the transcriptional start site in the pagC and ugtL promoters that are required for gene transcription ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	18221392	3	ver/dev	The pagC genes appear to be regulated by both SlyA , by a mechanism .	67	The mig-14 and pagC genes appear to be regulated by both SlyA and PhoP , by a mechanism that is not yet understood ( Navarre et al. , 2005 ) .	9	SALMONELLA VIRULENCE GENES ARE SPECIFICALLY EXPRESSED IN VIVO DURING INFECTION OF C. ELEGANS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	18270203	20	ver/dev	pagC genes entails binding of both SlyA proteins to the promoters of these two genes .	187	pagC and ugtL genes entails binding of both the PhoP and SlyA proteins to the promoters of these two genes .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	pagC	regulator	18270203	51	ver/dev	The SlyA proteins bind to several sites in the pagC promoter .	247	The H-NS and SlyA proteins bind to several sites in the pagC promoter .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	pagC	regulator	18270203	56	ver/dev	the pagC promoter els for the ugtL mRNAs are probably due to the less are bound by the SlyA proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	18270203	56	ver/dev	the pagC promoter els for the pagC mRNAs are probably due to the less are bound by the SlyA proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	18270203	56	ver/dev	the pagC promoter els for the pagC mRNAs are probably due to the less are bound by the SlyA proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	18270203	70	ver/dev	Therefore , the role of PhoP in pagC transcription is 2-fold : as a regulator of SlyA at transcriptional and/or post-transcriptional levels .	295	Therefore , the role of PhoP in pagC transcription is 2-fold : as a direct transcriptional activator of the pagC promoter and as a regulator of SlyA at transcriptional ( 23 , 24 ) and/or post-transcriptional ( 8 ) levels .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	19091955	0	ver/dev	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including pagC , in Salmonella .	18	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL and pagC , in Salmonella ( 2 , 3 , 9 -- 11 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	pagC	regulator	19091955	8	ver/dev	Although the previous result suggested that SlyA could bind to downstream of the transcription start of pagC , the ATTATT direct repeat we identified should represent namely , the SlyA box .	64	Although the previous result suggested that SlyA could bind to 6 different DNA sequences located both upstream and downstream of the transcription start of pagC ( 13 ) , the ATTATT direct repeat we identified should represent the SlyA recognition site ( namely , the SlyA box ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	19091955	8	ver/dev	Although the previous result suggested that SlyA could bind to downstream of the transcription start of pagC , the ATTATT direct repeat we identified should represent the SlyA recognition site .	64	Although the previous result suggested that SlyA could bind to 6 different DNA sequences located both upstream and downstream of the transcription start of pagC ( 13 ) , the ATTATT direct repeat we identified should represent the SlyA recognition site ( namely , the SlyA box ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	19091955	11	ver/dev	twice that _ controlled by up-1 in wild-type cells , indicating that SlyA also facilitates PhoP binding to the pagC promoter	71	Similar to our previous study in which SlyA enhanced PhoP binding to the promoter of phoP ( 29 ) , lacZ expression controlled by up-52 is about twice that controlled by up-1 in wild-type cells , indicating that SlyA also facilitates PhoP binding to the pagC promoter ( Fig. 1C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagC	regulator	25135218	80	ver/dev	pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	29857034	10	ver/dev	Moreover , the pagC gene is positively regulated by SlyA .	290	Moreover , the pagC gene that encodes a membrane protein involved in bacterial virulence is positively regulated by SlyA .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	29857034	14	ver/dev	Within the virulence coincident genes , we determined that pagC is positively regulated by SlyA .	309	Within the virulence coincident genes , we determined that pagC is positively regulated by SlyA , which is consistent with previous reports [ 7,13,14 ] .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagC	regulator	29857034	22	ver/dev	To determine whether SlyA regulates pagC genes in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in DslyA strains under conditions of oxidative-stress .	341	To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP , and pagC genes in vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT and DslyA strains under conditions of oxidative stress .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	29857034	22	ver/dev	To determine whether SlyA regulates pagC genes in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT strains under conditions of oxidative-stress .	341	To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP , and pagC genes in vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT and DslyA strains under conditions of oxidative stress .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	regulator	29857034	32	ver/dev	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of Fig. 4G , suggesting that SlyA directly regulates pagC expression .	367	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM ( Fig. 4G ) , suggesting that SlyA positively and directly regulates pagC expression , which is similar to previous findings [ 7,13,14 ] .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagC	regulator	29857034	32	ver/dev	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM , suggesting that SlyA directly regulates pagC expression .	367	SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM ( Fig. 4G ) , suggesting that SlyA positively and directly regulates pagC expression , which is similar to previous findings [ 7,13,14 ] .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	pagC	regulator	29857034	33	ver/dev	Direct regulation of pagC genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	arcA	regulator	12420160	0	ver/dev	As both ArcA and Fnr contribute to regulation of respiration , the same explanation may be relevant for the GNS phenotype of the arcA mutants .	257	As both ArcA and Fnr contribute to regulation of respiration and therefore generation of a membrane potential , in addition to the regulatory effect on central metabolism , the same explanation may be relevant for the GNS phenotype of the arcA and fnr mutants .	22	GNS MUTANTS WHOSE PHENOTYPES MAY BE LINKED WITH A DECREASED CAPACITY TO UTILIZE NUTRIENTS REMAINING IN THE STATIONARY-PHASE BROTH CULTURES	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
FNR	gene	arcA	regulator	33341307	0	ver/dev	As Fnr are involved in the regulation of 120 genes in a similar fashion during anaerobiosis , we hypothesized that deletion of arcA simultaneously could cause maximum virulence attenuation of S. Typhimurium	55	As ArcA and Fnr are involved in the regulation of 120 genes in a similar fashion during anaerobiosis [ 22 ] , we hypothesized that deletion of arcA and fnr simultaneously could cause maximum virulence attenuation of S. Typhimurium , and the resulting mutant could have the potential to be a novel live vaccine strain .	3	1. INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	regulator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	11036033	1	ver/dev	Like marRAB , acrAB are positively regulated by MarA .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	16377664	0	ver/dev	Expression of acrAB is controlled by MarA .	20	Expression of acrAB is controlled by either acrR , the MarRAB operon , including MarA , a positive regulator , or the SoxRS operon ( 36 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	16492722	0	ver/dev	In S. enterica the global regu-2 MarA regulate the acrAB operon by binding to mar/sox boxes .	21	In both E. coli and S. enterica the global regu-2 -- 4 lators MarA and SoxS regulate the acrAB operon by binding to mar/sox boxes found downstream of the local repressor acrR .	4	INTRODUCTION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	acrAB	regulator	18407759	1	ver/dev	Expression of acrAB-tolC is regulated by the global regulator , MarA .	254	Expression of acrAB-tolC is regulated by the global regulator , MarA , which is a positive regulator ( Alekshun and Levy , 1999 ) and by AcrR ( decreased expression in 2a ) , which is a repressor specific for the acrAB operon ( Ma et al. , 1996 ) .	19	EFFLUX SYSTEMS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	18577510	2	ver/dev	Other regulators of MarA did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
MarA	TU	acrAB	regulator	19120970	0	ver/dev	In E. coli , the transcription of acrAB is controlled by the homologous proteins MarA .	23	In E. coli , the transcription of acrAB and micF is controlled by the homologous proteins MarA , SoxS and Rob ( 9 , 10 ) , but may be affected by other proteins such as AcrR ( 11 ) .	4	ABSTRACT	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	23503095	1	ver/dev	In the expression of acrAB is regulated by MarA et al. , Abouzeed et al. ,	28	In particular , the expression of acrAB is regulated by the global regulators , RamA , SoxS , MarA , and Rob ( Rosenberg et al. , 2003 ; Abouzeed et al. ,	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	23503095	1	ver/dev	In the expression of acrAB is regulated by MarA et al. , 2003 ,	28	In particular , the expression of acrAB is regulated by the global regulators , RamA , SoxS , MarA , and Rob ( Rosenberg et al. , 2003 ; Abouzeed et al. ,	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	28650690	1	ver/dev	At a global level , acrAB expression is regulated by MarA .	32	At a global level , acrAB expression is regulated by stressful conditions and by global transcriptional regulators , such as MarA and SoxS .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	acrAB	regulator	34202800	5	ver/dev	The level of the acrAB expression is controlled by the positive MarA regulator .	248	The level of the acrAB expression is controlled by acrR ( MarRAB operon ) , including the positive MarA regulator or the SoxRS operon [ 94 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	STM3138	regulator	27564394	9	ver/dev	STM3138 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HilA	gene	STM3138	regulator	27564394	9	ver/dev	STM3138 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsB	gene	dam	activator	31486760	5	ver/dev	Detection of repression in both dam backgrounds suggests that RcsB binding may counter transcriptional activation by the StdE-StdF-HdfR regulatory loop .	146	Detection of RcsCDB-mediated + repression in both dam and dam backgrounds ( Fig. 1d , c ) suggests that RcsB binding may counter transcriptional activation by the StdE-StdF-HdfR regulatory loop [ 24 ] .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	dam	activator	31486760	5	ver/dev	Detection of repression in both dam suggests that RcsB binding may counter transcriptional activation by the StdE-StdF-HdfR regulatory loop .	146	Detection of RcsCDB-mediated + repression in both dam and dam backgrounds ( Fig. 1d , c ) suggests that RcsB binding may counter transcriptional activation by the StdE-StdF-HdfR regulatory loop [ 24 ] .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RstA	gene	feoB	repressor	18790861	38	ver/dev	Activation of feoB transcription by the RstA protein is necessary for repression of iron-responsive genes .	215	Activation of feoB transcription by the RstA protein is necessary for repression of iron-responsive genes .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoB	repressor	18790861	41	ver/dev	To investigate further whether the Fe transporter FeoB is necessary for repression of iron-responsive genes by the RstA protein , we constructed a strain with a deletion of the feoB gene .	220	To investigate further whether the Fe ( II ) transporter FeoB is necessary for repression of iron-responsive genes by the RstA protein , we constructed a strain with a deletion of the feoB gene .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RstA	gene	feoB	repressor	18790861	43	ver/dev	Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels .	230	Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels which are simply accomplished by iron .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	treR	regulator	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	regulator	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	treR	regulator	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
H	gene	csgD	repressor	26880544	22	att	Taken together , these results identified a regulatory role for unphosphorylated SsrB by orchestrating anti-silencing at the H-NS-repressed csgD locus .	265	Taken together , these results identified a regulatory role for unphosphorylated SsrB by orchestrating anti-silencing at the H-NS-repressed csgD locus .	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	ugtL	activator	31484980	46	ver/dev	In this regulatory cascade , HilD induces expression of the ugtL virulence genes through SprB .	219	In this regulatory cascade , HilD induces expression of the yobH , slrP and ugtL virulence genes through SprB , a Salmonella-specific LuxR-like regulator encoded in SPI-1 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	ugtL	activator	31484980	46	ver/dev	In this regulatory cascade , HilD induces expression of the ugtL virulence genes through a Salmonella-specific LuxR-like regulator .	219	In this regulatory cascade , HilD induces expression of the yobH , slrP and ugtL virulence genes through SprB , a Salmonella-specific LuxR-like regulator encoded in SPI-1 .	3	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	TU	ilvIH	activator	10931352	3	ver/dev	Alternatively , the LeuO protein stimulate transcription of the ilvIH operon to leucine limitation .	138	Alternatively , the LeuO protein might act as a classical transcriptional regulator and stimulate transcription of the ilvIH operon or of the leu operon in response to leucine limitation .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	repressor	24885225	53	ver/dev	Fis might participate in downregulation of hlyE via RpoS	208	As with CRP , Fis might participate in downregulation of hlyE via RpoS , and this regulation could be exerted directly due to the presence of several putative Fis binding boxes in S. Typhi rpoS promoter ( Figure 2C ) .	6	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PmrA	gene	pmrC	activator	15205413	1	att	Here we address both of these questions by establishing that the PmrA-activated pmrC gene encodes an inner membrane protein that is required for the incorporation of phosphoethanolamine into lipid-A and for polymyxin B resistance .	9	Here we address both of these questions by establishing that the PmrA-activated pmrC gene encodes an inner membrane protein that is required for the incorporation of phosphoethanolamine into lipid A and for polymyxin B resistance .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrC	activator	15205413	15	att	We have now established that the PmrA-activated pmrC gene is necessary for the phosphoethanolamine modification of lipid-A ( Fig. 2 ) and for resistance to polymyxin B ( Fig. 3 ) .	237	We have now established that the PmrA-activated pmrC gene is necessary for the phosphoethanolamine modification of lipid A ( Fig. 2 ) and for resistance to polymyxin B ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrC	activator	15205413	17	att	It has been hypothesized that two promoters mediate the transcription of the pmrA and pmrB genes : a PmrA-activated promoter located upstream of the pmrC gene in the pmrCAB operon and a constitutive promoter located within the pmrC open reading frame .	271	It has been hypothesized that two promoters mediate the transcription of the pmrA and pmrB genes : a PmrA-activated promoter located upstream of the pmrC gene in the pmrCAB operon and a constitutive promoter located within the pmrC open reading frame .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	15205413	18	att	Whereas the PmrA-regulated promoter has been defined by S1-mapping experiments ( 47 ) , evidence for the constitutive promoter is based on the ability of a 346-bp fragment from the pmrC coding region to promote transcription from a plasmid-linked promoterless reporter gene ( 14 ) and the fact that pmrC-lac fusions generated with the MudJ transposon near the 3 end , but within the pmrC coding region , exhibit normal PmrA-dependent transcription ( 41 ) .	272	Whereas the PmrA-regulated promoter has been defined by S1 mapping experiments ( 47 ) , evidence for the constitutive promoter is based on the ability of a 346-bp fragment from the pmrC coding region to promote transcription from a plasmid-linked promoterless reporter gene ( 14 ) and the fact that pmrC-lac fusions generated with the MudJ transposon near the 3 end , but within the pmrC coding region , exhibit normal PmrA-dependent transcription ( 41 ) .	5	DISCUSSION	unidentified plasmid	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	15205413	4	att	The PmrA/PmrB system is encoded by the pmrCAB operon and is apparently expressed from both a PmrA-activated promoter upstream of the pmrC gene ( 47 ) and a constitutive promoter within the pmrC coding region ( 14 , 41 ) .	31	The PmrA/PmrB system is encoded by the pmrCAB operon and is apparently expressed from both a PmrA-activated promoter upstream of the pmrC gene ( 47 ) and a constitutive promoter within the pmrC coding region ( 14 , 41 ) .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	15205413	5	att	In this paper , we demonstrate that the PmrA-activated pmrC gene encodes an inner membrane protein that is required for polymyxin resistance and for the incorporation of phosphoeth-anolamine into lipid-A .	32	In this paper , we demonstrate that the PmrA-activated pmrC gene encodes an inner membrane protein that is required for polymyxin resistance and for the incorporation of phosphoeth-anolamine into lipid A .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrC	activator	15205413	9	att	To examine whether the pmrC gene is necessary for the incorporation of phosphoethanolamine into lipid-A , we used negative-ion-mode MALDI-TOF mass spectrometry to analyze the lipid-A species from wild-type pbgP , pmrC1 .1 , and pmrA strains and strains grown at a low pH and with a low level of Mg2 , which are conditions that promote the transcription of PmrA-activated genes ( 41 ) .	155	To examine whether the pmrC gene is necessary for the incorporation of phosphoethanolamine into lipid A , we used negative-ion-mode MALDI-TOF mass spectrometry to analyze the lipid A species from wild-type pbgP , pmrC1 .1 , and pmrA strains and strains grown at a low pH and with a low level of Mg2 , which are conditions that promote the transcription of PmrA-activated genes ( 41 ) .	4	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	activator	15866924	13	ver/dev	Activation of pmrC by PmrA suggests that the consequent pEtN modifications , are up-regulated during infection of the mouse	274	Activation of pmrC and cptA by PmrA suggests that these loci , and the consequent pEtN modifications , are up-regulated during infection of the mouse ( 17 ) , but the function of pEtN LPS modifications remain unclear .	5	DISCUSSION	Mus musculus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	15866924	13	ver/dev	Activation of pmrC by PmrA suggests that these loci , are up-regulated during infection of the mouse	274	Activation of pmrC and cptA by PmrA suggests that these loci , and the consequent pEtN modifications , are up-regulated during infection of the mouse ( 17 ) , but the function of pEtN LPS modifications remain unclear .	5	DISCUSSION	Mus musculus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	17158330	12	att	For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .	66	For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .	5	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	activator	23019341	0	att	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	16	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	activator	23690578	23	att	S1 ) and that the ssrB promoter mutation had no effect on the expression of the PmrA-activated pmrC gene ( Fig. 5C ) .	92	S1 ) and that the ssrB promoter mutation had no effect on the expression of the PmrA-activated pmrC gene ( Fig. 5C ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	pmrC	activator	29739882	13	att	This analysis suggests a correlation between PhoP activation of lpxT transcription and the presence of a PmrA-activated pmrC gene .	157	This analysis suggests a correlation between PhoP activation of lpxT transcription and the presence of a PmrA-activated pmrC gene .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	activator	29739882	9	att	When wild-type Salmonella was shifted from non-inducing conditions to media with a mildly acidic pH , the mRNA amounts of the PmrA-activated genes pbgP , pmrC , and pmrR reached a maximum within 5 min ( Fig. 5A ) .	128	When wild-type Salmonella was shifted from non-inducing conditions to media with a mildly acidic pH , the mRNA amounts of the PmrA-activated genes pbgP , pmrC , and pmrR reached a maximum within 5 min ( Fig. 5A ) .	5	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	trkH	activator	26039089	7	att	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	164	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
EvgA	gene	safA	activator	33045730	104	att	It is also dependent on EvgA-activated safA ( 83 ) , a horizontally acquired gene that specifies a post-translational activator of the PhoQ protein ( 84 ) .	441	It is also dependent on EvgA-activated safA ( 83 ) , a horizontally acquired gene that specifies a post-translational activator of the PhoQ protein ( 84 ) .	37	DIFFERENT HORIZONTALLY ACQUIRED GENES ENABLE ESCHERICHIA COLI TO ACTIVATE PHOP/PHOQ IN MILDLY ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsB	gene	yddX	regulator	27601571	16	ver/dev	We also observed negative regulation of yddX by RtsB .	180	We also observed negative regulation of flgM and yddX by RtsB ( Fig. 2 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
PtsJ	gene	pdxK	regulator	27987384	0	ver/dev	PtsJ from Salmonella typhimur-ium controls the expression of the pdxK gene	8	In the present work , we identified a new MocR-like regulator , PtsJ from Salmonella typhimur-ium , which controls the expression of the pdxK gene encoding one of the two PLKs expressed in this organism ( PLK1 ) .	0	Unknown	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PtsJ	gene	pdxK	regulator	27987384	5	ver/dev	In the present study , we showed that PtsJ is actually involved in the regulation of pdxK and therefore in the transcriptional control of B6 vitamers salvage pathway .	408	In the present study , we showed that PtsJ is actually involved in the regulation of pdxK and therefore in the transcriptional control of B6 vitamers salvage pathway ( Scheme 1 ) .	18	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PtsJ	gene	pdxK	regulator	27987384	5	ver/dev	In the present study , we showed that PtsJ is actually involved in the regulation of pdxK and therefore in the transcriptional control of B6 vitamers salvage pathway .	408	In the present study , we showed that PtsJ is actually involved in the regulation of pdxK and therefore in the transcriptional control of B6 vitamers salvage pathway ( Scheme 1 ) .	18	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
ZntR	gene	copA	regulator	24858080	10	att	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	336	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
ZntR	gene	copA	regulator	24858080	3	att	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	264	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	lon	activator	27185788	19	ver/dev	Of note , it seems unlikely that the increased degradation of HilD is mediated by changes in protease expression or activity , as the expression of lon is not increased by bile treatment .	345	Of note , it seems unlikely that the increased degradation of HilD is mediated by changes in protease expression or activity , as the expression of lon is not increased by bile treatment ( 18 ) .	6	DISCUSSION	nan	1	L2	SPEC	Other	NEG	Other	Level 1
HilD	gene	lon	activator	30941426	12	ver/dev	Deleting lon increased the HilD protein level in all three strains , with the highest fold-increase .	252	Deleting lon increased the HilD protein level in all three strains , with the highest fold-increase observed in the rpsD * strain ( Figure 6D and E ) .	25	NON-OPTIMAL TRANSLATIONAL FIDELITY PROMOTES DEGRADATION OF HILD BY LON	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lon	activator	30941426	32	ver/dev	-LRB- C , D -RRB- Deleting lon increased the HilD protein level in the rpsD * .	326	( C , D ) Deleting lon increased the HilD protein level in the rpsD * and rpsL * strains .	26	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	fljB	activator	22179129	4	ver/dev	Our previous study showed that OmpR activates the transcription of fljB by promoting fliA expression , and indirectly increases the secretion of FljB : z66 by repressing Vi capsular antigen at high-osmolarity .	165	Our previous study showed that OmpR activates the transcription of fljB : z66 in S. Typhi by promoting flhDC and fliA expression , and indirectly increases the secretion of FljB : z66 by repressing Vi capsular antigen at high osmolarity [ 24 ] .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	fljB	activator	22179129	4	ver/dev	Our previous study showed that OmpR activates the transcription of fljB by promoting flhDC expression , and indirectly increases the secretion of FljB : z66 by repressing Vi capsular antigen at high-osmolarity .	165	Our previous study showed that OmpR activates the transcription of fljB : z66 in S. Typhi by promoting flhDC and fliA expression , and indirectly increases the secretion of FljB : z66 by repressing Vi capsular antigen at high osmolarity [ 24 ] .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	katE	activator	17293430	14	ver/dev	Therefore , even though decreased S abundance increased the magnitude of Crl activation of gene expression , it did not affect the differential responsiveness of the katE genes to Crl activation .	254	Therefore , even though decreased S abundance increased the magnitude of Crl activation of gene expression , it did not affect the differential responsiveness of the katE and katN genes to Crl activation .	5	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
Crl	gene	katE	activator	17293430	18	ver/dev	Decreasing the concentration of E S led to higher levels of katE activation by Crl .	274	Decreasing the concentration of E S ( 4 nM core and 8 nM S ) led to higher levels of katE activation by Crl , which were observed even after 40 min of incubation ( data not shown ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	16707690	1	ver/dev	potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD promoters .	11	In vitro transcription assays and potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD and adrA promoters .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	16707690	1	ver/dev	In vitro transcription assays with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD promoters .	11	In vitro transcription assays and potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD and adrA promoters .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	16707690	6	ver/dev	In vitro transcription experiments with purified Crl protein of Salmonella showed that Crl stimulates S-dependent transcription at the csgD promoters .	52	In vitro transcription experiments with purified Crl protein of Salmonella showed that Crl stimulates S-dependent transcription at the adrA and csgD promoters .	2	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	16707690	10	ver/dev	Together , these results demonstrated that Crl plays a role in the transcription activation of the csgD , csgB , adrA required for developing a typical rdar morphotype in Salmo-nella .	297	Together , these results demonstrated that Crl plays a role in the transcription activation of the csgD , csgB , adrA , and bcsA genes required for developing a typical rdar morphotype in Salmo-nella .	4	RESULTS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
Crl	gene	csgD	activator	16707690	14	ver/dev	Crl protein activates in-vitro-transcription by E S from the csgD promoters .	314	Crl protein activates in vitro transcription by E S from the csgD and adrA promoters .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	16707690	21	ver/dev	Together , these results showed that Crl enhanced both the rate of formation of open complexes by E S from the csgD promoters .	369	Together , these results showed that Crl enhanced both the quantity of open complexes and the rate of formation of open complexes by E S from the csgD and adrA promoters .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	16707690	21	ver/dev	Together , these results showed that Crl enhanced both the quantity of open complexes by E S from the csgD promoters .	369	Together , these results showed that Crl enhanced both the quantity of open complexes and the rate of formation of open complexes by E S from the csgD and adrA promoters .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	csgD	activator	17293430	2	ver/dev	In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the csgD genes ; these genes are involved in the biosynthesis of cellulose .	38	In vitro transcription experiments with the purified Salmonella Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA and csgD genes ; these genes are involved in the biosynthesis of curli and cellulose ( 32 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	csgD	activator	17293430	2	ver/dev	In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the csgD genes ; these genes are involved in the biosynthesis of curli .	38	In vitro transcription experiments with the purified Salmonella Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA and csgD genes ; these genes are involved in the biosynthesis of curli and cellulose ( 32 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YqhC	gene	sipB	activator	22004521	12	ver/dev	Our RNA-seq data showed a significant down-regulation of sipB in the yqhC mutant , suggesting that YqhC therefore modulates induction of cytotoxicity in host cells .	333	Our RNA-seq data showed a significant down-regulation of sipB in the yqhC mutant , suggesting that YqhC affects expression of these genes , and therefore modulates induction of cytotoxicity in host cells .	25	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarR	gene	slyA	regulator	17029709	0	ver/dev	AE008762 slyA Pathogenicity MarR family transcriptional regulator for hemolysin	395	AE008762 slyA Pathogenicity MarR family transcriptional regulator for hemolysin	17	3.3.2. FIMBRIAL CLUSTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	gene	iagA	repressor	17725646	1	ver/dev	In S. Typhi , TviA in conjunction with RcsB represses transcription of iagA .	94	In S. Typhi , TviA in conjunction with RcsB represses transcription of hilA ( iagA ) ( Arricau et al. , 1998 ) , which encodes a regulator of the invasion-associated type III secretion system ( T3SS-1 ) .	7	THE TVIA-DEPENDENT DECREASE IN IL-8 EXPRESSION IS INDEPENDENT OF THE INVASION-ASSOCIATED TYPE III SECRETION SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	tolB	activator	12519186	22	att	On the other hand , the tolB mutant produced two S1 products : the large PmrA-dependent product , and a small product whose presence is RcsB dependent because it was produced at higher levels in a mutant harbouring a constitutive allele of rcsC -- rcsC11 ( Costa and Anton , 2001 ) , and it was not detected in RNA harvested from rcsB and tolB rcsB mutants ( Fig. 4A ) .	73	On the other hand , the tolB mutant produced two S1 products : the large PmrA-dependent product , and a small product whose presence is RcsB dependent because it was produced at higher levels in a mutant harbouring a constitutive allele of rcsC -- rcsC11 ( Costa and Anton , 2001 ) , and it was not detected in RNA harvested from rcsB and tolB rcsB mutants ( Fig. 4A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Lrp	TU	ilvIH	activator	11591661	1	ver/dev	The expression of ilvIH gene products is inhibited by leucine , apparently due to a requirement for Lrp for activation of ilvIH transcription .	49	The expression of AHAS III ( ilvIH gene products ) is inhibited by leucine , apparently due to a requirement for the leucine-responsive regulatory protein ( Lrp ) for activation of ilvIH transcription .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Lrp	TU	ilvIH	activator	11591661	1	ver/dev	The expression of AHAS III is inhibited by leucine , apparently due to a requirement for Lrp for activation of ilvIH transcription .	49	The expression of AHAS III ( ilvIH gene products ) is inhibited by leucine , apparently due to a requirement for the leucine-responsive regulatory protein ( Lrp ) for activation of ilvIH transcription .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Lrp	TU	ilvIH	activator	11591661	2	ver/dev	In the presence of leucine , binding of Lrp is reduced , resulting in reduced transcriptional activation of ilvIH expression .	50	In the presence of leucine , binding of Lrp is reduced , resulting in reduced transcriptional activation of ilvIH expression ( references 60 and 61 and references therein ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	TU	ilvIH	activator	11591661	7	ver/dev	As mentioned in the Introduction , the expression of ilvIH in E. coli K-12 is activated by Lrp .	290	As mentioned in the Introduction , the expression of ilvIH ( AHAS III ) in E. coli K-12 is activated by Lrp ( 11 , 40 , 60 ) whose expression in turn is strongly dependent on ppGpp ( 32 ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	TU	ilvIH	activator	11591661	9	ver/dev	Lrp activates ilvIH expression .	345	Lrp activates ilvIH expression ( 60 ) and is thought to repress ilvGM expression ( 46 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	ilvIH	activator	11591661	20	ver/dev	Lrp , activates transcription of ilvIH .	843	Lrp , a global regulatory protein of Esch-erichia coli , binds co-operatively to multiple sites and activates transcription of ilvIH .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csrA	regulator	23676436	7	ver/dev	Together these results indicate that the csrA expression level in Salmonella is controlled by RpoS , consistent with previous observations in S. Typhimurium , E. coli and Er .	184	Together these results indicate that the csrA expression level in Salmonella is controlled by RpoS , consistent with previous observations in S. Typhimurium , E. coli and Er .	7	IDENTIFICATION OF GENES AFFECTED BY THE CLPP PROTEASE	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	csrA	regulator	23676436	24	ver/dev	the stationary sigma factor RpoS controls the expression of csrA	454	Through proteolysis , the ClpP protease controls the level of the stationary sigma factor RpoS , which controls the expression of csrA .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csrA	regulator	23676436	26	ver/dev	the stationary sigma factor RpoS controls the expression of csrA	480	Through proteolysis , the ClpP protease controls the level of the stationary sigma factor RpoS , which controls the expression of csrA .	10	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csrA	regulator	25123657	28	ver/dev	csrA expression is controlled by RpoS at 37 °	228	csrA expression is controlled by RpoS at 37 °C [ 13 ] , and the results are consistent with this also being the case at 10 °C .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rflM	activator	30373755	12	att	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	221	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PrpR	gene	prpBCDE	activator	12700259	1	ver/dev	needed for transcriptional activation of the prpBCDE operon by the PrpR activator protein .	27	needed for transcriptional activation of the prpBCDE operon by the PrpR activator protein ( 23 , 31 , 42 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpBCDE	activator	12700259	4	ver/dev	citrate synthase enzyme , provides sufficient 2-methylcitrate for the activation of prpBCDE expression by PrpR	285	An alternative scenario is that there is no residual transcription of prpBCDE but the GltA ( citrate synthase ) enzyme , which is known to synthesize 2-methylcitrate from Pro-CoA and oxaloacetate ( 20 ) , provides sufficient 2-methylcitrate for the activation of prpBCDE expression by PrpR .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PrpR	gene	prpBCDE	activator	12700259	4	ver/dev	the GltA enzyme , provides sufficient 2-methylcitrate for the activation of prpBCDE expression by PrpR	285	An alternative scenario is that there is no residual transcription of prpBCDE but the GltA ( citrate synthase ) enzyme , which is known to synthesize 2-methylcitrate from Pro-CoA and oxaloacetate ( 20 ) , provides sufficient 2-methylcitrate for the activation of prpBCDE expression by PrpR .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PrpR	gene	prpBCDE	activator	15528672	16	att	2-Methylcitrate, not propionate or propionyl-CoA, triggers PrpR-dependent transcription of the prpBCDE operon	435	2-Methylcitrate, not propionate or propionyl-CoA, triggers PrpR-dependent transcription of the prpBCDE operon	16	2-METHYLCITRATE, NOT PROPIONATE OR PROPIONYL-COA, TRIGGERS PRPR-DEPENDENT TRANSCRIPTION OF THE PRPBCDE OPERON	nan	1	L3	OTHER	Other	NEG	New	Level 1
PrpR	gene	prpBCDE	activator	15528672	19	att	The fact that a single amino-acid change ( PrpR ) can A162T completely bypass the need for 2-MC without affecting the ATPase activity of the protein indicates that the effect of 2-MC binding on PrpR-dependent activation of prpBCDE expression is not due to an increase in the ATPase activity of the protein .	476	The fact that a single amino acid change ( PrpR ) can A162T completely bypass the need for 2-MC without affecting the ATPase activity of the protein indicates that the effect of 2-MC binding on PrpR-dependent activation of prpBCDE expression is not due to an increase in the ATPase activity of the protein .	19	ROLE OF 2-MC	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PrpR	gene	prpBCDE	activator	15528672	2	ver/dev	In vitro studies provide insights into how PrpR may activate prpBCDE expression .	45	In vitro studies reported here provide insights into how PrpR may activate prpBCDE expression .	4	MAIN	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PrpR	gene	prpBCDE	activator	15528672	11	ver/dev	To determine whether 2-MC was required for the trans-criptional activation of the prpBCDE genes or not , co-activator-dependent transcription of the prpB promoter by PrpR was tested in-vitro .	362	To determine whether 2-MC was required for the trans-criptional activation of the prpBCDE genes or not , co-activator-dependent transcription of the prpB promoter by PrpR was tested in vitro .	12	2-MC IS A POSITIVE EFFECTOR OF PRPR ACTIVITY	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
PrpR	gene	prpBCDE	activator	15528672	19	ver/dev	The fact that PrpR can A162T completely bypass the need for 2-MC without affecting the ATPase activity of the protein indicates that the effect of 2-MC binding on PrpR-dependent activation of prpBCDE expression is not due to an increase in the ATPase activity of the protein .	476	The fact that a single amino acid change ( PrpR ) can A162T completely bypass the need for 2-MC without affecting the ATPase activity of the protein indicates that the effect of 2-MC binding on PrpR-dependent activation of prpBCDE expression is not due to an increase in the ATPase activity of the protein .	19	ROLE OF 2-MC	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PrpR	gene	prpBCDE	activator	15528672	19	ver/dev	The fact that a single amino-acid change can A162T completely bypass the need for 2-MC without affecting the ATPase activity of the protein indicates that the effect of 2-MC binding on PrpR-dependent activation of prpBCDE expression is not due to an increase in the ATPase activity of the protein .	476	The fact that a single amino acid change ( PrpR ) can A162T completely bypass the need for 2-MC without affecting the ATPase activity of the protein indicates that the effect of 2-MC binding on PrpR-dependent activation of prpBCDE expression is not due to an increase in the ATPase activity of the protein .	19	ROLE OF 2-MC	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PrpR	gene	prpBCDE	activator	16616438	2	ver/dev	The 2-MC-activated PrpR nd activates transcription of prpBCDE from Pp .	38	The 2-MC-activated PrpR binds to an enhancer-like element located at a distance 5 ′ to the P , contacts the σ54 prpBdependent RNA polymerase by means of DNA loop formation , and activates transcription of prpBCDE from PprpB .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpBCDE	activator	20970504	1	ver/dev	2-Methylcitrate-dependent activation of the propionate catabolic operon ( prpBCDE ) of Salmonella enterica by the PrpR protein .	561	2-Methylcitrate-dependent activation of the propionate catabolic operon ( prpBCDE ) of Salmonella enterica by the PrpR protein .	39	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpBCDE	activator	27583250	6	ver/dev	2-Methylcitrate-dependent activation of thepropionate catabolic operon ( prpBCDE ) of Salmonella enterica by the PrpR protein .	479	2-Methylcitrate-dependent activation of thepropionate catabolic operon ( prpBCDE ) of Salmonella enterica by the PrpR protein .	19	ACKNOWLEDGMENTS	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpBCDE	activator	9006051	3	ver/dev	Homology of PrpR to failure of an RpoN-deficient strain to grow on propionate support the idea that PrpR is likely responsible for the transcriptional activation of the prpBCDE operon .	361	Homology of PrpR to the sigma-54 ( RpoN ) family of transcriptional activators and failure of an RpoN-deficient strain to grow on propionate support the idea that PrpR is likely responsible for the transcriptional activation of the prpBCDE operon .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PrpR	gene	prpBCDE	activator	9006051	3	ver/dev	Homology of PrpR to RpoN family of transcriptional activators support the idea that PrpR is likely responsible for the transcriptional activation of the prpBCDE operon .	361	Homology of PrpR to the sigma-54 ( RpoN ) family of transcriptional activators and failure of an RpoN-deficient strain to grow on propionate support the idea that PrpR is likely responsible for the transcriptional activation of the prpBCDE operon .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PrpR	gene	prpBCDE	activator	9006051	3	ver/dev	Homology of PrpR to the sigma-54 family of transcriptional activators support the idea that PrpR is likely responsible for the transcriptional activation of the prpBCDE operon .	361	Homology of PrpR to the sigma-54 ( RpoN ) family of transcriptional activators and failure of an RpoN-deficient strain to grow on propionate support the idea that PrpR is likely responsible for the transcriptional activation of the prpBCDE operon .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Lrp	gene	ybaO	activator	22752112	15	ver/dev	the activation of ybaO expression present homology with the transcription factors Lrp and AstB	265	In this context , overexpression of Rob in E. coli results in the activation of ybaO and aslB expression , which present homology with the transcription factors Lrp and AstB ( Bennik et al. 2000 ) .	17	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	stiB	repressor	8045891	3	ver/dev	Interestingly , the regulation of the stiB locus ( unlike that of stiC ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .	36	Interestingly , the regulation of the stiB locus ( unlike that of stiA and stiC ) was unaffected by a cya mutation , suggesting that cAMP receptor protein acts alone or with a different signal molecule in the repression of stiB ( 44 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stiB	repressor	8045891	3	ver/dev	Interestingly , the regulation of the stiB locus ( unlike that of stiA ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .	36	Interestingly , the regulation of the stiB locus ( unlike that of stiA and stiC ) was unaffected by a cya mutation , suggesting that cAMP receptor protein acts alone or with a different signal molecule in the repression of stiB ( 44 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stiB	repressor	8045891	22	ver/dev	This putative repressor would not function during log phase ; the repression of stiB during log phase is mediated by cAMP-receptor-protein in a cAMP-independent manner .	213	This putative repressor would not function during log phase ; the repression of stiB during log phase is mediated by cAMP receptor protein ( 22 ) in a cAMP-independent manner ( 44 ) .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
LeuO	gene	cas5	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	prgH	regulator	28439039	9	ver/dev	It is known that prgH is under the regulation of PhoP .	327	It is known that prgH is under the regulation of many global regulators , such as HilA , InvF , PhoP , and SirA .	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	orgBC	regulator	29555922	16	ver/dev	PhoP also independently regulate the expression of the orgBC SPI-1 operon .	267	HilD and PhoP also positively and independently regulate the expression of the orgBC SPI-1 operon , in SPI-1-inducing growth conditions , PhoP directly and HilD through HilA8 ,56 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	tviA	activator	20363312	0	ver/dev	The level of expression of tviA in the ompR mutant is nearly 10-fold lower than that in the wild type strain , suggesting that the expression of tviA in S. typhi is activated by OmpR at the early stage of osmotic-stress .	69	The level of expression of tviA in the ompR mutant is nearly 10-fold lower than that in the wild type strain , suggesting that the expression of tviA in S. typhi is activated by OmpR at the early stage of osmotic stress .	3	2. RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	tviA	activator	20363312	1	ver/dev	The result demonstrates that the expression of tviA is activated by OmpR .	115	The result demonstrates that the expression of tviA is activated by OmpR , which is just opposite to the action of Hfq .	4	3. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	tviA	activator	29417203	11	att	S2 ) , and thus the OmpR-dependent transcription of ompR and tviA may belong to the class I transcriptional stimulation [ 36 ] .	119	S2 ) , and thus the OmpR-dependent transcription of ompR and tviA may belong to the class I transcriptional stimulation [ 36 ] .	14	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
NsrR	gene	nsrR	repressor	24021902	0	att	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	77	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
zur	gene	znuC	regulator	12117991	15	ver/dev	Figure 2 shows how the expression of znuC was higher in Cm cells , indicating that , as happens in E. coli , expression of the Salmonella serovar Typhimurium znuC gene is negatively controlled by the product of the zur gene .	70	Figure 2 shows how the expression of znuC was higher in the zur : : Cm cells than in both the wild-type and znuC : : Cm cells , indicating that , as happens in E. coli , expression of the Salmonella serovar Typhimurium znuC gene is negatively controlled by the product of the zur gene .	2	MAIN	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
zur	gene	znuC	regulator	12117991	15	ver/dev	Figure 2 shows how the expression of znuC was higher in the zur : : Cm cells than in both znuC : , indicating that , as happens in E. coli , expression of the Salmonella serovar Typhimurium znuC gene is negatively controlled by the product of the zur gene .	70	Figure 2 shows how the expression of znuC was higher in the zur : : Cm cells than in both the wild-type and znuC : : Cm cells , indicating that , as happens in E. coli , expression of the Salmonella serovar Typhimurium znuC gene is negatively controlled by the product of the zur gene .	2	MAIN	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
zur	gene	znuC	regulator	12117991	15	ver/dev	Figure 2 shows how the expression of znuC was higher in the zur : : Cm cells than in both the wild-type : , indicating that , as happens in E. coli , expression of the Salmonella serovar Typhimurium znuC gene is negatively controlled by the product of the zur gene .	70	Figure 2 shows how the expression of znuC was higher in the zur : : Cm cells than in both the wild-type and znuC : : Cm cells , indicating that , as happens in E. coli , expression of the Salmonella serovar Typhimurium znuC gene is negatively controlled by the product of the zur gene .	2	MAIN	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
GntR	gene	srfN	regulator	28674150	14	ver/dev	YdcR Directly Binds to the Promoter Region of the srfN Gene -- Like other transcriptional regulators of the GntR family , YdcR also has an HTH DNA-binding domain .	230	YdcR Directly Binds to the Promoter Region of the srfN Gene -- Like other transcriptional regulators of the GntR family , YdcR also has an N-terminal helix-turn-helix ( HTH ) DNA-binding domain .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
GntR	gene	srfN	regulator	28674150	14	ver/dev	YdcR Directly Binds to the Promoter Region of the srfN Gene -- Like other transcriptional regulators of the GntR family , YdcR also has an N-terminal helix-turn-helix DNA-binding domain .	230	YdcR Directly Binds to the Promoter Region of the srfN Gene -- Like other transcriptional regulators of the GntR family , YdcR also has an N-terminal helix-turn-helix ( HTH ) DNA-binding domain .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	Cantareus apertus;Cornu aspersum;Cantareus apertus;Cornu aspersum	0	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	rpoN	activator	19076233	2	att	Here , it was observed that inactivation of the rpoN gene markedly increases the resistance of S. enterica to PM by a mechanism that is not linked to the classical PmrA-dependent pathway .	38	Here , it was observed that inactivation of the rpoN gene markedly increases the resistance of S. enterica to PM by a mechanism that is not linked to the classical PmrA-dependent pathway .	6	INTRODUCTION	Salmonella;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
SprB	gene	avrA	regulator	21168230	2	ver/dev	SprB , regulates the expression of avrA .	212	SprB , a transcriptional regulator , is encoded within the SPI1 and regulates the expression of sipC , sptP , avrA , sopB and sopE ( Eichelberg et al. , 1999 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	pgtE	activator	29487214	0	ver/dev	Expression of the pgtE transcript is is activated by OmpR / SsrA/B .	91	Expression of the pgtE transcript is induced during intramacrophage replication ( 26 , 27 ) , controlled by the SPI2-associated regulators PhoPQ and SlyA ( 19 , 28 ) , and is activated by OmpR / EnvZ and SsrA/B ( 15 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	pgtE	activator	29487214	0	ver/dev	Expression of the pgtE transcript is is activated by OmpR / EnvZ .	91	Expression of the pgtE transcript is induced during intramacrophage replication ( 26 , 27 ) , controlled by the SPI2-associated regulators PhoPQ and SlyA ( 19 , 28 ) , and is activated by OmpR / EnvZ and SsrA/B ( 15 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	prgJ	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhD	gene	lacZ	activator	16430704	15	ver/dev	expression of activity of FlhD proteins in initiating the transcription of fliA-fused lacZ gene after induction of IPTG-controlled flhDC genes in cells depleted either of DnaK or of both DnaK and ClpP .	224	Accumulation and expression of activity of FlhD and FlhC proteins in initiating the transcription of fliA-fused lacZ gene after induction of IPTG-controlled flhDC genes in cells depleted either of DnaK or of both DnaK and ClpP .	7	PHYSICAL INTERACTION OF FLHD, FLHC AND DNAK PROTEINS IN VIVO	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	invF	regulator	10844688	14	ver/dev	Furthermore , preliminary results indicate that HilD can bind directly to the invF promoter , supporting the hypothesis that there is an alternative HilA-independent mechanism for C. P. Lostroh , unpublished results .	286	Furthermore , preliminary results indicate that HilD can bind directly to the invF promoter , supporting the hypothesis that there is an alternative HilA-independent mechanism for activating invF ( C. P. Lostroh , unpublished results ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	invF	regulator	10844688	14	ver/dev	Furthermore , preliminary results indicate that HilD can bind directly to the invF promoter , supporting the hypothesis that there is an alternative HilA-independent mechanism for activating invF .	286	Furthermore , preliminary results indicate that HilD can bind directly to the invF promoter , supporting the hypothesis that there is an alternative HilA-independent mechanism for activating invF ( C. P. Lostroh , unpublished results ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	invF	regulator	12535071	16	ver/dev	We show that HilD can directly bind invF .	63	We show that HilD and HilC can directly bind and activate invF , which leads to the non-co-ordinate expression of a subset of SPI1 genes .	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	regulator	12535071	28	ver/dev	In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	regulator	12535071	28	ver/dev	In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilC , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	regulator	12535071	28	ver/dev	In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilD , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	regulator	12535071	73	ver/dev	These results suggest that HilD might directly activate invF expression by binding to sequences upstream of invF .	188	These results suggest that HilD and HilC might directly activate invF expression by binding to sequences upstream of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	invF	regulator	12535071	76	ver/dev	HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilD	gene	invF	regulator	12535071	76	ver/dev	HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilD	gene	invF	regulator	12535071	87	ver/dev	In addition to binding upstream of invF , HilD also bind to sites upstream of hilC .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	12535071	87	ver/dev	In addition to binding upstream of invF , HilD also bind within S. Akbar , unpublished results .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	12535071	87	ver/dev	In addition to binding upstream of invF , HilD also bind within the prgH-hilD intergenic region .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	20028809	2	ver/dev	given the cross regulation of SPI-2 by the SPI-1-encoded HilD regulator , it is possible that in-vivo invF is needed to control other genes in Salmonella	248	InvF is a transcriptional factor , and given the cross regulation of SPI-1 and SPI-2 by the SPI-1-encoded HilD regulator ( 17 ) , it is possible that in vivo invF is needed to control other genes in Salmonella involved in systemic disease .	4	RESULTS	Salmonella	1	L1	SPEC	Other	OTHER	Other	Level 1
HilD	gene	invF	regulator	20028809	2	ver/dev	given the cross regulation of SPI-1 by the SPI-1-encoded HilD regulator , it is possible that in-vivo invF is needed to control other genes in Salmonella	248	InvF is a transcriptional factor , and given the cross regulation of SPI-1 and SPI-2 by the SPI-1-encoded HilD regulator ( 17 ) , it is possible that in vivo invF is needed to control other genes in Salmonella involved in systemic disease .	4	RESULTS	Salmonella	1	L1	SPEC	Other	OTHER	Other	Level 1
HilD	gene	invF	regulator	22479568	2	ver/dev	In addition , invF has been shown to be directly regulated by HilD through a HilA-independent pathway .	33	In addition , invF has been shown to be directly regulated by HilD and HilC through a HilA-independent pathway [ 18 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	invF	regulator	25135218	6	ver/dev	HilD also directly controls the expression of invF .	23	HilD also directly controls the expression of the SPI-1 genes hilD , hilC , and invF , as well as other acquired and ancestral genes located outside SPI-1 , such as rtsA , flhDC , siiA , lpxR , ytfK , STM14_1282 , and STM14_2342 ( 2 , 25 -- 31 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	25135218	72	ver/dev	However , HilD regulates invF by binding to downstream of the HilC/Ddependent invF promoter .	215	However , HilD regulates invF by binding to regions located both upstream and downstream of the HilC/Ddependent invF promoter ( 28 , 60 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	25135218	72	ver/dev	However , HilD regulates invF by binding to downstream of the HilC/Ddependent invF promoter .	215	However , HilD regulates invF by binding to regions located both upstream and downstream of the HilC/Ddependent invF promoter ( 28 , 60 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	25135218	72	ver/dev	However , HilD regulates invF by binding to downstream of the HilC/Ddependent invF promoter .	215	However , HilD regulates invF by binding to regions located both upstream and downstream of the HilC/Ddependent invF promoter ( 28 , 60 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	25135218	72	ver/dev	However , HilD regulates invF by binding to regions upstream .	215	However , HilD regulates invF by binding to regions located both upstream and downstream of the HilC/Ddependent invF promoter ( 28 , 60 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	25135218	72	ver/dev	However , HilD regulates invF by binding to regions located .	215	However , HilD regulates invF by binding to regions located both upstream and downstream of the HilC/Ddependent invF promoter ( 28 , 60 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	regulator	27886269	5	ver/dev	invF is positively regulated by HilD through HilA	65	As a control , the expression of a cat transcriptional fusion of invF , which is positively regulated by HilD through HilA , was also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	invF	regulator	28329249	4	ver/dev	HilD , can bind to the promoters of invF .	91	HilD , a member of the AraC/XylS family , can bind to the promoters of hilA and invF [ 4 , 19 ] .	12	INVOLVEMENT OF K297 IN HILD’S DNA-BINDING ABILITY	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	regulator	33101243	5	ver/dev	HilD is also able to bind to the promoters of invF to active SPI-1 .	242	HilD is also able to bind to the promoters of hilA and invF to active SPI-1 ( Schechter and Lee , 2001 ) .	25	MYRICANOL INTERFERES WITH THE DNA-BINDING ABILITY OF HILD	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	invF	regulator	33101243	7	ver/dev	The EMSA results suggest that HilD protein does bind specifically to the invF promoters as described .	260	The EMSA results suggest that HilD protein does bind specifically to the hilA and invF promoters as described ( Akbar et al. , 2003 ; Bustamante et al. , 2008 ) .	25	MYRICANOL INTERFERES WITH THE DNA-BINDING ABILITY OF HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	cld	regulator	18467098	6	att	PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid-A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .	136	PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .	10	PMRAB-MEDIATED LPS MODIFICATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	0	ver/dev	Previous work has shown that the global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site .	10	Previous work has shown that the global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FNR	gene	hlyE	activator	14996792	10	ver/dev	Previous studies have shown that FNR contribute to hlyE expression when E. coli is grown on a solid medium .	72	Previous studies have shown that FNR , CRP , and H-NS contribute to hlyE expression when E. coli is grown on a solid medium ( 10 , 36 ) .	7	RESULTS	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	14	ver/dev	Thus , we concluded that FNR all contribute towards the regulation of hlyE expression .	83	Thus , we concluded that CRP , FNR , and H-NS all contribute towards the regulation of hlyE expression .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FNR	gene	hlyE	activator	14996792	26	ver/dev	Footprinting studies have shown that FNR activate hlyE expression from the same site centered 61.5 bp upstream of the SlyA-associated transcription start site .	128	Footprinting studies have shown that FNR and CRP activate hlyE expression from the same site centered 61.5 bp upstream of the SlyA-associated transcription start site ( 10 , 36 ) .	7	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
FNR	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	activator	19835951	3	ver/dev	In E. coli , global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site at the promoter region in response to oxygen depletion and glucose-starvation , respectively .	46	In E. coli , global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site at the promoter region in response to oxygen depletion and glucose starvation , respectively [ 46,60,63 ] .	5	1. INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	assT	activator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	assT	activator	18156266	32	ver/dev	the transcriptional results showed that LeuO positively induced assT at different points of the growth curve	329	Interestingly , the transcriptional results showed that LeuO positively induced STY3070 , assT , and ompS1 at different points of the growth curve , and the highest activity was observed in stationary phase ( Fig. 2a to c ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	assT	activator	22343301	0	att	The H-NS nucleoid protein repressed the expression of the assT-dsbL-dsbI LeuO-dependent operon , as well as of the assT transcriptional units .	8	The H-NS nucleoid protein repressed the expression of the assT-dsbL-dsbI LeuO-dependent operon , as well as of the assT transcriptional units .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	assT	activator	22343301	1	att	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal-medium which is used for induction of Salmonella SPI-2 ( 16 ) .	27	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal medium which is used for induction of Salmonella SPI-2 ( 16 ) .	2	MAIN	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	assT	activator	22343301	2	att	Previous studies performed in our laboratory with the S. Typhi IMSS-1 wild-type strain showed that the assT transcriptional expression depends on the transcriptional regulator LeuO and , by primer-extension experiments , a LeuO-dependent promoter ( PLeuO ) , located 164 bp upstream of the putative assT translation start site , was reported ( 26 ) .	120	Previous studies performed in our laboratory with the S. Typhi IMSS-1 wild-type strain showed that the assT transcriptional expression depends on the transcriptional regulator LeuO and , by primer extension experiments , a LeuO-dependent promoter ( PLeuO ) , located 164 bp upstream of the putative assT translation start site , was reported ( 26 ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;synthetic construct	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	2	att	Previous studies performed in our laboratory with the S. Typhi IMSS-1 wild-type strain showed that the assT transcriptional expression depends on the transcriptional regulator LeuO and , by primer-extension experiments , a LeuO-dependent promoter ( PLeuO ) , located 164 bp upstream of the putative assT translation start site , was reported ( 26 ) .	120	Previous studies performed in our laboratory with the S. Typhi IMSS-1 wild-type strain showed that the assT transcriptional expression depends on the transcriptional regulator LeuO and , by primer extension experiments , a LeuO-dependent promoter ( PLeuO ) , located 164 bp upstream of the putative assT translation start site , was reported ( 26 ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;synthetic construct	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	4	att	The transcriptional-fusions assT 688/dsbL 105 and assT 688/dsbI 107 , containing the assT LeuO-dependent promoter , as well as the upstream regions of dsbL and dsbI , respectively , also showed null transcriptional activity in the wild-type strain with the plasmid vector ( data not shown ) .	124	The transcriptional fusions assT 688/dsbL 105 and assT 688/dsbI 107 , containing the assT LeuO-dependent promoter , as well as the upstream regions of dsbL and dsbI , respectively , also showed null transcriptional activity in the wild-type strain with the plasmid vector ( data not shown ) .	4	RESULTS	unidentified plasmid;unidentified	1	L3	OTHER	Analysis	NEG	New	Level 1
LeuO	gene	assT	activator	22343301	5	att	Elimination of the assT regulatory region , including the LeuO-dependent promoter ( assT 78/dsbL 105 , dsbL 297 / dsbI 107 , and dsbI 498/dsbI 107 cat fusions ) , abolished the transcriptional activation generated by LeuO , indicating that the regulatory region of assT is essential for assT-dsbL-dsbI expression mediated by LeuO , and suggesting a LeuO-dependent operon in S. Typhi IMSS-1 .	127	Elimination of the assT regulatory region , including the LeuO-dependent promoter ( assT 78/dsbL 105 , dsbL 297 / dsbI 107 , and dsbI 498/dsbI 107 cat fusions ) , abolished the transcriptional activation generated by LeuO , indicating that the regulatory region of assT is essential for assT-dsbL-dsbI expression mediated by LeuO , and suggesting a LeuO-dependent operon in S. Typhi IMSS-1 .	4	RESULTS	Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	5	att	Elimination of the assT regulatory region , including the LeuO-dependent promoter ( assT 78/dsbL 105 , dsbL 297 / dsbI 107 , and dsbI 498/dsbI 107 cat fusions ) , abolished the transcriptional activation generated by LeuO , indicating that the regulatory region of assT is essential for assT-dsbL-dsbI expression mediated by LeuO , and suggesting a LeuO-dependent operon in S. Typhi IMSS-1 .	127	Elimination of the assT regulatory region , including the LeuO-dependent promoter ( assT 78/dsbL 105 , dsbL 297 / dsbI 107 , and dsbI 498/dsbI 107 cat fusions ) , abolished the transcriptional activation generated by LeuO , indicating that the regulatory region of assT is essential for assT-dsbL-dsbI expression mediated by LeuO , and suggesting a LeuO-dependent operon in S. Typhi IMSS-1 .	4	RESULTS	Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	7	att	These data indicate that assT , dsbL , and dsbI are functionally organized as a LeuO-dependent operon in the rich MA medium .	130	These data indicate that assT , dsbL , and dsbI are functionally organized as a LeuO-dependent operon in the rich MA medium .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	1	ver/dev	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for the dsbL-dsbI transcriptional units in the absence of cloned leuO SPI-2 .	27	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal medium which is used for induction of Salmonella SPI-2 ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	assT	activator	22343301	1	ver/dev	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for assT transcriptional units in the absence of cloned leuO SPI-2 .	27	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal medium which is used for induction of Salmonella SPI-2 ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	assT	activator	22343301	1	ver/dev	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for the dsbL-dsbI transcriptional units in a leuO background , in N-minimal-medium SPI-2 .	27	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal medium which is used for induction of Salmonella SPI-2 ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	assT	activator	22343301	1	ver/dev	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for assT transcriptional units in a leuO background , in N-minimal-medium SPI-2 .	27	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal medium which is used for induction of Salmonella SPI-2 ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	assT	activator	22343301	13	ver/dev	Because LeuO still activates assT , although at 25 % of the wild-type levels , we analyzed , by footprinting of a DNA fragment lacking II sites , whether there are other LeuO-binding sites in this region .	146	Because LeuO still activates assT when both LBS I and II have been deleted ( assT 688/assT 80 LBS I-II construction ) , although at 25 % of the wild-type levels , we analyzed , by footprinting of a DNA fragment lacking both LBS I and II sites , whether there are other LeuO-binding sites in this region .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	13	ver/dev	Because LeuO still activates assT , although at 25 % of the wild-type levels , we analyzed , by footprinting of a DNA fragment lacking both LBS I sites , whether there are other LeuO-binding sites in this region .	146	Because LeuO still activates assT when both LBS I and II have been deleted ( assT 688/assT 80 LBS I-II construction ) , although at 25 % of the wild-type levels , we analyzed , by footprinting of a DNA fragment lacking both LBS I and II sites , whether there are other LeuO-binding sites in this region .	4	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	assT	activator	22343301	15	ver/dev	LBS II _ involved in assT activation by LeuO	153	In order to determine the nucleotides in LBS II involved in assT activation by LeuO , substitutions were generated on the assT 688/assT 80 gene fusion ( Fig. 3B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	assT	activator	22343301	18	ver/dev	The data indicate that assT is induced in N-minimal-medium in the absence of LeuO , since the same activity was observed in all of the constructions in a leuO isogenic background -LRB- data not shown -RRB- .	165	The data indicate that assT is induced in N-minimal medium in the absence of LeuO , since the same activity was observed in all of the constructions in a leuO isogenic background ( data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	assT	activator	25566242	12	ver/dev	In a subsequent study to pursue more targets in Salmonella Typhi , LeuO was found to also positively regulate assT .	84	In a subsequent study to pursue more targets in Salmonella Typhi , LeuO was found to also positively regulate assT and STY3070 ; and negatively ompX , tpx and STY1978 ( Figure 1 ) .	5	THE LEUO REGULATOR IN OTHER GRAM-NEGATIVE BACTERIA	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	sirC	repressor	11083793	4	ver/dev	As shown in Fig. 3 , the bile-mediated repression of sirC : : luc does not occur in the strain background without a functional SirA .	136	As shown in Fig. 3 , the bile-mediated repression of sirC : : luc does not occur in the strain background without a functional SirA ( ; 2-fold repression versus 8 - to 10-fold repression ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
SirA	gene	sirC	repressor	11083793	5	ver/dev	Bile-mediated repression of sirC transcription is dependent upon SirA .	149	Bile-mediated repression of sirC transcription is dependent upon SirA .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	cspD	regulator	32159509	12	ver/dev	Uppal S , Shetty DM , Jawali N. Cyclic-AMP-receptor-protein regulates cspD , in Escherichia coli .	564	Uppal S , Shetty DM , Jawali N. Cyclic AMP receptor protein regulates cspD , a bacterial toxin gene , in Escherichia coli .	64	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	lldD	activator	30682134	47	ver/dev	CsrA also activated lldD S2 Table .	343	CsrA also activated L-lactate dehydrogenase ( lldD ) 5.3-fold ( S2 Table ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	lldD	activator	30682134	47	ver/dev	CsrA also activated lldD 5.3-fold .	343	CsrA also activated L-lactate dehydrogenase ( lldD ) 5.3-fold ( S2 Table ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	spvR	activator	21388802	2	ver/dev	CsrA activates spvR expression .	151	CsrA activates spvR and rpoE expression and represses himD .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	spvR	activator	21388802	7	ver/dev	spvR transcription is activated by CsrA .	209	spvR transcription is activated by Hnr , CRP , RpoE , HimD and CsrA and is repressed by PhoP .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	spvR	activator	30682134	20	ver/dev	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM encoded effectors , slyA in LB .	227	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM and repressing the regulator of SPI-2 encoded effectors , slyA in LB .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	Salmonella;unidentified plasmid	1	L3	OTHER	Analysis	OTHER	New	Level 2
Fur	gene	gpmA	regulator	18554972	0	att	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	215	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	15	3.1. TRANSPOSON MUTAGENESIS IDENTIFIES IRON RESPONSE GENES INVOLVED IN NOREPINEPHRINE-ENHANCED GROWTH OF SALMONELLA TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1703	repressor	17322315	9	ver/dev	Although the STM4264 mutant showed the highest c-di-GMP concentration , CsgD expression was lower than in the STM1703 mutant .	206	Although the STM4264 mutant showed the highest c-di-GMP concentration , CsgD expression was lower than in the STM1703 mutant .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1703	repressor	17322315	43	ver/dev	STM4264 is located upstream of STM1703 , since STM1703 can complement an STM4264 defect by downregulation of CsgD versa .	405	STM4264 is located upstream of STM1703 , since STM1703 can complement an STM4264 defect by downregulation of CsgD but not vice versa .	5	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	STM1703	repressor	19376870	28	ver/dev	STM1344 positively affects the expression of the major regulator of CsgD , through the downregulation of the expression of the phosphodiesterases STM1703 and STM3611 .	342	STM1344 positively affects the expression of the major regulator of the multicellular rdar morphotype behavior , CsgD , through the downregulation of the expression of the phosphodiesterases STM1703 and STM3611 ( 37 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1703	repressor	19376870	34	ver/dev	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 , required for the downregulation of CsgD expression .	380	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 and STM3611 , required for the downregulation of CsgD expression ( 37 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1703	repressor	25153529	3	ver/dev	The GGDEF/EAL domain protein STM1703 inhibit expression of CsgD .	130	The GGDEF/EAL domain protein STM1703 ( yciR ) and GGDEF domain proteins STM3611 ( yhjH ) and STM4264 ( yjcC ) each inhibit expression of CsgD and hence rdar morphotype development [ 57 ] .	8	GGDEF/EAL DOMAIN PROTEINS AND RDAR MORPHOTYPE DEVELOPMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1703	repressor	26655751	2	ver/dev	STM1703 inhibit CsgD function .	43	PDEs ( STM1703 , STM3611 , STM4264 , and STM1827 ) inhibit CsgD function ( 13 , 14 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1703	repressor	26655751	5	ver/dev	During growth on low salt agar plates , STM1703 is the major inhibitor of CsgD , while the other three PDEs play more minor roles .	387	During growth on low salt agar plates , STM1703 is the major inhibitor of CsgD , while the other three PDEs play more minor roles ( 14 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	slyA	repressor	30682134	17	ver/dev	CsrA repressed slyA translation 1.8-fold in LB .	223	CsrA repressed slyA translation 1.8-fold in LB but not in mLPM ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	slyA	repressor	30682134	17	ver/dev	CsrA repressed slyA translation 1.8-fold in S2 Table .	223	CsrA repressed slyA translation 1.8-fold in LB but not in mLPM ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	slyA	repressor	30682134	17	ver/dev	CsrA repressed slyA translation 1.8-fold in mLPM .	223	CsrA repressed slyA translation 1.8-fold in LB but not in mLPM ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	slyA	repressor	30682134	38	ver/dev	In LB , CsrA also repressed expression of slyA , regulators .	279	In LB , CsrA also repressed expression of slyA , rpoS , and soxS , regulators that contribute to resistance to oxidative stress in Salmonella [ 71,109,110 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	slyA	repressor	30682134	40	ver/dev	In contrast , the stress resistant phenotype may be apparent in LB because CsrA represses the expression of slyA	287	In contrast , the stress resistant phenotype may be apparent in LB because CsrA represses the expression of multiple regulators ( slyA , soxS , and rpoS ) that induce expression of	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	dcp	regulator	24272778	24	att	Intriguingly , association of AraC with the site in dcp , as measured by ChIP/qPCR , is the highest of all AraC-bound regions in the E. coli genome ( Fig. 1A ) .	258	Intriguingly , association of AraC with the site in dcp , as measured by ChIP/qPCR , is the highest of all AraC-bound regions in the E. coli genome ( Fig. 1A ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	dcp	regulator	24272778	37	att	Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .	377	Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
AraC	gene	dcp	regulator	24272778	22	ver/dev	AraC binding within dcp is not associated with detectable regulation of transcription .	254	AraC binding within dcp is not associated with detectable regulation of transcription .	4	RESULTS	nan	1	L2	OTHER	Other	NEG	Other	Level 1
AraC	gene	dcp	regulator	24272778	23	ver/dev	We detected binding of AraC within dcp .	255	We detected binding of AraC within dcp ( Fig. 1A ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	ompW	regulator	17618087	0	ver/dev	Shine-Dalgarno sequences along with a SoxS binding site were found , suggesting that ompW expression could be positively regulated by intracellular ROS concentration -LRB- not shown -RRB- .	174	Consensus-10 , -35 and Shine-Dalgarno sequences along with a SoxS binding site were found , suggesting that ompW expression could be positively regulated by intracellular ROS concentration [ 25,30 ] ( not shown ) .	16	3.1. MV INDUCES OMPW EXPRESSION	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
SoxS	gene	ompW	regulator	17618087	0	ver/dev	-35 along with a SoxS binding site were found , suggesting that ompW expression could be positively regulated by intracellular ROS concentration -LRB- not shown -RRB- .	174	Consensus-10 , -35 and Shine-Dalgarno sequences along with a SoxS binding site were found , suggesting that ompW expression could be positively regulated by intracellular ROS concentration [ 25,30 ] ( not shown ) .	16	3.1. MV INDUCES OMPW EXPRESSION	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
SoxS	gene	ompW	regulator	17618087	0	ver/dev	Consensus-10 along with a SoxS binding site were found , suggesting that ompW expression could be positively regulated by intracellular ROS concentration -LRB- not shown -RRB- .	174	Consensus-10 , -35 and Shine-Dalgarno sequences along with a SoxS binding site were found , suggesting that ompW expression could be positively regulated by intracellular ROS concentration [ 25,30 ] ( not shown ) .	16	3.1. MV INDUCES OMPW EXPRESSION	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
SoxS	gene	ompW	regulator	19460824	0	ver/dev	SoxS regulates the expression of the Salmonella enterica serovar Typhimurium ompW gene	2	SoxS regulates the expression of the Salmonella enterica serovar Typhimurium ompW gene	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	ompW	regulator	19460824	5	ver/dev	To define the role of SoxS in the regulation of ompW expression , we constructed transcriptional-fusions .	130	To define the role of SoxS in the regulation of ompW expression and to confirm the activity of the putative promoter , we constructed transcriptional fusions encompassing different lengths of the ompW promoter region ( Fig. 3 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SoxS	gene	ompW	regulator	19460824	8	ver/dev	SoxS binds to the regulatory region of the ompW gene	145	SoxS binds to the regulatory region of the ompW gene	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	ompW	regulator	21148209	37	ver/dev	SoxS regulates the expression of the Salmonella enterica serovar Typhimurium ompW gene .	343	SoxS regulates the expression of the Salmonella enterica serovar Typhimurium ompW gene .	42	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	ompW	regulator	29018419	5	ver/dev	SoxS regulates the expression of the S. Typhimurium ompW gene .	566	SoxS regulates the expression of the S. Typhimurium ompW gene .	30	REFERENCES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	ompW	regulator	31838175	5	ver/dev	However , while SoxS could bind the ompW promoter region , as previously reported , we could not detect SoxS binding to ssrB promoter regions -LRB- Supplementary Fig .	207	However , while SoxS could bind the ompW promoter region , as previously reported [ 16 ] , we could not detect SoxS binding to the ssrA and ssrB promoter regions ( Supplementary Fig .	20	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
SoxS	gene	ompW	regulator	31838175	5	ver/dev	However , while SoxS could bind the ompW promoter region , as previously reported , we could not detect SoxS binding to the ssrA .	207	However , while SoxS could bind the ompW promoter region , as previously reported [ 16 ] , we could not detect SoxS binding to the ssrA and ssrB promoter regions ( Supplementary Fig .	20	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
FlhC	gene	dnaK	activator	16430704	8	ver/dev	Therefore , the slower increasing of FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of s ClpAP , HslVU and L .	175	Therefore , the slower increasing of FlhD and FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of protease ( s ) such as ClpAP , HslVU and Lon .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	dnaK	activator	16430704	8	ver/dev	Therefore , the slower increasing of FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of f protea .	175	Therefore , the slower increasing of FlhD and FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of protease ( s ) such as ClpAP , HslVU and Lon .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	tviB	regulator	29417203	5	ver/dev	These results indicated that the transcription of tviB was under negative control of OmpR , respectively .	92	These results indicated that the transcription of tviA and tviB was under positive and negative control of OmpR and Hfq , respectively .	12	REGULATION OF TVIA AND TVIB BY OMPR AND HFQ	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	tviB	regulator	29417203	5	ver/dev	These results indicated that the transcription of tviB was under positive control of OmpR , respectively .	92	These results indicated that the transcription of tviA and tviB was under positive and negative control of OmpR and Hfq , respectively .	12	REGULATION OF TVIA AND TVIB BY OMPR AND HFQ	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	tviB	regulator	29417203	7	ver/dev	Fig. 3 OmpR regulate tviB transcription under osmotic-stress condition .	101	Fig. 3 OmpR and Hfq regulate tviA and tviB transcription under osmotic stress condition .	13	AUTOREGULATION AND RECIPROCAL REGULATION OF OMPR AND HFQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	10856650	2	ver/dev	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	209	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	24	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	11036033	0	ver/dev	MarA is a transcriptional activator for marRAB .	13	MarA is a transcriptional activator for marRAB and binds to the marbox located within the operator marO .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	marRAB	activator	12528827	0	ver/dev	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	314	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	17	R E F E R E N C E S	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	15073288	19	ver/dev	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	409	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	15155237	4	ver/dev	MarA is a transcriptional activator for marRAB .	72	MarA is a transcriptional activator for marRAB and binds to the mar box located within marO .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	marRAB	activator	16006078	0	ver/dev	By far the greatest impact induction of marRAB has is the overexpression and accumulation of MarA .	36	By far the greatest impact induction of marRAB has is the overexpression and accumulation of MarA .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	TU	marRAB	activator	16842216	2	ver/dev	The MarA homologs SoxS activate marRAB transcription .	345	The MarA homologs SoxS and Rob can also bind to the marO marbox and activate marRAB transcription .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	22752112	28	ver/dev	Mol Microbiol 44:1611 -- 1624 Martin RG , Jair KW , Wolf RE Jr , Rosner JL Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	338	Mol Microbiol 44:1611 -- 1624 Martin RG , Jair KW , Wolf RE Jr , Rosner JL ( 1996 ) Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	24	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	32210923	1	ver/dev	Different effects of transcriptional regulators MarA on susceptibility of Escherichia coli to CAMPs : rob-dependent CAMP induction of the marRAB operon .	837	Different effects of transcriptional regulators MarA , SoxS and Rob on susceptibility of Escherichia coli to cationic antimicrobial peptides ( CAMPs ) : rob-dependent CAMP induction of the marRAB operon .	32	TIME: 17:30 # 16	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	32210923	1	ver/dev	Different effects of transcriptional regulators MarA on susceptibility of Escherichia coli to cationic antimicrobial peptides : rob-dependent CAMP induction of the marRAB operon .	837	Different effects of transcriptional regulators MarA , SoxS and Rob on susceptibility of Escherichia coli to cationic antimicrobial peptides ( CAMPs ) : rob-dependent CAMP induction of the marRAB operon .	32	TIME: 17:30 # 16	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	activator	9068629	5	ver/dev	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	639	Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .	25	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CspE	gene	cspA	regulator	32159509	5	ver/dev	To understand whether the CspE mediated biofilm regulatory pathway overlapped with the regulation of swarming motility , cspA over-expression system was used .	217	To understand whether the CspE mediated biofilm regulatory pathway overlapped with the regulation of swarming motility , the cspE complementation ( pcspE ) and cspA over-expression system ( pcspA ) was used .	13	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CspE	gene	cspA	regulator	32159509	7	ver/dev	The probable mechanism of transcriptional repression of CspA by CspE involves physical binding of CspE to the cold box region ' proximal part of 5 ′ - UTR of cspA mRNA .	273	The probable mechanism of transcriptional repression of CspA by CspE involves physical binding of CspE to the cold box region which is located in the 5 ' proximal part of 5 ′ - UTR of cspA mRNA .	14	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
Lrp	gene	fimZ	activator	18776023	2	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	615	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	34	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	activator	19074398	48	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	979	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	39	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	activator	23938383	0	ver/dev	a global gene regulator controls genes in Salmonella , among which fimZ was shown to be activated by Lrp	26	In addition , the leucine-responsive regulatory protein ( Lrp ) is a global gene regulator that controls a variety of genes in Salmonella , among which fimZ was shown to be activated by Lrp and consequently allows S. Typhimurium to produce type 1 fimbriae ( McFarland et al. 2008 ) .	3	1. INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimZ	activator	23938383	0	ver/dev	a global gene regulator controls a variety in Salmonella , among which fimZ was shown to be activated by Lrp	26	In addition , the leucine-responsive regulatory protein ( Lrp ) is a global gene regulator that controls a variety of genes in Salmonella , among which fimZ was shown to be activated by Lrp and consequently allows S. Typhimurium to produce type 1 fimbriae ( McFarland et al. 2008 ) .	3	1. INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimZ	activator	23938383	0	ver/dev	a global gene regulator controls genes in Salmonella , among which fimZ was shown to be activated by Lrp	26	In addition , the leucine-responsive regulatory protein ( Lrp ) is a global gene regulator that controls a variety of genes in Salmonella , among which fimZ was shown to be activated by Lrp and consequently allows S. Typhimurium to produce type 1 fimbriae ( McFarland et al. 2008 ) .	3	1. INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimZ	activator	23938383	0	ver/dev	a global gene regulator controls a variety in Salmonella , among which fimZ was shown to be activated by Lrp	26	In addition , the leucine-responsive regulatory protein ( Lrp ) is a global gene regulator that controls a variety of genes in Salmonella , among which fimZ was shown to be activated by Lrp and consequently allows S. Typhimurium to produce type 1 fimbriae ( McFarland et al. 2008 ) .	3	1. INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimZ	activator	24462182	35	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	328	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	25	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	activator	27909434	10	ver/dev	Among them , fimZ are shown to be activated by Lrp .	338	Among them , fimZ and fimA are shown to be activated by Lrp and consequently allow S. Typhimurium to produce type 1 fimbriae ( McFarland et al. , 2008 ) .	25	ACETYLATION OF K36 AFFECTS THE EXPRESSION OF LRP REGULON	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimZ	activator	27909434	13	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene .	543	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene .	40	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	activator	28922626	6	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene .	565	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene .	39	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	activator	31139165	13	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene .	1059	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene .	18	TIME: 14:52 # 17	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimZ	activator	33201432	7	ver/dev	Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	461	The leucine-responsive regulatory protein , Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .	31	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliC	activator	9765212	12	att	TH3920 is deleted for the flgM locus , and contains a transcriptional-fusion of lacZ to the fliC gene , which serves as a reporter for s28-dependent transcription .	328	TH3920 is deleted for the flgM locus , and contains a transcriptional fusion of lacZ to the fliC gene , which serves as a reporter for s28-dependent transcription .	9	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	fliC	activator	9765212	2	att	The purified mutant proteins , His -- FlgM * L66S and His -- FlgM * I82T , were then compared with His -- FlgM for their ability to inhibit s28-dependent transcription from the fliC promoter in-vitro .	59	The purified mutant proteins , His -- FlgM * L66S and His -- FlgM * I82T , were then compared with His -- FlgM for their ability to inhibit s28-dependent transcription from the fliC promoter in vitro .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Sigma28	gene	fliC	activator	9765212	3	att	Reconstituted Es28 specifically transcribed the s28-dependent fliC promoter and reached a near-maximal rate of transcription at a 1:1 ratio between s28 and core RNAP ( Fig. 1A ) .	60	Reconstituted Es28 specifically transcribed the s28-dependent fliC promoter and reached a near-maximal rate of transcription at a 1:1 ratio between s28 and core RNAP ( Fig. 1A ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliC	activator	9765212	5	att	Reaction mixtures contained 30 nM His-core RNAP ( E ) and 3 nM template DNA [ either the s28-dependent fliC promoter ( s ) , or the s70-dependent tac promoter ( d ) ] .	77	Reaction mixtures contained 30 nM His-core RNAP ( E ) and 3 nM template DNA [ either the s28-dependent fliC promoter ( s ) , or the s70-dependent tac promoter ( d ) ] .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliC	activator	9765570	1	att	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	71	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	sifB	activator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sifB by both direct activation of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	invH	regulator	28575106	5	att	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	167	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	8	THE GENE LOIA IS THE VIRULENCE DETERMINANT IN SPI-14	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	flhD	regulator	27601571	32	ver/dev	We note that two previous studies provided strong evidence that flhD is not regulated by HilA .	270	We note that two previous studies provided strong evidence that flhD is not regulated by HilA ( 18 , 54 ) .	3	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
HU	gene	narH	regulator	21212121	8	ver/dev	HU has been reported to regulate narH positively in E. coli whereas hupA acts negatively on narH transcription in Salmonella -LRB- Supplementary Fig .	307	HU has been reported to regulate narH positively in E. coli ( Oberto et al. , 2009 ) whereas hupA acts negatively on narH transcription in Salmonella ( Supplementary Fig .	9	RESPIRATION AND METABOLISM	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	yejABEF	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	yejABEF	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	yejABEF	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	yejABEF	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	yejABEF	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilE	repressor	31428589	8	ver/dev	Interestingly , H-NS also represses the promoters of hilE .	170	Interestingly , H-NS also represses the promoters of leuO and hilE , which are regarded as negative regulatory genes .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	TU	STM4509	regulator	12437215	0	ver/dev	Two proteins also have a 28 % identity to a 130 aa central portion of STM4509 , a modulator of HilA expression , the master regulator of pathogenicity island 1 type III secretion system in S. enterica .	343	Two proteins also have a 28 % identity to a 130 aa central portion of the HilE protein ( STM4509 ) [ 9 ] , a modulator of HilA expression , the master regulator of pathogenicity island 1 type III secretion system in S. enterica .	11	3.1. THE SCI GENOMIC ISLAND IN S. ENTERICA SEROVAR TYPHIMURIUM ENCODES NOVEL PROTEINS WITH BOTH CYTOPLASMIC AND EXTRACELLULAR LOCALIZATIONS	Phaeoacremonium santali;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	ytfE	repressor	23651595	17	ver/dev	Expression of ytfE is repressed by NsrR	621	Expression of ytfE is repressed by NsrR and it has been suggested that ytfE becomes activated by NarL upon exposure to nitrate and nitrite ( Constantinidou et al. , 2006 ; Filenko et al. , 2007 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Overton et al. , 2008 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	12068808	47	ver/dev	Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	236	Consistent with OmpR being an acid-induced regulator important to Salmonella pathogenicity , Lee et al. ( 2000 ) have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	12080060	47	ver/dev	Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	236	Consistent with OmpR being an acid-induced regulator important to Salmonella pathogenicity , Lee et al. ( 2000 ) have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	20861532	0	ver/dev	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrB proteins .	120	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA and SsrB proteins [ 16 ] .	6	3.1.1 SALMONELLA PATHOGENICITY ISLAND 1 (SPI-1)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	20861532	0	ver/dev	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA proteins .	120	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA and SsrB proteins [ 16 ] .	6	3.1.1 SALMONELLA PATHOGENICITY ISLAND 1 (SPI-1)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	27404739	3	ver/dev	Further , as mentioned previously , OmpR is a direct transcriptional activator of ssrAB .	165	Further , as mentioned previously , OmpR is a direct transcriptional activator of ssrAB , a two-component regulatory system that activates SPI-2 gene transcription ( Lee et al. , 2000 ) .	9	ANTIGENS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	30663891	8	ver/dev	The activated OmpR also induces the transcription of ssrAB genes .	345	The activated OmpR has reported effects on SPI-1 and also induces the transcription of ssrAB genes , the regulatory system required for SPI-2 gene expression ( Fabrega and Vila , 2013 ) .	14	5.2.1. STRESS PROTEINS RELATED WITH VIRULENCE RESPONSE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	30718301	4	ver/dev	One involves the additive action of HilD , whereas the other involves SlyA , but not HilD , to counteract H-NS-mediated repression on ssrAB , thus favoring in both cases the activation of ssrAB by OmpR .	16	One involves the additive action of SlyA and HilD , whereas the other involves SlyA , but not HilD , to counteract H-NS-mediated repression on ssrAB , thus favoring in both cases the activation of ssrAB by OmpR .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	TU	ssrAB	activator	30718301	4	ver/dev	One involves the additive action of SlyA , whereas the other involves SlyA , but not HilD , to counteract H-NS-mediated repression on ssrAB , thus favoring in both cases the activation of ssrAB by OmpR .	16	One involves the additive action of SlyA and HilD , whereas the other involves SlyA , but not HilD , to counteract H-NS-mediated repression on ssrAB , thus favoring in both cases the activation of ssrAB by OmpR .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	TU	ssrAB	activator	30718301	5	ver/dev	One involves the additive action of the regulators SlyA and HilD , whereas the other involves SlyA , but not HilD , to counteract H-NS-mediated repression on the ssrAB operon , thus favoring its activation by the OmpR regulator .	20	One involves the additive action of the regulators SlyA and HilD , whereas the other involves SlyA , but not HilD , to counteract H-NS-mediated repression on the ssrAB operon , thus favoring its activation by the OmpR regulator .	2	MAIN	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	TU	ssrAB	activator	30718301	6	ver/dev	HilD counteract H-NS-mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	24	SlyA and HilD counteract H-NS-mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	30718301	6	ver/dev	SlyA counteract H-NS-mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	24	SlyA and HilD counteract H-NS-mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	30718301	41	ver/dev	SlyA act additively as anti-H-NS factors , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during-growth in LB .	126	FIG 5 HilD and SlyA act additively as anti-H-NS factors , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during growth in LB .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	30718301	41	ver/dev	FIG 5 HilD act additively as anti-H-NS factors , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during-growth in LB .	126	FIG 5 HilD and SlyA act additively as anti-H-NS factors , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during growth in LB .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	30718301	42	ver/dev	HilD , acts as an anti-H-NS factor , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during-growth in N-MM .	131	FIG 6 SlyA , but not HilD , acts as an anti-H-NS factor , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during growth in N-MM .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	30718301	42	ver/dev	FIG 6 SlyA , acts as an anti-H-NS factor , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during-growth in N-MM .	131	FIG 6 SlyA , but not HilD , acts as an anti-H-NS factor , whereas OmpR acts independently of H-NS , to induce expression of ssrAB during growth in N-MM .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	activator	30718301	43	ver/dev	LB would favor the activation of ssrAB by OmpR	136	Collectively , these results indicate that SlyA and HilD act additively to counteract H-NS-mediated repression on ssrAB during the growth of S. Typhimurium in LB , which would favor the activation of ssrAB by OmpR .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
OmpR	TU	ssrAB	activator	30718301	43	ver/dev	LB would favor the activation of ssrAB by OmpR	136	Collectively , these results indicate that SlyA and HilD act additively to counteract H-NS-mediated repression on ssrAB during the growth of S. Typhimurium in LB , which would favor the activation of ssrAB by OmpR .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	V.H. SlyA counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	Bustamante counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	D. counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	Perez-Morales counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	C. counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	Zavala-Alvarado counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	M.M. counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	TU	ssrAB	activator	33045730	109	ver/dev	Banda counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	555	Banda , M.M. , Zavala-Alvarado , C. , Perez-Morales , D. and Bustamante , V.H. ( 2019 ) SlyA and HilD counteract H-NS-Mediated repression on the ssrAB virulence operon of Salmonella enterica serovar Typhimurium and thus promote its activation by OmpR .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	phoP	activator	21388802	3	ver/dev	OmpR activates phoP expression .	160	OmpR activates slyA , phoP and ssrB expression and represses rpoS .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
UvrY	gene	csrB	activator	15765064	22	ver/dev	UvrY in turn activates the expression of csrB	125	It appears that csrA is necessary to regulate the activity of UvrY , which in turn activates the expression of csrB ( Suzuki et al. , 2002 ) .	6	OTHER INVASION GENE ACTIVATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
UvrY	gene	csrB	activator	16949866	32	ver/dev	UvrY of E. coli both control the csr system by directly activating the csrB gene .	458	SirA of Salmonella and UvrY of E. coli both control the csr system by directly binding and activating the csrB gene ( Pernestig et al. , 2001 ; Teplitski et al. , 2003 ) .	19	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	sbp	regulator	18957594	2	att	With the exception of cysK and sbp , mutants in all other CysB-regulated genes showed little or no activity on swim plates .	233	With the exception of cysK and sbp , mutants in all other CysB-regulated genes showed little or no activity on swim plates .	7	CYSTEINE AUXOTROPHS HAVE ALTERED SWARM COLONY MORPHOLOGY	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
CysB	gene	sbp	regulator	20600858	3	att	Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9-minimal-medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative-stress .	181	Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9 minimal medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative stress .	16	3.4. CYSTEINE BIOSYNTHESIS IS CRITICAL DURING PERIODS OF OXIDATIVE STRESS	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Zur	gene	zinT	regulator	24430377	1	ver/dev	that zinT are coregulated by Zur	147	Lack of ZupT determines changes in intracellular zinc concentration Previous studies have shown that zinT and znuABC are coregulated by Zur and that ZinT accumulation is strongly induced by	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Zur	gene	zinT	regulator	24430377	2	ver/dev	As zinT expression is under the direct control of Zur , the main transcriptional regulator strongly support the hypothesis that the absence of zupT further reduces the ability of Salmonella enterica to import zinc from the environment .	153	As zinT expression is under the direct control of Zur , the main transcriptional regulator activated in response to zinc deprivation , the observed differences in the ZinT accumulation pattern in the two mutant strains strongly support the hypothesis that the absence of zupT further reduces the ability of Salmonella enterica to import zinc from the environment .	11	RESULTS	Salmonella;Salmonella enterica;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Zur	gene	zinT	regulator	24858080	12	att	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	408	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CytR	gene	udp	regulator	14499937	3	ver/dev	The absence of consensus sequences for the CytR protein within the udp regulatory region of V. cholerae suggests that reduced CytR regulation of udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	186	The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis and V. cholerae ( Fig. 3 ) suggests that reduced CytR regulation of udpPYp and udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	17	3.4. EXPRESSION OF HETERLOGOUS UDP PROMOTERS IN E. COLI CELLS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CytR	gene	udp	regulator	14499937	3	ver/dev	The absence of consensus sequences for the CytR protein within the udp regulatory region of V. cholerae suggests that reduced CytR regulation of udpPYp c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	186	The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis and V. cholerae ( Fig. 3 ) suggests that reduced CytR regulation of udpPYp and udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	17	3.4. EXPRESSION OF HETERLOGOUS UDP PROMOTERS IN E. COLI CELLS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CytR	gene	udp	regulator	14499937	3	ver/dev	The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis suggests that reduced CytR regulation of udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	186	The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis and V. cholerae ( Fig. 3 ) suggests that reduced CytR regulation of udpPYp and udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	17	3.4. EXPRESSION OF HETERLOGOUS UDP PROMOTERS IN E. COLI CELLS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CytR	gene	udp	regulator	14499937	3	ver/dev	The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis suggests that reduced CytR regulation of udpPYp c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	186	The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis and V. cholerae ( Fig. 3 ) suggests that reduced CytR regulation of udpPYp and udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters	17	3.4. EXPRESSION OF HETERLOGOUS UDP PROMOTERS IN E. COLI CELLS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CytR	gene	udp	regulator	14499937	7	ver/dev	Both cdd and udp are members of the CytR regulon , i.e. , the expression of these genes is negatively regulated by the CytR repressor protein .	204	Both cdd and udp are members of the CytR regulon , i.e. , the expression of these genes is negatively regulated by the CytR repressor protein .	17	3.4. EXPRESSION OF HETERLOGOUS UDP PROMOTERS IN E. COLI CELLS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	sefR	activator	11577150	0	att	β-Galactosidase assays were used to measure sefR-dependent expression of the sef operon in these mutants by comparing expression levels before and after the addition of arabinose to strains containing the AraC-dependent sefR expression plasmid ( Fig. 4 ) .	207	β-Galactosidase assays were used to measure sefR-dependent expression of the sef operon in these mutants by comparing expression levels before and after the addition of arabinose to strains containing the AraC-dependent sefR expression plasmid ( Fig. 4 ) .	9	SEFR REGULATES SEF GENE EXPRESSION	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhD	gene	spiC	activator	19706157	9	ver/dev	We next examined the expression of FlhD at bacterial growth phase of OD600 of 0.7 in LB , because the spiC expression is induced at over an OD600 of 1.5 when the bacteria are grown in LB .	250	We next examined the expression of FlhD at bacterial growth phase of OD600 of 0.7 in LB , because the spiC expression is induced at over an OD600 of 1.5 when the bacteria are grown in LB .	7	RELATIVE EXPRESSION LEVELS RELATIVE EXPRESSION LEVELS (FOLD) (FOLD)	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	hit	regulator	31611347	2	att	These results further substantiated the selection of compounds , showing that the two hit compounds exerted a 36 % to 80 % repressive effect on the - galactosidase activity levels measured from the six PhoP-controlled reporters tested .	73	These results further substantiated the selection of compounds , showing that the two hit compounds exerted a 36 % to 80 % repressive effect on the - galactosidase activity levels measured from the six PhoP-controlled reporters tested .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	lon	activator	31370702	0	att	SPI-11 includes the PhoP-activated genes pagD and pagC , which are involved in intramacrophage survival [ 40 ] ; pagD and pagC were downregulated 2.5 - and 2.6-fold in the lon mutant , respectively ( Supplementary Table 2 ) .	219	SPI-11 includes the PhoP-activated genes pagD and pagC , which are involved in intramacrophage survival [ 40 ] ; pagD and pagC were downregulated 2.5 - and 2.6-fold in the lon mutant , respectively ( Supplementary Table 2 ) .	15	LON REGULATES THE EXPRESSION OF SEVERAL SPIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	spvR	activator	11101680	0	att	A majority of stress-sensitive DT 104 and PT 4 strains harboured mutations in the rpoS gene or showed reduced expression of the RpoS protein as measured indirectly using the RpoS-dependent spvR } A `` : : luxCDABE fusion .	53	A majority of stress-sensitive DT 104 and PT 4 strains harboured mutations in the rpoS gene or showed reduced expression of the RpoS protein as measured indirectly using the RpoS-dependent spvR } A `` : : luxCDABE fusion .	3	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium DT104	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	spvR	activator	11101680	3	att	In the five sensitive DT 104 and PT 4 strains examined , three harboured mutations in the rpoS gene , while two DT 104 strains had intact rpoS genes and one of those demonstrated a reduced level of RpoS-dependent spvR } A `` : : luxCDABE expression .	332	In the five sensitive DT 104 and PT 4 strains examined , three harboured mutations in the rpoS gene , while two DT 104 strains had intact rpoS genes and one of those demonstrated a reduced level of RpoS-dependent spvR } A `` : : luxCDABE expression .	8	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium DT104;Salmonella enterica subsp. enterica serovar Typhimurium DT104	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	spvR	activator	11101680	4	att	It is therefore possible that the reduced expression the RpoS-dependent spvR } A `` : : luxCDABE fusion in DT 104 strain 11 is due to mutations affecting the translational processing of the RpoS protein or , alternatively , to protein instability .	334	It is therefore possible that the reduced expression the RpoS-dependent spvR } A `` : : luxCDABE fusion in DT 104 strain 11 is due to mutations affecting the translational processing of the RpoS protein or , alternatively , to protein instability .	8	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium DT104;Bauldia consociata;Serratia fonticola;Paenibacillus aquistagni	0.5	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvR	activator	11101680	6	att	The level of expression of the RpoS-dependent spvR } A `` : : luxCDABE fusion in strain 11 was lower than in the stress-resistant strain 30 , but with a similar induction , while strain 10 encoded a highly truncated protein .	351	The level of expression of the RpoS-dependent spvR } A `` : : luxCDABE fusion in strain 11 was lower than in the stress-resistant strain 30 , but with a similar induction , while strain 10 encoded a highly truncated protein .	8	DISCUSSION	Bauldia consociata;Serratia fonticola;Paenibacillus aquistagni;Azospirillum palatum;Leptospira inadai	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	spvR	activator	11553591	3	ver/dev	This lack of an in-vitro phenotype agrees with the fact that RpoS positively regulates spvR expression .	350	This lack of an in vitro phenotype agrees with the fact that RpoS positively regulates spvR expression ( 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	spvR	activator	15790293	5	ver/dev	Indeed , RpoS participates in the induction of spvR .	237	Indeed , RpoS also promotes expression of AgfA fimbriae ( Römling et al. , 1998a , b ) and participates in the induction of spvR ( Chen et al. , 1995 ; Heiskanen et al. , 1994 ) .	14	ALTERNATIVE R-FACTORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	spvR	activator	25217722	0	ver/dev	It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvR	activator	25217722	0	ver/dev	It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvR	activator	25217722	0	ver/dev	It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvR	activator	25217722	0	ver/dev	It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvR	activator	29763647	0	att	One hundred and twenty six compounds that inhibited light production by > 3 standard deviations above the mean ( cutoff > 64 % inhibition ) were re-tested for inhibition of growth and expression of the RpoS-dependent spvR gene ( Kowarz et al. , 1994 ) in Samonella strain SL1344 ( data not shown ) .	66	One hundred and twenty six compounds that inhibited light production by > 3 standard deviations above the mean ( cutoff > 64 % inhibition ) were re-tested for inhibition of growth and expression of the RpoS-dependent spvR gene ( Kowarz et al. , 1994 ) in Samonella strain SL1344 ( data not shown ) .	0	Unknown	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	adrA	activator	15790293	13	att	While CsgD activates the two divergent csg promoters for csgABC and csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	319	While CsgD activates the two divergent csg promoters for csgABC and csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	18	THE LUXR FAMILY OF GENE REGULATORS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	15790293	13	ver/dev	While CsgD activates the two divergent csg promoters for csgABC transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	319	While CsgD activates the two divergent csg promoters for csgABC and csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	18	THE LUXR FAMILY OF GENE REGULATORS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	16629664	9	ver/dev	The other known target of activation by CsgD is the adrA promoter .	182	The other known target of activation by CsgD is the adrA promoter ( Römling et al. , 2000 ) .	9	CSGD EXPRESSION IS REGULATED BY C-DI-GMP ON A TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL LEVEL	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	16629664	17	ver/dev	the regulatory network where CsgD activates transcription of adrA	200	Consequently , the regulatory network where CsgD activates transcription of adrA , whose gene product subsequently produces c-di-GMP is still valid ( Simm et al. , 2004 ) .	9	CSGD EXPRESSION IS REGULATED BY C-DI-GMP ON A TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL LEVEL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	16707690	4	ver/dev	CsgD also stimulates cellulose production via activation of transcription of adrA .	48	CsgD also stimulates cellulose production via activation of transcription of adrA , which encodes a diguanyl-ate cyclase protein ( 40 , 52 , 58 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	16707690	4	ver/dev	CsgD also stimulates cellulose production via activation of transcription of adrA .	48	CsgD also stimulates cellulose production via activation of transcription of adrA , which encodes a diguanyl-ate cyclase protein ( 40 , 52 , 58 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	16707690	33	ver/dev	Experiments with purified CsgD are needed to determine whether CsgD can activate transcription by E S and/or E 70 at the adrA promoters .	433	Experiments with purified CsgD are needed to determine whether CsgD can activate transcription by E S and/or E 70 at the adrA and csgB promoters .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	adrA	activator	17322315	40	ver/dev	CsgD , in turn , is required for the transcriptional activation of adrA encoding a GGDEF domain protein .	397	CsgD , in turn , is required for the transcriptional activation of adrA encoding a GGDEF domain protein , which is required for the expression of cellulose ( 29 , 35 ) and , partially , curli fimbriae ( 20 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	20545866	44	att	In agreement with in-vivo findings ( Romling et al. , 2000 ) , CsgD-activated transcription at the adrA promoter occurred with RNA polymerase loaded with RpoS and RpoD .	287	In agreement with in vivo findings ( Romling et al. , 2000 ) , CsgD-activated transcription at the adrA promoter occurred with RNA polymerase loaded with RpoS and RpoD .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	20545866	49	att	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	294	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	activator	20545866	3	ver/dev	In addition , CsgD contributes indirectly to cellulose production by activating the transcription of adrA .	27	In addition , CsgD contributes indirectly to cellulose production by activating the transcription of adrA .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	adrA	activator	20545866	23	ver/dev	To investigate whether c-di-GMP plays a role in the transcriptional activation of adrA by CsgD , we added c-di-GMP to the in-vitro-transcription assays .	125	To investigate whether c-di-GMP plays a role in the transcriptional activation of csgBA and adrA by CsgD , we added c-di-GMP to the in vitro transcription assays .	7	CSGD IS CRUCIAL FOR THE TRANSCRIPTION OF CSGBA AND ADRA IN VITRO	nan	1	L3	SPEC	Other	OTHER	New	Level 1
CsgD	gene	adrA	activator	20545866	34	ver/dev	In this study , we dem-onstrated for the first time that CsgD activates transcription of the promoter regions of adrA .	251	In this study , we dem-onstrated for the first time that CsgD interacts directly and activates transcription of the promoter regions of csgBA and adrA .	9	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CsgD	gene	adrA	activator	21388802	1	ver/dev	CsgD activates transcription of adrA .	148	CsgD interacts directly and activates transcription of csgBA and adrA .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	22235813	0	ver/dev	CsgD is also indirectly involved in cellulose production by activating transcription of adrA .	62	CsgD is also indirectly involved in cellulose production by activating transcription of adrA .	1	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	22235813	3	ver/dev	CsgD positively regulates the expression of adrA	378	This latter culture condition conceivably activates CsgD , which positively regulates the expression of the csg operons ( curli fimbriae ) and adrA ( Zakikhany et al. 2010 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	24735176	9	ver/dev	CsgD is essential for , among other things , biofilm matrix production by inducing curli cellulose production , via adrA .	412	CsgD is essential for , among other things , biofilm matrix production by inducing curli production ( via csgBAC regulation ) and cellulose production , via adrA ( see review by Steenac-kers et al. 2012 ) .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	24735176	9	ver/dev	CsgD is essential for , among other things , biofilm matrix production by inducing curli production -LRB- via csgBAC regulation -RRB- , via adrA .	412	CsgD is essential for , among other things , biofilm matrix production by inducing curli production ( via csgBAC regulation ) and cellulose production , via adrA ( see review by Steenac-kers et al. 2012 ) .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	25437188	4	ver/dev	CsgD also positively controls expression of the diguanylate cyclase AdrA by direct binding to the promoter region upstream of adrA .	112	CsgD also positively controls expression of the diguanylate cyclase AdrA by direct binding to the promoter region upstream of adrA [ 76,77 ] .	5	REGULATION OF THE RDAR PHENOTYPE IN S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	25437188	6	ver/dev	In contrast , CsgD activated adrA transcription only with RNA polymerase .	116	In contrast , CsgD activated adrA transcription only with RNA polymerase loaded with sigma factor RpoS ( Figure 2 ) [ 76 ] .	5	REGULATION OF THE RDAR PHENOTYPE IN S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	25437188	43	ver/dev	In contrast to the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .	525	In contrast to VpsT , the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA and csgBAC is unaffected by c-di-GMP in vitro [ 76 ] .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	Vibrio cholerae	0	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	activator	25437188	43	ver/dev	In contrast to the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .	525	In contrast to VpsT , the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA and csgBAC is unaffected by c-di-GMP in vitro [ 76 ] .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	Vibrio cholerae	0	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	activator	25437188	43	ver/dev	In contrast to VpsT , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .	525	In contrast to VpsT , the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA and csgBAC is unaffected by c-di-GMP in vitro [ 76 ] .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	activator	25437188	43	ver/dev	In contrast to VpsT , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .	525	In contrast to VpsT , the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA and csgBAC is unaffected by c-di-GMP in vitro [ 76 ] .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	activator	26655751	0	att	Cellulose production is initiated through CsgD-activated transcription of adrA ( 11 ) .	22	Cellulose production is initiated through CsgD-activated transcription of adrA ( 11 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	26880544	3	ver/dev	CsgD also activates expression of adrA , activating the cellulose biosynthetic operon bcsABZC .	64	CsgD also activates expression of adrA , increasing intracellular c-di-GMP levels , and activating the cellulose biosynthetic operon bcsABZC ( Zogaj et al. , 2001 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	26880544	3	ver/dev	CsgD also activates expression of adrA , increasing intracellular c-di-GMP levels .	64	CsgD also activates expression of adrA , increasing intracellular c-di-GMP levels , and activating the cellulose biosynthetic operon bcsABZC ( Zogaj et al. , 2001 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	29163440	1	ver/dev	Expression of the two biofilm-promoting factors is co-regulated , since the response regulator CsgD stimulates expression of both adrA .	179	Expression of the two biofilm-promoting factors is co-regulated , since the response regulator CsgD stimulates expression of both adrA and the genes coding for the structural curli subunits , csgBAC .	14	TRANSCRIPTIONAL EXPRESSION OF GENES INVOLVED IN CURLI AND CELLULOSE SYNTHESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	32307570	0	ver/dev	The CsgD protein also promotes cellulose production by inducing adrA gene transcription .	32	The CsgD protein also promotes cellulose production by inducing adrA gene transcription ( Brombacher et al. 2003 ; Zogaj et al. 2001 ; Gerstel and Römling 2003 ; García et al. 2004 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	32604994	6	ver/dev	In this manuscript , we analyzed the activity of CsgD through activation of csgBAC and cellulose production ( adrA ) .	62	In this manuscript , we analyzed the regulation of csgD transcription and the activity of CsgD through activation of curli biosynthesis ( csgBAC ) and cellulose production ( adrA ) .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	32604994	6	ver/dev	In this manuscript , we analyzed the activity of CsgD through activation of curli biosynthesis and cellulose production ( adrA ) .	62	In this manuscript , we analyzed the regulation of csgD transcription and the activity of CsgD through activation of curli biosynthesis ( csgBAC ) and cellulose production ( adrA ) .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	activator	32769186	0	ver/dev	In turn , CsgD activates expression of the diguanylate cyclase adrA .	188	In turn , CsgD activates expression of curli fimbriae and the diguanylate cyclase adrA , leading to an increase in cellular cyclic-di-GMP ( 34 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	activator	34368016	0	ver/dev	In Salmonella , the MlrA transcription factor promotes csgD transcription whose gene product CsgD stimulates both adrA .	49	In Salmonella , the MlrA transcription factor promotes csgD transcription whose gene product CsgD stimulates both adrA and curli genes ( Brown et al. , 2001 ) .	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	hilA	repressor	25375226	28	ver/dev	While the two single point mutations , significantly enhanced StpA 's silencing activity at the yciG promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While the two single point mutations , significantly enhanced StpA 's silencing activity at the ssrA promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While the two single point mutations , significantly enhanced StpA 's silencing activity at the proV promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While A77D , significantly enhanced StpA 's silencing activity at the yciG promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While A77D , significantly enhanced StpA 's silencing activity at the ssrA promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While A77D , significantly enhanced StpA 's silencing activity at the proV promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While M4T , significantly enhanced StpA 's silencing activity at the yciG promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While M4T , significantly enhanced StpA 's silencing activity at the ssrA promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
StpA	gene	hilA	repressor	25375226	28	ver/dev	While M4T , significantly enhanced StpA 's silencing activity at the proV promoters regions these substitutions did not provide increased repression of hilA .	401	While the two single point mutations , M4T and A77D , significantly enhanced StpA 's silencing activity at the proV , ssrA and yciG promoters regions these substitutions did not provide increased repression of hilA , encoding the SPI-1 transcriptional activator HilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
EmrR	gene	emrR	repressor	32514543	0	ver/dev	Our data indicate that in S. Typhi mutation of emrR conferred reduced susceptibility to ciprofloxacin , as would be expected if emrAB became overexpressed due to loss of repression by EmrR .	91	Our data indicate that in S. Typhi mutation of emrR conferred reduced susceptibility to ciprofloxacin ( Table 2 ) , as would be expected if emrAB became overexpressed due to loss of repression by EmrR .	13	EFFLUX AND PORIN GENES INVOLVED IN CIPROFLOXACIN SUSCEPTIBILITY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
InvF	gene	sopE	activator	15765064	6	ver/dev	InvF also activate transcription of sopE , found elsewhere on the chromosome .	59	InvF and SicA also activate transcription of sopB/sigD , and sopE , found elsewhere on the chromosome , that encode secreted effector proteins that enhance invasion ( Ahmer et al. , 1999 ; Darwin and Miller , 1999 ; Eichelberg and Galán , 1999 ; Darwin and Miller , 2000 ; Darwin and Miller , 2001 ) .	3	THE HILA REGULATOR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopE	activator	21320585	0	ver/dev	InvF induces the expression of sopE -LSB- 14e16 -RSB- .	42	InvF is required for the efficient invasion of Salmonella into host epithelial cells , and induces the expression of other genes involved in invasion , such as sipB , sipC , and sopE [ 14e16 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopE	activator	22291596	2	ver/dev	InvF activates expression of sopE .	597	InvF activates expression of effector genes inside SPI1 and also effector genes outside SPI-1 such as sopB and sopE [ 47 ] .	27	EXPRESSION OF SPI-1 AND SPI-2 TYPE 3 SECRETION SYSTEM REGULATORY GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopE	activator	25128737	0	ver/dev	Along with InvF , SicA is required for transcription activation of several virulence genes like sopE .	187	Along with InvF , SicA is required for transcription activation of several virulence genes like sigDE ( sopB , pipC ) , sipBCDA , and sopE ( Darwin et al. , 2001 ) .	19	3.3. THE FIVE INDIVIDUAL SPI AND COMBINED INTERACTOMES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	sapA	activator	18407759	0	att	Synthesis of vitamin-B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin ( enterochelin ) and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F ( sigma-28 ) factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR ( or CreC ) PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB ( OmpR family ) aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold-shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine-sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor ( Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	222	Synthesis of vitamin B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin ( enterochelin ) and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F ( sigma 28 ) factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR ( or CreC ) PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB ( OmpR family ) aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor ( Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	18	RESULTS AND DISCUSSION	Salmonella;Salmonella;Enterobacteria phage Ox2;Salmonella	0.5	L2	SPEC	Other	OTHER	Other	Level 1
FliZ	TU	flhDC	regulator	18469103	6	ver/dev	To test the hypothesis that FliZ may operate through FliT , we compared tetRA background to control for flhDC autoregulation -LRB- Fig. 4B -RRB- .	268	To test the hypothesis that FliZ may operate through FliT , we compared Pclass2 activity in fliZ , fliT , and fliZ fliT mutants in the PflhDC : : tetRA background to control for flhDC autoregulation ( Fig. 4B ) .	5	RESULTS	Triportheus paranensis	0	L2	SPEC	Analysis	OTHER	New	Level 1
FliZ	TU	flhDC	regulator	18469103	10	ver/dev	One possibility is that FliZ regulates flhDC transcription .	299	One possibility is that FliZ regulates flhDC transcription , resulting in an indirect effect on Pclass2 activity due to changes in FlhD4C2 expression .	5	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FliZ	TU	flhDC	regulator	18469103	17	ver/dev	In the related insect pathogen Xenorhabdus nematophila , FliZ was recently shown to bind to the flhDC promoter .	387	In the related insect pathogen Xenorhabdus nematophila , FliZ was recently shown to bind to the flhDC promoter and increase the rate of transcription ( 38 ) .	6	DISCUSSION	Xenorhabdus nematophila	0	L3	OTHER	Analysis	OTHER	Other	Level 2
FliZ	TU	flhDC	regulator	18469103	18	ver/dev	Likewise , our data show that FliZ is not a transcriptional regulator of the flhDC operon in S. enterica serovar Typhimurium , whereas it is in X. nematophila .	391	Likewise , our data show that FliZ is not a transcriptional regulator of the flhDC operon in S. enterica serovar Typhimurium , whereas it is in X. nematophila .	6	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	NEG	Other	Level 1
FliZ	TU	flhDC	regulator	30420601	2	ver/dev	However , regulation of flagellar gene expression in S. enterica via FliZ must take in to consideration its impact on flhDC gene expression9 ,28,29 .	317	However , regulation of flagellar gene expression in S. enterica via FliZ must take in to consideration other regulators such as HilD and its impact on flhDC gene expression9 ,28,29 .	4	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , others .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , a nutritional regulator .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , YdiV .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , a fimbrial regulator .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , FimZ .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	asd	regulator	22666539	0	ver/dev	In the resulting YB1 strain , the FNR related anaerobic capable promoter PpepT controls asd transcription while PsodA , facilitates transcription of antisense asd .	47	In the resulting YB1 strain , the FNR related anaerobic capable promoter PpepT controls asd transcription while an aerobic promoter , PsodA , facilitates transcription of antisense asd that blocks any leakage of asd expression under aerobic conditions ( Fig. 1a ) .	1	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
FNR	gene	asd	regulator	22666539	0	ver/dev	In the resulting YB1 strain , the FNR related anaerobic capable promoter PpepT controls asd transcription while an aerobic promoter , facilitates transcription of antisense asd .	47	In the resulting YB1 strain , the FNR related anaerobic capable promoter PpepT controls asd transcription while an aerobic promoter , PsodA , facilitates transcription of antisense asd that blocks any leakage of asd expression under aerobic conditions ( Fig. 1a ) .	1	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
LexA	gene	sulA	repressor	28874380	2	att	A LexA-repressed gene , sulA , is not constitutively expressed , allowing detection of SOS response activation .	129	A LexA-repressed gene , sulA , is not constitutively expressed , allowing detection of SOS response activation .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	hilC	activator	16045614	1	ver/dev	that HilD are each capable of independently inducing expression of the hilC genes	14	We demonstrate that HilC , HilD and RtsA are each capable of independently inducing expression of the hilC , hilD and rtsA genes , and that each can independently activate hilA .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	activator	16045614	20	ver/dev	We demonstrate that HilD are each capable of inducing expression of hilC .	82	We demonstrate that HilC , HilD and RtsA are each capable of inducing expression of hilC , hilD and rtsA .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilC	activator	16045614	21	ver/dev	HilD can independently induce expression of hilC	85	HilC , HilD and RtsA can independently induce expression of hilC , hilD and rtsA	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilC	activator	16045614	24	ver/dev	We wanted to determine if HilD could induce expression of hilC in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	hilC	activator	16045614	28	ver/dev	HilD also induced expression of hilC .	131	RtsA , HilC and HilD also induced expression of hilC , hilD and rtsA ( Fig. 2 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilC	activator	16045614	29	ver/dev	HilD induced expression of hilC approximately threeto fourfold 12-fold .	133	RtsA , HilC and HilD induced expression of hilC approximately threeto fourfold and hilD ~ 10 - to 12-fold .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilC	activator	16045614	30	ver/dev	These data show that HilD are each capable of independently inducing expression of hilC , consistent with our model that HilD constitute a feed forward regulatory loop .	134	These data show that HilC , HilD and RtsA are each capable of independently inducing expression of hilC , hilD and rtsA , consistent with our model that HilC , HilD and RtsA constitute a feed forward regulatory loop ( Fig. 1 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	activator	16045614	69	ver/dev	We show that HilD can each independently activate expression of the hilC genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilC	activator	17993530	6	ver/dev	HilD are all also capable of activating expression of hilC independent of each other and comprise a complex feed forward regulatory loop .	39	HilC , HilD , and RtsA are all also capable of activating expression of hilC , hilD , and rtsA independent of each other and comprise a complex feed forward regulatory loop that controls hilA expression ( Fig. 1 ) ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD is consistent with our model for SPI1 regulation ; transcription of hilC were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD be present ; transcription of hilC were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilC	activator	22479568	0	ver/dev	HilD can activate expression of hilC of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilC	activator	25991823	14	att	For this purpose , we analyzed the effect of L-arabinose on the expression of three HilD-activated genes ( hilC , rtsA , and invH ) .	249	For this purpose , we analyzed the effect of L-arabinose on the expression of three HilD-activated genes ( hilC , rtsA , and invH ) .	14	L-ARABINOSE-DEPENDENT REPRESSION OF SPI-1 IS TRANSMITTED VIA HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	activator	25991823	2	ver/dev	Furthermore , HilD activates transcription of hilC and of hilD itself by direct binding to both promoters .	26	Furthermore , HilD activates transcription of hilC and of hilD itself ( Ellermeier et al. 2005 ) by direct binding to both promoters ( Olekhnovich and Kadner 2002 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilC	activator	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilC	activator	32041797	4	ver/dev	Thus , HilD acts as a switch to initiate activation of hilC .	43	Thus , HilD acts as a switch to integrate environmental cues and initiate activation of hilC , rtsA , and hilA expression .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilC	activator	32041797	5	ver/dev	The AraC-like proteins HilD activate transcription of hilC , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	soxS	regulator	19917752	0	ver/dev	SoxS _ regulated , including soxS itself	266	Among the genes that were upregulated in 104-cip , a number were SoxS regulated , including acnA , fpr , ribA , sodA , lpxC , and soxS itself .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	soxS	regulator	24858080	9	att	In our experiments , we observed a marked upregulation of soxS in the presence of CuSO4 in SLB , but no induction of any known SoxS-controlled genes ( Fig. 1b , Table S3 ) .	296	In our experiments , we observed a marked upregulation of soxS in the presence of CuSO4 in SLB , but no induction of any known SoxS-controlled genes ( Fig. 1b , Table S3 ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	fliC	activator	11681212	2	ver/dev	These results suggest that activation of the PhoP system indirectly represses the transcription of fliC too .	224	These results suggest that activation of the PhoP system directly or indirectly represses the transcription of fliC and possibly other classes of flagellar genes too .	21	3.7 PHOPQ REPRESSES TRANSCRIPTION OF THE CLASS 3 FLAGELLAR GENE FLIC WHEREAS RPOS MILDLY INDUCES IT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	fliC	activator	11681212	2	ver/dev	These results suggest that activation of the PhoP system directly represses the transcription of fliC too .	224	These results suggest that activation of the PhoP system directly or indirectly represses the transcription of fliC and possibly other classes of flagellar genes too .	21	3.7 PHOPQ REPRESSES TRANSCRIPTION OF THE CLASS 3 FLAGELLAR GENE FLIC WHEREAS RPOS MILDLY INDUCES IT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	fliC	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in sopE229 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in sopE , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in sopF28 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in SPI-527 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in sopE229 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in sopE , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in sopF28 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	siiB	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in SPI-527 , encoding for T3SS-1 effectors , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CpxR	TU	tatABC	regulator	30716090	33	ver/dev	To investigate the binding of CpxR to the tatABC promoter region , the CpxR recognition motif was subjected to DNase I footprint analysis .	381	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment including the CpxR recognition motif was subjected to DNase I footprint analysis ( Fig 7A and 7B ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	TU	tatABC	regulator	30716090	33	ver/dev	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment was subjected to DNase I footprint analysis .	381	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment including the CpxR recognition motif was subjected to DNase I footprint analysis ( Fig 7A and 7B ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	TU	tatABC	regulator	30716090	33	ver/dev	To investigate the binding of CpxR to the tatABC promoter region , the CpxR recognition motif was subjected to 7B .	381	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment including the CpxR recognition motif was subjected to DNase I footprint analysis ( Fig 7A and 7B ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	Terfezia eliocrocae	0	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	TU	tatABC	regulator	30716090	33	ver/dev	To investigate the binding of CpxR to the tatABC promoter region , the CpxR recognition motif was subjected to Fig 7A .	381	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment including the CpxR recognition motif was subjected to DNase I footprint analysis ( Fig 7A and 7B ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	TU	tatABC	regulator	30716090	33	ver/dev	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment was subjected to 7B .	381	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment including the CpxR recognition motif was subjected to DNase I footprint analysis ( Fig 7A and 7B ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	Terfezia eliocrocae	0	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	TU	tatABC	regulator	30716090	33	ver/dev	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment was subjected to Fig 7A .	381	To investigate the binding of CpxR to the tatABC promoter region , a 250 bp DIG-labelled DNA fragment including the CpxR recognition motif was subjected to DNase I footprint analysis ( Fig 7A and 7B ) .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1697	activator	25437188	40	ver/dev	Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .	446	Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1697	activator	25437188	40	ver/dev	Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .	446	Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DgoR	gene	dgoT	activator	23483857	0	ver/dev	Furthermore , increasing the level of DgoR by providing the corresponding gene on pFPV-dgoR was able to abolish induction of dgoT : : MudK by P22 wt , but had no obvious effect on phage infection per se .	48	Furthermore , increasing the level of DgoR by providing the corresponding gene on a multicopy plasmid ( pFPV-dgoR ) was able to abolish induction of dgoT : : MudK by P22 wt , but had no obvious effect on phage infection per se ( Figure 2C ) .	6	MUDK OF LT2K7 MAPS TO THE DGOT GENE	Salmonella virus P22	1	L2	OTHER	Analysis	NEG	Other	Level 1
DgoR	gene	dgoT	activator	23483857	0	ver/dev	Furthermore , increasing the level of DgoR by providing the corresponding gene on a multicopy plasmid was able to abolish induction of dgoT : : MudK by P22 wt , but had no obvious effect on phage infection per se .	48	Furthermore , increasing the level of DgoR by providing the corresponding gene on a multicopy plasmid ( pFPV-dgoR ) was able to abolish induction of dgoT : : MudK by P22 wt , but had no obvious effect on phage infection per se ( Figure 2C ) .	6	MUDK OF LT2K7 MAPS TO THE DGOT GENE	unidentified plasmid;Salmonella virus P22	1	L2	OTHER	Analysis	NEG	Other	Level 1
Fur	gene	fhuA	activator	27564394	17	att	STnc3250 is intergenic and transcribed divergently from fhuA , which is the first gene in a Fur-dependent operon that encodes ferrichrome-iron associated proteins .	465	STnc3250 is intergenic and transcribed divergently from fhuA , which is the first gene in a Fur-dependent operon that encodes ferrichrome-iron associated proteins .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	iroB	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	iroB	regulator	14633100	2	att	Fur-regulated gene ( iroB )	90	Fur-regulated gene ( iroB )	5	PRIMER PAIR TARGET PRIMER SEQUENCE (5¢ FI 3¢)* ANNEALING CYCLES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	iroB	regulator	14633100	3	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	190	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	iroB	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	araC	activator	24272778	43	att	Unlike AraC-dependent repression of araC and ytfQ , repression of ydeN occurs only in the presence of arabinose ( Table 2 and Fig. 3 ) .	410	Unlike AraC-dependent repression of araC and ytfQ , repression of ydeN occurs only in the presence of arabinose ( Table 2 and Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	araC	activator	24272778	5	att	These targets include two araC ) and AMD115 were constructed by P1 transduction of the Kanr-novel , cotranscribed , AraC-activated genes ( and linked araC from BW25113 araC ( 17 ) into MG1655 and AMD054 , ) that encode a putative arabinoside transporter and respectively .	83	These targets include two araC ) and AMD115 were constructed by P1 transduction of the Kanr-novel , cotranscribed , AraC-activated genes ( STM14_0178 and linked araC from BW25113 araC ( 17 ) into MG1655 and AMD054 , STM14_0177 ) that encode a putative arabinoside transporter and respectively .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoB	gene	mgtC	activator	31346161	8	att	We speculated that such an increase in the mRNA levels of the PhoB / PhoR-controlled genes during infection might be due to the presence of the MgtC protein because the mgtC gene is one of the most highly expressed genes inside macrophages18 , and also because MgtC activates PhoR autophosphorylation to promote PhoB-dependent gene expression ( Figs. 1 and 4 ) .	289	We speculated that such an increase in the mRNA levels of the PhoB / PhoR-controlled genes during infection might be due to the presence of the MgtC protein because the mgtC gene is one of the most highly expressed genes inside macrophages18 , and also because MgtC activates PhoR autophosphorylation to promote PhoB-dependent gene expression ( Figs. 1 and 4 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Sigma32	gene	opdA	activator	10629202	0	att	The opdA operon is a s32-dependent heat-shock operon .	25	The opdA operon is a s32-dependent heat shock operon .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma32	gene	opdA	activator	10629202	1	att	A near-consensus s32-dependent promoter sequence is present upstream from the start of translation of opdA ( Fig. 3 ) ( 2 , 4 ) .	26	A near-consensus s32-dependent promoter sequence is present upstream from the start of translation of opdA ( Fig. 3 ) ( 2 , 4 ) .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with tRNA hydroxylase STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with tRNA hydroxylase STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with miaE STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with first gene of a putative operon with miaE STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with tRNA hydroxylase STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with tRNA hydroxylase STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with miaE STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with arginine ornithine transferase with miaE STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with tRNA hydroxylase STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with tRNA hydroxylase STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with miaE STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with putative inner membrane protein	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	STM1631	regulator	14759259	7	ver/dev	-LRB- SW : -RRB- putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI with miaE STM1631 secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630	442	( SW : YJGD_SALTY ) putative cytoplasmic protein ; Putative binding site for ArgR ; shared intergenic regions with argI ( arginine ornithine transferase ) ; first gene of a putative operon with miaE ( tRNA hydroxylase ) STM1631 ; S. typhimurium secreted effector ; regulated by SPI-2 ; shared intergenic with STM1630 ( putative inner membrane protein )	6	IDENTIFICATION OF CLOSE HOMOLOGS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsB	TU	flhDC	repressor	16045614	5	ver/dev	RtsB negatively regulates flhDC	41	HilC and HilD are encoded within SPI1 , whereas RtsA is encoded in an operon at 93.9 centisomes that also encodes RtsB , which negatively regulates flhDC and hence the flagellar regulon ( Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsB	TU	flhDC	repressor	16045614	5	ver/dev	RtsB negatively regulates flhDC	41	HilC and HilD are encoded within SPI1 , whereas RtsA is encoded in an operon at 93.9 centisomes that also encodes RtsB , which negatively regulates flhDC and hence the flagellar regulon ( Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsB	TU	flhDC	repressor	17993530	4	ver/dev	RtsB negatively regulates expression of flhDC .	37	RtsB negatively regulates expression of flhDC and therefore the entire flagellar regulon ( 18 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsB	TU	flhDC	repressor	24706743	9	ver/dev	RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon .	255	One HilD-activated gene product , RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon ( 49 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsB	TU	flhDC	repressor	26561851	5	ver/dev	In turn , RtsB represses the flhDC promoter .	210	In turn , RtsB represses the flhDC promoter [ 57 ] .	8	RELATING INTRA-MACROPHAGE GENE EXPRESSION TO GENE FUNCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsB	TU	flhDC	repressor	31262841	12	ver/dev	We have previously shown that RtsB regulates flagellar gene expression by repressing the transcription of flhDC , encoding the master regulator of the flagellar regulon .	180	We have previously shown that RtsB regulates flagellar gene expression by repressing the transcription of flhDC , encoding the master regulator of the flagellar regulon ( 19 , 70 , 71 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsB	TU	flhDC	repressor	31262841	16	ver/dev	Certainly , under the conditions , the negative effect of PinT on flhDC transcription via CRP seems to outweigh the repression of RtsB .	274	Certainly , under the conditions used in this study , the negative effect of PinT on flhDC transcription via CRP seems to outweigh the repression of RtsB .	5	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	New	Level 1
LysR	gene	ompS1	regulator	17908208	56	ver/dev	a regulator of the LysR family , was found to be a positive effector of the ompS1 gene in Salmonella .	238	LeuO , a regulator of the LysR family , was found to be a positive effector of the ompS1 gene in Salmonella .	13	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	regulator	17158330	15	att	mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .	158	mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .	10	REFERENCES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagD	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagD	regulator	30373755	8	att	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	regulator	30967459	12	ver/dev	In vitro binding of PhoP to the pagD promoter with or without EIIANtr .	168	( B ) In vitro binding of PhoP to the pagD promoter with or without EIIANtr .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagD	regulator	30967459	15	ver/dev	Purified PhoP bound to the pagD promoter DNA Fig. 4B .	172	Purified PhoP bound to the pagD promoter DNA and formed a complex with the probe DNA in vitro ( Fig. 4B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagD	regulator	30967459	15	ver/dev	Purified PhoP bound to the pagD promoter DNA in-vitro .	172	Purified PhoP bound to the pagD promoter DNA and formed a complex with the probe DNA in vitro ( Fig. 4B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	csgD	regulator	16313619	2	att	In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 : : csgD ] , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of its own promoter , which exclusively activates cellulose	169	In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 : : csgD ] , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of its own promoter , which exclusively activates cellulose	8	RELATIONSHIP BETWEEN BAPA AND OTHER COMPONENTS OF THE BIOFILM MATRIX	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	csgD	regulator	19376870	15	ver/dev	To investigate on which level the regulation of CsgD expression occurs , the transcription of csgD was measured by real-time RT-PCR analysis .	258	To investigate on which level the regulation of CsgD expression occurs , the transcription of csgD was measured by real-time RT-PCR analysis .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgD	regulator	23443158	14	att	Group III is represented by OmrA/B , which by binding directly to flhDC and csgD mRNA [ 62,75 ] , can down-regulate both motility and the expression of CsgD-controlled curli fibres and cellulose .	169	Group III is represented by OmrA/B , which by binding directly to flhDC and csgD mRNA [ 62,75 ] , can down-regulate both motility and the expression of CsgD-controlled curli fibres and cellulose .	6	3. SRNAS CONTRIBUTE TO INVERSE REGULATION OF FLAGELLA AND BIOFILM COMPONENTS IN DIFFERENT REGULATORY PATTERNS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	26655751	7	ver/dev	Alternatively , the leaf persistence competition defect of the STM4264 mutant may be unrelated to the regulation of CsgD since the csgD mutant had no defect in the phyllosphere .	391	Alternatively , the leaf persistence competition defect of the STM4264 mutant may be unrelated to the regulation of CsgD since the csgD mutant had no defect in the phyllosphere .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	csgD	regulator	27260360	2	ver/dev	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD , coding for curli fimbria production , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	315	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD and csgB , coding for curli fimbria production , and adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	csgD	regulator	30936374	2	auto	CsgD did not regulate its own expression , in accordance with previous reports ( 17 ) , as high expression of the csgDEFG genes was observed in M9 plus glucose in a csgD mutant background ( Fig. 4c and d ) .	129	CsgD did not regulate its own expression , in accordance with previous reports ( 17 ) , as high expression of the csgDEFG genes was observed in M9 plus glucose in a csgD mutant background ( Fig. 4c and d ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	csgD	regulator	31233504	10	att	Therefore , any increases in csgD transcription , which can be caused by known promoter mutations [ 16,24 ] or potentially host-related environmental signals such as iron limitation [ 16 ] or the presence of human bile [ 37 ] , may be enough to restore CsgD-regulated biofilm phenotypes in S. Typhi .	303	Therefore , any increases in csgD transcription , which can be caused by known promoter mutations [ 16,24 ] or potentially host-related environmental signals such as iron limitation [ 16 ] or the presence of human bile [ 37 ] , may be enough to restore CsgD-regulated biofilm phenotypes in S. Typhi .	16	FOR SALMONELLA SEROVAR TYPHI, WE SHOWED THAT A PREMATURE STOP CODON, RESULTING IN LOSS OF	Homo sapiens;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L1	SPEC	Fact	OTHER	Other	Level 1
CsgD	gene	csgD	regulator	31233504	5	att	This experiment showed that the SNP at the 3 ' end of csgD was sufficient to disrupt CsgD-regulated biofilm phenotypes in S. Ty CT18 .	248	This experiment showed that the SNP at the 3 ' end of csgD was sufficient to disrupt CsgD-regulated biofilm phenotypes in S. Ty CT18 .	13	CONSERVATION OF BIOFILM-ALTERING SNPS IN INVASIVE LINEAGES OF S. TYPHIMURIUM AND S. ENTERITIDIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgD	regulator	31233504	9	att	Conservation of the csgD promoter SNP in all 167 strains of the Central/East African clade of S. Enteritidis from sub-Saharan Africa , and lack of the SNP in 250 ` global ' S. Enteritidis isolates , is strong evidence that loss of this CsgD-regulated biofilm phenotype has being selectively maintained in the invasive population since the most recent common ancestor , circa 1945 [ 10 ] .	284	Conservation of the csgD promoter SNP in all 167 strains of the Central/East African clade of S. Enteritidis from sub-Saharan Africa , and lack of the SNP in 250 ` global ' S. Enteritidis isolates , is strong evidence that loss of this CsgD-regulated biofilm phenotype has being selectively maintained in the invasive population since the most recent common ancestor , circa 1945 [ 10 ] .	15	DISCUSSION	Salmonella;Salmonella	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RcsB	gene	rflM	activator	27206164	24	att	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma70	gene	invF	activator	11466291	1	att	HilA behaves as a repressor when the HilA box from invF is cloned between the 235 and 210 hexamers of a s70-dependent promoter ( -35 INVWT-10 ) .	177	HilA behaves as a repressor when the HilA box from invF is cloned between the 235 and 210 hexamers of a s70-dependent promoter ( -35 INVWT-10 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	cspH	repressor	15235764	20	ver/dev	This might explain the inhibition of cspH expression by gyrase inhibitor , i.e. a reduction of Fis levels and a decrease in the superhelical density of the cspH promoter .	184	This might explain the inhibition of cspH expression by gyrase inhibitor , i.e. a reduction of Fis levels and a decrease in the superhelical density of the cspH promoter .	17	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	mcpC	repressor	33441540	0	ver/dev	Expression of mcpC is repressed by the universal regulator H-NS .	15	Expression of mcpC is repressed by the universal regulator H-NS , which can be displaced by HilD .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	pstS	regulator	26386064	0	ver/dev	the former _ being regulated by a promoter located upstream of the pstS gene regulated by PhoB	148	Both operons have been shown to be induced under phosphate starvation conditions , with the former being regulated by a promoter located upstream of the pstS gene and the latter regulated by RpoS , PhoB , and CRP ( 16 , 17 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	pstS	regulator	26386064	0	ver/dev	the former _ being regulated by a promoter located upstream of the pstS gene regulated by PhoB	148	Both operons have been shown to be induced under phosphate starvation conditions , with the former being regulated by a promoter located upstream of the pstS gene and the latter regulated by RpoS , PhoB , and CRP ( 16 , 17 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	TU	aceEF	regulator	20851888	6	ver/dev	aceEF , , do not appear to be regulated by DksA .	179	Several other genes of the pentose phosphate pathway , glycolysis , and tricarboxylic acid cycle such as gnd , aceEF , and mdh , which are also associated with production of reductive power , do not appear to be regulated by DksA .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
RpoS	gene	fliC	repressor	27564394	15	ver/dev	fliC expression decreases in the absence of RpoS .	392	fliC expression decreases in the absence of RpoS [ 63 ] .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	repressor	10844688	18	ver/dev	If a condition exists in which hilA is repressed while invF expression is induced through HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilA	repressor	11755416	22	ver/dev	Loss of hns , however , does not relieve repression of hilA by oxygen -LRB- as opposed to osmolarity -RRB- and expression of hilA in an hns mutant still requires HilD under inducing -LRB- high-osmolarity , low oxygen -RRB- growth-conditions .	262	Loss of hns , however , does not relieve repression of hilA by oxygen ( as opposed to osmolarity ) and expression of hilA in an hns mutant still requires HilD under inducing ( high osmolarity , low oxygen ) growth conditions ( L. Schechter and C. Lee , unpublished observations ) .	8	6. P AS A LOCUS OF SIGNAL INTEGRATION HILA	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	11755416	22	ver/dev	Loss of hns , however , does not relieve repression of hilA by oxygen -LRB- as opposed to osmolarity -RRB- and expression of hilA in an hns mutant still requires HilD under inducing L. C. Lee , unpublished observations .	262	Loss of hns , however , does not relieve repression of hilA by oxygen ( as opposed to osmolarity ) and expression of hilA in an hns mutant still requires HilD under inducing ( high osmolarity , low oxygen ) growth conditions ( L. Schechter and C. Lee , unpublished observations ) .	8	6. P AS A LOCUS OF SIGNAL INTEGRATION HILA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	hilA	repressor	11755416	22	ver/dev	Loss of hns , however , does not relieve repression of hilA by oxygen -LRB- as opposed to osmolarity -RRB- and expression of hilA in an hns mutant still requires HilD under inducing L. Schechter Lee , unpublished observations .	262	Loss of hns , however , does not relieve repression of hilA by oxygen ( as opposed to osmolarity ) and expression of hilA in an hns mutant still requires HilD under inducing ( high osmolarity , low oxygen ) growth conditions ( L. Schechter and C. Lee , unpublished observations ) .	8	6. P AS A LOCUS OF SIGNAL INTEGRATION HILA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	hilA	repressor	15765064	30	ver/dev	This finding suggests that HilE functions as a repressor by binding to HilD to prevent its activation of the hilA promoter .	160	This finding suggests that HilE functions as a repressor by binding to HilD to prevent its activation of the hilA promoter .	7	NEGATIVE REGULATORS OF INVASION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	repressor	17993530	54	ver/dev	For example , hilA expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	363	For example , hilA expression , rtsA expression , and hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilA	repressor	20008574	1	ver/dev	Transcriptional activation by HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha .	36	Transcriptional activation by HilC and HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	repressor	25991823	1	ver/dev	HilD relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha .	25	HilC and HilD relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) and can activate expression of the invF and sicA/sip transcriptional units independently of HilA ( Rakeman et al. 1999 ; Akbar et al. 2003 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	repressor	27185788	15	ver/dev	Coincident with this reduction in HilD protein , hilA = was potently repressed by 9.7-fold repression .	246	Coincident with this reduction in HilD protein , hilA = - lacZ expression was potently repressed by bile ( 9.7-fold repression ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	repressor	27185788	15	ver/dev	Coincident with this reduction in HilD protein , hilA = was potently repressed by bile .	246	Coincident with this reduction in HilD protein , hilA = - lacZ expression was potently repressed by bile ( 9.7-fold repression ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	repressor	28335027	10	ver/dev	H-NS repression of hilA counteracts transcriptional activation by HilD	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including repression of hilA by preventing HilD function .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including repression of hilA by binding to .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
HilD	gene	hilA	repressor	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of rtsA .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilA	repressor	31428589	15	ver/dev	a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression through the degradation of HilD .	202	Lon protease , a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression and intracellular survival after the invasion of epithelial cells through the degradation of HilC and HilD ( Boddicker and Jones , 2004 ; Takaya et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilA	repressor	31428589	15	ver/dev	Lon protease , is important for the downregulation of hilA expression through the degradation of HilD .	202	Lon protease , a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression and intracellular survival after the invasion of epithelial cells through the degradation of HilC and HilD ( Boddicker and Jones , 2004 ; Takaya et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	repressor	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
RcsAB	gene	rcsB	regulator	27558204	2	att	Microarray analyses of rcsB - and / or rcsB rcsA-dependent changes in genes expression in S. enterica , E. coli and Erwinia amylovora identified dozens of genes that are directly or indirectly controlled by these regulators ( Wang et al. , 2007 ; 2012 ) To determine which members of the Rcs regulon contribute to persistence within tomatoes , we chose a two-pronged approach : we first defined a set of likely direct RcsAB targets , and then que-ried results of a recently completed high-throughput screen of transposon-tagged Salmonella mutants ( de Moraes et al. , submitted ) to determine which of the RcsAB-regulated genes contribute to the reduced fitness of the	95	Microarray analyses of rcsB - and / or rcsB rcsA-dependent changes in genes expression in S. enterica , E. coli and Erwinia amylovora identified dozens of genes that are directly or indirectly controlled by these regulators ( Wang et al. , 2007 ; 2012 ) To determine which members of the Rcs regulon contribute to persistence within tomatoes , we chose a two-pronged approach : we first defined a set of likely direct RcsAB targets , and then que-ried results of a recently completed high-throughput screen of transposon-tagged Salmonella mutants ( de Moraes et al. , submitted ) to determine which of the RcsAB-regulated genes contribute to the reduced fitness of the	8	KNOWN AND PREVIOUSLY UNCHARACTERIZED MEMBERS OF THE RCS REGULON CONTRIBUTE TO PERSISTENCE WITHIN TOMATOES	Salmonella;Salmonella;Escherichia coli;Erwinia amylovora;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrF	regulator	19076233	6	att	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	138	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	14	INACTIVATION OF RPON INDUCES PM RESISTANCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	leuO	activator	24354910	3	ver/dev	Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions .	27	Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions that impair H-NS-mediated silencing .	7	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sopE	regulator	10844688	9	ver/dev	For example , sopE seem to be regulated directly by InvF through modulation of invF expression .	273	For example , sopE and sopB seem to be regulated directly by InvF and indirectly by HilA through modulation of invF expression ( Darwin and Miller , 1999b ; Eichelberg and GalaÂn , 1999 ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Other	OTHER	New	Level 1
InvF	gene	sopE	regulator	15567133	0	ver/dev	Expression of sopE is controlled by the SPI-1-encoded proteins InvF and SicA .	241	Expression of sopE is controlled by the SPI-1-encoded proteins InvF and SicA ( Eichelberg and Galan , 1999 ; Darwin and Miller , 2000 ; Tucker and Galan , 2000 ) .	25	8. INTEGRATION OF THE MORON-ENCODED GENE SOPE INTO THE TTSS NETWORK	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopE	regulator	28887382	0	ver/dev	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of sopE .	258	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of SPI-1 T3SS genes such as sopB , sicA and sopE ( 35 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopE	regulator	28887382	0	ver/dev	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of sopE .	258	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of SPI-1 T3SS genes such as sopB , sicA and sopE ( 35 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopE	regulator	31428589	0	ver/dev	sopE are regulated cooperatively by InvF .	125	sopA , sopB , and sopE are regulated cooperatively by HilA and InvF ( Thijs et al. , 2007 ) .	3	THE ROLE OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of RpoS to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of RpoS to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	proV	repressor	23515315	40	ver/dev	We identified a mutation in the N-terminal dimerization domain of I11A / H-NS interaction while retaining other properties of H-NS required for normal repression of the proV locus .	354	We identified a mutation in the N-terminal dimerization domain of H-NS ( I11A ) that abolishes the Hha / H-NS interaction while retaining other properties of H-NS required for normal repression of the proV locus .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	proV	repressor	23515315	40	ver/dev	We identified a mutation in the N-terminal dimerization domain of H-NS / H-NS interaction while retaining other properties of H-NS required for normal repression of the proV locus .	354	We identified a mutation in the N-terminal dimerization domain of H-NS ( I11A ) that abolishes the Hha / H-NS interaction while retaining other properties of H-NS required for normal repression of the proV locus .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	proV	repressor	27564394	18	ver/dev	The proV promoter were used as negative control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FNR	gene	fnr	activator	16495536	4	att	In particular , we generated a mutant lacking the global anaerobiosis regulator fnr to test the combined relevance of several identified Fnr-dependent genes associated with anaerobic respiration and mixed acid fermentation that were selectively expressed during enteritis .	309	In particular , we generated a mutant lacking the global anaerobiosis regulator fnr to test the combined relevance of several identified Fnr-dependent genes associated with anaerobic respiration and mixed acid fermentation that were selectively expressed during enteritis .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	fnr	activator	28575106	13	ver/dev	Our study showed that Fnr , is not involved in the low O2-induced LoiA-mediated activation of SPI-1 genes as the expression of loiA was not affected by the deletion of fnr .	305	Our study showed that Fnr , another well-known global regulator that senses and responds to O2 limitation , is not involved in the low O2-induced LoiA-mediated activation of SPI-1 genes as the expression of loiA was not affected by the deletion of fnr .	13	DISCUSSION	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
PhoP	gene	phoQ	regulator	14507376	2	att	PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl . ) .	126	PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl . ) .	6	TRANSCRIPTIONAL PROFILING INDICATES ACTIVATION OF THE PHOP AND RPOS REGULONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoQ	regulator	14742517	4	ver/dev	Transcriptional regulation of Salmonella virulence -- a phoQ periplasmic domain mutation results in increased net phosphotransfer to PhoP .	334	Transcriptional regulation of Salmonella virulence -- a phoQ periplasmic domain mutation results in increased net phosphotransfer to PhoP .	14	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoQ	regulator	15208313	7	att	The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .	30	The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoQ	regulator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	phoQ	regulator	17158330	13	ver/dev	that harbored a plasmid with the phoQ genes under the control of a derivative of the lac promoter because a strain with a chromosomal phoQ mutation would constitutively activate the PhoP protein	91	We used strains in which the chromosomal copy of the phoPQ operon had been deleted and that harbored a plasmid with the phoP-HA and phoQ genes under the control of a derivative of the lac promoter ( 14 ) because a strain with a chromosomal phoQ mutation encoding a phosphatase-defective PhoQ would constitutively activate the PhoP protein .	5	MAIN	unidentified plasmid	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	phoQ	regulator	17158330	13	ver/dev	that harbored a plasmid with the phoP-HA genes under the control of a derivative of the lac promoter because a strain with a chromosomal phoQ mutation would constitutively activate the PhoP protein	91	We used strains in which the chromosomal copy of the phoPQ operon had been deleted and that harbored a plasmid with the phoP-HA and phoQ genes under the control of a derivative of the lac promoter ( 14 ) because a strain with a chromosomal phoQ mutation encoding a phosphatase-defective PhoQ would constitutively activate the PhoP protein .	5	MAIN	unidentified plasmid	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	phoQ	regulator	31182495	7	att	Therefore , PhoPQ repression of hilA was demonstrated using an allele of phoQ , phoQ24 , which has been shown to have a reduced sensitivity to Ca2 and activates PhoP-regulated genes in an essentially constitutive manner ( 44 , 51 ) .	61	Therefore , PhoPQ repression of hilA was demonstrated using an allele of phoQ , phoQ24 , which has been shown to have a reduced sensitivity to Ca2 and activates PhoP-regulated genes in an essentially constitutive manner ( 44 , 51 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	acrB	activator	28874380	1	ver/dev	that CRP activates expression of acrB in stationary-phase	114	These data suggest that CRP activates expression of acrB in stationary phase and that upregulation of the AcrAB efflux pump may contribute to the ciprofloxacin resistance of SL1344 : Δcrp .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	lacZ	activator	19091955	9	att	The up-52 fragment in pYS1033 controls lacZ expression in a SlyA-dependent manner because - galactosidase activity is 4.7-fold lower in the slyA mutant than in wild type ( Fig. 1C ) .	68	The up-52 fragment in pYS1033 controls lacZ expression in a SlyA-dependent manner because - galactosidase activity is 4.7-fold lower in the slyA mutant than in wild type ( Fig. 1C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	pduA	repressor	33853321	0	ver/dev	.24 This CRP-dependent regulation mediates the catabolite-repression of pdu genes _ resulting in a decrease of pduA expression as the glucose concentration increased	104	This is probably because a lack of CRP reduced pdu expression ( Figure 2B , C ) , consistent with the previous report .24 This CRP-dependent regulation mediates the catabolite repression of pdu genes , resulting in a decrease of pduA expression as the glucose concentration increased ( Figure 2B ) .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	10844687	0	ver/dev	Recent work by Lee et al. revealed that the expression of ssrAB itself is regulated by OmpR ± Env .	127	Recent work by Lee et al. ( 2000 ) revealed that the expression of ssrAB itself is regulated by OmpR ± EnvZ , another two-component system with global regulatory function .	14	THE ROLE OF THE SSRAB SYSTEM FOR EXPRESSION OF SPI2 GENES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	12068808	47	ver/dev	Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	236	Consistent with OmpR being an acid-induced regulator important to Salmonella pathogenicity , Lee et al. ( 2000 ) have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	12080060	47	ver/dev	Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	236	Consistent with OmpR being an acid-induced regulator important to Salmonella pathogenicity , Lee et al. ( 2000 ) have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	12949164	0	ver/dev	turn _ regulated by the OmpR -- EnvZ two-component system , by direct binding of OmpR to the ssrAB promoter	13	The expression of SsrA -- B is in turn regulated by the OmpR -- EnvZ two-component system , by direct binding of OmpR to the ssrAB promoter .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	12949164	0	ver/dev	turn _ regulated by the OmpR -- EnvZ two-component system , by direct binding of OmpR to the ssrAB promoter	13	The expression of SsrA -- B is in turn regulated by the OmpR -- EnvZ two-component system , by direct binding of OmpR to the ssrAB promoter .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	12949164	1	ver/dev	OmpR binds directly to the ssrAB promoter .	45	OmpR binds directly to the ssrAB promoter ( Lee et al. , 2000 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	12949164	6	ver/dev	These results indicate that other than ssrAB , is not a result of direct binding of OmpR to their promoters .	583	These results indicate that the effect of OmpR -- EnvZ on the expression of SPI-2 genes , other than ssrAB , is not a result of direct binding of OmpR to their promoters but is indirect , probably as a consequence of its binding to the ssrAB promoter ( Lee et al. , 2000 ) .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to cation chelation .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to cation chelation .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to acidic pH .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to acidic pH .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to low-osmolarity .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	16777370	4	ver/dev	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to low-osmolarity .	27	The regulation of ssrAB by OmpR-EnvZ two-component system through a direct binding of phosphorylated OmpR to the ssrAB promoter has been analyzed extensively to investigate the transcriptional activation pathway of SPI2 in response to several environmental signals such as low osmolarity , acidic pH , and cation chelation , which are known to promote SPI2 gene expression [ 11 -- 15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	19609351	1	ver/dev	OmpR is also known to interact with the endogenous two-component regulator of SPI-2 , ssrAB in S. Typhimurium .	304	OmpR is also known to interact with the endogenous two-component regulator of SPI-2 , ssrAB in S. Typhimurium [ 39,40 ] .	6	NON-CODING (NC) RNA SEQUENCES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	TU	ssrAB	regulator	20861532	0	ver/dev	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrB proteins .	120	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA and SsrB proteins [ 16 ] .	6	3.1.1 SALMONELLA PATHOGENICITY ISLAND 1 (SPI-1)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	20861532	0	ver/dev	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA proteins .	120	OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA and SsrB proteins [ 16 ] .	6	3.1.1 SALMONELLA PATHOGENICITY ISLAND 1 (SPI-1)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	21320585	1	ver/dev	The expression of the SsrA-SsrB two-component system is regulated by the OmpR-EnvZ two-component system by OmpR binding directly to the ssrAB promoter .	47	The expression of the SsrA-SsrB two-component system is regulated by the OmpR-EnvZ two-component system by OmpR binding directly to the ssrAB promoter [ 24 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	25135218	82	ver/dev	Since OmpR binds to the 83 / 6 region , it is possible that the sequence is involved in the positive regulation of ssrAB by OmpR .	229	Since OmpR binds to the 83 / 6 region ( 32 , 33 ) , it is possible that the sequence spanning positions 106 to 55 is involved in the positive regulation of ssrAB by OmpR .	5	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	25135218	86	ver/dev	To determine how OmpR to regulate the expression of ssrAB in response to different growth-conditions is a matter of future studies .	238	To determine how HilD , OmpR , and SlyA coordinate to regulate the expression of ssrAB in response to different growth conditions is a matter of our current and future studies .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	25135218	86	ver/dev	To determine how OmpR to regulate the expression of ssrAB in response to different growth-conditions is a matter of our current .	238	To determine how HilD , OmpR , and SlyA coordinate to regulate the expression of ssrAB in response to different growth conditions is a matter of our current and future studies .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	HilD have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	SlyA have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing SlyA by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	HilD have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	HilD have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing SlyA by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	SlyA have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	53	ver/dev	SlyA have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing SlyA by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	regulator	30718301	69	ver/dev	FIG 8 Model for the regulation of ssrAB by OmpR .	211	FIG 8 Model for the regulation of ssrAB by SlyA , HilD , OmpR , and H-NS .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	33854491	17	ver/dev	OmpR regulates the expression of ssrAB , the main regulators of pathogenicity islands 2 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	33854491	17	ver/dev	OmpR regulates the expression of ssrAB , the main regulators of pathogenicity islands 2 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	33854491	17	ver/dev	OmpR regulates the expression of ssrAB , the main regulators of pathogenicity islands 1 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	ssrAB	regulator	33854491	17	ver/dev	OmpR regulates the expression of ssrAB , the main regulators of pathogenicity islands 1 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	sopB	regulator	10844688	9	ver/dev	For example , sopB seem to be regulated directly indirectly by HilA through modulation of invF expression .	273	For example , sopE and sopB seem to be regulated directly by InvF and indirectly by HilA through modulation of invF expression ( Darwin and Miller , 1999b ; Eichelberg and GalaÂn , 1999 ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HilA	gene	sopB	regulator	22694285	0	ver/dev	Surprisingly , no correlation was found between the expression of SPI-1 genes sopB for a certain strain , although this can be due to the fact that expression of the effector protein SopB is only partly regulated by HilA .	426	Surprisingly , no correlation was found between the expression of SPI-1 genes hilA and sopB for a certain strain , although this can be due to the fact that expression of the effector protein SopB is only partly regulated by HilA [ 22 ] .	16	DISCUSSION	nan	1	L2	OTHER	Other	NEG	Other	Level 1
HilA	gene	sopB	regulator	24947562	0	ver/dev	However , it is important to mention that sopB , is cooperatively regulated by lowered levels of HilA were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control .	232	However , it is important to mention that sopB , is cooperatively regulated by InvF and HilA [ 30 ] and lowered levels of all SPI-1-encoded transcriptional regulators ( HilA , HilC , HilD , and InvF ) were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control [ 24 ] .	19	4. DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	sopB	regulator	31428589	0	ver/dev	sopB are regulated cooperatively by HilA .	125	sopA , sopB , and sopE are regulated cooperatively by HilA and InvF ( Thijs et al. , 2007 ) .	3	THE ROLE OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IscR	gene	torS	regulator	33751923	19	ver/dev	Carey et al. showed that the E. coli global regulator IscR binds the intergenic region between torS .	589	Carey et al. ( 2018 ) showed that the E. coli global regulator IscR binds the intergenic region between torT and torS , repressing their regulation in aerobic conditions ( Carey et al. 2018 ) .	20	TORSR	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CspA	gene	gyrA	activator	16940079	0	ver/dev	CspA is involved in the cold-shock response by stimulating the transcription of the cold-shock-inducible promoters of gyrA .	410	CspA is involved in the cold shock response by binding to and stimulating the transcription of the cold shock-inducible promoters of hns and gyrA .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseB	regulator	19202096	3	ver/dev	sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	335	pagC and sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	orgBC	activator	29555922	16	ver/dev	PhoP also positively regulate the expression of the orgBC SPI-1 operon .	267	HilD and PhoP also positively and independently regulate the expression of the orgBC SPI-1 operon , in SPI-1-inducing growth conditions , PhoP directly and HilD through HilA8 ,56 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	orgBC	activator	29555922	19	ver/dev	In SPI-2-inducing growth-conditions , PhoP also positively controls transcription of the orgBC operon .	281	In SPI-2-inducing growth conditions , PhoP also positively controls transcription of the orgBC operon and the slrP gene independently of HilD37 ,56 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	invF	activator	10692170	5	att	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	92	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	invF	activator	10844688	18	att	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
InvF	gene	invF	activator	24018968	4	att	The luxS gene , which encodes a synthase that produces a quorum-sensing signal-molecule termed autoinducer ( AI-2 ) , is necessary for the growth-dependent induction of a subset of SPI1 genes , including invF and InvF-dependent genes , but not hilA [ 9 ] .	139	The luxS gene , which encodes a synthase that produces a quorum-sensing signal molecule termed autoinducer ( AI-2 ) , is necessary for the growth-dependent induction of a subset of SPI1 genes , including invF and InvF-dependent genes , but not hilA [ 9 ] .	14	STATIONARY PHASE UNDER SHAKING CULTURE CONDITIONS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsA	TU	flhDC	activator	33638994	3	ver/dev	Phosphorylated RcsB can act in combination with RcsA to enhance activation of the cps operon , to repress flhDC .	45	Phosphorylated RcsB can act in combination with RcsA to enhance activation of the cps operon , to activate expression of the rcsA gene or to repress flhDC ( 14,16 ) .	6	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	fliZ	repressor	31182495	28	ver/dev	Deletion of fliZ led to decreased hilA expression as expected ; however , PhoP repressed hilA to similar levels in the presence or absence of fliZ .	130	Deletion of fliZ led to decreased hilA expression as expected ; however , PhoP repressed hilA to similar levels in the presence or absence of fliZ ( Fig. 5B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
sigma-70	TU	csgBA	activator	14643403	32	ver/dev	A. Arnqvist , A. Olsen , S. Normark , Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in-vivo by sigma-70 in the absence of ol .	236	[ 1 ] A. Arnqvist , A. Olsen , S. Normark , Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS , Mol .	24	REFERENCES	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
sigma-70	TU	csgBA	activator	14643403	32	ver/dev	A. Arnqvist , A. Olsen , S. Normark , Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in-vivo by sigma-70 in the absence of he nucleoid-associated protein H-NS .	236	[ 1 ] A. Arnqvist , A. Olsen , S. Normark , Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS , Mol .	24	REFERENCES	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
sigma-70	TU	csgBA	activator	16629664	43	ver/dev	Normark , S. Sigma Sdependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in-vivo by sigma-70 in the absence of the nucleoid-associated protein H-NS .	557	Arnqvist , A. , Olsen , A. , and Normark , S. ( 1994 ) Sigma Sdependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS .	25	REFERENCES	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
CpxR	gene	mgrB	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium indirectly through mgrB .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	mgrB	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by regulating mgrB through other regulators .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	mgrB	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium indirectly through mgrB .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	mgrB	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of CRRGs , binding directly to mgrB .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	mgrB	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of colistin resistance-related genes , binding directly to mgrB .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ssrA	activator	17259627	12	ver/dev	in-vitro analyses of the point-mutated SlyA proteins revealed that the amino-acid-residues of SlyA are critical for the transcriptional activation of the ssrA gene .	69	In vivo and in vitro analyses of the point-mutated SlyA proteins revealed that the amino acid residues of SlyA involved in the interaction with DNA and in dimerization are critical for the transcriptional activation of the ssrA gene .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ssrA	activator	17259627	12	ver/dev	In vivo revealed that the amino-acid-residues of SlyA are critical for the transcriptional activation of the ssrA gene .	69	In vivo and in vitro analyses of the point-mutated SlyA proteins revealed that the amino acid residues of SlyA involved in the interaction with DNA and in dimerization are critical for the transcriptional activation of the ssrA gene .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ssrA	activator	17259627	24	ver/dev	Two of 10 mutant SlyA proteins were significantly defective in terms of the activation of ssrA transcription .	243	Two of 10 mutant SlyA proteins ( L12A and L126A ) were significantly defective in terms of the activation of ssrA transcription ( Fig. 5b ) .	10	IDENTIFICATION OF AMINO ACID RESIDUES OF SLYA THAT ARE IMPORTANT FOR DIMERIZATION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SlyA	gene	ssrA	activator	19091955	30	att	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	187	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ssrA	activator	19091955	30	att	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	187	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ssrA	activator	27564394	4	ver/dev	SlyA activates transcription from the ssrA promoter of the SPI2-encoded TCS SsrA/B .	224	SlyA binds to and activates transcription from the ssrA promoter of the SPI2-encoded TCS SsrA/B [ 44 , 110 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoB	gene	hilC	regulator	11755416	13	ver/dev	This pstS mutation only reduces hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC .	218	This pstS mutation only reduces hilC and hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC or hilD ( R. Lucas and C. Lee , unpublished observations ) .	7	5. SIGNALS AND SIGNAL TRANSDUCERS INVOLVED IN TTSS-1 REGULATION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoB	gene	hilC	regulator	11755416	13	ver/dev	This pstS mutation only reduces hilC expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC .	218	This pstS mutation only reduces hilC and hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC or hilD ( R. Lucas and C. Lee , unpublished observations ) .	7	5. SIGNALS AND SIGNAL TRANSDUCERS INVOLVED IN TTSS-1 REGULATION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	spvA	regulator	18790861	7	att	In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary-phase ( 4 ) .	33	In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary phase ( 4 ) .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	glpA	regulator	29857034	33	ver/dev	Direct regulation of glpA genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	TU	glmUS	activator	24450479	49	ver/dev	Plumbridge , the NagC repressor acts as an activator for the transcription of the glmUS operon .	326	Plumbridge , J. ( 1995 ) Co-ordinated regulation of aminosugar biosynthesis and degradation : the NagC repressor acts as an activator for the transcription of the glmUS operon and requires two separated NagC binding sites .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM1674	gene	barA	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased fitness in the macrophage infection model , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA rfbJ .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	barA	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased fitness in the macrophage infection model , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA biosynthetic genes abe .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	barA	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased fitness in the macrophage infection model , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA rfbA .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	barA	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased fitness in the macrophage infection model , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA rmlA .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	rpoS	regulator	12882514	18	ver/dev	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	820	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	61	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	15126450	37	ver/dev	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	489	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	24	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	17908208	83	ver/dev	Hengge-Aronis , R. The LysR-like regulator LeuO n Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	458	Klauck , E. , Bohringer , J. , and Hengge-Aronis , R. ( 1997 ) The LysR-like regulator LeuO ( I ) n Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	24	ACKNOWLEDGEMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	22343301	41	ver/dev	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	494	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	45	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	22804842	34	ver/dev	Hengge-Aronis , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	678	Klauck , E. , Bohringer , J. , and Hengge-Aronis , R. ( 1997 ) The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	30	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	22804842	34	ver/dev	Klauck , E. , Bohringer , J. , , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	678	Klauck , E. , Bohringer , J. , and Hengge-Aronis , R. ( 1997 ) The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	30	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	24354910	60	ver/dev	Hengge-Aronis , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	444	Klauck , E. , Bohringer , J. , and Hengge-Aronis , R. ( 1997 ) The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	40	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	24354910	60	ver/dev	Klauck , E. , Bohringer , J. , , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	444	Klauck , E. , Bohringer , J. , and Hengge-Aronis , R. ( 1997 ) The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	40	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	24659766	21	ver/dev	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	377	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	14	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	rpoS	regulator	25566242	18	ver/dev	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	381	The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .	44	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RtcR	gene	rtcA	activator	30201777	27	att	( B ) The RNA repair operon map is shown with the 70-type promoter for the dinJ-yafQ operon , dinJp , and the potential promoters for RtcR-dependent expression of the dinJ-yafQ operon : the 54-dependent promoter for the RNA repair operon ( rsrp ) and the E 54 binding site within rtcA .	267	( B ) The RNA repair operon map is shown with the 70-type promoter for the dinJ-yafQ operon , dinJp , and the potential promoters for RtcR-dependent expression of the dinJ-yafQ operon : the 54-dependent promoter for the RNA repair operon ( rsrp ) and the E 54 binding site within rtcA .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcA	activator	30201777	29	att	Although RtcR-dependent expression of the dinJ-yafQ operon appears to be due to transcription read-through from the 54-dependent promoter of the RNA repair operon ( rsrp ) , RtcR-dependent transcription of the TA operon could additionally initiate from a recently identified 54 binding site at the 3 = end of rtcA , which is oriented toward the 5 = end of dinJ ( 5 ) ( Fig. 6B ) .	295	Although RtcR-dependent expression of the dinJ-yafQ operon appears to be due to transcription read-through from the 54-dependent promoter of the RNA repair operon ( rsrp ) , RtcR-dependent transcription of the TA operon could additionally initiate from a recently identified 54 binding site at the 3 = end of rtcA , which is oriented toward the 5 = end of dinJ ( 5 ) ( Fig. 6B ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcA	activator	30201777	3	ver/dev	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcA were measured in a WT strai .	103	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcA or rtcB were measured in a ΔrtcR mutant and a WT strain ( Fig. 3 ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcA	activator	30201777	3	ver/dev	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcA were measured in a ΔrtcR mutan .	103	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcA or rtcB were measured in a ΔrtcR mutant and a WT strain ( Fig. 3 ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcA	activator	30201777	8	ver/dev	Because rtcA was upregulated by nitrogen-limitation but independently of RtcR , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen-limitation .	115	Because rtcA was upregulated by nitrogen limitation but independently of RtcR ( Fig. 3C ) , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen limitation .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcA	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express Fig. 3B , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for ΔrpoN strai .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcA	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express Fig. 3B , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for Δrtc .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcA	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express Fig. 3B , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcA	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for ΔrpoN strai .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcA	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for Δrtc .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcA	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RpoS	gene	corA	activator	26039089	7	att	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	164	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	ecnB	activator	22275872	0	att	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	125	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	9	ADAPTATION OF S. ENTERICA TO LETHAL CONCENTRATIONS OF SODIUM DEOXYCHOLATE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	sopB	repressor	11244064	11	ver/dev	Therefore , under these conditions , the activity of SirA appears to be minimal , although the magnitude of repression of the flagellar genes mirrors the magnitude of activation of sopB .	249	Therefore , under these conditions , the activity of SirA appears to be minimal , although the magnitude of repression of the flagellar genes mirrors the magnitude of activation of sopB .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	pduA	activator	33853321	0	att	This is probably because a lack of CRP reduced pdu expression ( Figure 2B , C ) , consistent with the previous report .24 This CRP-dependent regulation mediates the catabolite-repression of pdu genes , resulting in a decrease of pduA expression as the glucose concentration increased ( Figure 2B ) .	104	This is probably because a lack of CRP reduced pdu expression ( Figure 2B , C ) , consistent with the previous report .24 This CRP-dependent regulation mediates the catabolite repression of pdu genes , resulting in a decrease of pduA expression as the glucose concentration increased ( Figure 2B ) .	3	SI SUPPORTING INFORMATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	soxS	regulator	27199934	12	ver/dev	To our knowledge , the influence of CpxR on the mRNA levels of soxS genes has not been demonstrated .	362	To our knowledge , the influence of CpxR on the mRNA levels of marA and soxS genes has not been demonstrated .	16	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of OmpR to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of OmpR to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	feoA	regulator	18790861	55	att	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtB	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RtsA	gene	rtsA	activator	31428589	3	auto	Each activator among HilC , RtsA , and HilD can bind to the hilA promoter to activate the expression of hilA , and HilA can also induce its own expression significantly as well as activate the other two regulators ( Schechter and Lee , 2001 ; Boddicker et al. , 2003 ; Ellermeier et al. , 2005 ) .	154	Each activator among HilC , RtsA , and HilD can bind to the hilA promoter to activate the expression of hilA , and HilA can also induce its own expression significantly as well as activate the other two regulators ( Schechter and Lee , 2001 ; Boddicker et al. , 2003 ; Ellermeier et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L2	OTHER	Other	OTHER	New	Level 1
FNR	gene	sodCI	regulator	18362154	3	ver/dev	Unexpectedly , we have found that sodCI is also regulated by FNR .	319	Unexpectedly , we have found that sodCI is also regulated by FNR , but in the opposite fashion .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	sodCI	regulator	18362154	6	ver/dev	The phage-associated sodCI gene is regulated by a network of FNR .	346	The phage-associated sodCI gene is regulated by a network of regulators including PhoPQ and FNR , which promote expression in the intracellular environment to protect Salmonella from reactive oxygen and nitrogen species produced by the host phagocytes ( 4 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rstA	activator	18248433	1	att	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rstA	activator	32209674	25	att	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	206	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rstA	activator	32209674	34	att	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	292	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rstA	activator	32392214	32	att	This was also true for strains harboring gfp transcriptional-fusions to the PhoP-activated rstA gene ( S17 Fig ) and the OmpR-activated ompC gene ( S18 Fig ) .	328	This was also true for strains harboring gfp transcriptional fusions to the PhoP-activated rstA gene ( S17 Fig ) and the OmpR-activated ompC gene ( S18 Fig ) .	17	BARA IS DISPENSABLE FOR ACTIVATION OF THE REGULATORS ARCA, OMPR, AND PHOP UNDER CONDITIONS IN WHICH IT ACTIVATES RCSB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rstA	activator	33045730	97	ver/dev	PhoP is a direct transcriptional activator of the rstA genes	413	And second , SsrB activation of PhoP is likely to have genome-wide effects , beyond the genes directly controlled by PhoP because : ( i ) PhoP is a direct transcriptional activator of the rstA and slyA genes , which specify DNA binding regulatory proteins ( 63,64,68,69 ) ; ( ii ) PhoP activates the transcriptional regulator PmrA post-translationally ( 70,71 ) ; ( iii ) PhoP promotes degradation of the gene silencer H-NS ( 72 ) ; and ( iv ) PhoP reduces proteolysis by different proteases that target pleiotropic regulators ( 73 -- 75 ) .	35	CONTROL OF THE VIRULENCE REGULATOR PHOP BY THE SSRB PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	cueO	regulator	24858080	10	att	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	336	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
ZntR	gene	cueO	regulator	24858080	3	att	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	264	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	regulator	11036033	1	ver/dev	Like marRAB , acrAB are positively regulated by SoxS .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	regulator	16492722	0	ver/dev	In S. enterica the global regu-2 SoxS regulate the acrAB operon by binding to mar/sox boxes .	21	In both E. coli and S. enterica the global regu-2 -- 4 lators MarA and SoxS regulate the acrAB operon by binding to mar/sox boxes found downstream of the local repressor acrR .	4	INTRODUCTION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	regulator	18577510	2	ver/dev	Other regulators of SoxS did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
SoxS	TU	acrAB	regulator	19120970	0	ver/dev	In E. coli , the transcription of acrAB is controlled by SoxS .	23	In E. coli , the transcription of acrAB and micF is controlled by the homologous proteins MarA , SoxS and Rob ( 9 , 10 ) , but may be affected by other proteins such as AcrR ( 11 ) .	4	ABSTRACT	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	regulator	23503095	1	ver/dev	In the expression of acrAB is regulated by SoxS et al. , Abouzeed et al. ,	28	In particular , the expression of acrAB is regulated by the global regulators , RamA , SoxS , MarA , and Rob ( Rosenberg et al. , 2003 ; Abouzeed et al. ,	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	regulator	23503095	1	ver/dev	In the expression of acrAB is regulated by SoxS et al. , 2003 ,	28	In particular , the expression of acrAB is regulated by the global regulators , RamA , SoxS , MarA , and Rob ( Rosenberg et al. , 2003 ; Abouzeed et al. ,	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	regulator	28650690	1	ver/dev	At a global level , acrAB expression is regulated by SoxS .	32	At a global level , acrAB expression is regulated by stressful conditions and by global transcriptional regulators , such as MarA and SoxS .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sopE	regulator	10844688	9	ver/dev	For example , sopE seem to be regulated directly indirectly by HilA through modulation of invF expression .	273	For example , sopE and sopB seem to be regulated directly by InvF and indirectly by HilA through modulation of invF expression ( Darwin and Miller , 1999b ; Eichelberg and GalaÂn , 1999 ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HilA	gene	sopE	regulator	31428589	0	ver/dev	sopE are regulated cooperatively by HilA .	125	sopA , sopB , and sopE are regulated cooperatively by HilA and InvF ( Thijs et al. , 2007 ) .	3	THE ROLE OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sopE	regulator	33691799	0	ver/dev	As a T3SS effector protein , the expression of sopE SPI1 T3SS is tightly regulated by its central activators HilA .	345	As a T3SS effector protein , the expression of sopE and other SPI1 T3SS is tightly regulated by its central activators HilA and HilD , which are activated by ferric uptake regulator ( Fur ) [ 49 ] .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	14563863	10	att	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	125	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	14563863	16	ver/dev	PhoP binds to the promoter region of mgtC .	155	PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL , and pmrC genes but not to the promoter region of phoN , pagC , or mgtC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtC	regulator	15703297	12	att	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	15703297	5	att	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	105	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to promoters in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to promoters in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to promoters in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to promoters in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to different classes in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to different classes in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to different classes in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	15703297	18	ver/dev	The experimental verification that the PhoP protein binds to different classes in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	18620040	1	att	The level of PagC protein is lowered in a mgtC null mutant : ( A ) , 1-D SDS-PAGE of outer-membrane proteins isolated from 14028s ( wild-type ) or NM14 ( DmgtC ) grown in low Mg2þ medium ( conditions that activate PhoP-regulated genes ) .	112	The level of PagC protein is lowered in a mgtC null mutant : ( A ) , 1-D SDS-PAGE of outer-membrane proteins isolated from 14028s ( wild-type ) or NM14 ( DmgtC ) grown in low Mg2þ medium ( conditions that activate PhoP-regulated genes ) .	10	3. DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	19436747	2	ver/dev	The PhoP regulator controls mgtC expression in acidic environment	124	The PhoP regulator controls mgtC expression in a low Mg and acidic environment	14	2. MGTC IS REQUIRED FOR GROWTH OF S. TYPHI WITHIN EPITHELIAL AND MONOCYTIC HUMAN CELLS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtC	regulator	19436747	2	ver/dev	The PhoP regulator controls mgtC expression in a low Mg	124	The PhoP regulator controls mgtC expression in a low Mg and acidic environment	14	2. MGTC IS REQUIRED FOR GROWTH OF S. TYPHI WITHIN EPITHELIAL AND MONOCYTIC HUMAN CELLS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtC	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtC	regulator	25848006	0	ver/dev	This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	25848006	0	ver/dev	This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to recruiting RNA polymerase .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	25848006	0	ver/dev	This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	25848006	0	ver/dev	This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	26943369	4	att	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	26943369	4	ver/dev	To determine whether acetylation affects the activity of PhoP as a transcription factor , mgtC were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	regulator	27350030	1	ver/dev	gene because , like mgtC , it is regulated by the PhoP / absence of supporting inforPhoQ two component system at the transcription initia - mation Fig .	107	gene because , like mgtC , it is regulated by the PhoP / absence of the efp gene ( Fig. 2B and supporting inforPhoQ two component system at the transcription initia - mation Fig .	6	THE MGTP PROLINE CODONS ARE CRITICAL FOR EF-P MEDIATED INDUCTION OF THE MGTC GENE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	27350030	1	ver/dev	gene because , like mgtC , it is regulated by the PhoP / absence of the efp gene -LRB- Fig. 2B - mation Fig .	107	gene because , like mgtC , it is regulated by the PhoP / absence of the efp gene ( Fig. 2B and supporting inforPhoQ two component system at the transcription initia - mation Fig .	6	THE MGTP PROLINE CODONS ARE CRITICAL FOR EF-P MEDIATED INDUCTION OF THE MGTC GENE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	28181542	0	att	This makes physiological sense because Salmonella indeed decreases EF-P mRNA levels during infection21 and it explains why the mgtC gene is highly expressed among other PhoP-regulated genes inside macrophages22 ,23 .	43	This makes physiological sense because Salmonella indeed decreases EF-P mRNA levels during infection21 and it explains why the mgtC gene is highly expressed among other PhoP-regulated genes inside macrophages22 ,23 .	2	MAIN	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtC	regulator	31346161	14	ver/dev	However , PhoP-dependent transcription is not influenced by the PhoB/PhoR-activating signal because low phosphate does not affect mgtC transcription .	526	However , PhoP-dependent transcription is not influenced by the PhoB/PhoR-activating signal because low phosphate does not affect mgtC transcription ( Fig. 4 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Sigma32	gene	ibpA	regulator	17630972	0	ver/dev	Dual control by a s32 promoter in concert with a ROSE-like RNA thermometer was also shown for the ibpA genes of Salmonella .	361	Dual control by a s32 promoter in concert with a ROSE-like RNA thermometer was also shown for the ibpA genes of E. coli and Salmonella ( Waldminghaus et al. , 2005 ) .	11	G	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Sigma32	gene	ibpA	regulator	17630972	0	ver/dev	Dual control by a s32 promoter in concert with a ROSE-like RNA thermometer was also shown for the ibpA genes of E. coli .	361	Dual control by a s32 promoter in concert with a ROSE-like RNA thermometer was also shown for the ibpA genes of E. coli and Salmonella ( Waldminghaus et al. , 2005 ) .	11	G	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	pefI	regulator	25080967	12	ver/dev	Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of any other position along the whole operon .	102	Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of pefI , or any other position along the whole operon .	7	PROMOTERS PREDICTED UPSTREAM OF PEFI, BUT NOT THOSE UPSTREAM OF SRGA AND SRGC, ARE FUNCTIONAL	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	pefI	regulator	25080967	12	ver/dev	Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of pefI along the whole operon .	102	Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of pefI , or any other position along the whole operon .	7	PROMOTERS PREDICTED UPSTREAM OF PEFI, BUT NOT THOSE UPSTREAM OF SRGA AND SRGC, ARE FUNCTIONAL	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	pefI	regulator	25080967	28	ver/dev	Second , we described the mechanism of regulation by SdiA on the promoter region located upstream of pefI .	258	Second , we described the transcriptional organization of this operon and the mechanism of regulation by SdiA on the promoter region located upstream of pefI .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SdiA	gene	pefI	regulator	25080967	39	ver/dev	a relatively high affinity _ demonstrating a direct regulation of the pefI-srgC operon by SdiA	338	SdiA-AHLs binds to the distal promoter identified upstream of pefI with a relatively high affinity demonstrating a direct regulation of the pefI-srgC operon by SdiA and AHLs .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtCB	activator	11755422	0	att	Transcription of the mgtA and mgtCB loci occurs in a PhoP-dependent manner and is repressed by Mg2 + and Ca2 + [ 30 , 31 ] .	95	Transcription of the mgtA and mgtCB loci occurs in a PhoP-dependent manner and is repressed by Mg2 + and Ca2 + [ 30 , 31 ] .	6	5. THE SALMONELLA PHOP/PHOQ REGULON PROMOTES VIRULENCE AND RESISTANCE TO INNATE IMMUNITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCB	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCB	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtCB	activator	18248433	3	att	Here , it was shown that the expression of mgtA and mgtCB , both harbouring long 50UTR regions , is highly diminished in the presence of submillimolar Mg 21 concentrations in the culture medium , a condition in which the rest of the PhoP-activated genes are actively expressed ( Fig. 1 ) .	328	Here , it was shown that the expression of mgtA and mgtCB , both harbouring long 50UTR regions , is highly diminished in the presence of submillimolar Mg 21 concentrations in the culture medium , a condition in which the rest of the PhoP-activated genes are actively expressed ( Fig. 1 ) .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCB	activator	31182500	0	ver/dev	PhoP is known to repress the expression of SPI-1 genes , while activating the expression of mgtCB , inside macrophages .	177	PhoP is a response regulator and is known to repress the expression of SPI-1 genes ( 48 ) , while activating the expression of pag genes , including mgtCB , pmrB , and SPI-2 genes , inside macrophages .	4	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
MviA	gene	igaA	regulator	33717045	0	ver/dev	Regulation of igaA by the MviA response regulator in Salmonella enterica .	443	Regulation of igaA and the Rcs system by the MviA response regulator in Salmonella enterica .	27	WE ARE GRATEFUL TO MIGUEL A. DE PEDRO, LAURENT AUSSEL, AND AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB.2021.647305/ KAI PAPENFORT FOR ADVICE AND DISCUSSIONS, AND TO MODESTO FULL#SUPPLEMENTARY-MATERIAL	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	TU	flhDC	regulator	32032766	0	ver/dev	Furthermore , the flhDC operon was reported to be regulated by Fis .	151	Furthermore , the flhDC operon was reported to be activated during the stationary phase under high osmolarity stress and regulated by several regulators ( such as , RpoS , OmpR , and Fis ) [ 17,24 ] .	17	3.2. EXPRESSION AND REGULATION OF ASFD IN S. TYPHI	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	TU	flhDC	regulator	32032766	3	ver/dev	Furthermore , we utilized qRT-PCR to investigate the regulation of Fis on the flhDC operon .	194	Furthermore , we utilized qRT-PCR to investigate the regulation of RpoS , OmpR , Fis , and Hfq on AsfD and the flhDC operon .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	TU	flhDC	regulator	34202800	1	ver/dev	In S. Typhimurium , flhDC expression is regulated by several factors binding Fis nucleoid , histone-like protein .	191	In S. Typhimurium , flhDC expression is regulated by several factors such as cAMP ( CRP ) receptor protein , Fur , proteins binding Fis nucleoid , histone-like protein structuring the ( H-NS ) nucleoids , and SlyA [ 63 ] .	5	2. SALMONELLA PATHOGENESIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	TU	flhDC	regulator	34202800	1	ver/dev	In S. Typhimurium , flhDC expression is regulated by cAMP receptor protein , Fur , proteins binding Fis nucleoid , histone-like protein .	191	In S. Typhimurium , flhDC expression is regulated by several factors such as cAMP ( CRP ) receptor protein , Fur , proteins binding Fis nucleoid , histone-like protein structuring the ( H-NS ) nucleoids , and SlyA [ 63 ] .	5	2. SALMONELLA PATHOGENESIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	regulator	17024490	18	ver/dev	Paraquat regulation of hmp ( Xavohaemoglobin ) gene expression in Escherichia coli K-12 is SoxRS independent gene by the `` NO releaser '' S-nitrosoglutathione : nitrosation of modulatio of MetR binding to the glyA-hmp intergenic region .	290	Paraquat regulation of hmp ( Xavohaemoglobin ) gene expression in Escherichia coli K-12 is SoxRS independent but modulated by S. J Bacteriol 179:3164 -- 3170 Membrillo-Hernández J , Coopamah MD , Channa A , Hughes MN , Poole RK ( 1998 ) A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( Xavohaemoglobin ) gene by the `` NO releaser '' S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	26	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	hmp	regulator	17024490	18	ver/dev	Paraquat regulation of hmp ( Xavohaemoglobin ) gene expression in Escherichia coli K-12 is SoxRS independent gene by the `` NO releaser '' S-nitrosoglutathione : nitrosation of homocystein of MetR binding to the glyA-hmp intergenic region .	290	Paraquat regulation of hmp ( Xavohaemoglobin ) gene expression in Escherichia coli K-12 is SoxRS independent but modulated by S. J Bacteriol 179:3164 -- 3170 Membrillo-Hernández J , Coopamah MD , Channa A , Hughes MN , Poole RK ( 1998 ) A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( Xavohaemoglobin ) gene by the `` NO releaser '' S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region .	26	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with Venus , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with Venus , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with yfp , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with yfp , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with Venus , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with Venus , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with yfp , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	flhB	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhB with yfp , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	rcsB	activator	25028458	26	att	This rcsB dps phenotype could be explained assuming that expression of other RcsB-dependent genes is required for H2O2 resistance .	267	This rcsB dps phenotype could be explained assuming that expression of other RcsB-dependent genes is required for H2O2 resistance .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsB	activator	25028458	3	att	However , we observed that only elimination of the rcsB gene from the rcsC11 mutant fully restored virulence levels , suggesting that other RcsB-dependent gene products are involved in such an attenuation phenotype .	40	However , we observed that only elimination of the rcsB gene from the rcsC11 mutant fully restored virulence levels , suggesting that other RcsB-dependent gene products are involved in such an attenuation phenotype .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsB	activator	27558204	0	ver/dev	To better characterize the contribution of RcsB to persistence within tomatoes , rcsB genes were deleted	53	To better characterize the contribution of RcsA and RcsB to persistence within tomatoes , rcsA and rcsB genes were deleted and the abilities of the corresponding mutants to multiply in red and green tomatoes were tested ( strains and pri-mers used to construct them are listed in Supporting Information Tables S1 and S2 ) .	7	SALMONELLA RCSA AND RCSB GENES ARE INVOLVED IN PERSISTENCE WITHIN TOMATOES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsB	activator	30510144	30	att	To confirm the SlyA repression effect on rcsB , we used another RcsB-dependent gene , dps ( 32 ) .	136	To confirm the SlyA repression effect on rcsB , we used another RcsB-dependent gene , dps ( 32 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	rcsB	activator	30510144	31	att	Here , we have demonstrated that the repression of rcsB by the SlyA regulator results in the modulation of RcsB-dependent genes .	138	Here , we have demonstrated that the repression of rcsB by the SlyA regulator results in the modulation of RcsB-dependent genes .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	rcsB	activator	30510144	41	att	Taking into account that ( i ) the activity of P1flhDC ensures the synthesis of the flagellum to positively control motility , ( ii ) P1flhDC is negatively affected by RcsB , even at basal levels , and ( iii ) high levels of SlyA repress the expression of rcsB from its two promoters , hence no repression of P1flhDC takes place , we here propose that SlyA activation indirectly modulates Salmonella motility in a RcsB-dependent pathway .	185	Taking into account that ( i ) the activity of P1flhDC ensures the synthesis of the flagellum to positively control motility , ( ii ) P1flhDC is negatively affected by RcsB , even at basal levels , and ( iii ) high levels of SlyA repress the expression of rcsB from its two promoters , hence no repression of P1flhDC takes place , we here propose that SlyA activation indirectly modulates Salmonella motility in a RcsB-dependent pathway .	5	DISCUSSION	Salmonella	1	L3	SPEC	Analysis	NEG	Other	Level 1
RcsB	gene	rcsB	activator	30510144	42	att	A similar effect was observed using another RcsB-dependent gene , dps ; slyA overexpression decreased the levels of dps in the wild type but not in the rcsB strain .	186	A similar effect was observed using another RcsB-dependent gene , dps ; slyA overexpression decreased the levels of dps in the wild type but not in the rcsB strain .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsB	gene	rcsB	activator	31563538	16	att	We demonstrated here that increasing the concentration of either glucose , trehalose , mannose or mannitol is enough to observe changes in the expression of RcsB-dependent genes since in the absence of rcsB , no changes were observed .	266	We demonstrated here that increasing the concentration of either glucose , trehalose , mannose or mannitol is enough to observe changes in the expression of RcsB-dependent genes since in the absence of rcsB , no changes were observed .	16	4. DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsB	activator	31714197	0	att	On the other hand , deletion of the rcsB gene from the rcsC11 strain fully restored the levels of virulence , indicating that the attenuation was produced by the repression of RcsB-dependent virulence gene expression [ 7 ] .	29	On the other hand , deletion of the rcsB gene from the rcsC11 strain fully restored the levels of virulence , indicating that the attenuation was produced by the repression of RcsB-dependent virulence gene expression [ 7 ] .	2	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsB	activator	32392214	25	ver/dev	The SirA-mediated activation of the rcsD promoter occurs independently of RcsB , as pSirA increased the fluorescence from rcsD-gfp in the rcsB mutant .	220	The SirA-mediated activation of the rcsD promoter occurs independently of RcsB , a negative regulator of the rcsDB operon [ 34 ] , as pSirA increased the fluorescence from rcsD-gfp in the rcsB mutant ( S9 Fig ) .	14	SIRA PROMOTES RCSDB TRANSCRIPTION FROM A RCSD PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	ssrAB	repressor	30718301	26	ver/dev	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed EMSAs to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	83	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed competitive electrophoretic mobility shift assays ( EMSAs ) to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	3	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
SlyA	TU	ssrAB	repressor	30718301	26	ver/dev	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed competitive electrophoretic-mobility-shift assays to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	83	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed competitive electrophoretic mobility shift assays ( EMSAs ) to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	3	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
SlyA	TU	ssrAB	repressor	30718301	65	ver/dev	Therefore , the expression of ssrAB would involve two steps , as follows : the relief of H-NS-mediated repression by SlyA and the recruitment of the RNA polymerase by OmpR .	185	Therefore , the expression of ssrAB mediated by SyA , HilD , and OmpR would involve two steps , as follows : the relief of H-NS-mediated repression by SlyA and HilD or only SlyA and the recruitment of the RNA polymerase by OmpR ( Fig. 8 ) .	4	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	gltA	activator	30524381	15	ver/dev	OmpR binding to the gltA promoter was increased at acid-pH ompared to the addition of OmpR at neutral pH -LRB- Figures 7A , B -RRB- .	231	OmpR binding to the gltA promoter was increased at acid pH ompared to the addition of OmpR at neutral pH ( Figures 7A , B ) .	17	COMMON OMPR TARGETS IN ACID AND OSMOTIC STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	fliL	activator	31627387	1	ver/dev	Conversely , CpxR induced the expression of fimbrial stdAC operons only during fliL operons exclusively during the planktonic phase , indicating a responsive biofilm-associated loop of the CpxR regulator .	20	Conversely , CpxR induced the expression of curli csgAB and fimbrial stdAC operons only during biofilm development and flagellar motAB and fliL operons exclusively during the planktonic phase , indicating a responsive biofilm-associated loop of the CpxR regulator .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	fliL	activator	31627387	1	ver/dev	Conversely , CpxR induced the expression of curli csgAB only during fliL operons exclusively during the planktonic phase , indicating a responsive biofilm-associated loop of the CpxR regulator .	20	Conversely , CpxR induced the expression of curli csgAB and fimbrial stdAC operons only during biofilm development and flagellar motAB and fliL operons exclusively during the planktonic phase , indicating a responsive biofilm-associated loop of the CpxR regulator .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	rpoS	regulator	22256797	8	ver/dev	Although H-NS reduces the transcription of more than 100 genes , it also is shown to be a negative regulator for rpoS translation .	344	Although H-NS reduces the transcription of more than 100 genes , it also is shown to be a negative regulator for rpoS translation ( 44,45 ) .	15	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	22256797	9	ver/dev	H-NS binds directly to rpoS mRNA to enhance cleavage of the mRNA .	345	H-NS binds directly to rpoS mRNA to enhance cleavage of the mRNA ( 44 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	regulator	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	ompD	activator	27407104	4	ver/dev	Similarly , CRP controls OmpD expression , however , different from S , CRP activates ompD transcription .	379	Similarly , CRP controls OmpD expression , however , different from S , CRP activates ompD transcription ( 97 ) .	21	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	ompD	activator	27407104	5	ver/dev	In this case , SdsR will inhibit OmpD production by a dual mechanism : first , by inhibiting ompD translation through direct base-pairing with second , by restricting transcriptional activation of ompD by CRP .	380	In this case , SdsR will inhibit OmpD production by a dual mechanism : first , by inhibiting ompD translation through direct base-pairing with the mRNA ( 40 ) , and second , by restricting transcriptional activation of ompD by CRP .	21	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	ompD	activator	27407104	5	ver/dev	In this case , SdsR will inhibit OmpD production by a dual mechanism : first , by inhibiting ompD translation through direct base-pairing with the mRNA , by restricting transcriptional activation of ompD by CRP .	380	In this case , SdsR will inhibit OmpD production by a dual mechanism : first , by inhibiting ompD translation through direct base-pairing with the mRNA ( 40 ) , and second , by restricting transcriptional activation of ompD by CRP .	21	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CsgD	gene	STM1703	regulator	17322315	29	ver/dev	Overcoming the temperature regulation of Salmonella serovar Typhimurium UMR1 by mutations in STM1703 demonstrated that both gene products act as suppressors of the rdar morphotype expression upstream of CsgD at 37 °C .	284	Overcoming the temperature regulation of Salmonella serovar Typhimurium UMR1 by mutations in STM1703 and STM4264 demonstrated that both gene products act as suppressors of the rdar morphotype expression upstream of CsgD at 37 °C .	4	RESULTS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1703	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1703	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1703	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1703	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1703	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is either located downstream of STM1827 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	STM4264	activator	17322315	8	ver/dev	These data indicate that in STM4264 mutants , CsgD expression is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM4264	activator	17322315	8	ver/dev	These data indicate that in STM4264 mutants , the rdar morphotype is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM4264	activator	17322315	8	ver/dev	These data indicate that in STM1703 , STM1827 , STM3611 , CsgD expression is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM4264	activator	17322315	8	ver/dev	These data indicate that in STM1703 , STM1827 , STM3611 , the rdar morphotype is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	185	These data indicate that in STM1703 , STM1827 , STM3611 , and STM4264 mutants , the rdar morphotype and CsgD expression is upregulated , whereby STM1703 and STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM4264	activator	17322315	19	ver/dev	In order to demonstrate that upregulation of the rdar morphotype in the STM4264 mutants is mediated by CsgD , csgD was knocked out in the STM4264 mutants .	223	In order to demonstrate that upregulation of the rdar morphotype in the STM1703 and STM4264 mutants is mediated by CsgD , csgD was knocked out in the STM1703 and STM4264 mutants .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	STM1330	regulator	27564394	11	ver/dev	Furthermore , STM1330 are regulated by the master regulators of the SsrB regulon .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM1330	regulator	27564394	11	ver/dev	Furthermore , STM1330 are regulated by the master regulators of the SsrB regulon .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	hmp	regulator	26443513	4	ver/dev	Nitric oxide , nitrite , and Fnr regulation of hmp gene expression in Escherichia coli K-12 .	767	Nitric oxide , nitrite , and Fnr regulation of hmp ( flavohemoglobin ) gene expression in Escherichia coli K-12 .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	nfsA	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , nfsA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	nfsA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , nfsA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hemX	repressor	27564394	18	ver/dev	the hemX gene were used as negative control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	lon	regulator	32209674	42	ver/dev	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella -LRB- Fig. 3F -RRB- , reflecting the higher H-NS amounts Fig. 3A .	325	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella ( Fig. 3F ) , reflecting the higher H-NS amounts pre-sent in the former than the latter strain ( Fig. 3A ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	lon	regulator	32209674	42	ver/dev	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella -LRB- Fig. 3F -RRB- , reflecting the higher H-NS amounts pre-sent in the former than the latter strain .	325	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella ( Fig. 3F ) , reflecting the higher H-NS amounts pre-sent in the former than the latter strain ( Fig. 3A ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	lon	regulator	32209674	48	ver/dev	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella -LRB- Fig. 3F -RRB- , reflecting the higher H-NS amounts Fig. 3A .	387	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella ( Fig. 3F ) , reflecting the higher H-NS amounts pre-sent in the former than the latter strain ( Fig. 3A ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	lon	regulator	32209674	48	ver/dev	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella -LRB- Fig. 3F -RRB- , reflecting the higher H-NS amounts pre-sent in the former than the latter strain .	387	Chromatin immunoprecipitation experiments demonstrated that more H-NS bound to HTGs in the lon mutant than in wild-type Salmonella ( Fig. 3F ) , reflecting the higher H-NS amounts pre-sent in the former than the latter strain ( Fig. 3A ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
OxyR	gene	hcp	activator	23651595	15	ver/dev	that hcp transcription is activated by S-nitrosylation of OxyR during anaerobic nitrate respiration	613	They showed that OxyR is a key regulator in S-nitrosylation and that hcp transcription is activated by S-nitrosylation of OxyR during anaerobic nitrate respiration .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sirA	regulator	29555922	9	ver/dev	sirA , a gene not regulated by PhoP , was also tested	115	As positive and negative controls , the activity of transcriptional fusions to cat reporter of pagK , a gene positively regulated by PhoP , and sirA , a gene not regulated by PhoP , was also tested .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FliZ	gene	hilA	activator	11162188	5	ver/dev	However , activation of the hilA gene by FliZ occurs even in the absence of FlhD/FlhC .	227	However , activation of the hilA gene by FliZ occurs even in the absence of FlhD/FlhC [ 13 , our unpublished results ] .	9	EFFECT OF THE FLIZ MUTATION ON THE SURVIVAL WITHIN MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	hilA	activator	16045614	15	ver/dev	Several studies have identi-fied the class 3 flagellar protein FliZ as an activator of hilA expression .	70	Several studies have identi-fied the class 3 flagellar protein FliZ as an activator of hilA expression ( Eichelberg and Galan , 2000 ; Lucas et al. , 2000 ; Iyoda et al. , 2001 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	hilA	activator	22004521	11	ver/dev	Moreover , studies have shown that FliZ , under the control of FlhDC , positively regulates hilA expression by controlling HilD post-translationally , through a mechanism independent of the Lon protease .	326	Moreover , studies have shown that FliZ , under the control of FlhDC , positively regulates hilA expression by controlling HilD post-translationally , through a mechanism independent of the Lon protease ( 50 ) .	25	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	hilA	activator	23419780	6	ver/dev	In another pathway , FliZ positively regulates hilA .	238	In another pathway , FliZ positively regulates hilA and positively affects secretion of invasion proteins ( Iyoda et al. , 2001 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	hilA	activator	24992093	8	ver/dev	The regulatory protein FliZ is an activator of hilA , thus placing T3SS-1 gene expression under negative control of TviA ( Fig .	156	The regulatory protein FliZ is an activator of hilA [ 48 -- 50 ] , the master regulator of T3SS-1 genes [ 51,52 ] , thus placing T3SS-1 gene expression under negative control of TviA ( Fig .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliZ	gene	hilA	activator	27564394	3	ver/dev	FliZ also activates hilA expression phase through post-translational interaction with the HilD protein .	194	FliZ also activates hilA expression phase ( ESP ) through post-translational interaction with the HilD protein [ 22 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	activator	31428589	10	ver/dev	FliZ posttranscriptionally controls HilD to upregulate hilA expression .	180	FliZ posttranscriptionally controls HilD to upregulate hilA expression ( Chubiz et al. , 2010 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	iroB	activator	32560822	0	att	These results indicate that iroB expression is repressed by the ferric uptake regulator ( Fur ) protein under normal growth-conditions , but is strongly up-regulated upon iron-depletion in a Fur-dependent manner in Salmonella .	118	These results indicate that iroB expression is repressed by the ferric uptake regulator ( Fur ) protein under normal growth conditions , but is strongly up-regulated upon iron depletion in a Fur-dependent manner in Salmonella .	15	3.1. REGULATION OF IROB GENE EXPRESSION BY FUR IN RESPONSE TO IRON AVAILABILITY IN SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SpvR	gene	spvA	regulator	11705925	0	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	363	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	18	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	12011028	5	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	212	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	12	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	15256548	29	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	986	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	56	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	15790293	20	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	614	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	54	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	16430223	0	ver/dev	Grob , P. , and Guiney , D. G. In Vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA , J. Bacteriol .	274	Grob , P. , and Guiney , D. G. ( 1996 ) In Vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR , J. Bacteriol .	11	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	19447191	1	ver/dev	Gel mobility-shift assays revealed that the SpvR fusion proteins were able to bind 147-bp DNA fragments of the spvA , respectively .	80	Gel mobility shift assays revealed that the SpvR fusion proteins were able to bind to 125 - and 147-bp DNA fragments of the spvA and spvR promoter regions , respectively ( Grob and Guiney , 1996 ) .	5	4.1. SPVR	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SpvR	gene	spvA	regulator	19447191	21	ver/dev	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	206	In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	13	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	21716657	0	ver/dev	The SpvR protein is a positive transcriptional regulator of the LysR family and binds to inverted repeat recognition sequences upstream of the spvA promoter .	54	The SpvR protein is a positive transcriptional regulator of the LysR family and binds to inverted repeat recognition sequences upstream of its own promoter and the spvA promoter ( Krause et al. , 1991 , 1995 ; Grob and Guiney , 1996 ; Grob et al. , 1997 ) .	3	THE SPV VIRULENCE LOCUS IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SpvR	gene	spvA	regulator	24426086	0	ver/dev	SpvR binds to both spvA promoters .	33	SpvR binds to both the spvR and spvA promoters and is required for expression of the spvABCD genes [ 17 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	24426086	1	ver/dev	Grob P , Guiney DG In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter region of spvA .	162	Grob P , Guiney DG ( 1996 ) In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter region of spvA and spvR .	10	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	25175817	0	ver/dev	SpvR is recognized as a positive regulator of the spv operon via transcription of spvA .	236	SpvR is recognized as a positive regulator of the spv operon via transcription of itself and spvA ( Fabrega and Vila , 2013 ; Heiskanen et al. , 1994 ) , and is expressed in a temporal fashion during infection .	13	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SpvR	gene	spvA	regulator	30143595	12	ver/dev	As a result , in cells stochastically expressing a higher number of SpvR molecules , SpvR would be more prone to bind spvA promoter , thereby activating spv expression .	235	As a result , in cells stochastically expressing a higher number of SpvR molecules , SpvR would be more prone to bind the spvR ( establishing the positive feedback loop ) and spvA promoter , thereby activating spv expression .	13	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SpvR	gene	spvA	regulator	30143595	14	ver/dev	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and 1996 In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	406	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and D. G. Guiney , 1996 In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	26	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	30143595	14	ver/dev	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and D. G. Guiney In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .	406	https://doi.org/10.1074/jbc.M116.752782 Grob , P. , and D. G. Guiney , 1996 In vitro binding of the Salmonella Dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA and spvR .	26	REFERENCES	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	regulator	34202800	32	ver/dev	The SpvR binds above the spvA promoter in the presence of the alternative RpoS sigma factor .	491	The SpvR binds to sequences above its own promoter and above the spvA promoter in the presence of the alternative RpoS sigma factor .	17	3.7.1. SPVR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	activator	15208313	4	ver/dev	Although the SlyA protein is a transcriptional activator of the ugtL gene , it footprinted the ugtL promoter at a region located downstream of the transcription start site .	11	Although the SlyA protein is a transcriptional activator of the ugtL gene , it footprinted the ugtL promoter at a region located downstream of the transcription start site .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ugtL	activator	15208313	32	ver/dev	the ugtL promoter _ performed with increasing amounts of SlyA proteins	142	B , DNase I footprinting analysis of the ugtL promoter performed with probes for the coding and noncoding strands ( see `` Experimental Procedures '' ) and increasing amounts of PhoP ( 15 , 30 , and 60 pmol ) or SlyA ( 5 , 15 , and 30 pmol ) proteins .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
SlyA	gene	ugtL	activator	18270203	3	att	Thus , to understand this process , we investigated the expression of the PhoP - and SlyA-dependent ugtL and pagC genes , which are normally bound by the H-NS protein ( 4 , 5 ) .	37	Thus , to understand this process , we investigated the expression of the PhoP - and SlyA-dependent ugtL and pagC genes , which are normally bound by the H-NS protein ( 4 , 5 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ugtL	activator	18270203	71	att	This form of regulation is in striking parallel to that controlling expression of the ugtL gene ( 23 ) , and it may apply to other PhoP - and SlyA-dependent genes , such as mig-14 and virK ( which also seem to have been horizontally acquired ) , because the PhoP protein has been shown to bind to their respective promoters in-vitro and in-vivo ( 26 ) .3	296	This form of regulation is in striking parallel to that controlling expression of the ugtL gene ( 23 ) , and it may apply to other PhoP - and SlyA-dependent genes , such as mig-14 and virK ( which also seem to have been horizontally acquired ) , because the PhoP protein has been shown to bind to their respective promoters in vitro and in vivo ( 26 ) .3	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ugtL	activator	18270203	21	ver/dev	H-NS Remains Associated with the ugtL Promoters under Inducing Conditions -- The SlyA proteins could activate transcription of the ugtL genes by either displacing H-NS by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
SlyA	gene	ugtL	activator	18270203	21	ver/dev	H-NS Remains Associated with the ugtL Promoters under Inducing Conditions -- The SlyA proteins could activate transcription of the ugtL genes by either displacing H-NS from their respective promoters not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
SlyA	gene	ugtL	activator	18792679	10	att	The PhoP - and SlyA-dependent control ofthe ugtL gene appears to be a Coherent type 1AND feedforward loop , which isanticipated to shorten the periodoftime it takes for the ugtL gene to be expressed .	176	The PhoP - and SlyA-dependent control ofthe ugtL gene appears to be a Coherent type 1AND feedforward loop , which isanticipated to shorten the periodoftime it takes for the ugtL gene to be expressed .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ugtL	activator	19091955	5	att	A direct repeat , TAAAT - ( 6 nt ) - TCAAC , referred to as `` the reverse PhoP box , '' was identified in the ugtL promoter ( 2 ) , which is conserved in another PhoP and SlyA-dependent gene , pagC ( shown as TAAAT - ( 6 nt ) - TAAAC in Fig. 1A ) ( 13 , 14 ) .	58	A direct repeat , TAAAT - ( 6 nt ) - TCAAC , referred to as `` the reverse PhoP box , '' was identified in the ugtL promoter ( 2 ) , which is conserved in another PhoP and SlyA-dependent gene , pagC ( shown as TAAAT - ( 6 nt ) - TAAAC in Fig. 1A ) ( 13 , 14 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ugtL	activator	19091955	1	ver/dev	To activate transcription of ugtL , both SlyA must bind to its promoter simultaneously .	19	To activate transcription of ugtL , both PhoP and SlyA must bind to its promoter simultaneously ( 2 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	activator	31333620	0	att	According to our previous studies , transcription of many horizontally acquired genetic loci such as the ugtL and pagC genes are governed by a PhoP/PhoQ - and SlyA-dependent feedforward regulatory loop ( Shi et al. , 2004b ; Zhao et al. , 2008 ) .	55	According to our previous studies , transcription of many horizontally acquired genetic loci such as the ugtL and pagC genes are governed by a PhoP/PhoQ - and SlyA-dependent feedforward regulatory loop ( Shi et al. , 2004b ; Zhao et al. , 2008 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
OmpR	gene	ompR	repressor	24720747	7	ver/dev	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with Fig. 3D .	132	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation mediated by LtrR , since a clear decrease ( 80 % ) of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / D ( Fig. 3D ) , and also with the double substitution pKK8/ompR -134 -1 / E ( Fig. 3D ) .	6	IDENTIFICATION OF THE OMPR SEQUENCES THAT MEDIATE LTRR-DEPENDENT EXPRESSION IN S. TYPHI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	repressor	24720747	7	ver/dev	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / also with the double substitution pKK8/ompR -134 -1 / E .	132	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation mediated by LtrR , since a clear decrease ( 80 % ) of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / D ( Fig. 3D ) , and also with the double substitution pKK8/ompR -134 -1 / E ( Fig. 3D ) .	6	IDENTIFICATION OF THE OMPR SEQUENCES THAT MEDIATE LTRR-DEPENDENT EXPRESSION IN S. TYPHI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	repressor	24720747	7	ver/dev	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / Fig. 3D -134 -1 / E .	132	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation mediated by LtrR , since a clear decrease ( 80 % ) of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / D ( Fig. 3D ) , and also with the double substitution pKK8/ompR -134 -1 / E ( Fig. 3D ) .	6	IDENTIFICATION OF THE OMPR SEQUENCES THAT MEDIATE LTRR-DEPENDENT EXPRESSION IN S. TYPHI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	repressor	24720747	7	ver/dev	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / D -134 -1 / E .	132	However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation mediated by LtrR , since a clear decrease ( 80 % ) of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / D ( Fig. 3D ) , and also with the double substitution pKK8/ompR -134 -1 / E ( Fig. 3D ) .	6	IDENTIFICATION OF THE OMPR SEQUENCES THAT MEDIATE LTRR-DEPENDENT EXPRESSION IN S. TYPHI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at this locus	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at this locus	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at this locus	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at this locus	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at this locus	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	repressor	25875623	5	ver/dev	the ompR mutant _ suggesting that OmpR functions as a repressor at this locus	235	Transcripts for genes cadC ( 2.3-fold ) , cadB ( 3.2-fold ) and cadA ( 4.9-fold ) were all up-regulated in the ompR mutant , suggesting that OmpR functions as a repressor at this locus ( Fig 5A ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	flhDC	activator	24706743	9	att	One HilD-activated gene product , RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon ( 49 ) .	255	One HilD-activated gene product , RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon ( 49 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	flhDC	activator	24706743	10	ver/dev	Recent work has demonstrated that HilD activates flhDC transcription late in the cell 's growth phase under non-Spi1 induction conditions .	256	Recent work has demonstrated that HilD activates flhDC transcription late in the cell 's growth phase under non-Spi1 induction conditions ( 50 , 51 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	flhDC	activator	24706743	15	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	642	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	7	8	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	25135218	88	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	473	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	47	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	25547794	21	ver/dev	Additional work has demonstrated that the flhDC genes , the master operon of the flagellar hierarchy , activate transcription of the hilD gene at early stages of growth , while the HilD regulator activates promoter 5 of the flhDC genes at later stages of growth .	218	Additional work has demonstrated that the flhDC genes , the master operon of the flagellar hierarchy , activate transcription of the hilD gene at early stages of growth , while the HilD regulator activates promoter 5 of the flhDC genes at later stages of growth ( 62 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	flhDC	activator	26056383	3	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	595	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	18	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	26267246	1	ver/dev	Transcription of flhDC is also activated by the master regulator of the Salmonella pathogenicity island-1 encoded Spi-1 , HilD .	64	Transcription of flhDC is also activated by the ironregulatory protein Fur [ 21 ] and the master regulator of the Salmonella pathogenicity island-1 encoded injectisome ( Spi-1 ) , HilD .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	26267246	1	ver/dev	Transcription of flhDC is also activated by the master regulator of the Salmonella pathogenicity island-1 encoded injectisome , HilD .	64	Transcription of flhDC is also activated by the ironregulatory protein Fur [ 21 ] and the master regulator of the Salmonella pathogenicity island-1 encoded injectisome ( Spi-1 ) , HilD .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	26267246	2	ver/dev	HilD positively regulates flagellar gene expression through a direct binding to the P5 promoter of flhDC .	65	HilD positively regulates flagellar gene expression through a direct binding to the P5 promoter of flhDC [ 22 ] .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	26300871	43	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	832	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	19	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	26441883	14	ver/dev	FliZ is needed for eficient induction of the Spi-1 system via post-translational activation of the Spi-1 regulatory protein HilD , which in turn activates flhDC gene transcription .	350	FliZ is needed for eficient induction of the Spi-1 system via post-translational activation of the Spi-1 regulatory protein HilD , which in turn activates flhDC gene transcription ( Iyoda et al. , 2001 ; Chubiz et al. , 2010 ; Mouslim and Hughes , 2014 ; Singer et al. , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	26441883	31	ver/dev	Moreover , HilD coordinates hilA transcription with the expression of other crucial infection-relevant systems , e.g. , it induces expression of the flagellar operons through activation of flhDC transcription .	426	Moreover , HilD coordinates hilA transcription with the expression of other crucial infection-relevant systems , e.g. , it induces expression of the flagellar operons through activation of flhDC transcription and controls expression of Spi-2 genes ( see also the Sections Regulation of Motility and Regulatory Circuits Controlling Later Stages of Infection and Defense Systems against the Host 's Immune Response ) .	9	ATTACHMENT AND INVASION OF THE INTESTINAL EPITHELIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	26441883	49	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	1383	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	93	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27206164	69	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	525	Singer , H.M. , Ku $ hne , C. , Deditius , J.A. , Hughes , K.T. , and Erhardt , M. ( 2014 ) The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	41	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27206164	69	ver/dev	Singer , H.M. , Ku C. , Deditius , J.A. , Hughes , K.T. , The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	525	Singer , H.M. , Ku $ hne , C. , Deditius , J.A. , Hughes , K.T. , and Erhardt , M. ( 2014 ) The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	41	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27404739	4	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	376	Singer , H.M. , Kühne , C. , Deditius , J.A. , Hughes , K.T. , and Erhardt , M. ( 2014 ) The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	34	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27404739	4	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	376	Singer , H.M. , Kühne , C. , Deditius , J.A. , Hughes , K.T. , and Erhardt , M. ( 2014 ) The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	34	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27564394	24	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	1563	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	30	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27601571	51	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	644	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	26	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	27886269	20	ver/dev	Previously , by using ChIP-qPCR , it was found that HilD binds in-vivo to DNA regions -RRB- S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in flhDC + 31 .	129	Previously , by using chromatin immunoprecipitation-sequencing ( ChIP-seq ) and ChIP-qPCR , it was found that HilD binds in vivo to DNA regions associated with the sinR , lpxR and SL4247 ( STM14_5184 ) S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in the E. coli AMD054 strain ( flhDC + ) 31 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	TU	flhDC	activator	27886269	20	ver/dev	Previously , by using ChIP-seq , it was found that HilD binds in-vivo to DNA regions -RRB- S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in flhDC + 31 .	129	Previously , by using chromatin immunoprecipitation-sequencing ( ChIP-seq ) and ChIP-qPCR , it was found that HilD binds in vivo to DNA regions associated with the sinR , lpxR and SL4247 ( STM14_5184 ) S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in the E. coli AMD054 strain ( flhDC + ) 31 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	TU	flhDC	activator	27886269	20	ver/dev	Previously , by using chromatin immunoprecipitation-sequencing , it was found that HilD binds in-vivo to DNA regions -RRB- S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in flhDC + 31 .	129	Previously , by using chromatin immunoprecipitation-sequencing ( ChIP-seq ) and ChIP-qPCR , it was found that HilD binds in vivo to DNA regions associated with the sinR , lpxR and SL4247 ( STM14_5184 ) S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in the E. coli AMD054 strain ( flhDC + ) 31 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	TU	flhDC	activator	27886269	41	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	383	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	10	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	28329249	22	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	393	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	24	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	28389944	1	ver/dev	The activation of flhDC transcription by HilD were found using a T-POP transposon derivative of Tn10dTc .	33	The activation of flhDC transcription by HilD and inhibitors of FlhDC activity were found using a T-POP transposon derivative of Tn10dTc , described earlier [ 5 ] .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	28704543	52	ver/dev	HilD ndirectly activates the expression of everal other genes located outside SPI-1 , including he flagellar regulatory operon flhDC .	312	( A ) HilD directly or indirectly activates the expression of the SPI-1 genes and several other genes located outside SPI-1 , including the flagellar regulatory operon flhDC required for the invasion of host cells .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	28704543	52	ver/dev	HilD irectly activates the expression of everal other genes located outside SPI-1 , including he flagellar regulatory operon flhDC .	312	( A ) HilD directly or indirectly activates the expression of the SPI-1 genes and several other genes located outside SPI-1 , including the flagellar regulatory operon flhDC required for the invasion of host cells .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	28704543	64	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	800	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	30	3	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	29150501	1	ver/dev	Furthermore , HilD acts as a direct activator of flhDC expression , strengthening the transcriptional cross talk between the SPI-1 regulons in Salmonella .	227	Furthermore , HilD acts as a direct activator of flhDC expression , strengthening the transcriptional cross talk between the flagellar and SPI-1 regulons in Salmonella ( 52 ) .	4	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	29150501	1	ver/dev	Furthermore , HilD acts as a direct activator of flhDC expression , strengthening the transcriptional cross talk between the flagellar regulons in Salmonella .	227	Furthermore , HilD acts as a direct activator of flhDC expression , strengthening the transcriptional cross talk between the flagellar and SPI-1 regulons in Salmonella ( 52 ) .	4	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	activator	29555922	23	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	536	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	11	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	30355489	17	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	306	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	13	MULDER, D.T., MCPHEE, J.B., REID-YU, S.A., STOGIOS, P.J., SAVCHENKO, A., AND TJADEN, B. (2015). DE NOVO ASSEMBLY OF BACTERIAL TRANSCRIPTOMES FROM RNA- COOMBES, B.K. (2015). MULTIPLE HISTIDINES IN THE PERIPLASMIC DOMAIN OF THE SEQ DATA. GENOME BIOL. 16, 1.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	30420601	5	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	598	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	9	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	31484980	60	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	483	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	13	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	31488053	0	ver/dev	Moreover , HilD can activate the transcription of flhDC .	49	Moreover , HilD can activate the transcription of flhDC [ 7 ] , whereas RtsB , which is encoded in the same operon as RtsA , can repress the transcription of flhDC [ 10 ] .	5	BACKGROUND	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	TU	flhDC	activator	31488053	7	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	379	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	22	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	31501286	2	ver/dev	HilD , has also been shown to activate flhDC transcription , illustrating cross talk between pathogenicity-associated gene expression .	33	HilD , a key regulator of Salmonella pathogenicity island 1 ( SPI-1 ) , has also been shown to activate flhDC transcription , illustrating cross talk between flagellar and pathogenicity-associated gene expression ( 20 ) .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	flhDC	activator	31501286	2	ver/dev	HilD , has also been shown to activate flhDC transcription , illustrating cross talk between flagellar gene expression .	33	HilD , a key regulator of Salmonella pathogenicity island 1 ( SPI-1 ) , has also been shown to activate flhDC transcription , illustrating cross talk between flagellar and pathogenicity-associated gene expression ( 20 ) .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	flhDC	activator	33177235	0	ver/dev	The DNA binding protein HilD directly activates transcription of the flagellar master operon flhDC .	212	The DNA binding protein HilD is a dominant regulator of hilA transcription ( 39 ) and also directly activates transcription of the flagellar master operon flhDC ( 40 ) .	4	THE AUTHORS DECLARE NO COMPETING INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	33177235	4	ver/dev	H. M. Singer , C. Kühne , J. A. Deditius , K. T. Hughes , M. Erhardt , The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	664	H. M. Singer , C. Kühne , J. A. Deditius , K. T. Hughes , M. Erhardt , The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	6	MATERIALS AND METHODS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	33299016	13	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	489	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	16	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	33441540	1	ver/dev	HilD directly activates transcription of the agellar master operon flhDC by fl binding upstream of the P5 promoter21 .	38	HilD activates HilA16 ,25 and also directly activates transcription of the agellar master operon flhDC by fl binding upstream of the P5 promoter21 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	activator	33441540	26	ver/dev	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	535	The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .	8	RECEIVED: 15 SEPTEMBER 2020; ACCEPTED: 27 NOVEMBER 2020;	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	sseJ	activator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sseJ by both direct activation of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	pmrD	regulator	15703297	2	att	We used the model to analyze the intergenic regions of the Escherichia coli ( 40 ) and S. enterica ( 41 ) genomes by using relaxed thresholds ( 25 ) , which allowed the recovery of PhoP-regulated promoters with weak matching to the PhoP box consensus , such as the Salmonella pmrD promoter , that could not be detected by using consensus cutoffs ( 2 , 25 ) despite being regulated and footprinted by the PhoP protein ( 18 , 26 ) .	87	We used the model to analyze the intergenic regions of the Escherichia coli ( 40 ) and S. enterica ( 41 ) genomes by using relaxed thresholds ( 25 ) , which allowed the recovery of PhoP-regulated promoters with weak matching to the PhoP box consensus , such as the Salmonella pmrD promoter , that could not be detected by using consensus cutoffs ( 2 , 25 ) despite being regulated and footprinted by the PhoP protein ( 18 , 26 ) .	4	RESULTS	Escherichia coli;Salmonella;Salmonella;Salmonella	0.5	L1	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	pmrD	regulator	15703297	2	ver/dev	the Salmonella pmrD promoter could not be detected by using consensus cutoffs despite being regulated by the PhoP protein	87	We used the model to analyze the intergenic regions of the Escherichia coli ( 40 ) and S. enterica ( 41 ) genomes by using relaxed thresholds ( 25 ) , which allowed the recovery of PhoP-regulated promoters with weak matching to the PhoP box consensus , such as the Salmonella pmrD promoter , that could not be detected by using consensus cutoffs ( 2 , 25 ) despite being regulated and footprinted by the PhoP protein ( 18 , 26 ) .	4	RESULTS	Salmonella	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	pmrD	regulator	15703297	2	ver/dev	the Salmonella pmrD promoter could not be detected by using consensus cutoffs despite being regulated by the PhoP protein	87	We used the model to analyze the intergenic regions of the Escherichia coli ( 40 ) and S. enterica ( 41 ) genomes by using relaxed thresholds ( 25 ) , which allowed the recovery of PhoP-regulated promoters with weak matching to the PhoP box consensus , such as the Salmonella pmrD promoter , that could not be detected by using consensus cutoffs ( 2 , 25 ) despite being regulated and footprinted by the PhoP protein ( 18 , 26 ) .	4	RESULTS	Salmonella	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	pmrD	regulator	15703297	9	ver/dev	the pmrD promoter harbors binding sites for both the PhoP	115	We have previously identified a multicomponent loop in Sal-monella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA , and activated PmrA represses transcription from the pmrD promoter , which harbors binding sites for both the PhoP and PmrA proteins ( 18 ) ( Fig. 1D ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrD	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the pmrD promoters increased during the first 10 min .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the pmrD promoters increased during the first 10 min .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the pmrD promoters then asymptotically reached the steady-state levels .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the pmrD promoters then asymptotically reached the steady-state levels .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	regulator	18792679	20	att	PhoQlPhoP 's sole role in the PmrD-mediated pathway is to promote PmrD expression because transcription of the pmrD gene from a heterologous promoter renders production of PmrA-activated mRNAs phoP - and phoQ-independent .42 Moreover , the PhoP-regulated PmrD protein functions at a posttranslationallevel because expression ofPmrA-activared genes was still phoP - andpmrD-dependent when thepmrA andpmrBgenes were expressed using a heterologous promoter and ribosome-binding site .	234	PhoQlPhoP 's sole role in the PmrD-mediated pathway is to promote PmrD expression because transcription of the pmrD gene from a heterologous promoter renders production of PmrA-activated mRNAs phoP - and phoQ-independent .42 Moreover , the PhoP-regulated PmrD protein functions at a posttranslationallevel because expression ofPmrA-activared genes was still phoP - andpmrD-dependent when thepmrA andpmrBgenes were expressed using a heterologous promoter and ribosome-binding site .	9	PHOP AS A CO-ACTIVATOR PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	regulator	18792679	19	ver/dev	4-76 These PmrA-dependent changes increases bacterial resistance to serum '' to Fe3 +.78 When Salmonella experiences the PhoP protein binds to the pmrD promoter .	231	4-76 These PmrA-dependent changes increases bacterial resistance to serum '' to the antibiotic polymyxin B3S .42,49.7 S. 78.79 and to Fe3 +.78 When Salmonella experiences low Mg '' , the PhoP protein binds to the pmrD promoter and stimulates pmrD transcription.v The purified PmrD protein binds specifically to the phosphorylated form ofthe PmrA protein ( PmrA-P ) and protects it from dephosphorylation by the sensor PmrB .72 Because PmrA-P exhibits higher affinity for its target promoters than unphosphorylated PmrA , transcription ofPmrA-activated genes is stimulated and that ofPmrA-repressed genes are inhibited .	9	PHOP AS A CO-ACTIVATOR PROTEIN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrD	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RstA	gene	feoB	regulator	18790861	42	ver/dev	This result was correlated with regulation of the feoB gene in response to RstA activation : in the wild-type strain , iron decreased feoB transcription whereas RstA expression highly increased it .	229	This result was correlated with regulation of the feoB gene in response to iron and RstA activation : in the wild-type strain , iron decreased feoB transcription whereas RstA expression highly increased it , overcoming the Fur-Fe ( II ) protein-mediated repression ( Fig. 4 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoB	regulator	18790861	42	ver/dev	This result was correlated with regulation of the feoB gene in response to iron activation : in the wild-type strain , iron decreased feoB transcription whereas RstA expression highly increased it .	229	This result was correlated with regulation of the feoB gene in response to iron and RstA activation : in the wild-type strain , iron decreased feoB transcription whereas RstA expression highly increased it , overcoming the Fur-Fe ( II ) protein-mediated repression ( Fig. 4 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	ompR	regulator	14643403	27	ver/dev	For example , in E. coli , IHF has been shown to regulate transcription of the ompR .	208	For example , in E. coli , IHF has been shown to regulate transcription of the ompR -- envZ operon [ 49 ] , while rpoS , on the other hand , regulates the two spatially distant IHF subunits , especially ihfA at a transcriptional level [ 2 ] .	20	6.5. MLRA	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	argT	repressor	30682134	41	ver/dev	In LB , CsrA repressed the expression of the arginine permease argT .	290	In LB , CsrA repressed the expression of the arginine permease argT ( Fig 6A and S2 Table ) , which allows Salmonella to deplete arginine from its environment [ 107 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	csiD	regulator	14996792	54	att	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
CsrA	gene	pnp	repressor	30682134	48	ver/dev	CsrA in E. coli represses pnp expression	367	CsrA in E. coli represses hfq and pnp expression [ 121,122 ] , but we did not find effects on the expression of these genes in Salmonella ( S2 Table ) .	15	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrCAB	activator	10844688	3	ver/dev	Furthermore , PmrA activates the expression of several pags , including pmrCAB itself , under low cation conditions in a PhoP-dependent manner ; however , PmrA can also induce these genes under acid conditions in the absence of PhoPQ regardless of cation concentrations .	239	Furthermore , PmrA activates the expression of several pags , including pmrCAB itself , under low cation conditions in a PhoP-dependent manner ( Groisman , 1998 ) ; however , PmrA can also induce these genes under acid conditions in the absence of PhoPQ regardless of cation concentrations .	14	MISLEADING CLUES?	nan	1	L2	OTHER	Other	OTHER	New	Level 1
PmrA	gene	pmrCAB	activator	15205413	4	att	The PmrA/PmrB system is encoded by the pmrCAB operon and is apparently expressed from both a PmrA-activated promoter upstream of the pmrC gene ( 47 ) and a constitutive promoter within the pmrC coding region ( 14 , 41 ) .	31	The PmrA/PmrB system is encoded by the pmrCAB operon and is apparently expressed from both a PmrA-activated promoter upstream of the pmrC gene ( 47 ) and a constitutive promoter within the pmrC coding region ( 14 , 41 ) .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrCAB	activator	15205413	6	att	We recovered four open reading frames ( PmrC , YbiP , YhjW , and YijP ) ( Table 2 ) and decided to focus on the PmrC protein because it is encoded in the PmrA-dependent pmrCAB operon ( 41 ) and because we were interested in phosphoethanolamine modifications that are regulated by PmrA .	140	We recovered four open reading frames ( PmrC , YbiP , YhjW , and YijP ) ( Table 2 ) and decided to focus on the PmrC protein because it is encoded in the PmrA-dependent pmrCAB operon ( 41 ) and because we were interested in phosphoethanolamine modifications that are regulated by PmrA .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	spvA	regulator	21716657	0	ver/dev	The SpvR protein is a positive transcriptional regulator of the LysR family and binds to inverted repeat recognition sequences upstream of the spvA promoter .	54	The SpvR protein is a positive transcriptional regulator of the LysR family and binds to inverted repeat recognition sequences upstream of its own promoter and the spvA promoter ( Krause et al. , 1991 , 1995 ; Grob and Guiney , 1996 ; Grob et al. , 1997 ) .	3	THE SPV VIRULENCE LOCUS IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YdgT	gene	pefB	repressor	31661351	8	ver/dev	YdgT negatively regulate PefA expression by acting on the pefB promoter .	210	Hha and YdgT negatively regulate PefA expression by acting on the pefB promoter .	8	H-NS EXERTS ITS REPRESSION ACTIVITY MOSTLY ON THE PPEFB PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoB	gene	virK	activator	18407759	0	att	Synthesis of vitamin-B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin ( enterochelin ) and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F ( sigma-28 ) factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR ( or CreC ) PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB ( OmpR family ) aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold-shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine-sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor ( Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	222	Synthesis of vitamin B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin ( enterochelin ) and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F ( sigma 28 ) factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR ( or CreC ) PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB ( OmpR family ) aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor ( Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	18	RESULTS AND DISCUSSION	Salmonella;Salmonella;Enterobacteria phage Ox2;Salmonella	0.5	L2	SPEC	Other	OTHER	Other	Level 1
Lrp	gene	osmY	regulator	8045891	27	ver/dev	Complex transcriptional control of the osmotically regulated osmY gene suggests novel roles for Lrp .	382	Complex transcriptional control of the ars-dependent stationary-phase-in-duced and osmotically regulated osmY ( csi-5 ) gene suggests novel roles for Lrp , cyclic AMP ( cAMP ) receptor protein-cAMP complex , and integration host factor in the stationary-phase response of Eschenichia coli .	18	REFERENCES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	treA	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of treA .39 Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
OmpR	gene	hilD	repressor	28704543	51	ver/dev	OmpR is known to repress the expression of hilD .	308	OmpR is known to directly activate expression of ssrA-ssrB , and repress the expression of hilD [ 42 , 43 ] .	10	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PmrA	gene	ssrB	regulator	23690578	19	att	Importantly , the enrichment in ssrB promoter DNA was comparable to that of other known PmrA-regulated genes , including pmrC ( Fig. 4C ) .	86	Importantly , the enrichment in ssrB promoter DNA was comparable to that of other known PmrA-regulated genes , including pmrC ( Fig. 4C ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	ssrB	regulator	23690578	15	ver/dev	This analysis suggested that PmrA might bind to the ssrB promoter .	78	This analysis suggested that PmrA might bind to the ssrB promoter hampering ssrB transcription .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ssrB	regulator	23690578	18	ver/dev	Second , chromatin immunoprecipitation experiments revealed that an HA-tagged PmrA bound to the ssrB promoter in-vivo .	85	Second , chromatin immunoprecipitation experiments revealed that an HA-tagged PmrA expressed from its normal promoter and chromosomal location bound to the ssrB promoter in vivo but not to the ssaG promoter ( Fig. 4C ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	ssrB	regulator	23690578	30	ver/dev	PmrA binds to the promoter of the ssrB gene .	106	PmrA binds to the promoter of the ssrB gene .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssrB	regulator	23690578	32	ver/dev	Binding of PmrA to the ssrB promoter is required for PmrA-mediated repression of the SPI-2 ssaG gene .	119	Binding of PmrA to the ssrB promoter is required for PmrA-mediated repression of the SPI-2 ssaG gene .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ssrB	regulator	23690578	44	ver/dev	The PmrA protein directly binds to a specific sequence in the promoter of ssrB , repressing its expression .	170	The PmrA protein directly binds to a specific sequence in the promoter of ssrB , repressing its expression ( Figs. 4 and 5 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssrB	regulator	23690578	54	ver/dev	To identify the binding of PmrA to the promoter region of the ssrB gene were carried out as described .	202	To identify the binding of PmrA to the promoter region of the ssrB gene , chromatin immunoprecipitation ( 55 ) , electrophoretic mobility shift assay ( 55 ) , and DNase I footprinting assay ( 34 ) were carried out as described .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	ssrB	regulator	24643535	19	ver/dev	Interestingly , the PmrA protein repressed SPI-2 expression in a manner similar to the Fur regulator ; PmrA was shown to bind to a region overlapping with the SsrB-binding site on the ssrB promoter .	290	Interestingly , the PmrA protein repressed SPI-2 expression in a manner similar to the Fur regulator ; PmrA was shown to bind to a region overlapping with the SsrB-binding site on the ssrB promoter ( Fig. 4A ) and repress ssrB transcription ( 21 ) .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtcR	gene	malT	repressor	30201777	22	ver/dev	Although malT appeared to be downregulated in the absence of RtcR under MMC-induced stress conditions , visualization of the reads with Integrated Genome Viewer showed that this is most likely due to read-through transcription from rsrp into the 3 = end of the convergently transcribed malT gene -LRB- Fig. 6A -RRB- .	221	Although malT appeared to be downregulated in the absence of RtcR under MMC-induced stress conditions , visualization of the mapped reads with Integrated Genome Viewer showed that this is most likely due to read-through transcription from rsrp into the 3 = end of the convergently transcribed malT gene ( Fig. 6A ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	cdtB	regulator	29324231	0	ver/dev	Under PhoP-activating growth-conditions , PhoP was found to bind both cdtB promoter regions .	128	Under low magnesium ( PhoP-activating ) growth conditions , PhoP was found to bind both the pltB and cdtB promoter regions ( Figure 3D ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	cdtB	regulator	29324231	0	ver/dev	Under low magnesium growth-conditions , PhoP was found to bind both cdtB promoter regions .	128	Under low magnesium ( PhoP-activating ) growth conditions , PhoP was found to bind both the pltB and cdtB promoter regions ( Figure 3D ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
TviA	gene	hilA	repressor	17725646	1	ver/dev	In S. Typhi , TviA in conjunction with RcsB represses transcription of hilA .	94	In S. Typhi , TviA in conjunction with RcsB represses transcription of hilA ( iagA ) ( Arricau et al. , 1998 ) , which encodes a regulator of the invasion-associated type III secretion system ( T3SS-1 ) .	7	THE TVIA-DEPENDENT DECREASE IN IL-8 EXPRESSION IS INDEPENDENT OF THE INVASION-ASSOCIATED TYPE III SECRETION SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	pgtE	regulator	29487214	0	ver/dev	Expression of the pgtE transcript is controlled by the SPI2-associated regulators PhoPQ and SlyA .	91	Expression of the pgtE transcript is induced during intramacrophage replication ( 26 , 27 ) , controlled by the SPI2-associated regulators PhoPQ and SlyA ( 19 , 28 ) , and is activated by OmpR / EnvZ and SsrA/B ( 15 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	activator	18469103	8	ver/dev	Using the aTc-inducible expression system , we observed that FliZ is unable to increase the activity of Pclass2 promoters in the flhDC mutant -LRB- results not shown -RRB- .	281	Using the aTc-inducible expression system , we observed that FliZ is unable to increase the activity of Pclass2 promoters in the flhDC mutant ( results not shown ) .	5	RESULTS	unidentified	1	L2	OTHER	Analysis	NEG	Other	Level 1
FliZ	TU	flhDC	activator	18469103	15	ver/dev	FliZ is responsible for increased levels of FlhC protein independent of flhDC transcription .	359	FliZ is responsible for increased levels of FlhC protein independent of flhDC transcription .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	activator	26441883	14	ver/dev	FliZ is needed for eficient induction of the Spi-1 system via post-translational activation of the Spi-1 regulatory protein HilD , which in turn activates flhDC gene transcription .	350	FliZ is needed for eficient induction of the Spi-1 system via post-translational activation of the Spi-1 regulatory protein HilD , which in turn activates flhDC gene transcription ( Iyoda et al. , 2001 ; Chubiz et al. , 2010 ; Mouslim and Hughes , 2014 ; Singer et al. , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	activator	26561851	4	ver/dev	The flagellar regulator FliZ is a post-transcriptional activator of flhDC that positively regulates SPI1 by activating the hilD-rtsAB cascade .	209	The flagellar regulator FliZ is a post-transcriptional activator of flhDC that positively regulates SPI1 by activating the hilD-rtsAB cascade [ 74 ] .	8	RELATING INTRA-MACROPHAGE GENE EXPRESSION TO GENE FUNCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	activator	27206164	7	ver/dev	Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV .	48	Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV ( Chubiz et al. , 2010 ; Wada et al. , 2011 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	TU	flhDC	activator	29369799	0	ver/dev	FliZ increases flhDC synthesis through an unknown mechanism .	189	FliZ increases flhDC synthesis through an unknown mechanism [ 78 ] and represses ydiV transcription .	13	3.2. MOTILITY (FLIC)	unidentified	1	L3	SPEC	Fact	OTHER	Other	Level 1
CsrA	gene	rcsC	regulator	32392214	37	ver/dev	While this analysis suggests that CsrA may directly regulate rcsC translation , the rcsC mRNA was not identified as a CsrA target in a recent genome-wide mapping of CsrA binding sites in Salmonella .	359	While this analysis suggests that CsrA may directly regulate rcsC translation , the rcsC mRNA was not identified as a CsrA target in a recent genome-wide mapping of CsrA binding sites in Salmonella [ 29 ] .	18	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
PrpR	gene	prpB	activator	15528672	13	att	( a ) Quantitative analysis of the effect of 2-MC on the PrpR-dependent transcriptional activation of the prpB promoter .	372	( a ) Quantitative analysis of the effect of 2-MC on the PrpR-dependent transcriptional activation of the prpB promoter .	12	2-MC IS A POSITIVE EFFECTOR OF PRPR ACTIVITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PrpR	gene	prpB	activator	15528672	12	ver/dev	In vitro 2-MC-dependent activation of the prpB promoter by PrpR .	371	In vitro 2-MC-dependent activation of the prpB promoter by PrpR .	12	2-MC IS A POSITIVE EFFECTOR OF PRPR ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpB	activator	15528672	13	ver/dev	Quantitative analysis of the effect of 2-MC on the PrpR-dependent transcriptional activation of the prpB promoter .	372	( a ) Quantitative analysis of the effect of 2-MC on the PrpR-dependent transcriptional activation of the prpB promoter .	12	2-MC IS A POSITIVE EFFECTOR OF PRPR ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	lon	activator	26300871	34	ver/dev	CpxR , induces the transcription of lon .	480	FIGURE 7 | RpoH , but not CpxR , induces the transcription of lon , clpX , and clpP .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	lon	activator	26300871	35	ver/dev	Our results show that CpxR , induces the transcription of lon encoding the ClpXP protease .	491	Our results show that RpoH , but not CpxR , induces the transcription of lon , as well as of the clpX and clpP neighbor genes encoding the ClpXP protease .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	STM3176	regulator	24021902	2	ver/dev	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid-A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits modification of lipid-A STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	93	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits LpxO function ( modification of lipid A ) STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	6	INTRODUCTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	STM3176	regulator	24021902	2	ver/dev	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid-A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits LpxO function STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	93	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits LpxO function ( modification of lipid A ) STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	6	INTRODUCTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
Sigma28	gene	flgA	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgA by introduction of a null mutation in J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgA	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgA by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgA	repressor	9765570	4	ver/dev	Like all genes , mutations in any of the flgA result in FlgM-dependent inhibition of s28 activity .	90	Like all genes involved in HBB assembly , mutations in any of the flgA , flgH , and flgI genes result in FlgM-dependent inhibition of s28 activity ( 8 ) .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	narZ	regulator	31563538	7	ver/dev	To confirm the participation of RcsB in the transcriptional control of narZ , its expression was determined under other RcsCDB activation conditions .	198	To confirm the participation of RcsB in the transcriptional control of narZ , its expression was determined under other RcsCDB activation conditions .	12	3.3. EFFECT OF RCSCDB SUGAR-ACTIVATION ON NARZ GENE EXPRESSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	narZ	regulator	31563538	14	ver/dev	The results together demonstrate that RcsB can recognize a specific sequence in the nar promoter region to directly control narZ expression .	234	The results obtained from bioinformatic analysis of narZ gene expression and EMSA together demonstrate that RcsB can recognize a specific sequence in the nar promoter region to directly control narZ expression .	14	3.5. LOCATION OF RCSB BINDING SITE ON THE NAR OPERON PROMOTER REGION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
Lrp	gene	traJ	regulator	12067346	2	ver/dev	Gel retardation assays indicated that Lrp binds a DNA region upstream of the traJ promoter .	11	Gel retardation assays indicated that Lrp binds a DNA region upstream of the traJ promoter .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	traJ	regulator	12067346	11	ver/dev	Because the 84 bp fragments both contain the region homologous to the Lrp binding site , these observations provided evidence that Lrp binds to the UAS of traJ .	94	Because the 313 bp and the 84 bp fragments both contain the region homologous to the Lrp binding site , these observations provided evidence that Lrp binds to the UAS of traJ .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
Lrp	gene	traJ	regulator	12067346	11	ver/dev	Because the 313 bp both contain the region homologous to the Lrp binding site , these observations provided evidence that Lrp binds to the UAS of traJ .	94	Because the 313 bp and the 84 bp fragments both contain the region homologous to the Lrp binding site , these observations provided evidence that Lrp binds to the UAS of traJ .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
Lrp	gene	traJ	regulator	12067346	15	ver/dev	Retardation of the DNA fragment under study is clearly observed , thereby confirming that Lrp binds the traJ UAS .	105	Retardation of the DNA fragment under study is clearly observed , thereby confirming that Lrp binds the traJ UAS .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	traJ	regulator	12067346	21	ver/dev	We thus propose that binding of Lrp to the UAS upstream of traJ activates traJ transcription .	118	We thus propose that binding of Lrp to the UAS upstream of traJ activates traJ transcription .	5	DELETION ANALYSIS OF THE TRAJ UAS: EFFECT ON TRAJ EXPRESSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	traJ	regulator	12067346	21	ver/dev	We thus propose that binding of Lrp to the UAS upstream of traJ activates traJ transcription .	118	We thus propose that binding of Lrp to the UAS upstream of traJ activates traJ transcription .	5	DELETION ANALYSIS OF THE TRAJ UAS: EFFECT ON TRAJ EXPRESSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
Lrp	gene	traJ	regulator	18599829	2	ver/dev	In addition , Lrp controls the expression of the virulence plasmid traJ gene .	34	In addition , Lrp controls the expression of the virulence plasmid traJ gene ( Camacho & Casadesús , 2005 ) , allowing Lrp to influence the conjugal transfer of this episome ( Camacho & Casadesús , 2002 ) .	2	MAIN	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	traJ	regulator	19074398	4	att	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	25	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	2	MAIN	Salmonella;unidentified plasmid;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtBC	repressor	12492857	0	att	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtBC	repressor	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	map	activator	12535071	59	att	The 5 cents ends of the HilD-dependent products appear to map to an A and a T .	166	The 5 cents ends of the HilD-dependent products appear to map to an A and a T .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	sicA	activator	11755416	9	att	InvF requires SicA as a co-factor , so HilA-dependent expression of sicA may provide the SicA needed to initiate InvF/SicA-dependent PsicA-expression ( [ 55 ] ; K. Darwin and V. Miller , unpublished observations ) .	165	InvF requires SicA as a co-factor , so HilA-dependent expression of sicA may provide the SicA needed to initiate InvF/SicA-dependent PsicA-expression ( [ 55 ] ; K. Darwin and V. Miller , unpublished observations ) .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	sicA	activator	15765064	5	ver/dev	Apparently , HilA activates the expression of sicA .	58	Apparently , HilA activates the expression of invF and sicA , whose genes respectively encode an AraC/XylS transcriptional activator and a chaperone , that together activate transcription of the sip operon .	3	THE HILA REGULATOR	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilA	gene	sicA	activator	31428589	2	ver/dev	HilA directly activates the expression of sicA .	151	HilA directly activates the expression of two SPI-1 genes ( invF and sicA ) that encode SPI-1 T3SS apparatus components .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NarL	gene	narL	repressor	26099579	2	ver/dev	inactivation of narL did not reduce growth in the intes-tinal lumen , although NarL regulates metabolic genes	272	Remarkably , inactivation of narL did not reduce growth in the intes-tinal lumen , although NarL regulates a variety of metabolic genes , and this regulation includes activation of fdnGHI ( encoding formate dehydrogenase ) and repression of frdABCD ( encoding fumarate reductase ) , dmsABC ( encoding dimethyl sulfoxide [ DMSO ] reductase ) , dcuSR ( encoding a two-component system ) , and nrfABCDEFG and nirBDC ( encoding two nitrite reductases ) ( reviewed in reference 33 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
NarL	gene	narL	repressor	26099579	2	ver/dev	inactivation of narL did not reduce growth in the intes-tinal lumen , although NarL regulates a variety	272	Remarkably , inactivation of narL did not reduce growth in the intes-tinal lumen , although NarL regulates a variety of metabolic genes , and this regulation includes activation of fdnGHI ( encoding formate dehydrogenase ) and repression of frdABCD ( encoding fumarate reductase ) , dmsABC ( encoding dimethyl sulfoxide [ DMSO ] reductase ) , dcuSR ( encoding a two-component system ) , and nrfABCDEFG and nirBDC ( encoding two nitrite reductases ) ( reviewed in reference 33 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	pagO	regulator	21625519	8	ver/dev	various known PhoP _ regulated pagO	63	In the final pool of 93 sequenced clones we found a significant representation of various known PhoP regulated genes including pagO ( 5 times ) [ 26 ] ; mig-5 ( also known as PSLT046 ; 2 times ) [ 27 ] ; pmrD ( 2 times ) [ 28 ] ; and ybjX [ 29 ] , together with a dominant presence of sseL , which was hit 8 times .	5	RESULTS	nan	1	L3	OTHER	Fact	OTHER	New	Level 3
PhoP	gene	pagO	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Fur	gene	ftnA	repressor	17302823	1	ver/dev	Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
Fur	gene	ftnA	repressor	17302823	1	ver/dev	Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	katN	regulator	11260470	3	ver/dev	Consistent with a role for RpoS in the regulation of katN was not produced in the Salmonella rpoS Fig. 2A .	170	Consistent with a role for RpoS in the regulation of katN , the KatN protein was not produced in the Salmonella rpoS mutant SL1344K ( Fig. 2A ) .	8	TRANSCRIPTION OF KATN IS RPOS AND GROWTH PHASE DEPENDENT	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	katN	regulator	11260470	3	ver/dev	Consistent with a role for RpoS in the regulation of katN was not produced in the Salmonella rpoS mutant SL1344K .	170	Consistent with a role for RpoS in the regulation of katN , the KatN protein was not produced in the Salmonella rpoS mutant SL1344K ( Fig. 2A ) .	8	TRANSCRIPTION OF KATN IS RPOS AND GROWTH PHASE DEPENDENT	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	katN	regulator	34149657	1	att	yciE is in an operon with catalase katN and yciGF that contains a putative RpoS-regulated promoter ( Robbe-Saule et al. , 2001 ) .	418	yciE is in an operon with catalase katN and yciGF that contains a putative RpoS-regulated promoter ( Robbe-Saule et al. , 2001 ) .	24	TIME: 11:13 # 10	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RtsA	gene	hilD	regulator	17208038	32	ver/dev	Thus , RtsA are also apparently indirectly regulating hilD , contributing to the feedforward loop .	163	Thus , HilC and RtsA are also apparently indirectly regulating hilD , contributing to the feedforward loop .	11	REGULATION OF HILD	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RtsA	gene	hilD	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilD by RtsA .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilD	regulator	22479568	0	ver/dev	RtsA can activate expression of hilD of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilD	regulator	26039089	8	ver/dev	RtsA is a major regulator of both hilD expression of a feed-forward loop for activation of SPI1 expression .	181	RtsA is a major regulator of both hilA and hilD expression and forms part of a feed-forward loop for activation of SPI1 expression [ 53 ] .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	ompF	activator	30682134	28	ver/dev	CsrA activated expression of both ompF and ompC -LRB- S2 Table -RRB- .	255	CsrA activated expression of both ompF and ompC , which encode outer membrane porins ( S2 Table ) , and Holmqvist et al. identified a CLIP-seq peak in the 5 ' - UTR of ompC [ 52 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaL	activator	17630976	38	att	Our results indicated that transcription of ssaL and ssaM are indeed coupled in an SsrB-dependent manner ( Fig. 7B ) .	299	Our results indicated that transcription of ssaL and ssaM are indeed coupled in an SsrB-dependent manner ( Fig. 7B ) .	10	IDENTIFICATION OF SSRB-REGULATED GENES ON SPI-2	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	activator	15208313	1	att	We have recently established that the PhoP-activated ugtL gene is required for resistance to the antimicrobial peptides magainin 2 and polymyxin B .	8	We have recently established that the PhoP-activated ugtL gene is required for resistance to the antimicrobial peptides magainin 2 and polymyxin B .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15208313	10	att	The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .	33	The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15208313	15	att	The Regulatory Gene slyA Is Essential for Transcription of the PhoP-activated ugtL Gene -- We analyzed the 536-bp region upstream of the ugtL coding region but did not find an obvious PhoP box sequence resembling the ( T/G ) GTTTA-N5 - ( T / G ) GTTTA motif at an equivalent position as the PhoP box present in the promoter region of other PhoP-activated genes characterized in E. coli ( 14 , 15 , 30 ) and Salmonella ( 13 ) .	102	The Regulatory Gene slyA Is Essential for Transcription of the PhoP-activated ugtL Gene -- We analyzed the 536-bp region upstream of the ugtL coding region but did not find an obvious PhoP box sequence resembling the ( T/G ) GTTTA-N5 - ( T / G ) GTTTA motif at an equivalent position as the PhoP box present in the promoter region of other PhoP-activated genes characterized in E. coli ( 14 , 15 , 30 ) and Salmonella ( 13 ) .	4	RESULTS	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugtL	activator	15208313	15	att	The Regulatory Gene slyA Is Essential for Transcription of the PhoP-activated ugtL Gene -- We analyzed the 536-bp region upstream of the ugtL coding region but did not find an obvious PhoP box sequence resembling the ( T/G ) GTTTA-N5 - ( T / G ) GTTTA motif at an equivalent position as the PhoP box present in the promoter region of other PhoP-activated genes characterized in E. coli ( 14 , 15 , 30 ) and Salmonella ( 13 ) .	102	The Regulatory Gene slyA Is Essential for Transcription of the PhoP-activated ugtL Gene -- We analyzed the 536-bp region upstream of the ugtL coding region but did not find an obvious PhoP box sequence resembling the ( T/G ) GTTTA-N5 - ( T / G ) GTTTA motif at an equivalent position as the PhoP box present in the promoter region of other PhoP-activated genes characterized in E. coli ( 14 , 15 , 30 ) and Salmonella ( 13 ) .	4	RESULTS	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugtL	activator	15208313	16	att	Consistent with our previous results ( 22 ) , the low Mg2 activation of the ugtL gene was PhoP-dependent ( Fig. 1A ) .	107	Consistent with our previous results ( 22 ) , the low Mg2 activation of the ugtL gene was PhoP-dependent ( Fig. 1A ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15208313	52	att	Transcriptional Activation of the ugtL Promoter -- The majority of PhoP-activated promoters described to date harbor a conserved hexanucleotide repeat separated by 5 nucleotides , termed the PhoP box , located 12 bp upstream of the 10 region ( 14 ) .	193	Transcriptional Activation of the ugtL Promoter -- The majority of PhoP-activated promoters described to date harbor a conserved hexanucleotide repeat separated by 5 nucleotides , termed the PhoP box , located 12 bp upstream of the 10 region ( 14 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	activator	15208313	9	att	We have demonstrated recently that the PhoP-activated ugtL gene is required for a modification of the lipid-A mediating resistance to the antimicrobial peptides magainin 2 and poly-myxin B ( 21 ) .	32	We have demonstrated recently that the PhoP-activated ugtL gene is required for a modification of the lipid A mediating resistance to the antimicrobial peptides magainin 2 and poly-myxin B ( 21 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15208313	16	ver/dev	Consistent with the low Mg2 activation of the ugtL gene was PhoP-dependent .	107	Consistent with our previous results ( 22 ) , the low Mg2 activation of the ugtL gene was PhoP-dependent ( Fig. 1A ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15208313	32	ver/dev	the ugtL promoter _ performed with increasing amounts of PhoP proteins	142	B , DNase I footprinting analysis of the ugtL promoter performed with probes for the coding and noncoding strands ( see `` Experimental Procedures '' ) and increasing amounts of PhoP ( 15 , 30 , and 60 pmol ) or SlyA ( 5 , 15 , and 30 pmol ) proteins .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	15208313	41	ver/dev	the ugtL promoter _ performed with increasing amounts of the PhoP protein	160	B , DNase I footprinting analysis of the ugtL promoter performed with probes for the noncoding strand ( see `` Experimental Procedures '' ) and increasing amounts of the PhoP protein ( 15 , 30 , and 60 pmol ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	15225317	1	att	One of the clones harboured the PhoP-activated ugtL gene , deletion of which rendered Salmonella susceptible to magainin 2 and polymyxin B , but not defensin HNP-1 .	11	One of the clones harboured the PhoP-activated ugtL gene , deletion of which rendered Salmonella susceptible to magainin 2 and polymyxin B , but not defensin HNP-1 .	1	SUMMARY	Salmonella	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	ugtL	activator	15225317	13	att	The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .	156	The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	ugtL	activator	15225317	20	att	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	185	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15225317	25	att	The ugtL gene was first identified as part of a Salmonella-specific DNA region harbouring the PhoP-activated pcgL gene , which encodes a D-Ala-D-Ala dipeptidase ( Hilbert et al. , 1999 ) .	266	The ugtL gene was first identified as part of a Salmonella-specific DNA region harbouring the PhoP-activated pcgL gene , which encodes a D-Ala-D-Ala dipeptidase ( Hilbert et al. , 1999 ) .	9	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	15225317	28	att	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	338	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	ugtL	activator	15225317	6	att	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid-A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	37	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	3	2 ND POLYMYXIN B	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	activator	15225317	9	att	Three of the plasmids harboured two complete Salmonella-specific open reading frames ( ORFs ) : ugtL , a PhoP-activated gene of unknown function ( Hilbert et al. , 1999 ) ; and STM1600 , an uncharacterized ORF .	56	Three of the plasmids harboured two complete Salmonella-specific open reading frames ( ORFs ) : ugtL , a PhoP-activated gene of unknown function ( Hilbert et al. , 1999 ) ; and STM1600 , an uncharacterized ORF .	5	A SURVIVAL ENRICHMENT STRATEGY FOR RECOVERING PEPTIDE RESISTANCE GENES	Salmonella;Salmonella;unidentified	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	activator	15225317	2	ver/dev	both ugtL is post-tran-scriptionally activated by the PhoP	13	Inactivation of both ugtL and the regulatory gene pmrA , which controls lipid A modifications required for resistance to polymxyin B ( but not to magainin 2 ) and is post-tran-scriptionally activated by the PhoP -- PhoQ system , resulted in a strain that was as susceptible to poly-myxin B as a phoP mutant.The most frequently recovered clone harboured the yqjA gene , which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP-1 .	1	SUMMARY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	18270203	21	ver/dev	H-NS Remains Associated with the ugtL Promoters under Inducing Conditions -- The PhoP proteins could activate transcription of the ugtL genes by either displacing H-NS by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
PhoP	gene	ugtL	activator	18270203	21	ver/dev	H-NS Remains Associated with the ugtL Promoters under Inducing Conditions -- The PhoP proteins could activate transcription of the ugtL genes by either displacing H-NS from their respective promoters not involving removal of H-NS from the promoters .	188	H-NS Remains Associated with the pagC and ugtL Promoters under Inducing Conditions -- The PhoP and SlyA proteins could activate transcription of the pagC and ugtL genes by either displacing H-NS from their respective promoters or by counteracting its repressing effects in a manner not involving removal of H-NS from the promoters .	3	RESULTS	nan	1	L1	SPEC	Other	NEG	New	Level 1
PhoP	gene	ugtL	activator	18792679	8	att	The PhoP protein utilizes this architecture to promote expression of ugtL and possibly other PhoP-activated genes .	174	The PhoP protein utilizes this architecture to promote expression of ugtL and possibly other PhoP-activated genes .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	ugtL	activator	19091955	0	att	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL and pagC , in Salmonella ( 2 , 3 , 9 -- 11 ) .	18	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL and pagC , in Salmonella ( 2 , 3 , 9 -- 11 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	19091955	4	att	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	38	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus	0	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	ugtL	activator	19091955	1	ver/dev	To activate transcription of ugtL , both PhoP must bind to its promoter simultaneously .	19	To activate transcription of ugtL , both PhoP and SlyA must bind to its promoter simultaneously ( 2 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	21625519	58	att	The PhoP-activated promoters of ugtL [ 47 ] and iraP [ 48 ] harbor two PhoP binding sites , and one of the sites in each promoter overlaps with the 210 element .	202	The PhoP-activated promoters of ugtL [ 47 ] and iraP [ 48 ] harbor two PhoP binding sites , and one of the sites in each promoter overlaps with the 210 element .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	29739882	7	att	In addition , full activation of the PhoP/PhoQ system under mildly acidic pH requires the PhoP-activated gene ugtL , which encodes a protein that stimulates PhoQ autophosphorylation ( 30 ) .	124	In addition , full activation of the PhoP/PhoQ system under mildly acidic pH requires the PhoP-activated gene ugtL , which encodes a protein that stimulates PhoQ autophosphorylation ( 30 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	29739882	7	ver/dev	In addition , full activation of the PhoP/PhoQ system under mildly acidic pH requires the PhoP-activated gene ugtL .	124	In addition , full activation of the PhoP/PhoQ system under mildly acidic pH requires the PhoP-activated gene ugtL , which encodes a protein that stimulates PhoQ autophosphorylation ( 30 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	30373755	12	att	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	221	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	30373755	8	ver/dev	Using qRT-PCR , we validated the RNA-seq data for several PhoP-regulated genes and others , including upregulated PhoP-activated ugtL and pagD .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	30373755	8	ver/dev	Using qRT-PCR , we validated the RNA-seq data for several PhoP-regulated genes and others , including upregulated PhoP-activated ugtL and pagD .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	30373755	8	ver/dev	Using quantitative real-time PCR , we validated the RNA-seq data for several PhoP-regulated genes and others , including upregulated PhoP-activated ugtL and pagD .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	30373755	8	ver/dev	Using quantitative real-time PCR , we validated the RNA-seq data for several PhoP-regulated genes and others , including upregulated PhoP-activated ugtL and pagD .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	30992361	4	ver/dev	As shown previously , the PhoP / PhoQ two-component system built a feedforward loop in association with SlyA to activate transcription of ugtL , in a PhoP-activating condition .	75	As shown previously , the PhoP / PhoQ two-component system built a feedforward loop in association with SlyA to activate transcription of a polymyxin B resistance gene , ugtL , in a PhoP-activating condition ( 0.01 mM Mg2 ; referred to as low Mg2 ) ( 5 , 23 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	100	att	Given that PhoP-activated genes , including ugtL , are highly induced inside the vacuolar compartment of epithelial cells ( 76 ) , the PhoP activation mechanisms described in this paper may also take place in such cells during infection , and thus , promote Salmonella virulence .	424	Given that PhoP-activated genes , including ugtL , are highly induced inside the vacuolar compartment of epithelial cells ( 76 ) , the PhoP activation mechanisms described in this paper may also take place in such cells during infection , and thus , promote Salmonella virulence .	35	CONTROL OF THE VIRULENCE REGULATOR PHOP BY THE SSRB PROTEIN	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	activator	33045730	18	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	28	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	56	att	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	255	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	activator	33045730	64	att	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	283	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	72	att	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	316	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	30	B	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	75	att	The mRNA abundance of the PhoP-activated ugtL , pagC and ssrB genes was similar among wild-type , ugtL-sifBmu mutant and ssrB null strains at 1 h post bacterial internalization by macrophages ( Figure 5B ) .	328	The mRNA abundance of the PhoP-activated ugtL , pagC and ssrB genes was similar among wild-type , ugtL-sifBmu mutant and ssrB null strains at 1 h post bacterial internalization by macrophages ( Figure 5B ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	77	att	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	340	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	activator	33045730	45	ver/dev	Critically , ugtL transcription from a heterologous promoter bypasses the need for a mildly acidic pH for activation of the PhoP protein .	243	Critically , ugtL transcription from a heterologous promoter bypasses the SsrB requirement ( Supplemental Figure S8 ) but not the need for a mildly acidic pH ( Supplemental Figure S8 ) for activation of the PhoP protein .	26	SSRB ACTIVATES PHOP BY PROMOTING TRANSCRIPTION OF THE UGTL GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	33045730	45	ver/dev	Critically , ugtL transcription from a heterologous promoter bypasses the SsrB requirement for a mildly acidic pH for activation of the PhoP protein .	243	Critically , ugtL transcription from a heterologous promoter bypasses the SsrB requirement ( Supplemental Figure S8 ) but not the need for a mildly acidic pH ( Supplemental Figure S8 ) for activation of the PhoP protein .	26	SSRB ACTIVATES PHOP BY PROMOTING TRANSCRIPTION OF THE UGTL GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	activator	33045730	99	ver/dev	Our findings suggest that the SsrB-mediated induction of the ugtL gene contributes to virulence in an animal host by generating active PhoP protein .	423	Our findings suggest that the SsrB-mediated induction of the ugtL gene taking place inside macrophages ( Figure 5B ) contributes to virulence in an animal host ( Figure 5A and Supplemental Figure S9 ) by generating active PhoP protein ( Figure 5B ) .	35	CONTROL OF THE VIRULENCE REGULATOR PHOP BY THE SSRB PROTEIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	scsA	regulator	29866803	6	att	( C ) - Galactosidase activity determined for wild-type cells carrying scsA : : lacZ ( scsA-lacZ ) or cpxP : : lacZ ( cpxP-lacZ ) ( included as a CpxR-regulated positive control ) transcriptional-fusions and transformed either with the empty vector pUHE21-2lacIq ( vector ) or with pNlpE and then grown in LB-medium with the addition of 100 M IPTG .	118	( C ) - Galactosidase activity determined for wild-type cells carrying scsA : : lacZ ( scsA-lacZ ) or cpxP : : lacZ ( cpxP-lacZ ) ( included as a CpxR-regulated positive control ) transcriptional fusions and transformed either with the empty vector pUHE21-2lacIq ( vector ) or with pNlpE and then grown in LB medium with the addition of 100 M IPTG .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
RpoS	gene	STM0319	regulator	32044996	0	ver/dev	STM0319 NP .1 Binds RpoS	169	STM0319 NP_459316 .1 Binds RpoS and increases its activity	9	INFERRING SELECTION FOR INACTIVATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	ptsG	repressor	23935052	2	ver/dev	Expression of ptsG , is repressed by Mlc .	614	Expression of ptsG , the gene for the major glucose PTS transporter in Escherichia coli , is repressed by Mlc and induced by growth on glucose .	15	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM3138	repressor	27564394	9	ver/dev	STM3138 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI4-encoded genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM3138	repressor	27564394	9	ver/dev	STM3138 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-associated genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM3138	repressor	27564394	9	ver/dev	STM3138 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-encoded genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	regulator	18599829	7	ver/dev	Purified Lrp binds to the lrp promoter region	159	Purified Lrp binds to the lrp promoter region	7	PURIFIED LRP BINDS TO THE LRP PROMOTER REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	lrp	regulator	18599829	9	ver/dev	that Lrp could bind to the lrp regulatory region in the absence of amino-acids	165	These results showed that Lrp could bind to the lrp regulatory region in the absence of amino acids and that leucine could modulate this process .	7	PURIFIED LRP BINDS TO THE LRP PROMOTER REGION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
Lrp	gene	lrp	regulator	18599829	13	ver/dev	It has been shown previously that leucine does not alter the binding of Lrp to the regulatory region of the E. coli lrp gene .	200	It has been shown previously that leucine does not alter the binding of Lrp to the regulatory region of the E. coli lrp gene ( Wang et al. , 1994 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	NEG	Other	Level 1
Lrp	gene	lrp	regulator	18599829	18	ver/dev	The modifications to the patterns of hypersensitivity seen in the lrp regulatory region in the presence and absence of leucine are consistent with an adjustment to the Lrp -- DNA contacts due to the influence of the amino-acid on Lrp protein structure .	258	The modifications to the patterns of protection and hypersensitivity seen in the lrp regulatory region in the presence and absence of leucine are consistent with an adjustment to the Lrp -- DNA contacts due to the influence of the amino acid on Lrp protein structure .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	regulator	18599829	18	ver/dev	The modifications to the patterns of protection seen in the lrp regulatory region in the presence and absence of leucine are consistent with an adjustment to the Lrp -- DNA contacts due to the influence of the amino-acid on Lrp protein structure .	258	The modifications to the patterns of protection and hypersensitivity seen in the lrp regulatory region in the presence and absence of leucine are consistent with an adjustment to the Lrp -- DNA contacts due to the influence of the amino acid on Lrp protein structure .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	regulator	18599829	21	ver/dev	The effect of adding leucine is not to remodel it so that the negative influence of the Lrp protein on lrp promoter function is attenuated .	262	The effect of adding leucine is not to abolish Lrp -- DNA interaction , but to remodel it so that the negative influence of the Lrp protein on lrp promoter function is attenuated .	8	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Lrp	gene	lrp	regulator	18599829	21	ver/dev	The effect of adding leucine is not to abolish DNA interaction so that the negative influence of the Lrp protein on lrp promoter function is attenuated .	262	The effect of adding leucine is not to abolish Lrp -- DNA interaction , but to remodel it so that the negative influence of the Lrp protein on lrp promoter function is attenuated .	8	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Lrp	gene	lrp	regulator	18599829	21	ver/dev	The effect of adding leucine is not to abolish Lrp so that the negative influence of the Lrp protein on lrp promoter function is attenuated .	262	The effect of adding leucine is not to abolish Lrp -- DNA interaction , but to remodel it so that the negative influence of the Lrp protein on lrp promoter function is attenuated .	8	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Lrp	gene	lrp	regulator	19074398	26	ver/dev	Recently , expression of the lrp gene in serovar Typhimurium SL1344 was found to be autoregulated by direct interaction between Lrp .	342	Recently , expression of the lrp gene in serovar Typhimurium SL1344 was found to be autoregulated by direct interaction between Lrp and its promoter , Plrp ( 66 ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	regulator	27909434	8	att	of Lrp-regulated genes in chromosome lrp mutants .	287	of Lrp-regulated genes in chromosome lrp mutants .	25	ACETYLATION OF K36 AFFECTS THE EXPRESSION OF LRP REGULON	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	lrp	regulator	27909434	9	att	of Lrp-regulated genes in chromosome lrp mutants .	314	of Lrp-regulated genes in chromosome lrp mutants .	25	ACETYLATION OF K36 AFFECTS THE EXPRESSION OF LRP REGULON	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	lrp	regulator	32284321	4	ver/dev	The specific CAT activities were similar in the lrp mutant , indicating that Lrp alone is not involved in the regulation of the ltrR1 coding region .	145	The specific CAT activities observed were similar in the wild-type strain and the lrp mutant ( Fig. 4B ) , indicating that Lrp alone is not involved in the regulation of the ltrR1 coding region .	3	RESULTS	Felis catus	0	L2	SPEC	Analysis	NEG	Other	Level 1
AcrR	gene	acrR	regulator	19946377	2	ver/dev	Amplification of the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , RamR exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers .	492	Amplification of the QRDRs of gyrA , gyrB , parC , and parE , as well as the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , the transcriptional regulators SoxS , MarA and RamR exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers listed in Table 5 .	20	SUSCEPTIBILITY TESTING	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
AcrR	gene	acrR	regulator	19946377	2	ver/dev	Amplification of the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , MarA exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers .	492	Amplification of the QRDRs of gyrA , gyrB , parC , and parE , as well as the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , the transcriptional regulators SoxS , MarA and RamR exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers listed in Table 5 .	20	SUSCEPTIBILITY TESTING	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
AcrR	gene	acrR	regulator	19946377	2	ver/dev	Amplification of the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , the transcriptional regulators SoxS exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers .	492	Amplification of the QRDRs of gyrA , gyrB , parC , and parE , as well as the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , the transcriptional regulators SoxS , MarA and RamR exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers listed in Table 5 .	20	SUSCEPTIBILITY TESTING	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	pmrC	activator	12507481	1	att	The system consists of a set of two strains that harbor a lac transcriptional-fusion to the chromosomal copy of the PhoP-activated pmrC gene .	39	The system consists of a set of two strains that harbor a lac transcriptional fusion to the chromosomal copy of the PhoP-activated pmrC gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	12507481	10	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 harboring plasmids expressing wild-type ( phoQ ) , mutated phoQs or plasmid vector ( vector ) .	145	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 harboring plasmids expressing wild-type ( phoQ ) , mutated phoQs or plasmid vector ( vector ) .	5	THE PUTATIVE SITE PHOSPHORYLATION OF PHOQ IS DISPENSABLE FOR REPRESSION OF PHOP-MEDIATED TRANSCRIPTION DURING GROWTH IN HIGH MG21	unidentified plasmid	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	pmrC	activator	12507481	11	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) or by strain EG5931 ( b ) and ( c ) , and harboring plasmids expressing wild-type ( pphoQ ) , mutated phoQs or plasmid vector ( vector ) .	156	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) or by strain EG5931 ( b ) and ( c ) , and harboring plasmids expressing wild-type ( pphoQ ) , mutated phoQs or plasmid vector ( vector ) .	5	THE PUTATIVE SITE PHOSPHORYLATION OF PHOQ IS DISPENSABLE FOR REPRESSION OF PHOP-MEDIATED TRANSCRIPTION DURING GROWTH IN HIGH MG21	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	12507481	2	att	Mg2þ-dependent repression of the PhoP-activated pmrC gene requires the periplasmic domain of the PhoQ protein .	54	Mg2þ-dependent repression of the PhoP-activated pmrC gene requires the periplasmic domain of the PhoQ protein .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	12507481	3	att	( a ) The ZhoQ chimera consisting of the periplasmic domain of the sensor EnvZ fused to the cytoplasmic domain of the PhoQ protein promotes high expression of the PhoP-activated pmrC gene in high Mg2þ , and ( b ) fails to down-regulate PhoPp-mediated gene expression in high Mg2þ .	55	( a ) The ZhoQ chimera consisting of the periplasmic domain of the sensor EnvZ fused to the cytoplasmic domain of the PhoQ protein promotes high expression of the PhoP-activated pmrC gene in high Mg2þ , and ( b ) fails to down-regulate PhoPp-mediated gene expression in high Mg2þ .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrC	activator	12507481	4	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , or by strain EG5931 ( b ) , and harboring plasmids expressing plasmid vector ( vector ) , wild-type phoQ ( pphoQ ) or zhoQ ( pzhoQ ) .	56	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , or by strain EG5931 ( b ) , and harboring plasmids expressing plasmid vector ( vector ) , wild-type phoQ ( pphoQ ) or zhoQ ( pzhoQ ) .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	pmrC	activator	12507481	5	att	( a ) PhoQ derivatives with amino-acid substitutions in conserved residues in the periplasmic domain of PhoQ that do not alter transcription of the PhoP-activated pmrC gene in response to Mg2þ .	87	( a ) PhoQ derivatives with amino acid substitutions in conserved residues in the periplasmic domain of PhoQ that do not alter transcription of the PhoP-activated pmrC gene in response to Mg2þ .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	pmrC	activator	12507481	6	att	( b ) PhoQ derivatives with amino-acid substitutions in conserved residues in the periplasmic domain of PhoQ that allow transcription of the PhoP-activated pmrC gene in high Mg2þ .	88	( b ) PhoQ derivatives with amino acid substitutions in conserved residues in the periplasmic domain of PhoQ that allow transcription of the PhoP-activated pmrC gene in high Mg2þ .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	12507481	7	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , ( b ) and ( d ) or by strain EG5931 ( c ) , and harboring plasmids expressing wild-type ( pphoQ and pphoP phoQ ) , mutated phoQs or plasmid vector ( vector ) .	91	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , ( b ) and ( d ) or by strain EG5931 ( c ) , and harboring plasmids expressing wild-type ( pphoQ and pphoP phoQ ) , mutated phoQs or plasmid vector ( vector ) .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	12507481	8	att	( a ) b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 and harboring plasmids expressing plasmid vector ( vector ) , wild-type ( pphoQ ) , or PhoQ variants with mutations D149A , D150A , D151A and D152A .	97	( a ) b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 and harboring plasmids expressing plasmid vector ( vector ) , wild-type ( pphoQ ) , or PhoQ variants with mutations D149A , D150A , D151A and D152A .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	12507481	9	att	( c ) b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG5931 ( b ) , and harboring plasmids expressing plasmid vector ( vector ) , wild-type ( pphoQ ) , or PhoQ variants with mutations D149A , D150A , D151A and D152A .	99	( c ) b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG5931 ( b ) , and harboring plasmids expressing plasmid vector ( vector ) , wild-type ( pphoQ ) , or PhoQ variants with mutations D149A , D150A , D151A and D152A .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	activator	29739882	16	att	Likewise , the pmrC gene was highly induced in low Mg2 + ( Fig. 3 ) but the lipid-A did not contain detectable pEtN ( Fig. 4B ) , due to preceding PhoP-dependent lpxT transcription ( Fig. 3 ) favoring incorporation of L-Ara4N over incorporation of pEtN ( Fig. 4B ) .	194	Likewise , the pmrC gene was highly induced in low Mg2 + ( Fig. 3 ) but the lipid A did not contain detectable pEtN ( Fig. 4B ) , due to preceding PhoP-dependent lpxT transcription ( Fig. 3 ) favoring incorporation of L-Ara4N over incorporation of pEtN ( Fig. 4B ) .	6	DISCUSSION	nan	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	invB	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	STM3030	regulator	30448437	1	ver/dev	The binding of the regulator BaeR to the role of STM3030 in antibiotic resistance were also examined .	47	The binding of the regulator BaeR to the promoters of both genes and the role of STM3030 in antibiotic resistance were also examined .	3	INTRODUCTION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
SirA	gene	invF	regulator	10672185	7	ver/dev	The pattern of hilA-dependent regulation of prgH by BarA together with partially hilA-indepen-dent regulation of invF by BarA parallels the pattern recently reported for SirA .	155	The pattern of hilA-dependent regulation of prgH by BarA together with partially hilA-indepen-dent regulation of invF by BarA parallels the pattern recently reported for SirA ( Rakeman et al. , 1999 ) , which we have con ® rmed under our culture conditions ( Table 3 ) .	8	INTEGRATION OF MULTIPLE INVASION REGULATORS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Cra	gene	ppsA	activator	20676398	2	ver/dev	Cra protein activates ppsA , pckA , fbp	277	Under the conditions investigated , it is assumed that carbon flux is controlled by the catabolite repressor/activator ( Cra ) protein , which activates gluconeogenesis enzymes ( ppsA , pckA , fbp ) and represses sugar catabolism enzymes [ 61 ] .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CadC	gene	lysP	regulator	23066934	11	ver/dev	These results suggest that the lysine signal represses lysP expression , thereby eliminating the negative regulation of CadC activation by LysP .	212	These results suggest that the lysine signal represses lysP expression , thereby eliminating the negative regulation of CadC activation by LysP .	16	S. TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
AraC	gene	garL	regulator	24272778	16	att	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	222	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	wza	activator	33751923	21	ver/dev	When phosphorylated , RcsB binds RcsA to activate expression of wza .	645	When phosphorylated , RcsB binds RcsA to activate expression of several genes , such as osmB , osmC , bdm , ftsZ , rprA , wza , and rcsA .	25	RCSBCD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	fliA	regulator	24031550	8	ver/dev	fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of fliA by OmpR .	268	fljB : z66 at low osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC and fliA by OmpR .	5	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CpxR	gene	mdtA	regulator	23651595	8	ver/dev	Although CpxR also regulates transcription of mdtA , cpxR deletion strains is critically required for S. Typhimurium resistance to Na2WO4 .	337	Although CpxR also regulates transcription of mdtA and acrD , cpxR deletion strains do not possess a tungstate-sensitive phenotype , suggesting that BaeR is the primary regulator of these genes in response to tungstate waste removal and is critically required for S. Typhimurium resistance to Na2WO4 ( Appia-Ayme et al. , 2011 ) .	18	2.3.2. THE BAE PATHWAY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	mdtA	regulator	23651595	8	ver/dev	Although CpxR also regulates transcription of mdtA , cpxR deletion strains do not possess a tungstate-sensitive phenotype .	337	Although CpxR also regulates transcription of mdtA and acrD , cpxR deletion strains do not possess a tungstate-sensitive phenotype , suggesting that BaeR is the primary regulator of these genes in response to tungstate waste removal and is critically required for S. Typhimurium resistance to Na2WO4 ( Appia-Ayme et al. , 2011 ) .	18	2.3.2. THE BAE PATHWAY	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	STM1253	regulator	15681155	16	ver/dev	Using site directed mutagenesis , Marchal et al. demonstrated that the fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1253 promoters .	261	Using site directed mutagenesis , Marchal et al. [ 35 ] demonstrated that the third and fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 , STM1253 and STM4118 promoters .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM1253	regulator	15681155	16	ver/dev	Using site directed mutagenesis , Marchal et al. demonstrated that the third positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1253 promoters .	261	Using site directed mutagenesis , Marchal et al. [ 35 ] demonstrated that the third and fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 , STM1253 and STM4118 promoters .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	malT	activator	28373272	3	ver/dev	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cAMP and cAMP-receptor-protein -LRB- CRP -RRB- .	320	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT when bound by ATP and maltotriose ; transcription of malT is positively regulated by cyclic AMP ( cAMP ) and cAMP receptor protein ( CRP ) ( 58 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	malT	activator	28373272	3	ver/dev	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cyclic AMP and cAMP-receptor-protein -LRB- CRP -RRB- .	320	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT when bound by ATP and maltotriose ; transcription of malT is positively regulated by cyclic AMP ( cAMP ) and cAMP receptor protein ( CRP ) ( 58 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	csgBA	regulator	33251260	17	ver/dev	Both RpoD and RpoS regulate csgBA promoter expression in Salmonella .	360	Both RpoD and RpoS can interact with RNA polymerase and regulate csgBA promoter expression in Salmonella ( 5 ) .	18	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	sipC	activator	21168230	5	ver/dev	In addition , HilC directly activate sipC in non-HilA dependent manner .	344	In addition , HilD and HilC directly activate invF , sipA and sipC in non-HilA dependent manner ( Akbar et al. , 2003 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcnR	gene	rcnA	activator	21722794	8	ver/dev	The expression of rcnA is specifically induced by cobalt via the derepressor RcnR .	702	The expression of rcnA is specifically induced by nickel and cobalt via the derepressor RcnR .	24	6.2. TRANSCRIPTIONAL REGULATION BY RCNR AND RCNA METAL EXPORT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcnR	gene	rcnA	activator	21722794	8	ver/dev	The expression of rcnA is specifically induced by nickel via the derepressor RcnR .	702	The expression of rcnA is specifically induced by nickel and cobalt via the derepressor RcnR .	24	6.2. TRANSCRIPTIONAL REGULATION BY RCNR AND RCNA METAL EXPORT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	hilD	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the occurrence of autogenous activation of hilD transcription .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ams	activator	16045614	14	att	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	68	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	4	INTRODUCTION	unidentified	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	TU	acrAB	activator	18577510	2	ver/dev	Other regulators of AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
SlyA	gene	slyA	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
SlyA	gene	slyA	activator	19091955	9	att	The up-52 fragment in pYS1033 controls lacZ expression in a SlyA-dependent manner because - galactosidase activity is 4.7-fold lower in the slyA mutant than in wild type ( Fig. 1C ) .	68	The up-52 fragment in pYS1033 controls lacZ expression in a SlyA-dependent manner because - galactosidase activity is 4.7-fold lower in the slyA mutant than in wild type ( Fig. 1C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	activator	19091955	23	ver/dev	Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by SlyA because the mRNA level of transcripts is reduced significantly in the slyA mutants grown in low-Mg2 conditions -LRB- Fig .	147	Our results from primer extension demonstrate that transcriptions of the identified loci are activated by PhoP and SlyA because the mRNA level of transcripts is reduced significantly in the phoP and slyA mutants grown in low-Mg2 conditions ( Fig .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	synthetic construct	0	L2	OTHER	Analysis	OTHER	Other	Level 1
SlyA	gene	slyA	activator	32969666	2	att	SlyA ( encoded by slyA ) is a dimeric helix-turn-helix transcriptional regulator belonging to the MarR superfamily of bacterial transcription factors .3 It has been suggested that the full virulence of S. typhimurium , e.g. , resistance to the oxidative-stress and secretion of antimicrobial peptide , is SlyA-dependent .4 − 6 In addition , the LD50 value of a slyA null mutant is > 1000-fold higher than that of the wild-type ( WT )	31	SlyA ( encoded by slyA ) is a dimeric helix-turn-helix transcriptional regulator belonging to the MarR superfamily of bacterial transcription factors .3 It has been suggested that the full virulence of S. typhimurium , e.g. , resistance to the oxidative stress and secretion of antimicrobial peptide , is SlyA-dependent .4 − 6 In addition , the LD50 value of a slyA null mutant is > 1000-fold higher than that of the wild-type ( WT )	2	MAIN	Cantareus apertus;Cornu aspersum;Cantareus apertus;Cornu aspersum;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	slyA	activator	32969666	2	att	SlyA ( encoded by slyA ) is a dimeric helix-turn-helix transcriptional regulator belonging to the MarR superfamily of bacterial transcription factors .3 It has been suggested that the full virulence of S. typhimurium , e.g. , resistance to the oxidative-stress and secretion of antimicrobial peptide , is SlyA-dependent .4 − 6 In addition , the LD50 value of a slyA null mutant is > 1000-fold higher than that of the wild-type ( WT )	31	SlyA ( encoded by slyA ) is a dimeric helix-turn-helix transcriptional regulator belonging to the MarR superfamily of bacterial transcription factors .3 It has been suggested that the full virulence of S. typhimurium , e.g. , resistance to the oxidative stress and secretion of antimicrobial peptide , is SlyA-dependent .4 − 6 In addition , the LD50 value of a slyA null mutant is > 1000-fold higher than that of the wild-type ( WT )	2	MAIN	Cantareus apertus;Cornu aspersum;Cantareus apertus;Cornu aspersum;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	barA	activator	10672185	8	ver/dev	However , when SirA is overproduced in a barA mutant there is strong stimulation of invasion gene expression .	158	However , when SirA is overproduced in a barA mutant there is strong stimulation of invasion gene expression ( Table 3 ) , which we consider in the Discussion .	8	INTEGRATION OF MULTIPLE INVASION REGULATORS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	barA	activator	32392214	19	att	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
MarR	TU	marRAB	activator	10856650	1	ver/dev	While normally repressed by MarR , a mutation within the marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance .	29	While normally repressed by MarR , a mutation within the marR or marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance that can be overcome by overexpression of wild-type MarR [ 5 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	activator	10856650	1	ver/dev	While normally repressed by MarR , a mutation within the marR genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance .	29	While normally repressed by MarR , a mutation within the marR or marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance that can be overcome by overexpression of wild-type MarR [ 5 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	activator	15073288	6	ver/dev	an inducer of marRAB activity , has been shown to bind the repressor MarR , leading to an increase in transcriptional activity of the operon .	202	Salicylate , an inducer of marRAB activity , has been shown to bind the repressor MarR , leading to an increase in transcriptional activity of the operon ( Cohen et al. , 1993 ; Martin & Rosner , 1995 ) .	10	DEOXYCHOLATE SPECIFICALLY INTERACTS WITH MARR	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarR	TU	marRAB	activator	15073288	7	ver/dev	Because transcriptional activation of marRAB is specific for deoxycholate , studies concerning interactions of deoxycholate with the repressor MarR were initiated .	203	Because transcriptional activation of marRAB is specific for deoxycholate and because MarR has been observed to bind a variety of structurally different compounds ( Schumacher & Brennan , 2002 ) , studies concerning interactions of deoxycholate with the repressor MarR were initiated .	10	DEOXYCHOLATE SPECIFICALLY INTERACTS WITH MARR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	activator	15073288	7	ver/dev	Because transcriptional activation of marRAB is specific because MarR has been observed to bind structurally different compounds , studies concerning interactions of deoxycholate with the repressor MarR were initiated .	203	Because transcriptional activation of marRAB is specific for deoxycholate and because MarR has been observed to bind a variety of structurally different compounds ( Schumacher & Brennan , 2002 ) , studies concerning interactions of deoxycholate with the repressor MarR were initiated .	10	DEOXYCHOLATE SPECIFICALLY INTERACTS WITH MARR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	activator	15073288	7	ver/dev	Because transcriptional activation of marRAB is specific because MarR has been observed to bind a variety , studies concerning interactions of deoxycholate with the repressor MarR were initiated .	203	Because transcriptional activation of marRAB is specific for deoxycholate and because MarR has been observed to bind a variety of structurally different compounds ( Schumacher & Brennan , 2002 ) , studies concerning interactions of deoxycholate with the repressor MarR were initiated .	10	DEOXYCHOLATE SPECIFICALLY INTERACTS WITH MARR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	activator	19120970	7	ver/dev	Thus induction of marRAB by DEC without inhibition of the repression activity of MarR is expected to be less effective than induction with SAL .	195	Thus induction of marRAB by DEC without inhibition of the repression activity of MarR is expected to be less effective than induction with SAL .	18	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarR	TU	marRAB	activator	33024855	7	ver/dev	Salicylates , are known inducers of the marRAB operon by binding to MarR .	316	Salicylates , found in abundance in tomato , are known inducers of the marRAB operon by binding to MarR which represses expression of marRAB .	11	3.2. STRESS RESPONSE AND PLANT HOST ADAPTATION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilC	gene	hilC	repressor	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	clpP	activator	26300871	34	ver/dev	CpxR , induces the transcription of clpP .	480	FIGURE 7 | RpoH , but not CpxR , induces the transcription of lon , clpX , and clpP .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	clpP	activator	26300871	35	ver/dev	Our results show that CpxR , induces the transcription of clpP neighbor genes encoding the ClpXP protease .	491	Our results show that RpoH , but not CpxR , induces the transcription of lon , as well as of the clpX and clpP neighbor genes encoding the ClpXP protease .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	ompW	activator	19460824	2	att	The SoxS site is in the forward orientation and its location suggests that the ompW gene has a class I SoxS-dependent promoter .	20	The SoxS site is in the forward orientation and its location suggests that the ompW gene has a class I SoxS-dependent promoter .	0	Unknown	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxS	gene	ompW	activator	19460824	7	att	These results support the notion that the activation of ompW is SoxS-dependent .	139	These results support the notion that the activation of ompW is SoxS-dependent .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	ompW	activator	19460824	7	ver/dev	These results support the notion that the activation of ompW is SoxS-dependent .	139	These results support the notion that the activation of ompW is SoxS-dependent .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	ompW	activator	19460824	14	ver/dev	SoxS-mediated activation of ompW is the result of a direct interaction between the promoter and SoxS	187	Binding of purified SoxS to the ompW promoter strongly suggests that the PQ - and SoxS-mediated activation of ompW is the result of a direct interaction between the promoter and SoxS .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	osmY	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of osmY Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	14	ver/dev	Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of OFF subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -	79	Single cell analysis of gene expression by flow cytometry ( Fig. 2 ) confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : ( i ) activation of leuO expression decreased the activity of a sipB : : GFP fusion , abolishing bistable SPI-1 expression ; ( ii ) lack of LeuO restored the wild type pattern of sipB : : GFP expression , indicating that SPI-1 downregulation was caused by LeuO indeed ; ( iii ) a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 ( OFF ) subpopulation , in agreement with the role of HilE as a SPI-1 repressor ( Baxter et al. , 2003 ) ; ( iv ) activation of leuO expression in a HilE − background yielded a small subpopulation of sipB - : : GFP ( OFF ) cells ; and ( v ) absence of both LeuO and HilE restored the wild type pattern of sipB : : GFP expression .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	14	ver/dev	Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -	79	Single cell analysis of gene expression by flow cytometry ( Fig. 2 ) confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : ( i ) activation of leuO expression decreased the activity of a sipB : : GFP fusion , abolishing bistable SPI-1 expression ; ( ii ) lack of LeuO restored the wild type pattern of sipB : : GFP expression , indicating that SPI-1 downregulation was caused by LeuO indeed ; ( iii ) a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 ( OFF ) subpopulation , in agreement with the role of HilE as a SPI-1 repressor ( Baxter et al. , 2003 ) ; ( iv ) activation of leuO expression in a HilE − background yielded a small subpopulation of sipB - : : GFP ( OFF ) cells ; and ( v ) absence of both LeuO and HilE restored the wild type pattern of sipB : : GFP expression .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of OFF cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of OFF cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in a HilE a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of OFF cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in a HilE a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of OFF cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in a HilE a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	leuO	activator	24354910	15	ver/dev	However , activation of leuO transcription in a HilE a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 cells .	81	However , activation of leuO transcription in a HilE + background yields a homogeneous population of ( SPI-1 ) OFF cells while activation of leuO transcription in the absence of HilE yields a small subpopulation of SPI-1 ( OFF ) cells .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	leuO	activator	24354910	51	ver/dev	This conclusion is in agreement with the observation that activation of leuO transcription decreases epithelial cell invasion > 100-fold in the presence of only three - to fourfold in the absence of HilE .	204	This conclusion is in agreement with the observation that activation of leuO transcription decreases epithelial cell invasion > 100-fold in the presence of HilE and only three - to fourfold in the absence of HilE ( Fig. 7 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	leuO	activator	24354910	51	ver/dev	This conclusion is in agreement with the observation that activation of leuO transcription decreases epithelial cell invasion > 100-fold in the presence of HilE - to fourfold in the absence of HilE .	204	This conclusion is in agreement with the observation that activation of leuO transcription decreases epithelial cell invasion > 100-fold in the presence of HilE and only three - to fourfold in the absence of HilE ( Fig. 7 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	repressor	15569938	2	ver/dev	The PmrA protein represses transcription of the pmrD gene .	84	The PmrA protein represses transcription of the pmrD gene .	3	THIS PAPER WAS SUBMITTED DIRECTLY (TRACK II) TO THE PNAS OFFICE. FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrD	repressor	15569938	11	ver/dev	When system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein represses pmrD transcription .	169	When the Salmonella PmrA PmrB system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter and represses pmrD transcription ( 30 ) ( Fig. 1 A ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	repressor	15569938	11	ver/dev	When the Salmonella PmrA PmrB is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein represses pmrD transcription .	169	When the Salmonella PmrA PmrB system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter and represses pmrD transcription ( 30 ) ( Fig. 1 A ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	repressor	15569938	12	ver/dev	We reasoned that if the PmrA-mediated repression of the Salmonella pmrD gene is designed to prevent the potentially detrimental production of PmrD protein , this negative feedback loop would be absent from E. coli because its PmrD protein is unable to activate the PmrA protein .	170	We reasoned that if the PmrA-mediated repression of the Salmonella pmrD gene is designed to prevent the potentially detrimental production of PmrD protein , this negative feedback loop would be absent from E. coli because its PmrD protein is unable to activate the PmrA protein .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	pmrD	repressor	15569938	14	ver/dev	For example , the presence of a PmrA-binding site in the Salmonella pmrD promoter enables the PmrA protein to repress pmrD transcription	286	For example , the presence of a PmrA-binding site in the Salmonella pmrD promoter enables the PmrA protein to repress pmrD transcription ( 30 ) , but such regulatory site is absent from the E. coli pmrD promoter , whose transcription is not affected by the presence of the PmrA protein ( this work ) .	5	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrD	repressor	18467098	1	ver/dev	The PhoP -- PmrA loop is closed by repression of pmrD expression by PmrA .	71	The PhoP -- PmrD -- PmrA loop is closed by repression of pmrD expression by PmrA [ 49 ] .	8	INDIRECT ACTIVATION OF PMRAB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	repressor	18467098	1	ver/dev	The PhoP -- PmrD is closed by repression of pmrD expression by PmrA .	71	The PhoP -- PmrD -- PmrA loop is closed by repression of pmrD expression by PmrA [ 49 ] .	8	INDIRECT ACTIVATION OF PMRAB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	repressor	18467098	4	ver/dev	This loop can be deactivated by the transcriptional repression of pmrD by PmrA .	104	This loop can be deactivated by the transcriptional repression of pmrD by PmrA .	10	PMRAB-MEDIATED LPS MODIFICATIONS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SlyA	gene	msgA	activator	17379730	7	att	SlyA-activated ) , STM1056 ( msgA homologue )	441	SlyA-activated ) , STM1056 ( msgA homologue )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IciA	gene	dnaA	regulator	24659766	28	ver/dev	The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P .	730	The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P .	68	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IciA	gene	dnaA	regulator	24659766	28	ver/dev	The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P .	730	The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P .	68	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagP	activator	11108722	0	att	PhoP-activated gene pagP ( 29 ) .	47	PhoP-activated gene pagP ( 29 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagP	activator	15225317	13	att	The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .	156	The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pagP	activator	15225317	16	att	Thus , we investigated the role of the PhoP-activated pagP and pgtE genes , because they had been implicated in resistance to the alpha-helical peptide C18G ( Guo et al. , 1998 ; Guina et al. , 2000 ) .	170	Thus , we investigated the role of the PhoP-activated pagP and pgtE genes , because they had been implicated in resistance to the alpha-helical peptide C18G ( Guo et al. , 1998 ; Guina et al. , 2000 ) .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	pagP	activator	15225317	20	att	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	185	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagP	activator	15659161	4	att	It may be that pagP belongs to the subset of PhoP-dependent genes that require low pH for maximal transcription ( Alpu -	356	It may be that pagP belongs to the subset of PhoP-dependent genes that require low pH for maximal transcription ( Alpu -	7	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagP	activator	15659161	3	ver/dev	Our inability to observe hepta-acylated lipid-A in E. coli correlates with the fact that the E. coli homologue of pagP , requires the activation of at least one other 2-component regulatory system in addition to PhoP / PhoQ .	337	Our inability to observe hepta-acylated lipid A in E. coli correlates with the fact that elevated transcription of crcA , the E. coli homologue of pagP , requires the activation of at least one other 2-component regulatory system in addition to PhoP / PhoQ ( Eguchi et al. , 2004 ) .	7	DISCUSSION	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagP	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	pagP	activator	17693506	6	att	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid-A modifications explain most of the alterations in the passive permeability of the OM bilayer .	208	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid A modifications explain most of the alterations in the passive permeability of the OM bilayer .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	pagP	activator	18792679	1	att	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	113	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	5	DIRECT TRANSCRIPTIONAL CONTROL BYTHE PHOP PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagP	activator	20833808	0	ver/dev	PhoP _ leading to the activation of pagP	20	In response to specific environmental signals , PhoQ phosphorylates PhoP , leading to the activation of pagL and pagP , which encode outer membrane lipid A 3-O-deacylase and outer membrane lipid A palmitoyltransferase , respectively ( 2 , 22 ) .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagP	activator	21511762	0	att	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	217	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	4	METHODS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	sopA	activator	23419780	7	ver/dev	HilA are transcription activators of effectors downregulates sopA .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	spiC	activator	12753201	35	ver/dev	From the data , it is apparent that both OmpR activate the transcriptional-fusions to spiC .	222	From the data shown in Fig. 2C , it is apparent that both OmpR and SsrB activate the transcriptional fusions to spiC .	11	THE SSRA/B REGION CONTAINS TWO PROMOTERS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	katG	activator	23651595	1	ver/dev	Activated OxyR induces katG , dps ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katG	activator	23651595	1	ver/dev	Activated OxyR induces katG , dps lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katG	activator	23651595	1	ver/dev	Activated OxyR induces katG , DNA-protection ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katG	activator	23651595	1	ver/dev	Activated OxyR induces katG , DNA-protection lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katG	activator	29844422	0	ver/dev	The katG promoter is activated by the transcription factor OxyR upon exposure to H2O2 in a concentration-dependent manner 16,28 .	376	The katG promoter is activated by the transcription factor OxyR upon exposure to H2O2 in a concentration-dependent manner ( Fig. 4c ) 16,28 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	tum	regulator	12399494	12	ver/dev	To further test the idea that LexA regulates the Fels-2 tum promoter , we placed this promoter region adjacent to the lacZ gene on plasmid F 128 .	425	To further test the idea that LexA regulates the Fels-2 tum promoter , we placed this promoter region adjacent to the lacZ gene on plasmid F 128 ( see Materials and Methods ) .	4	RESULTS	unidentified plasmid;Plasmid F	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	tum	regulator	12399494	17	ver/dev	LexA-dependent control of a Fels-2 tum : : lac fusiona	469	LexA-dependent control of a Fels-2 tum : : lac fusiona	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tlpA	regulator	16782389	3	ver/dev	Likewise , lacZ in the phoP mutant indicated that PhoP is involved in the regulation of tlpA .	157	Likewise , the higher expression of tlpA : : lacZ in the phoP mutant indicated that PhoP is involved in the regulation of tlpA .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	tlpA	regulator	16782389	3	ver/dev	Likewise , the higher expression of tlpA : indicated that PhoP is involved in the regulation of tlpA .	157	Likewise , the higher expression of tlpA : : lacZ in the phoP mutant indicated that PhoP is involved in the regulation of tlpA .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	tlpA	regulator	16782389	4	ver/dev	To further investigate the possibility that PhoP regulates tlpA , we constructed OG2008 .	159	To further investigate the possibility that PhoP regulates tlpA , we constructed a double mutant strain lacking both tlpA and phoP genes ( OG2008 ) .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	tlpA	regulator	16782389	4	ver/dev	To further investigate the possibility that PhoP regulates tlpA , we constructed a double mutant strain .	159	To further investigate the possibility that PhoP regulates tlpA , we constructed a double mutant strain lacking both tlpA and phoP genes ( OG2008 ) .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	tlpA	regulator	16782389	5	ver/dev	These results indicate that PhoP plays a pivotal role as a repressor in the regulation of tlpA .	162	These results indicate that PhoP plays a pivotal role as a repressor in the regulation of tlpA .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	tlpA	regulator	16782389	10	ver/dev	Therefore , the regulation of tlpA by PhoP may provide a molecular mechanism to the suppressed expression of tlpA under MgM medium , containing low Mg 2þ concentration .	317	Therefore , the regulation of tlpA by PhoP may explain and provide a molecular mechanism to the suppressed expression of tlpA under MgM medium , containing low Mg 2þ concentration .	23	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	tlpA	regulator	16782389	10	ver/dev	Therefore , the regulation of tlpA by PhoP may explain a molecular mechanism to the suppressed expression of tlpA under MgM medium , containing low Mg 2þ concentration .	317	Therefore , the regulation of tlpA by PhoP may explain and provide a molecular mechanism to the suppressed expression of tlpA under MgM medium , containing low Mg 2þ concentration .	23	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	STM1344	repressor	19376870	14	ver/dev	CsgD protein levels are downregulated in the STM1344 mutant .	257	CsgD protein levels are downregulated in the STM1344 mutant .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in the STM4264 , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in the STM4264 , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in the STM4264 , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	22	ver/dev	Upon the deletion of STM1344 in the STM4264 , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .	296	Upon the deletion of STM1344 in the STM4264 and STM1827 mutant backgrounds , the downregulation of rdar morphotype and CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 and STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants ( Fig. 7 ; also data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM1344	repressor	19376870	34	ver/dev	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM3611 , required for the downregulation of CsgD expression .	380	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 and STM3611 , required for the downregulation of CsgD expression ( 37 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	repressor	19376870	34	ver/dev	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 , required for the downregulation of CsgD expression .	380	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 and STM3611 , required for the downregulation of CsgD expression ( 37 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	repressor	25437188	40	ver/dev	Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .	446	Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YncC	gene	yciGFE	regulator	20713450	2	ver/dev	Our results indicate that differences between E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by YncC in these two enterobacteria .	15	Our results indicate that differences between Salmonella and E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE ( katN ) genes by H-NS and YncC in these two enterobacteria .	0	Unknown	Escherichia coli	0	L2	SPEC	Analysis	OTHER	New	Level 1
YncC	gene	yciGFE	regulator	20713450	2	ver/dev	Our results indicate that differences between Salmonella , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by YncC in these two enterobacteria .	15	Our results indicate that differences between Salmonella and E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE ( katN ) genes by H-NS and YncC in these two enterobacteria .	0	Unknown	Salmonella	1	L2	SPEC	Analysis	OTHER	New	Level 1
YncC	gene	yciGFE	regulator	20713450	4	ver/dev	The results reveal differential regulation of the yciGFE locus by YncC in these two closely related bacteria .	40	The results reveal differential regulation of the yciGFE ( katN ) locus by YncC and H-NS ( the Histone-like Nucleoid Structuring protein , 14 -- 16 ) in these two closely related bacteria .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
YncC	gene	yciGFE	regulator	20713450	7	ver/dev	YncC also Binds to the E. coli K-12 yciGFE Promoter Region -- The ortholog of yncC in E. coli K-12 -LRB- named mcbR -RRB- , regulates colanic acid production by repressing expression of the ybiM gene .	290	YncC also Binds to the E. coli K-12 yciGFE Promoter Region -- The ortholog of yncC in E. coli K-12 ( named mcbR ) , regulates colanic acid production by repressing expression of the ybiM gene ( 13 ) .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
YncC	gene	yciGFE	regulator	20713450	23	ver/dev	However , the sequence , the length , , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / H-NS .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciGFE	regulator	20713450	23	ver/dev	However , the sequence , the length , , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciGFE	regulator	20713450	23	ver/dev	However , the position of H-NS binding regions , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / H-NS .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciGFE	regulator	20713450	23	ver/dev	However , the position of H-NS binding regions , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciGFE	regulator	20713450	23	ver/dev	However , the position of the McbR/YncC , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / H-NS .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciGFE	regulator	20713450	23	ver/dev	However , the position of the McbR/YncC , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciGFE	regulator	20713450	24	ver/dev	It is remarkable that in E. coli K-12 , regulation of yciGFE by YncC are intimately linked , whereas in Salmonella , YncC directly activates transcription	480	It is remarkable that in E. coli K-12 , regulation of yciGFE by YncC and by H-NS are intimately linked , whereas in Salmonella , YncC directly activates transcription , and thus , activation by YncC is , at least partly , disconnected from the H-NS network .	7	DISCUSSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	1	ver/dev	Here in-vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals .	11	Here in vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	1	ver/dev	Here in-vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation .	11	Here in vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	1	ver/dev	Here in-vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to oxygen .	11	Here in vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	5	ver/dev	Thus , CRP enhances hlyE expression in response to FNR enhances hlyE expression in response to oxygen starvation .	20	Thus , CRP enhances hlyE expression in response to glucose starvation ( 36 ) and FNR enhances hlyE expression in response to oxygen starvation ( 10 , 11 , 23 ) .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	hlyE	activator	14996792	5	ver/dev	Thus , CRP enhances hlyE expression in response to glucose-starvation enhances hlyE expression in response to oxygen starvation .	20	Thus , CRP enhances hlyE expression in response to glucose starvation ( 36 ) and FNR enhances hlyE expression in response to oxygen starvation ( 10 , 11 , 23 ) .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	hlyE	activator	14996792	10	ver/dev	Previous studies have shown that CRP contribute to hlyE expression when E. coli is grown on a solid medium .	72	Previous studies have shown that FNR , CRP , and H-NS contribute to hlyE expression when E. coli is grown on a solid medium ( 10 , 36 ) .	7	RESULTS	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	14	ver/dev	Thus , we concluded that CRP all contribute towards the regulation of hlyE expression .	83	Thus , we concluded that CRP , FNR , and H-NS all contribute towards the regulation of hlyE expression .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	hlyE	activator	14996792	26	ver/dev	Footprinting studies have shown that CRP activate hlyE expression from the same site centered 61.5 bp upstream of the SlyA-associated transcription start site .	128	Footprinting studies have shown that FNR and CRP activate hlyE expression from the same site centered 61.5 bp upstream of the SlyA-associated transcription start site ( 10 , 36 ) .	7	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
CRP	gene	hlyE	activator	14996792	47	ver/dev	CRP are known to activate hlyE expression	237	Both proteins occupy a common region of PhlyE that overlaps the binding site for the global transcription factors FNR and CRP , which are known to activate hlyE expression ( 10 , 36 ) .	8	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CRP	gene	hlyE	activator	14996792	50	ver/dev	once CRP is bound , CRP-mediated activation of hlyE expression is efficient	241	These observations may be explained by a mechanism in which FNR recognizes PhlyE efficiently but acts only as a relatively poor activator of hlyE transcription ( 10 , 11 ) , whereas , conversely , the recognition of PhlyE by CRP is poor , but once CRP is bound , CRP-mediated activation of hlyE expression is efficient .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	19835951	0	att	RpoS- and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes: role of environmental conditions	2	RpoS- and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes: role of environmental conditions	0	Unknown	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	activator	19835951	15	att	Moreover , hlyE also presents Crp-dependent repression .	195	Moreover , hlyE also presents Crp-dependent repression .	17	4. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	hlyE	activator	19835951	1	ver/dev	On the other hand , the transcriptional regulator Crp , previously described as an activator of hlyE transcription in Escherichia coli , is involved in transcriptional repression of hlyE in S. Typhi .	12	On the other hand , the transcriptional regulator Crp , previously described as an activator of hlyE transcription in Escherichia coli , is involved in transcriptional repression of hlyE in S. Typhi .	2	ABSTRACT	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	19835951	9	ver/dev	Crp is a transcriptional regulator previously reported to be an activator of hlyE transcription in E. coli .	163	Crp is a transcriptional regulator previously reported to be an activator of hlyE transcription in E. coli [ 62 ] .	16	3.2. THE CRP REGULATOR IS INVOLVED IN TRANSCRIPTIONAL REPRESSION OF S. TYPHI HLYE	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	21148209	36	att	RpoS-and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	329	RpoS-and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	35	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	activator	24885225	65	att	Fuentes JA , Jofre MR , Villagra NA , Mora GC : RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	398	Fuentes JA , Jofre MR , Villagra NA , Mora GC : RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	23	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	activator	24885225	18	ver/dev	CRP is a transcriptional regulator previously reported as an activator of the hlyE transcription in E. coli .	60	CRP is a transcriptional regulator previously reported as an activator of the hlyE transcription in E. coli [ 16 ] .	4	RESULTS	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	activator	27260307	2	att	RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	739	RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	51	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	activator	30778340	4	att	RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	521	RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	20	SUPPLEMENTARY MATERIAL	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	ansB	regulator	18559530	0	ver/dev	In E. coli , ansB is positively coregulated by CRP .	145	In E. coli , ansB is positively coregulated by Fnr and by CRP ( cyclic AMP receptor protein ) , a carbon source utilization regulator ( 24 ) .	6	RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	ansB	regulator	18559530	1	ver/dev	In S. enterica , the anaerobic regulation of ansB may require only CRP .	146	In S. enterica , the anaerobic regulation of ansB may require only CRP ( 25 , 26 ) .	6	RESULTS AND DISCUSSION	Salmonella;Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	pbgP	activator	15205413	10	att	( B ) - Galactosidase activity ( in Miller units ) expressed by strains harboring a chromosomal lac transcriptional-fusion to the PmrA-activated pbgP gene that were grown logarithmically in N-min-imal medium , pH-5.8 , with 10 M MgCl2 .	170	( B ) - Galactosidase activity ( in Miller units ) expressed by strains harboring a chromosomal lac transcriptional fusion to the PmrA-activated pbgP gene that were grown logarithmically in N-min-imal medium , pH 5.8 , with 10 M MgCl2 .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	15205413	11	att	Transcription of the PmrA-activated pbgP gene was similar in the wild-type and pmrC1 strains , but it was decreased in the pmrC2 mutant .	173	Transcription of the PmrA-activated pbgP gene was similar in the wild-type and pmrC1 strains , but it was decreased in the pmrC2 mutant .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	15205413	14	att	The synthesis of aminoarabinose is mediated by the PmrA-activated ugd gene and pbgP operon ( 43 ) , which are necessary for resistance to polymyxin B .	236	The synthesis of aminoarabinose is mediated by the PmrA-activated ugd gene and pbgP operon ( 43 ) , which are necessary for resistance to polymyxin B .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	15205413	8	att	The generated mutation ( designated pmrC1 ) was not polar on the pmrA and pmrB genes because the same levels of transcription of the PmrA-activated pbgP gene were displayed by isogenic wildtype and pmrC1 strains ( Fig. 1B ) .	149	The generated mutation ( designated pmrC1 ) was not polar on the pmrA and pmrB genes because the same levels of transcription of the PmrA-activated pbgP gene were displayed by isogenic wildtype and pmrC1 strains ( Fig. 1B ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	pbgP	activator	15205413	9	att	To examine whether the pmrC gene is necessary for the incorporation of phosphoethanolamine into lipid-A , we used negative-ion-mode MALDI-TOF mass spectrometry to analyze the lipid-A species from wild-type pbgP , pmrC1 .1 , and pmrA strains and strains grown at a low pH and with a low level of Mg2 , which are conditions that promote the transcription of PmrA-activated genes ( 41 ) .	155	To examine whether the pmrC gene is necessary for the incorporation of phosphoethanolamine into lipid A , we used negative-ion-mode MALDI-TOF mass spectrometry to analyze the lipid A species from wild-type pbgP , pmrC1 .1 , and pmrA strains and strains grown at a low pH and with a low level of Mg2 , which are conditions that promote the transcription of PmrA-activated genes ( 41 ) .	4	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
PmrA	gene	pbgP	activator	15569938	13	att	This behavior is due to the highly divergent PmrD protein ( Figs. 6 and 7 ) , because replacement of the E. coli pmrD gene by the Salmonella pmrD gene endowed E. coli with the ability to transcribe the PmrA-activated pbgP gene and to exhibit resistance to polymyxin B in response to the low Mg2 signal ( Fig. 3 ) .	182	This behavior is due to the highly divergent PmrD protein ( Figs. 6 and 7 ) , because replacement of the E. coli pmrD gene by the Salmonella pmrD gene endowed E. coli with the ability to transcribe the PmrA-activated pbgP gene and to exhibit resistance to polymyxin B in response to the low Mg2 signal ( Fig. 3 ) .	5	DISCUSSION	Escherichia coli;Salmonella;Escherichia coli	0.5	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pbgP	activator	15569938	3	att	This phenotype was reflected also at the level of transcription ; the PmrA-activated pbgP gene was expressed by E. coli cells experiencing Fe3 but not in response to the low Mg2 signal ( Fig. 2C ) , whereas a pbgP transcript was made by Salmo-nella in both conditions ( Fig. 2D ) .	103	This phenotype was reflected also at the level of transcription ; the PmrA-activated pbgP gene was expressed by E. coli cells experiencing Fe3 but not in response to the low Mg2 signal ( Fig. 2C ) , whereas a pbgP transcript was made by Salmo-nella in both conditions ( Fig. 2D ) .	4	RESULTS	Escherichia coli;Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PmrA	gene	pbgP	activator	15569938	6	att	Low Mg2 promotes transcription of the PmrA-activated pbgP gene and polymyxin B resistance in Salmonella but not in E. coli .	121	Low Mg2 promotes transcription of the PmrA-activated pbgP gene and polymyxin B resistance in Salmonella but not in E. coli .	4	RESULTS	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pbgP	activator	15569938	7	att	The Salmonella pmrD gene enables E. coli to promote transcription of the PmrA-activated pbgP gene and to be resistant to polymyxin B after 2 growth in low Mg .	138	The Salmonella pmrD gene enables E. coli to promote transcription of the PmrA-activated pbgP gene and to be resistant to polymyxin B after 2 growth in low Mg .	4	RESULTS	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	17158330	12	att	For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .	66	For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .	5	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	17158330	12	ver/dev	For example , activation of the PmrA/PmrB system by growing Salmonella in media resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP .	66	For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .	5	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pbgP	activator	17158330	12	ver/dev	For example , activation of the PmrA/PmrB system by shifting it to media resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP .	66	For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pbgP	activator	20593264	1	att	Synthesis of Ara4N and addition to the lipid-A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .	173	Synthesis of Ara4N and addition to the lipid A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .	10	5.2.2 PMRA–PMRB REGULATORY SYSTEM	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
PmrA	gene	pbgP	activator	22921935	2	att	To test this hypothesis , we determined the β2 galactosidase activity produced by strains harboring chromosomal lac transcriptional-fusions to the PmrA-activated pbgP operon and ugd gene .	106	To test this hypothesis , we determined the β2 galactosidase activity produced by strains harboring chromosomal lac transcriptional fusions to the PmrA-activated pbgP operon and ugd gene .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pbgP	activator	22921935	6	att	By 120 min , the PmrA-dependent lipid-A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	141	By 120 min , the PmrA-dependent lipid A modifications were visible ( Figure 6C ) and wild-type Salmonella bound less Fe3 + ( Figure 6A ) and expressed lower amounts of pbgP transcript than the ugd mutant ( Figures 6B ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	29739882	9	att	When wild-type Salmonella was shifted from non-inducing conditions to media with a mildly acidic pH , the mRNA amounts of the PmrA-activated genes pbgP , pmrC , and pmrR reached a maximum within 5 min ( Fig. 5A ) .	128	When wild-type Salmonella was shifted from non-inducing conditions to media with a mildly acidic pH , the mRNA amounts of the PmrA-activated genes pbgP , pmrC , and pmrR reached a maximum within 5 min ( Fig. 5A ) .	5	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pbgP	activator	29739882	10	ver/dev	its pbgP promoter _ being directly activated by both PmrA proteins	147	For example , Yersinia pestis differs from Salmonella in lacking a pmrC gene and in its pbgP promoter being directly activated by both the PhoP and PmrA proteins ( 32 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pcgL	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pcgL	activator	15208313	10	att	The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .	33	The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pcgL	activator	15225317	25	att	The ugtL gene was first identified as part of a Salmonella-specific DNA region harbouring the PhoP-activated pcgL gene , which encodes a D-Ala-D-Ala dipeptidase ( Hilbert et al. , 1999 ) .	266	The ugtL gene was first identified as part of a Salmonella-specific DNA region harbouring the PhoP-activated pcgL gene , which encodes a D-Ala-D-Ala dipeptidase ( Hilbert et al. , 1999 ) .	9	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pcgL	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	pcgL	activator	19091955	28	att	This phenotype is not associated with the PhoP/PhoQ system because transcriptional levels of PhoP-dependent but SlyA-independent genes , such as pcgL , are reduced 2-fold overall in a relA spoT mutant ( data not shown ) .	183	This phenotype is not associated with the PhoP/PhoQ system because transcriptional levels of PhoP-dependent but SlyA-independent genes , such as pcgL , are reduced 2-fold overall in a relA spoT mutant ( data not shown ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pcgL	activator	23782700	2	att	A , - galactosidase activity from lacZ-transcriptional-fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	168	A , - galactosidase activity from lacZ transcriptional fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pcgL	activator	30992361	10	att	In contrast , EmrR did not exert an effect on transcription merely dependent on the PhoP/PhoQ system because transcription of two PhoP-activated genes , pcgL and STM3595 ( 36 ) , remained at similar levels in wild-type and ΔemrR strains ( Fig .	91	In contrast , EmrR did not exert an effect on transcription merely dependent on the PhoP/PhoQ system because transcription of two PhoP-activated genes , pcgL and STM3595 ( 36 ) , remained at similar levels in wild-type and ΔemrR strains ( Fig .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	pcgL	activator	30992361	14	att	On the other hand , dopamine could not act on the PhoP/PhoQ system because the PhoP-activated transcription of the pcgL and STM3595 genes remained unchanged under the conditions with 2 mM dopamine or without dopamine ( Fig .	123	On the other hand , dopamine could not act on the PhoP/PhoQ system because the PhoP-activated transcription of the pcgL and STM3595 genes remained unchanged under the conditions with 2 mM dopamine or without dopamine ( Fig .	3	RESULTS	nan	1	L1	OTHER	Other	NEG	New	Level 1
PhoP	gene	pcgL	activator	33045730	18	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	pcgL	activator	33045730	28	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiA	activator	8045891	1	ver/dev	RpoS ( as ) was found to be required for N starvation induction of stiA .	10	RpoS ( as ) was found to be required for the P , C , and N starvation induction of stiA and sfiC .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	pilS	repressor	27601577	0	ver/dev	Moreover , downregulation of pilS expression in the absence of FNR was not observed under data not shown , consistent with the inactive form of FNR under aerobiosis .	108	Moreover , downregulation of pilV and pilS expression in the absence of FNR was not observed under aerobic growth conditions ( data not shown ) , consistent with the inactive form of FNR under aerobiosis ( 24 ) .	4	2	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	pilS	repressor	27601577	0	ver/dev	Moreover , downregulation of pilS expression in the absence of FNR was not observed under aerobic-growth-conditions , consistent with the inactive form of FNR under aerobiosis .	108	Moreover , downregulation of pilV and pilS expression in the absence of FNR was not observed under aerobic growth conditions ( data not shown ) , consistent with the inactive form of FNR under aerobiosis ( 24 ) .	4	2	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	pilS	repressor	27601577	4	ver/dev	Under microaerobic conditions , the absence of FNR resulted in a downregulation of pilS , demonstrating the integration of the pilus gene expression with the global metabolic regulatory setup of Salmonella .	224	Under microaerobic conditions , the absence of FNR resulted in a downregulation of pilV , pilS , and pilT transcription and lower pESI conjugation , demonstrating the integration of the pilus gene expression with the global metabolic regulatory setup of Salmonella .	5	DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
FNR	gene	pflD	regulator	21887378	1	ver/dev	Furthermore , Fnr is involved in regulation of pflD , encoding the ` pyruvate formate lyase activase II ' and ` putative formate acetyltransferase 2 ' respectively , that were also identified from in IVET screening .	374	Furthermore , Fnr is involved in regulation of pflC and pflD , encoding the ` pyruvate formate lyase activase II ' and ` putative formate acetyltransferase 2 ' respectively , that were also identified from in IVET screening .	19	QUORUM SENSING AND ANAEROBIC GROWTH	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hns	repressor	31333620	3	ver/dev	Our previous study also showed that H-NS is essential for establishing the Mg2 + - responsive transcriptional regulation of the PhoP regulon in Salmonella because deletion of the hns gene abolished the transcriptional repression of PhoP/PhoQ-activated genes in the millimolar levels of Mg2 + .	58	Our previous study also showed that H-NS is essential for establishing the Mg2 + - responsive transcriptional regulation of the PhoP regulon in Salmonella because deletion of the hns gene abolished the transcriptional repression of PhoP/PhoQ-activated genes in the millimolar levels of Mg2 + ( Kong et al. , 2008 ) .	3	INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	pagJ	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	gene	flhC	activator	16430704	6	ver/dev	The FlhC levels were determined by immunoblotting analysis at various times after flhC transcription was induced by 50 µM IPTG .	171	The FlhD and FlhC levels were determined by immunoblotting analysis at various times after flhD and flhC transcription was induced by 50 µM IPTG .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	csrA	regulator	17379730	4	ver/dev	csrA encodes the CsrA regulator of Salmonella pathogeni-city	353	Interestingly , both the eut and the pdu operons are repressed in a mutant of csrA , which encodes the CsrA regulator of Salmonella pathogeni-city ( Lawhon et al. , 2003 ) , and a fivefold abundance of Pdu proteins of strain 14028 in comparison with the less virulent variant LT2 was detected in acidic minimal medium ( Adkins et al. , 2006 ) .	13	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	csrA	regulator	17379730	4	ver/dev	csrA encodes the CsrA regulator of Salmonella pathogeni-city	353	Interestingly , both the eut and the pdu operons are repressed in a mutant of csrA , which encodes the CsrA regulator of Salmonella pathogeni-city ( Lawhon et al. , 2003 ) , and a fivefold abundance of Pdu proteins of strain 14028 in comparison with the less virulent variant LT2 was detected in acidic minimal medium ( Adkins et al. , 2006 ) .	13	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	fur	regulator	11932449	0	ver/dev	The presence of a putative sequence to which the cAMP-CRP complex binds in the E. coli fur promoter has been suggested on the basis of computational analysis .	39	The presence of a putative sequence to which the cAMP-CRP complex binds in the E. coli fur promoter has been suggested on the basis of computational analysis ( Zheng et al. , 1999 ; Gelfand et al. , 2000 ) .	3	INTRODUCTION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	fur	regulator	11932449	1	ver/dev	In agreement with this possibility , it has been recently demonstrated that the fur gene of Pasteurella multocida , is positively regulated by the cAMP-CRP complex .	40	In agreement with this possibility , it has been recently demonstrated that the fur gene of Pasteurella multocida , which belongs to the γ-Proteobacteria , as does E. coli , is positively regulated by the cAMP-CRP complex ( Bosch et al. , 2001 ) .	3	INTRODUCTION	Pasteurella multocida	0	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	TU	flhDC	activator	32032766	2	ver/dev	The qRT-PCR results showed that both flhDC were upregulated by RpoS .	176	The qRT-PCR results showed that both asfD and flhDC were downregulated by the regulators , OmpR and Fis , and upregulated by RpoS .	19	3.4. ASFD OVEREXPRESSION PROMOTES S. TYPHI BIOFILM FORMATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	STM3154	activator	22356617	6	att	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	358	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
FliA	gene	fliC	activator	23977202	0	att	The loss of virulence in FlgM defective Salmonella requires fliA and fliC [ 35 ] , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	165	The loss of virulence in FlgM defective Salmonella requires fliA and fliC [ 35 ] , indicating that FlgM inhibition of FliA-dependent flagellin expression is necessary for virulence .	24	IN VITRO CHARACTERIZATION OF FLGM-DEFICIENT SALMONELLA	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	TU	araBAD	regulator	15208313	68	ver/dev	CRP together with AraC , which is active only in the presence of i.e. the secondary signal , bind to the araBAD promoter	225	The CRP protein directs the synthesis of the AraC protein in response to high levels of cAMP ( i.e. the primary signal ) , and then CRP together with AraC , which is active only in the presence of L-arabinose ( i.e. the secondary signal ) , bind to the araBAD promoter and stimulate transcription ( 36 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	TU	araBAD	regulator	15208313	68	ver/dev	CRP together with AraC , which is active only in the presence of L-arabinose , bind to the araBAD promoter	225	The CRP protein directs the synthesis of the AraC protein in response to high levels of cAMP ( i.e. the primary signal ) , and then CRP together with AraC , which is active only in the presence of L-arabinose ( i.e. the secondary signal ) , bind to the araBAD promoter and stimulate transcription ( 36 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilD	repressor	24354910	11	ver/dev	LeuO downregulates SPI-1 expression via hilD	70	LeuO downregulates SPI-1 expression via hilE and hilD	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	osmB	regulator	21311887	1	ver/dev	Among the 38 genes , osmB were previously reported to be regulated by RpoS .	120	Among the 38 genes , four ( osmC , osmY , osmB , and otsBA ) were previously reported to be regulated by RpoS [ 4 , 7 , 10 , 12 , 16 , 37 ] .	9	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	osmB	regulator	33638994	1	ver/dev	In this context , phosphorylated RcsB activates expression of cps operon ; rprA ; osmB , two genes also regulated by RpoS ; and , the cell division gene ftsZ , among others .	43	In this context , phosphorylated RcsB activates expression of the capsule ( cps ) operon ( 10 ) ; rprA , which encodes the small RNA RprA ( 11 ) ; osmC and osmB , two genes also regulated by RpoS ( 12 ) ; and , the cell division gene ftsZ ( 13 ) , among others .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmB	regulator	33638994	1	ver/dev	In this context , phosphorylated RcsB activates expression of the capsule operon ; rprA ; osmB , two genes also regulated by RpoS ; and , the cell division gene ftsZ , among others .	43	In this context , phosphorylated RcsB activates expression of the capsule ( cps ) operon ( 10 ) ; rprA , which encodes the small RNA RprA ( 11 ) ; osmC and osmB , two genes also regulated by RpoS ( 12 ) ; and , the cell division gene ftsZ ( 13 ) , among others .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	pipC	activator	20221735	3	ver/dev	Among the SPI-5 genes , primer-extension analysis revealed that pipC were induced at entry into the stationary-phase under standard growt conditions independently of RpoS .	314	Among the SPI-5 genes , which include pipA ~ D and sopB ( Wood et al. , 1998 ) , primer extension analysis revealed that sopB and pipC were induced at entry into the stationary phase under standard growt conditions independently of RpoS .	9	DISCUSSION	synthetic construct	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	osmC	regulator	19389776	1	ver/dev	Interplay between global regulators of Escherichia coli : effect of H-NS on the transcription of the gene osmC .	493	Interplay between global regulators of Escherichia coli : effect of RpoS , Lrp and H-NS on the transcription of the gene osmC .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	osmC	regulator	19843227	46	ver/dev	Gutierrez , C. Interplay between global regulators of Escherichia coli : effect of H-NS on transcription of the gene osmC .	469	Bouvier , J. , Gordia , S. , Kampmann , G. , Lange , R. , Hengge-Aronis , R. , and Gutierrez , C. ( 1998 ) Interplay between global regulators of Escherichia coli : effect of RpoS , Lrp and H-NS on transcription of the gene osmC .	32	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	rpoS	repressor	19843227	30	ver/dev	However , despite the fact that the deletion of stpA did not affect s38 protein levels at LEP , our data showed that rpoS mRNA levels were significantly lower in the absence of StpA -LRB- in strain JH3003 -RRB- at LEP compared with Table S1 , Fig. 7C .	189	However , despite the fact that the deletion of stpA did not affect s38 protein levels at LEP , our data showed that rpoS mRNA levels were significantly lower in the absence of StpA ( in strain JH3003 ) at LEP compared with wild type ( Table S1 , Fig. 7C ) .	13	STPA MODULATES S38 STABILITY	nan	1	L2	OTHER	Other	NEG	Other	Level 1
StpA	gene	rpoS	repressor	19843227	30	ver/dev	However , despite the fact that the deletion of stpA did not affect s38 protein levels at LEP , our data showed that rpoS mRNA levels were significantly lower in the absence of StpA -LRB- in strain JH3003 -RRB- at LEP compared with wild type .	189	However , despite the fact that the deletion of stpA did not affect s38 protein levels at LEP , our data showed that rpoS mRNA levels were significantly lower in the absence of StpA ( in strain JH3003 ) at LEP compared with wild type ( Table S1 , Fig. 7C ) .	13	STPA MODULATES S38 STABILITY	nan	1	L2	OTHER	Other	NEG	Other	Level 1
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	23651595	3	ver/dev	The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .	172	The small RNAs ( sRNAs ) DsrA and RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis and turnover of σS indirectly through the repression of the antiadapter protein encoding gene iraM ( rssC ) at various stages throughout the exponential phase of growth ( Brown & Elliott , 1996 ; Jones , Goodwill , & Elliott , 2006 ; Lucchini , McDermott , Thompson , & Hinton , 2009 ) .	11	1.2.4. STARVATION STRESS RESPONSE	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	rpoS	repressor	25375226	38	ver/dev	StpA in S. Typhimurium was recently proposed to repress the rpoS regulon during exponential-growth	535	StpA in S. Typhimurium was recently proposed to repress the rpoS regulon during exponential growth and the major caveat of our study is that we started with strain encoding a defective RpoS , which would alleviate the selective pressure to maintain a wild type copy of StpA [ 48 ] .	11	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	fur	repressor	17993530	53	ver/dev	Since one of our models proposes that Fur represses a repressor of HilD , we performed random mutagenesis of a strain with a fur deletion .	351	Since one of our models proposes that Fur represses a repressor of HilD , we used Tn10dTc and performed random mutagenesis of a strain with a fur deletion and a hilA-lacZ transcriptional fusion .	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	fur	repressor	17993530	54	ver/dev	For example , hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	363	For example , hilA expression , rtsA expression , and hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	fur	repressor	17993530	54	ver/dev	For example , rtsA expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	363	For example , hilA expression , rtsA expression , and hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	fur	repressor	17993530	54	ver/dev	For example , hilA expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	363	For example , hilA expression , rtsA expression , and hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	hup	repressor	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfB .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
IHF	gene	hup	repressor	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
IHF	gene	hup	repressor	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between HU at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfB .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
IHF	gene	hup	repressor	21212121	16	ver/dev	These results revealed a reciprocal regulatory relationship between HU at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA .	356	These results revealed a reciprocal regulatory relationship between HU and IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA and ihfB .	12	HU AND INTEGRATION HOST FACTOR (IHF)	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Hha	gene	hilA	repressor	15661008	29	ver/dev	Hha , is one of repressors of hilA transcription .	382	Hha , a small DNA-binding protein , is one of repressors of hilA transcription ( Fahlen et al. , 2001 ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include HilD , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include CsrB , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include FadD , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include EnvZ/OmpR , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include FliZ , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include BarA/SirA , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include Fis , HU , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include some nucleoid binding proteins , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	19074398	39	ver/dev	Fahlen et al. have shown that the histonelike protein Hha acts as a repressor of hilA .	504	Fahlen et al. have shown that the histonelike protein Hha acts as a repressor of hilA ( 29 ) and have speculated that another repressor also plays an important role in modulating hilA expression in response to growth conditions ( 29 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Hha	gene	hilA	repressor	21680637	21	ver/dev	In exponential phase cells , the results provided evidence that Hha repress hilA expression .	209	In exponential phase cells , the results obtained provided evidence that H-NS and Hha repress hilA expression .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
Hha	gene	hilA	repressor	21680637	58	ver/dev	Our work shows that Hha repress hilA under account for SPI1 gene silencing .	316	Our work shows that H-NS and Hha repress hilA under a set of well-defined environmental and physiological conditions and consequently account for SPI1 gene silencing .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	21680637	58	ver/dev	Our work shows that Hha repress hilA under a set of physiological conditions .	316	Our work shows that H-NS and Hha repress hilA under a set of well-defined environmental and physiological conditions and consequently account for SPI1 gene silencing .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	hilA	repressor	21680637	58	ver/dev	Our work shows that Hha repress hilA under a set of well-defined environmental .	316	Our work shows that H-NS and Hha repress hilA under a set of well-defined environmental and physiological conditions and consequently account for SPI1 gene silencing .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
AcrR	TU	acrAB	repressor	15336432	3	ver/dev	The AcrR protein is known in E. coli to repress transcription of the acrAB operon .	179	The AcrR protein is known in E. coli to repress transcription of the acrAB operon [ 12 ] .	5	3. RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
AcrR	TU	acrAB	repressor	18083849	0	ver/dev	In S. enterica , AcrR represses expression of acrAB .	368	In E. coli and S. enterica , AcrR represses expression of acrAB ( 28 , 36 ) .	6	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	repressor	18083849	0	ver/dev	In E. coli , AcrR represses expression of acrAB .	368	In E. coli and S. enterica , AcrR represses expression of acrAB ( 28 , 36 ) .	6	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	repressor	19230852	0	ver/dev	AcrR repress the expression of acrAB .	180	AcrR and AcrS repress the expression of acrAB ( Table 3 ) [ 54,55 ] .	7	4. REGULATORY NETWORK OF DRUG EFFLUX PUMPS IN E. COLI	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AcrR	TU	acrAB	repressor	19230852	8	ver/dev	AcrR are repressors of acrAB .	300	AcrR and AcrS are repressors of acrAB .	8	5. DRUG EFFLUX PUMPS IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	TU	acrAB	repressor	28631419	1	ver/dev	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor by the AraC/XylS-like regulators RamA , MarA , SoxS and	25	For example , acrAB transcription in Salmonella is controlled by AcrR , a TetR-like repressor encoded nearby , and by the AraC/XylS-like regulators RamA , MarA , SoxS and	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	TU	acrAB	repressor	28650690	0	ver/dev	AcrR represses the expression of acrAB locally .	31	AcrR represses the expression of acrAB locally .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	sipC	regulator	25028458	29	att	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	322	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	rflM	regulator	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rflM	regulator	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to csgD were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rflM	regulator	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to dps were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rflM	regulator	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to wzzB were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	rpoS	repressor	21388802	3	ver/dev	OmpR represses rpoS .	160	OmpR activates slyA , phoP and ssrB expression and represses rpoS .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	rpoS	repressor	30524381	0	ver/dev	In S. Typhimurium , OmpR represses rpoS , .	66	In S. Typhimurium , OmpR represses the alternative stationary phase sigma factor , rpoS , relieving RpoS repression of yghA .	4	NTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	rpoS	repressor	30524381	31	ver/dev	In Salmonella , YciF was reported to be under positive control of RpoS , yet our previous study showed that OmpR repressed rpoS during osmotic-stress .	319	In Salmonella , YciF was reported to be under positive control of RpoS ( Ibanez-Ruiz et al. , 2000 ) , yet our previous study showed that OmpR repressed rpoS during osmotic stress ( Chakraborty et al. , 2017 ) , which would decrease yciF transcription .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	rpoS	repressor	30524381	48	ver/dev	if they are mediated through OmpR regulation of an intermediating regulator , as we observed with the OmpR repression of the stationary-phase sigma factor rpoS	394	The challenge will be to determine whether these are direct effects or if they are mediated through OmpR regulation of an intermediating regulator , as we observed with the OmpR repression of the stationary phase sigma factor rpoS ( Chakraborty et al. , 2017 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DnaA	gene	dnaA	regulator	10905311	2	ver/dev	When DnaA IV-affinity gel was mixed with the DNAs , DnaA IV was found to bind with the dnaA box in the oriC fragment .	133	When DnaA IV-affinity gel was mixed with the DNAs amplified by PCR , DnaA IV was found to bind with the dnaA box in the oriC fragment .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	yhjB	regulator	29857034	20	ver/dev	two genes encode response regulators are regulated by SlyA yhjB	320	We also found two genes that encode response regulators that are regulated by SlyA yhjB ( STM14_4338 ) and creB ( STM14_5509 ) , which are involved in citrate fermentation and phosphate metabolism , respectively .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS	regulator	19609351	5	att	Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .	338	Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .	6	NON-CODING (NC) RNA SEQUENCES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	ansB	activator	18559530	0	ver/dev	In E. coli , ansB is positively coregulated by CRP .	145	In E. coli , ansB is positively coregulated by Fnr and by CRP ( cyclic AMP receptor protein ) , a carbon source utilization regulator ( 24 ) .	6	RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	pefI	activator	25080967	12	att	Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of pefI , or any other position along the whole operon .	102	Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of pefI , or any other position along the whole operon .	7	PROMOTERS PREDICTED UPSTREAM OF PEFI, BUT NOT THOSE UPSTREAM OF SRGA AND SRGC, ARE FUNCTIONAL	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	pefI	activator	25080967	14	att	The region upstream of pefI contains two promoters one of which is SdiA-dependent	146	The region upstream of pefI contains two promoters one of which is SdiA-dependent	8	THE REGION UPSTREAM OF PEFI CONTAINS TWO PROMOTERS ONE OF WHICH IS SDIA-DEPENDENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	pefI	activator	25080967	21	att	A and B. Analysis of the fluorescent primer-extension products specific for the SdiA-dependent PefIP2 promoter located upstream of the pefI ORF .	194	A and B. Analysis of the fluorescent primer extension products specific for the SdiA-dependent PefIP2 promoter located upstream of the pefI ORF .	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	synthetic construct	0	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	pefI	activator	25080967	33	ver/dev	Moreover , Michael et al. showed a strong activation of the promoter region located upstream of pefI in absence of AHLs when SdiA was expressed from a low-copy-number plasmid .	298	Moreover , Michael et al. ( 2001 ) showed a strong activation of the promoter region located upstream of pefI in absence of AHLs when SdiA was expressed from a low-copy-number plasmid .	13	DISCUSSION	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	csgBA	activator	16629664	2	ver/dev	While CsgD is suggested to activate biosynthesis of curli fimbriae directly by binding to the promoter of the csgBA operon , activation of cellulose biosynthesis by CsgD is indirect .	43	While CsgD is suggested to activate biosynthesis of curli fimbriae directly by binding to the promoter of the csgBA operon encoding the structural genes for curli fimbriae ( Hammar et al. , 1995 ; Brombacher et al. , 2003 ) , activation of cellulose biosynthesis by CsgD is indirect ( Römling et al. , 2000 ) .	6	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	TU	csgBA	activator	16629664	2	ver/dev	While CsgD is suggested to activate biosynthesis of curli fimbriae directly by binding to the promoter of the csgBA operon , activation of cellulose biosynthesis by CsgD is indirect .	43	While CsgD is suggested to activate biosynthesis of curli fimbriae directly by binding to the promoter of the csgBA operon encoding the structural genes for curli fimbriae ( Hammar et al. , 1995 ; Brombacher et al. , 2003 ) , activation of cellulose biosynthesis by CsgD is indirect ( Römling et al. , 2000 ) .	6	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	TU	csgBA	activator	16629664	6	ver/dev	Therefore , in the next step the level of the CsgD protein , the proposed transcriptional activator of the csgBA promoter was investigated .	127	Therefore , in the next step the level of the CsgD protein , the proposed transcriptional activator of the csgBA promoter was investigated .	9	CSGD EXPRESSION IS REGULATED BY C-DI-GMP ON A TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL LEVEL	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	csgBA	activator	17650335	1	ver/dev	csgBA is positively regulated by the global regulator CsgD	47	The curli subunits CsgA and CsgB are encoded by csgBA , which is positively regulated by the global regulator CsgD [ 20 ] .	5	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgBA	activator	20545866	49	att	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	294	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	TU	csgBA	activator	20545866	2	ver/dev	CsgD positively regulates the transcription of the csgBA operon .	26	CsgD positively regulates the transcription of the csgBA operon leading to the bio-synthesis of curli fimbriae ( Hammar et al. , 1995 ; Romling et al. , 1998b ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	TU	csgBA	activator	20545866	23	ver/dev	To investigate whether c-di-GMP plays a role in the transcriptional activation of csgBA by CsgD , we added c-di-GMP to the in-vitro-transcription assays .	125	To investigate whether c-di-GMP plays a role in the transcriptional activation of csgBA and adrA by CsgD , we added c-di-GMP to the in vitro transcription assays .	7	CSGD IS CRUCIAL FOR THE TRANSCRIPTION OF CSGBA AND ADRA IN VITRO	nan	1	L3	SPEC	Other	OTHER	New	Level 1
CsgD	TU	csgBA	activator	20545866	34	ver/dev	In this study , we dem-onstrated for the first time that CsgD activates transcription of the promoter regions of csgBA .	251	In this study , we dem-onstrated for the first time that CsgD interacts directly and activates transcription of the promoter regions of csgBA and adrA .	9	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CsgD	TU	csgBA	activator	21388802	1	ver/dev	CsgD activates transcription of csgBA .	148	CsgD interacts directly and activates transcription of csgBA and adrA .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	TU	csgBA	activator	22336758	1	ver/dev	The rdar -LRB- red , dry and rough -RRB- morphotype formed by Salmonella enterica serovar typhimurium -LRB- from here on S. Typhimurium -RRB- and Escherichia coli species constitutes a multicellular biofilm behavior characterized by the expression of extracellular matrix components , proteinaceous curli fimbriae and the exopolysaccharide cellulose .1 A major contributor to rdar development is the response regulator CsgD which acts as a transcriptional activator of csgBA encoding curli fimbrial subunits and adrA encoding a di-guanylate cyclase stimulating cellulose biosynthesis .2,3 The second messenger c-di-GMP produced by AdrA and other di-guanylate cyclases is a key molecule in the switch between sessility and motility4 and facilitates csgD expression at the transcriptional and post-transcriptional level .5 Transcriptional control of csgD is complex and integrates various outside stimuli such as temperature , osmolarity and nutritional status through a variety of regulatory factors , e.g. , two-component systems and nucleoid binding proteins .6,7 The alternative sigma factor RpoS -LRB- δS -RRB- activates csgD expression in stationary-phase , a process which is aided by the auxiliary protein Crl .8 Therefore RpoS constitutes a crucial factor for multicellular behavior and rdar morphotype development in S. Typhimurium and E. coli .	31	The rdar ( red , dry and rough ) morphotype formed by Salmonella enterica serovar typhimurium ( from here on S. Typhimurium ) and Escherichia coli species constitutes a multicellular biofilm behavior characterized by the expression of extracellular matrix components , proteinaceous curli fimbriae and the exopolysaccharide cellulose .1 A major contributor to rdar development is the response regulator CsgD which acts as a transcriptional activator of csgBA encoding curli fimbrial subunits and adrA encoding a di-guanylate cyclase stimulating cellulose biosynthesis .2,3 The second messenger c-di-GMP produced by AdrA and other di-guanylate cyclases is a key molecule in the switch between sessility and motility4 and facilitates csgD expression at the transcriptional and post-transcriptional level .5 Transcriptional control of csgD is complex and integrates various outside stimuli such as temperature , osmolarity and nutritional status through a variety of regulatory factors , e.g. , two-component systems and nucleoid binding proteins .6,7 The alternative sigma factor RpoS ( δS ) activates csgD expression in stationary phase , a process which is aided by the auxiliary protein Crl .8 Therefore RpoS constitutes a crucial factor for multicellular behavior and rdar morphotype development in S. Typhimurium and E. coli .	1	INTRODUCTION	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	csgBA	activator	28148244	1	ver/dev	The transcriptional regulator CsgD activates the expression of csgBA , encoding the diguanylate cyclase AdrA .	42	The transcriptional regulator CsgD activates the expression of csgBA , encoding the minor and major subunit of curli and adrA , encoding the diguanylate cyclase AdrA .	5	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagJ	activator	12775700	0	att	The genes pagJ and pagK are PhoP-activated genes and are nearly identical to each other ( 14 ) .	402	The genes pagJ and pagK are PhoP-activated genes and are nearly identical to each other ( 14 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagJ	activator	12864810	0	att	DNA sequence analysis of the chromosomal region surrounding the PhoP-activated gene pagJ led to the identi-fication of a gene encoding a 700-amino-acid protein that was designated SspH1 ( Miao et al. , 1999 ) .	100	DNA sequence analysis of the chromosomal region surrounding the PhoP-activated gene pagJ led to the identi-fication of a gene encoding a 700-amino-acid protein that was designated SspH1 ( Miao et al. , 1999 ) .	9	SEVERAL EFFECTORS CONTAIN A CONSERVED N-TERMINAL TRANSLOCATION MOTIF	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrCAB	activator	10844688	3	att	Furthermore , PmrA activates the expression of several pags , including pmrCAB itself , under low cation conditions in a PhoP-dependent manner ( Groisman , 1998 ) ; however , PmrA can also induce these genes under acid conditions in the absence of PhoPQ regardless of cation concentrations .	239	Furthermore , PmrA activates the expression of several pags , including pmrCAB itself , under low cation conditions in a PhoP-dependent manner ( Groisman , 1998 ) ; however , PmrA can also induce these genes under acid conditions in the absence of PhoPQ regardless of cation concentrations .	14	MISLEADING CLUES?	nan	1	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	pmrCAB	activator	33932721	1	ver/dev	Subsequently , PhoP phosphorylated PmrA activates the pmrCAB operon to produce pEtN .	232	Subsequently , PhoP modulates the activity of PmrD to activate the PmrAB regulator and phosphorylated PmrA activates the pmrHIJKLM and pmrCAB operon to produce LAra4N and pEtN ( Quesada et al. , 2015 ) .	23	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrCAB	activator	33932721	1	ver/dev	Subsequently , PhoP phosphorylated PmrA activates the pmrCAB operon to produce LAra4N .	232	Subsequently , PhoP modulates the activity of PmrD to activate the PmrAB regulator and phosphorylated PmrA activates the pmrHIJKLM and pmrCAB operon to produce LAra4N and pEtN ( Quesada et al. , 2015 ) .	23	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	spiC	activator	12874347	3	ver/dev	In contrast , the activation of the spiC promoter was shown to be modulated by PhoP .	289	In contrast , the activation of the spiC promoter was shown to require SsrB and to be modulated by PhoP ( 9 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where N all bases - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where N all bases - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where D not C - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where D not C - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where H not G - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where H not G - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where T - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where T - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where W A - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where W A - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where 5 - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where 5 - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where none -RSB- - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella;unidentified	1	L3	OTHER	Fact	NEG	Other	Level 1
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where none -RSB- - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella;unidentified	1	L3	OTHER	Fact	NEG	Other	Level 1
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where all bases - GNN TTTT-3 , termed consensus IV , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	gene	spvA	regulator	19074398	29	ver/dev	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 -LSB- where all bases - GNN TTTT-3 , termed consensus III , respectively .	358	Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella ( 64 , 67 , 74 , 93 ) , the upstream regions of these genes have short Lrp-binding motifs , 5 - HNDWTTATTHND-3 [ where H not G ; W A or T ; D not C ; N all bases ; and ( N ) all bases or none ] and 5 - GNN ( N ) TTTT-3 ( 75 ) , termed consensus III and IV , respectively .	4	RESULTS	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	gene	ompR	activator	12068808	50	att	The finding that reduced supercoiling imposed by a DNA-gyrase-inhibitor stimulates OmpR-dependent ompR expression at neutral pH suggests that acid-induced changes in DNA supercoiling around the ompR promoter may influence OmpR-P binding .	261	The finding that reduced supercoiling imposed by a DNA gyrase inhibitor stimulates OmpR-dependent ompR expression at neutral pH suggests that acid-induced changes in DNA supercoiling around the ompR promoter may influence OmpR-P binding .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	activator	12068808	5	ver/dev	In this paper , we examine the details of ompR induction by the potential roles of alternative OmpR phosphodonors in acid tolerance .	58	In this paper , we examine the details of ompR induction by low pH and the potential roles of alternative OmpR phosphodonors in acid tolerance .	4	INTRODUCTION	nan	1	L1	OTHER	Investigation	OTHER	Other	Level 1
OmpR	gene	ompR	activator	12068808	12	ver/dev	OmpR _ serving as an activator of ompR transcription during P1 , transcript	102	Consistent with OmpR serving as an activator of ompR transcription during acid shock , the P2 , but not P1 , transcript was eliminated by an insertion into the OmpR open reading frame ( ORF ; Fig. 4 , lanes 9 and 10 ) .	8	ACID SHOCK INDUCES OMPR TRANSCRIPTION FROM A SECOND PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	12068808	12	ver/dev	OmpR _ serving as an activator of ompR transcription during the P2	102	Consistent with OmpR serving as an activator of ompR transcription during acid shock , the P2 , but not P1 , transcript was eliminated by an insertion into the OmpR open reading frame ( ORF ; Fig. 4 , lanes 9 and 10 ) .	8	ACID SHOCK INDUCES OMPR TRANSCRIPTION FROM A SECOND PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	12068808	12	ver/dev	OmpR _ serving as an activator of ompR transcription during acid shock	102	Consistent with OmpR serving as an activator of ompR transcription during acid shock , the P2 , but not P1 , transcript was eliminated by an insertion into the OmpR open reading frame ( ORF ; Fig. 4 , lanes 9 and 10 ) .	8	ACID SHOCK INDUCES OMPR TRANSCRIPTION FROM A SECOND PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	12068808	24	ver/dev	A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR -LRB- as indicated -RRB- for 2 h at room temperature .	166	A radiolabelled ompR promoter DNA fragment and two control fragments ( 5000 c.p.m. ) were incubated with increasing quantities of OmpR or OmpR-P ( as indicated ) for 2 h at room temperature and assayed for an electrophoretic mobility shift .	10	OMPR FOOTPRINT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	activator	12068808	38	ver/dev	A. Western blot analysis of OmpR was used to examine the effect of hns on the acid shock induction of ompR .	206	A. Western blot analysis of OmpR was used to examine the effect of hns on the acid shock induction of ompR .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
OmpR	gene	ompR	activator	12080060	50	att	The finding that reduced supercoiling imposed by a DNA-gyrase-inhibitor stimulates OmpR-dependent ompR expression at neutral pH suggests that acid-induced changes in DNA supercoiling around the ompR promoter may influence OmpR-P binding .	261	The finding that reduced supercoiling imposed by a DNA gyrase inhibitor stimulates OmpR-dependent ompR expression at neutral pH suggests that acid-induced changes in DNA supercoiling around the ompR promoter may influence OmpR-P binding .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	activator	12080060	5	ver/dev	In this paper , we examine the details of ompR induction by the potential roles of alternative OmpR phosphodonors in acid tolerance .	58	In this paper , we examine the details of ompR induction by low pH and the potential roles of alternative OmpR phosphodonors in acid tolerance .	4	INTRODUCTION	nan	1	L1	OTHER	Investigation	OTHER	Other	Level 1
OmpR	gene	ompR	activator	12080060	12	ver/dev	OmpR _ serving as an activator of ompR transcription during P1 , transcript	102	Consistent with OmpR serving as an activator of ompR transcription during acid shock , the P2 , but not P1 , transcript was eliminated by an insertion into the OmpR open reading frame ( ORF ; Fig. 4 , lanes 9 and 10 ) .	8	ACID SHOCK INDUCES OMPR TRANSCRIPTION FROM A SECOND PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	12080060	12	ver/dev	OmpR _ serving as an activator of ompR transcription during the P2	102	Consistent with OmpR serving as an activator of ompR transcription during acid shock , the P2 , but not P1 , transcript was eliminated by an insertion into the OmpR open reading frame ( ORF ; Fig. 4 , lanes 9 and 10 ) .	8	ACID SHOCK INDUCES OMPR TRANSCRIPTION FROM A SECOND PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	12080060	12	ver/dev	OmpR _ serving as an activator of ompR transcription during acid shock	102	Consistent with OmpR serving as an activator of ompR transcription during acid shock , the P2 , but not P1 , transcript was eliminated by an insertion into the OmpR open reading frame ( ORF ; Fig. 4 , lanes 9 and 10 ) .	8	ACID SHOCK INDUCES OMPR TRANSCRIPTION FROM A SECOND PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	12080060	24	ver/dev	A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR -LRB- as indicated -RRB- for 2 h at room temperature .	166	A radiolabelled ompR promoter DNA fragment and two control fragments ( 5000 c.p.m. ) were incubated with increasing quantities of OmpR or OmpR-P ( as indicated ) for 2 h at room temperature and assayed for an electrophoretic mobility shift .	10	OMPR FOOTPRINT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	activator	12080060	38	ver/dev	A. Western blot analysis of OmpR was used to examine the effect of hns on the acid shock induction of ompR .	206	A. Western blot analysis of OmpR was used to examine the effect of hns on the acid shock induction of ompR .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
OmpR	gene	ompR	activator	12753201	7	att	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	73	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	activator	15491370	22	ver/dev	In our previous study , we observed that the levels of activation of our transcriptional-fusions to spiC were similar in the absence of ompR , suggesting that EnvZ was signalling through OmpR for activation .	376	In our previous study , we observed that the levels of activation of our transcriptional fusions to ssrA/B or spiC were similar in the absence of ompR or envZ , suggesting that EnvZ was signalling through OmpR for activation ( Feng et al. , 2003 ) .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	activator	15491370	22	ver/dev	In our previous study , we observed that the levels of activation of our transcriptional-fusions to ssrA/B were similar in the absence of ompR , suggesting that EnvZ was signalling through OmpR for activation .	376	In our previous study , we observed that the levels of activation of our transcriptional fusions to ssrA/B or spiC were similar in the absence of ompR or envZ , suggesting that EnvZ was signalling through OmpR for activation ( Feng et al. , 2003 ) .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	activator	16905537	9	att	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	197	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ompR	activator	25875623	2	att	OmpR-dependent intracellular acidification was completely restored upon supplying ompR in trans on a plasmid ( Fig 2A and 2B ) .	140	OmpR-dependent intracellular acidification was completely restored upon supplying ompR in trans on a plasmid ( Fig 2A and 2B ) .	7	EXTRACELLULAR ACID STRESS ACIDIFIES THE SALMONELLA CYTOPLASM AND REQUIRES ENVZ/OMPR ACTIVATION	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompR	activator	29214489	9	auto	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase .	107	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase .	13	CADC INTERACTS DIRECTLY WITH OMPR	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ompR	activator	29417203	11	att	S2 ) , and thus the OmpR-dependent transcription of ompR and tviA may belong to the class I transcriptional stimulation [ 36 ] .	119	S2 ) , and thus the OmpR-dependent transcription of ompR and tviA may belong to the class I transcriptional stimulation [ 36 ] .	14	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompR	activator	30524381	17	att	We compared OmpR-dependent pathways induced by acid , sucrose and salt stress from the expression profiles of wildtype and the ompR null strain of S. Typhimurium ( Figure 8 ) .	241	We compared OmpR-dependent pathways induced by acid , sucrose and salt stress from the expression profiles of wildtype and the ompR null strain of S. Typhimurium ( Figure 8 ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	30524381	6	att	In order to identify OmpR-dependent pathways induced during acid stress , gene expression profiles between wild-type and an ompR null strain of S. Typhimurium and E. coli were compared .	160	In order to identify OmpR-dependent pathways induced during acid stress , gene expression profiles between wild-type and an ompR null strain of S. Typhimurium and E. coli were compared .	16	IDENTIFICATION OF THE OMPR ACID STRESS REGULON	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ompR	activator	30524381	17	ver/dev	OmpR-dependent pathways _ induced by salt stress from the ompR null strain of S. Typhimurium	241	We compared OmpR-dependent pathways induced by acid , sucrose and salt stress from the expression profiles of wildtype and the ompR null strain of S. Typhimurium ( Figure 8 ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	30524381	17	ver/dev	OmpR-dependent pathways _ induced by sucrose stress from the ompR null strain of S. Typhimurium	241	We compared OmpR-dependent pathways induced by acid , sucrose and salt stress from the expression profiles of wildtype and the ompR null strain of S. Typhimurium ( Figure 8 ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompR	activator	30524381	17	ver/dev	OmpR-dependent pathways _ induced by acid stress from the ompR null strain of S. Typhimurium	241	We compared OmpR-dependent pathways induced by acid , sucrose and salt stress from the expression profiles of wildtype and the ompR null strain of S. Typhimurium ( Figure 8 ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	fhuF	repressor	18790861	22	ver/dev	Real-time PCR analysis revealed that upon RstA expression , transcriptional repression of the fhuF gene by the FLAG-tagged Fur protein was as efficient as in the strain with the wild-type Fur protein ( see Fig .	164	Real-time PCR analysis revealed that upon RstA expression , transcriptional repression of the fhuF gene by the FLAG-tagged Fur protein was as efficient as in the strain with the wild-type Fur protein ( see Fig .	4	RESULTS	Iris germanica	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RstA	gene	fhuF	repressor	18790861	40	ver/dev	We next compared the mRNA levels of fhuF between the feoA promoter mutant strains found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain .	219	We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	fhuF	repressor	18790861	40	ver/dev	We next compared the mRNA levels of fhuF between the wild-type promoter mutant strains found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain .	219	We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steC	activator	33535041	1	att	Together , the complex regulatory network , with the PhoP-induced sRNA PinT repressing PhoP-activated SteC , both directly and indirectly ( Figure 6 ) , makes the steC mRNA a particularly interesting PinT target , encouraging future studies of the relevance of these individual	322	Together , the complex regulatory network , with the PhoP-induced sRNA PinT repressing PhoP-activated SteC , both directly and indirectly ( Figure 6 ) , makes the steC mRNA a particularly interesting PinT target , encouraging future studies of the relevance of these individual	7	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
SsrB	gene	STM2239	regulator	24021902	5	ver/dev	III secretion system effector protein c STM2239 SPI-12-encoded genes _ regulated by SsrB	127	pipB2 STM2780 Type III secretion system effector protein , regulated by SlyA siiA STM4257 SPI-4 genes that encode an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein , regulated by SlyA c srcA STM2138 SPI-2 effector chaperone required for systemic infection in c mice sseK2 STM2137 Type III secretion system effector protein c sseL STM2287 Type III secretion system effector protein , functions as a c deubiquitinase in vivo , regulated by SlyA steB STM1629 Type III secretion system effector protein c steC STM1698 Type III secretion system effector protein c STM2239 SPI-12-encoded genes regulated by SsrB , enhance fitness in c vivo , STM2239 encodes a transcriptional regulator STM2340 STM3117 SPI-13-encoded genes with suggested function in c biosynthesis of the cell wall peptidoglycan layer STM3118 c STM3119	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EmrR	gene	ugtL	activator	30992361	5	ver/dev	Actually , EmrR was able to activate ugtL transcription in a low-Mg2 condition -LRB- Fig. 2A -RRB- .	76	Actually , EmrR was able to activate ugtL transcription in a low-Mg2 condition in which the - galactosidase activity in a strain harboring the chromosomal ugtL-lacZY fusion was 15.5-fold higher than that in its isogenic ΔemrR mutant ( Fig. 2A ) .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	fepE	activator	21719537	0	ver/dev	Our results indicate that only the PmrA regulator binds to the wzz promoter , inducing fepE gene expression .	35	Our results indicate that only the PmrA regulator binds to the wzz promoter , inducing fepE gene expression , which increases the amount of VL O-Ag .	3	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	sopB	repressor	33119619	11	ver/dev	Our reasoning was that if H-NS represses sopB just acts as an anti-H-NS factor , then the expression of this gene should be induced in the absence of H-NS independently of InvF similarly as it has been observed with other virulence genes in Salmo-nella .	177	Our reasoning was that if H-NS represses sopB and InvF just acts as an anti-H-NS factor , then the expression of this gene should be induced in the absence of H-NS independently of InvF similarly as it has been observed with other virulence genes in Salmo-nella .	21	THE INVF/SICA COMPLEX DOES NOT ACT AS AN ANTI-HNS FACTOR ON SOPB	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	STM3388	activator	16629664	35	ver/dev	On the other hand , STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a post-transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3388	activator	16629664	35	ver/dev	On the other hand , STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a post-transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3388	activator	16629664	35	ver/dev	On the other hand , STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3388	activator	16629664	35	ver/dev	On the other hand , STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional level .	396	On the other hand , STM2123 and STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional and post-transcriptional level .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	ramA	repressor	18984645	7	ver/dev	the 9 bp deletion in the promoter region of mutant ramA in fluoroquinolone-resistant Salmonella _ suggesting that it might be the 51 binding site for a local repressor of RamA	313	Our study independently identified the 9 bp deletion in the promoter region of mutant ramA in fluoroquinolone-resistant Salmonella , which includes the 2 bp deletion of Abouzeed et al. , suggesting that it might be the 51 binding site for RamR , a local repressor of RamA .	17	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	tpx	repressor	22336758	35	ver/dev	On the other hand , ArcZ contributes indirectly to csgD expression as the direct ArcZ target tpx contributes to downregulation of CsgD levels -LRB- data not shown -RRB- .	357	On the other hand , ArcZ contributes indirectly to csgD expression as the direct ArcZ target tpx encoding thiol peroxidase17 partially contributes to downregulation of CsgD levels ( data not shown ) .	3	DISCUSSION	unidentified	1	L3	OTHER	Analysis	OTHER	New	Level 2
NagC	gene	nagE	repressor	24450479	5	ver/dev	NagC is the repressor of the divergent nagE -- nagBACD operon .	61	NagC is the repressor of the divergent nagE -- nagBACD operon , which encodes proteins involved in N-acetylglucosamine ( GlcNAc ) transport and metabolism .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CreB	gene	pta	activator	25136333	2	ver/dev	Furthermore , CreB is also known to positively regulate pta .	1092	Furthermore , CreB is also known to positively regulate phosphate acetyltransferase ( pta ) , which was also up-regulated in ST24CHX at the transcriptomic and proteomic levels , along with acetate kinase ( ackA ) , which was up-regulated at the protein level .	14	MODIFICATIONS IN GENERAL CELL METABOLISM COMPARING ST24WT AND ST24CHX	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	hilC	regulator	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating hilC , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	18792679	7	ver/dev	the atypical cascade in which the PhoP protein binds to the ssrB promoter to activate ssrB transcription	171	Model illustrating the atypical cascade in which the PhoP protein binds to the ssrB promoter to activate ssrB transcription and to a yet unidentified gene z that promotes SpiR expression .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L3	SPEC	Other	OTHER	New	Level 1
PhoP	gene	ssrB	regulator	20861532	6	ver/dev	PhoP was reported to bind to the ssrB promoter when Salmonella are inside macrophages .	629	PhoP was reported to bind to the ssrB promoter when Salmonella are inside macrophages [ 46 ] .	13	DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	21625519	50	ver/dev	PhoP has been shown to bind the ssrB promoter .	179	PhoP has been shown to bind the ssrB promoter and to affect SsrA levels post-transcrip-tionally [ 25 ] .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	25972862	1	ver/dev	The role of SsrB in the regulation by PhoP was investigated in a double mutant phoQ24 ssrB .	366	The role of SsrB in the regulation by PhoP was investigated in a double mutant phoQ24 ssrB .	21	SYNTHESIS AND TRANSLOCATION INTO MAMMALIAN CELLS OF SSEK1 UNDER SPI1 AND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	26441883	1	ver/dev	PhoP also controls expression of Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .	73	PhoP also controls expression of Salmonella pathogenicity island-2 ( Spi-2 ) by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	26441883	1	ver/dev	PhoP also controls expression of Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .	73	PhoP also controls expression of Salmonella pathogenicity island-2 ( Spi-2 ) by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	26441883	1	ver/dev	PhoP also controls expression of Salmonella pathogenicity island-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .	73	PhoP also controls expression of Salmonella pathogenicity island-2 ( Spi-2 ) by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	26441883	1	ver/dev	PhoP also controls expression of Salmonella pathogenicity island-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .	73	PhoP also controls expression of Salmonella pathogenicity island-2 ( Spi-2 ) by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	26441883	37	ver/dev	The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .	479	The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Bijlsma and Groisman , 2005 ) .	10	REGULATORY CIRCUITS CONTROLLING LATER STAGES OF INFECTION AND DEFENSE SYSTEMS AGAINST THE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	26441883	37	ver/dev	The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .	479	The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region and the 5 ′ - UTR of the spiR transcript ( Bijlsma and Groisman , 2005 ) .	10	REGULATORY CIRCUITS CONTROLLING LATER STAGES OF INFECTION AND DEFENSE SYSTEMS AGAINST THE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	26880544	1	ver/dev	Under low osmolality , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	26880544	1	ver/dev	Under acidic pH , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	29270156	4	ver/dev	Since PhoP regulates expression of ssrB , it also regulates expression of genes in the SsrB regulon .	437	Since PhoP regulates expression of ssrA and ssrB ( Bijlsma and Groisman , 2005 ) , it also regulates expression of genes in the SsrB regulon .	32	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	regulator	33045730	4	ver/dev	Transcription of the horizontally acquired ssrB is regulated by PhoP .	29	Transcription of the horizontally acquired ssrB and spiR genes is regulated by several ancestral regulators , including SlyA ( 20 ) , OmpR ( 6 ) , and PhoP ( 7 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	33751923	3	ver/dev	Groisman showed , using chromatin immunoprecipitation in Salmonella-infected macro-phages , that PhoP regulates ssrB by binding to its promoter region .	358	Bijlsma and Groisman ( 2005 ) showed , using chromatin immunoprecipitation in Salmonella-infected macro-phages , that PhoP regulates ssrB by binding to its promoter region .	7	PHOPQ	Salmonella;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	regulator	33751923	3	ver/dev	Bijlsma showed , using chromatin immunoprecipitation in Salmonella-infected macro-phages , that PhoP regulates ssrB by binding to its promoter region .	358	Bijlsma and Groisman ( 2005 ) showed , using chromatin immunoprecipitation in Salmonella-infected macro-phages , that PhoP regulates ssrB by binding to its promoter region .	7	PHOPQ	Salmonella;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	thiM	repressor	30742606	0	ver/dev	For example , translational repression of thiMD genes promotes Rho-dependent premature termination in a region located between codons 20 and 34 of thiM .	54	For example , translational repression of thiMD genes caused by the binding of TPP to thiM riboswitch promotes Rho-dependent premature termination in a region located between codons 20 and 34 of thiM [ 13 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	activator	31262841	11	ver/dev	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both rtsA ( and hilD ) .	169	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both hilA and rtsA ( and hilD ) ( 60 ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	prgH	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
AraC	gene	araC	repressor	24272778	42	auto	AraC has previously been shown to repress its own transcription by binding to a region overlapping the araC promoter elements ( 32 ) .	403	AraC has previously been shown to repress its own transcription by binding to a region overlapping the araC promoter elements ( 32 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	araC	repressor	24272778	3	ver/dev	In the absence-of-arabinose , AraC represses transcription of araC by forming a repression loop .	15	In the absence of arabinose , AraC represses transcription of araBAD and araC by forming a repression loop mediated by dimerization of distally bound AraC monomers ( 5 , 6 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	araC	repressor	24272778	43	ver/dev	Unlike AraC-dependent repression of araC , repression of ydeN occurs only in the presence of arabinose .	410	Unlike AraC-dependent repression of araC and ytfQ , repression of ydeN occurs only in the presence of arabinose ( Table 2 and Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	araC	repressor	24272778	43	ver/dev	Unlike AraC-dependent repression of araC , repression of ydeN occurs only in the presence of arabinose .	410	Unlike AraC-dependent repression of araC and ytfQ , repression of ydeN occurs only in the presence of arabinose ( Table 2 and Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	slyA	regulator	11882648	12	ver/dev	The locations of the SlyA sites within PslyA were consistent with the observed autoregulation of slyA expression .	275	The locations of the SlyA sites within PslyA were consistent with the observed autoregulation of slyA expression observed in vivo .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	15208313	26	att	The region protected by SlyA includes the imperfect palindrome TTTAG-N7-CTTAA , which is similar to the SlyA binding sequence TTAG-N4-CTAA described for the slyA promoter ( 32 ) , the only SlyA-regulated promoter investigated in molecular detail .	130	The region protected by SlyA includes the imperfect palindrome TTTAG-N7-CTTAA , which is similar to the SlyA binding sequence TTAG-N4-CTAA described for the slyA promoter ( 32 ) , the only SlyA-regulated promoter investigated in molecular detail .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	15208313	70	att	The polymyxin B susceptibility of the slyA mutant was the same as that exhibited by the ugtL mutant ( Fig. 5A ) and could be complemented to wild-type levels by a plasmid that expressed the ugtL gene from a heterologous promoter ( Fig. 5B ) , suggesting that ugtL is the only SlyA-regulated gene mediating polymyxin B resistance .	234	The polymyxin B susceptibility of the slyA mutant was the same as that exhibited by the ugtL mutant ( Fig. 5A ) and could be complemented to wild-type levels by a plasmid that expressed the ugtL gene from a heterologous promoter ( Fig. 5B ) , suggesting that ugtL is the only SlyA-regulated gene mediating polymyxin B resistance .	5	DISCUSSION	unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	slyA	regulator	16413221	0	ver/dev	Sensitivity to CAMPs is also regulated by SlyA ; mutation of slyA renders S. typhimurium highly sensitive to the CAMP polymyxin B .	154	Sensitivity to CAMPs is also regulated by SlyA , a transcriptional regulator found in Salmonella and Escherichia coli ; mutation of slyA renders S. typhimurium highly sensitive to the CAMP polymyxin B [ 24 ] .	6	DEFINING SALMONELLA REGULONS AND STIMULONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	17259627	7	ver/dev	the SlyA-binding site is involved in the autoregulation of the slyA gene	59	The 12 bp consensus sequence , TTAGCAAGCTAA , is located in the slyA promoter , and has been identified as the SlyA-binding site , which is involved in the autoregulation of the slyA gene ( Stapleton et al. , 2002 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	17259627	7	ver/dev	the SlyA-binding site is involved in the autoregulation of the slyA gene	59	The 12 bp consensus sequence , TTAGCAAGCTAA , is located in the slyA promoter , and has been identified as the SlyA-binding site , which is involved in the autoregulation of the slyA gene ( Stapleton et al. , 2002 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	30510144	9	ver/dev	SlyA whose activation increases virulence via positive control of SPI-2 genes , as the virulence of a slyA gene mutant was attenuated in a mouse infection model	53	In contrast , an opposite effect was reported for SlyA , whose overproduction or activation increases virulence via positive control of SPI-2 genes ( 12 ) , as the virulence of a slyA gene mutant was attenuated in a mouse infection model ( 10 ) .	3	KEYWORDS RCSCDB SYSTEM, SALMONELLA, SLYA, GENE REGULATION	Mus musculus	0	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	30510144	9	ver/dev	SlyA whose overproduction increases virulence via positive control of SPI-2 genes , as the virulence of a slyA gene mutant was attenuated in a mouse infection model	53	In contrast , an opposite effect was reported for SlyA , whose overproduction or activation increases virulence via positive control of SPI-2 genes ( 12 ) , as the virulence of a slyA gene mutant was attenuated in a mouse infection model ( 10 ) .	3	KEYWORDS RCSCDB SYSTEM, SALMONELLA, SLYA, GENE REGULATION	Mus musculus	0	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	slyA	regulator	30510144	36	ver/dev	Accordingly , other authors also reported an functional palindrome for SlyA binding at slyA promoter regions , indicating that those motifs might function as SlyA regulatory sites .	165	Accordingly , other authors also reported an imperfect but functional palindrome for SlyA binding at the ugtL and slyA promoter regions ( 15 , 40 ) , indicating that those motifs identified in the PrcsDB and PrcsB sequences might function as SlyA regulatory sites .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	slyA	regulator	30510144	36	ver/dev	Accordingly , other authors also reported an imperfect palindrome for SlyA binding at slyA promoter regions , indicating that those motifs might function as SlyA regulatory sites .	165	Accordingly , other authors also reported an imperfect but functional palindrome for SlyA binding at the ugtL and slyA promoter regions ( 15 , 40 ) , indicating that those motifs identified in the PrcsDB and PrcsB sequences might function as SlyA regulatory sites .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	slyA	regulator	9284144	8	att	Although slyA mutants are able to invade deep tissues , they are unable to proliferate efficiently within the reticuloendothelial cells of murine hosts , suggesting that Salmonella strains are unable to withstand host cellular antimicrobial mechanisms in the absence of SlyA-regulated genes .	160	Although slyA mutants are able to invade deep tissues , they are unable to proliferate efficiently within the reticuloendothelial cells of murine hosts , suggesting that Salmonella strains are unable to withstand host cellular antimicrobial mechanisms in the absence of SlyA-regulated genes .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsB	gene	wza	regulator	28588134	4	att	We did not observe a decrease in Δ in a wza yjb rcsB mutant beyond what is observed in the rcsB mutant , suggesting that no additional RcsB-regulated factors are required for PMF maintenance ( see Fig .	256	We did not observe a decrease in Δ in a wza yjb rcsB mutant beyond what is observed in the rcsB mutant , suggesting that no additional RcsB-regulated factors are required for PMF maintenance ( see Fig .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	ompC	activator	32392214	32	att	This was also true for strains harboring gfp transcriptional-fusions to the PhoP-activated rstA gene ( S17 Fig ) and the OmpR-activated ompC gene ( S18 Fig ) .	328	This was also true for strains harboring gfp transcriptional fusions to the PhoP-activated rstA gene ( S17 Fig ) and the OmpR-activated ompC gene ( S18 Fig ) .	17	BARA IS DISPENSABLE FOR ACTIVATION OF THE REGULATORS ARCA, OMPR, AND PHOP UNDER CONDITIONS IN WHICH IT ACTIVATES RCSB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	phoPQ	regulator	31333620	7	ver/dev	Although H-NS was shown to bind the phoPQ promoter , the PhoPHA level in T13E mutant remained similar to that in the WT strain .	345	Although H-NS was shown to bind the phoPQ promoter ( Kong et al. , 2008 ) , the PhoPHA level in T13E mutant remained similar to that in the WT strain ( Figure 3A ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YncC	gene	yciG	regulator	20713450	3	ver/dev	The binding of YncC upstream of the yciG promoter were investigated .	37	The binding of YncC upstream of the yciG promoter and its effects on S-dependent transcription were investigated .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR-P	gene	ssrB	regulator	12753201	3	ver/dev	OmpR-P also binds to the ssrB region	50	Phosphorylation of OmpR has a large effect on DNA binding at ssrA , and OmpR-P also binds to the ssrB region .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ssrB	regulator	12753201	34	ver/dev	The effect of OmpR appears to be direct , based on our observation that OmpR-P binds to the intergenic region between ssrB .	218	The effect of OmpR appears to be direct , based on our observation that OmpR-P binds upstream of ssrA and to the intergenic region between ssrA and ssrB ( Fig. 6 ) .	11	THE SSRA/B REGION CONTAINS TWO PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR-P	gene	ssrB	regulator	12753201	45	ver/dev	Altogether , our data indicate that OmpR-P binds around the intergenic region between ssrB .	242	Altogether , our data indicate that OmpR-P binds to the upstream region of ssrA and around the intergenic region between ssrA and ssrB ( Fig. 6 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR-P	gene	ssrB	regulator	24079299	3	ver/dev	In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrB genes .	123	In low osmolarity conditions , OmpR and/or OmpR-P ( phosphorylayted OmpR present in low levels ) can bind to the upstream regions of ssrA and ssrB genes .	5	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
RpoS	gene	spoT	activator	8045891	19	att	Thus , the ppGpp-dependent induction of RpoS , and consequently RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	191	Thus , the ppGpp-dependent induction of RpoS , and consequently RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	5	DISCUSSION	Leiostomus xanthurus	0	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spoT	activator	8045891	19	ver/dev	Thus , the ppGpp-dependent induction of RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	191	Thus , the ppGpp-dependent induction of RpoS , and consequently RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	5	DISCUSSION	Leiostomus xanthurus	0	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spoT	activator	8045891	19	ver/dev	Thus , the ppGpp-dependent induction of RpoS , would be spoT dependent during P starvation and relA dependent during C starvation .	191	Thus , the ppGpp-dependent induction of RpoS , and consequently RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	5	DISCUSSION	Leiostomus xanthurus	0	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	stiB	regulator	8045891	0	ver/dev	The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiB , has been characterized .	9	The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiA , stiB , and stiC , has been characterized .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiB	regulator	8045891	2	ver/dev	In contrast , RpoS was found to be required for the negative regulation of stiB during logarithmic phase .	11	In contrast , RpoS was found to be required for the negative regulation of stiB during P and C starvation-induced stationary phase but not during logarithmic phase .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiB	regulator	8045891	2	ver/dev	In contrast , RpoS was found to be required for the negative regulation of stiB during C starvation-induced stationary-phase .	11	In contrast , RpoS was found to be required for the negative regulation of stiB during P and C starvation-induced stationary phase but not during logarithmic phase .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiB	regulator	8045891	2	ver/dev	In contrast , RpoS was found to be required for the negative regulation of stiB during P starvation-induced stationary-phase .	11	In contrast , RpoS was found to be required for the negative regulation of stiB during P and C starvation-induced stationary phase but not during logarithmic phase .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiB	regulator	8045891	9	ver/dev	RpoS functions in the negative regulation of stiB .	93	RpoS functions in the negative regulation of stiB .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	stiB	regulator	8045891	10	ver/dev	The rpoS mutation resulted in a two - to threefoldhigher level of induction of a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	99	The rpoS mutation resulted in a two - to threefoldhigher level of induction of stiB during P starvation and a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	stiB	regulator	8045891	10	ver/dev	The rpoS mutation resulted in a two - to threefoldhigher level of induction of stiB during P starvation during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	99	The rpoS mutation resulted in a two - to threefoldhigher level of induction of stiB during P starvation and a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	stiB	regulator	8045891	12	ver/dev	The fact that RpoS is an alternative a factor suggests that rpoS controls the expression of a negative regulator of stiB .	106	The fact that RpoS is an alternative a factor ( 47 ) suggests that rpoS controls the expression of a negative regulator of stiB , rather than stiB itself .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	stiB	regulator	8045891	13	ver/dev	Since stiB are regulated by RpoS , we wanted to examine the combined effects of sti mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiB	regulator	8045891	13	ver/dev	Since stiB are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiB	regulator	8045891	20	ver/dev	Role of the alternative a factor RpoS , or a ' , in the regulation of the starvation survival gene stiB .	199	Role of the alternative a factor RpoS , or a ' , in the regulation of the starvation survival gene stiB .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	stiB	regulator	8045891	24	ver/dev	On the basis of the fact that stiB are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	225	On the basis of the fact that stiA , stiB , and stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA and stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RpoS	gene	stiB	regulator	8045891	24	ver/dev	On the basis of the fact that stiB are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA are not induced and/or because stiB is overexpressed in an rpoS mutant .	225	On the basis of the fact that stiA , stiB , and stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA and stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
CRP	gene	aer	regulator	16949866	38	ver/dev	Of these genes , a master regulator of the flagellar operon , aer are known to bind CRP .	501	Of these genes , flhD ( a master regulator of the flagellar operon ) , aer and tsr ( chemotaxis genes ) , the malB region , and the phs operon are known to bind CRP or are predicted to have CRP -- cAMP-binding sites in their regulatory regions ( Brown and Callan , 2004 ; Heinzinger et al. , 1995 ; Yanagihara et al. , 1999 ) .	19	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CRP	gene	aer	regulator	16949866	38	ver/dev	Of these genes , flhD , aer are known to bind CRP .	501	Of these genes , flhD ( a master regulator of the flagellar operon ) , aer and tsr ( chemotaxis genes ) , the malB region , and the phs operon are known to bind CRP or are predicted to have CRP -- cAMP-binding sites in their regulatory regions ( Brown and Callan , 2004 ; Heinzinger et al. , 1995 ; Yanagihara et al. , 1999 ) .	19	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CRP	gene	aer	regulator	16949866	38	ver/dev	Of these genes , a master regulator of the flagellar operon , aer are predicted to have CRP .	501	Of these genes , flhD ( a master regulator of the flagellar operon ) , aer and tsr ( chemotaxis genes ) , the malB region , and the phs operon are known to bind CRP or are predicted to have CRP -- cAMP-binding sites in their regulatory regions ( Brown and Callan , 2004 ; Heinzinger et al. , 1995 ; Yanagihara et al. , 1999 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YeiE	gene	STM1697	regulator	34098734	6	ver/dev	To test whether YeiE influences the expression of STM1697 , we determined the relative expression of STM1697 in the DyeiE mutant .	166	To test whether YeiE influences the expression of STM1697 , we determined the relative expression of STM1697 in the WT and the DyeiE mutant .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
YeiE	gene	STM1697	regulator	34098734	6	ver/dev	To test whether YeiE influences the expression of STM1697 , we determined the relative expression of STM1697 in the WT .	166	To test whether YeiE influences the expression of STM1697 , we determined the relative expression of STM1697 in the WT and the DyeiE mutant .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
YeiE	gene	STM1697	regulator	34098734	12	ver/dev	YeiE may indirectly influence STM1697 expression by regulating the expression of an activator or inhibitor of STM1697 transcription .	186	YeiE may indirectly influence STM1697 expression by regulating the expression of an activator or inhibitor of STM1697 transcription .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
YeiE	gene	STM1697	regulator	34098734	12	ver/dev	YeiE may indirectly influence STM1697 expression by regulating the expression of an activator or inhibitor of STM1697 transcription .	186	YeiE may indirectly influence STM1697 expression by regulating the expression of an activator or inhibitor of STM1697 transcription .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
YeiE	gene	STM1697	regulator	34098734	23	ver/dev	We propose that YeiE serves as a control point for flagellar regulation through inhibition of the antiFlhD4C2 factor STM1697 , although additional work is needed to establish the mechanism by which YeiE influences STM1697 expression .	220	We propose that YeiE serves as a control point for flagellar regulation through inhibition of the antiFlhD4C2 factor STM1697 , although additional work is needed to establish the mechanism by which YeiE influences STM1697 expression .	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	fimB	regulator	29417203	18	ver/dev	Rentschler AE , Lovrich SD , Fitton R , Enos-Berlage J , Schwan WR OmpR regulation of the uropathogenic Escherichia coli fimB gene in an acidic/high osmolality environment .	248	Rentschler AE , Lovrich SD , Fitton R , Enos-Berlage J , Schwan WR ( 2013 ) OmpR regulation of the uropathogenic Escherichia coli fimB gene in an acidic/high osmolality environment .	32	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	sodB	regulator	17993530	2	att	Fur activation of SPI1 is not mediated through the Fur-regulated small RNAs RfrA and RfrB , which are the Salmonella ortholog and paralog of RyhB that control expression of sodB .	14	Fur activation of SPI1 is not mediated through the Fur-regulated small RNAs RfrA and RfrB , which are the Salmonella ortholog and paralog of RyhB that control expression of sodB .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
Fur	gene	sodB	regulator	17993530	27	ver/dev	Known `` Fur-activated '' genes , like sodB , are regulated at the level of translation initiation and/or mRNA stability .	218	Known `` Fur-activated '' genes , like sodB , are regulated at the level of translation initiation and/or mRNA stability .	4	RESULTS	nan	1	L2	OTHER	Other	NEG	Other	Level 1
HNS	gene	ftnA	repressor	21722794	1	ver/dev	H-NS acts as a direct repressor of ftnA transcription , causing derepression of ftnA expression	404	Fur binding at this site directly competes with the binding of the his-tone-like nucleoid-associated protein ( H-NS ) that acts as a direct repressor of ftnA transcription , thereby displacing H-NS and causing derepression of ftnA expression ( Nandal et al. , 2010 ) .	11	3.1. TRANSCRIPTIONAL REGULATION BY FUR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ftnA	repressor	21722794	1	ver/dev	H-NS acts as a direct repressor of ftnA transcription , thereby displacing H-NS	404	Fur binding at this site directly competes with the binding of the his-tone-like nucleoid-associated protein ( H-NS ) that acts as a direct repressor of ftnA transcription , thereby displacing H-NS and causing derepression of ftnA expression ( Nandal et al. , 2010 ) .	11	3.1. TRANSCRIPTIONAL REGULATION BY FUR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ftnA	repressor	21722794	1	ver/dev	the his-tone-like nucleoid-associated protein acts as a direct repressor of ftnA transcription , thereby displacing H-NS	404	Fur binding at this site directly competes with the binding of the his-tone-like nucleoid-associated protein ( H-NS ) that acts as a direct repressor of ftnA transcription , thereby displacing H-NS and causing derepression of ftnA expression ( Nandal et al. , 2010 ) .	11	3.1. TRANSCRIPTIONAL REGULATION BY FUR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	tviA	regulator	30145252	1	ver/dev	Also , the EMSA revealed that OxyR directly binds to the promoter region of tviA .	17	Also , the EMSA revealed that OxyR directly binds to the promoter region of tviA .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OxyR	gene	tviA	regulator	30145252	3	ver/dev	In this study , we found that OxyR positively regulated the gene expression of Vi antigen in S. Typhi by directly binding to the promoter region of tviA .	41	In this study , we found that OxyR positively regulated the gene expression of Vi antigen in S. Typhi by directly binding to the promoter region of tviA .	3	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
OxyR	gene	tviA	regulator	30145252	6	ver/dev	These results confirmed that transcription of tviA is under positive control of OxyR .	188	These results confirmed that transcription of tviA is under positive control of OxyR .	17	3.3. OXYR ACTIVATES THE PROMOTER ACTIVITY OF TVIA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OxyR	gene	tviA	regulator	30145252	7	ver/dev	The EMSA results showed that OxyR bound to the promoter region of tviA	229	The EMSA results showed that OxyR bound to the promoter region of tviA , but it was unable to bind to the upstream region of tviB .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	tviA	regulator	30145252	8	ver/dev	The results indicated that OxyR directly regulates the expression of the viaB locus by binding to tviA promoter .	230	The results indicated that OxyR directly regulates the expression of the viaB locus by binding to tviA promoter .	20	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OxyR	gene	tviA	regulator	30145252	8	ver/dev	The results indicated that OxyR directly regulates the expression of the viaB locus by binding to tviA promoter .	230	The results indicated that OxyR directly regulates the expression of the viaB locus by binding to tviA promoter .	20	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OxyR	gene	tviA	regulator	30145252	9	ver/dev	In summary , OxyR is involved in the regulation of Vi polysaccharide capsular antigen expression by directly binding to the promoter regions of tviA .	231	In summary , OxyR is involved in the regulation of Vi polysaccharide capsular antigen expression by directly binding to the promoter regions of tviA .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	tviA	regulator	30145252	9	ver/dev	In summary , OxyR is involved in the regulation of Vi polysaccharide capsular antigen expression by directly binding to the promoter regions of tviA .	231	In summary , OxyR is involved in the regulation of Vi polysaccharide capsular antigen expression by directly binding to the promoter regions of tviA .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FruR	gene	icd	regulator	19136587	16	ver/dev	In vitro binding of FruR , to icd operons of Salmonella typhimurium .	551	In vitro binding of the pleiotropic transcriptional regulatory protein , FruR , to the fru , pps , ace , pts and icd operons of Esche-richia coli and Salmonella typhimurium .	20	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FruR	gene	icd	regulator	19136587	16	ver/dev	In vitro binding of FruR , to icd operons of Esche-richia coli .	551	In vitro binding of the pleiotropic transcriptional regulatory protein , FruR , to the fru , pps , ace , pts and icd operons of Esche-richia coli and Salmonella typhimurium .	20	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	12753201	1	ver/dev	Emerging evidence indicates that OmpR regulates cryptic porins ompS1 .	29	Emerging evidence indicates that OmpR regulates many additional genes outside the porin repertoire ( Oshima et al. , 2002 ) , including regulation of the flagellar operon flhDC ( Shin and Park , 1995 ) , curli fimbrial expression ( Vidal et al. , 1998 ) and cryptic porins ompS1 and ompS2 in S. typhi ( Fernandez-Mora et al. , 1995 ; Oropeza et al. , 1999 ) .	3	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS1	regulator	17908208	22	ver/dev	To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .	74	To elucidate how LeuO , OmpR and H-NS regulate ompS1 expression , the effect of LeuO was evaluated in the wild type ( IMSS-1 ) , in the ompR mutant ( IMSS-41 ) , in the hns mutant ( STYhns99 ) and in the hns ompR double mutant ( STY9941 ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	acrA	regulator	18577510	23	ver/dev	RamA binds to the upstream region of acrA .	222	RamA binds to the upstream region of acrA and tolC .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	acrA	regulator	21148208	0	ver/dev	acrA binds RamA	19	region of acrA that binds RamA .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	acrA	regulator	21148208	21	ver/dev	This suggests that RamA competitively bind to the upstream region of acrA .	263	This suggests that RamA and SoxS competitively bind to the upstream region of acrA .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	entF	regulator	18554972	0	att	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	215	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	15	3.1. TRANSPOSON MUTAGENESIS IDENTIFIES IRON RESPONSE GENES INVOLVED IN NOREPINEPHRINE-ENHANCED GROWTH OF SALMONELLA TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	ompF	repressor	11796342	1	ver/dev	Repression of ompF by MarA is thought to occur indirectly through its activation of micF .	227	Repression of ompF by MarA is thought to occur indirectly through its activation of micF , whose RNA product interacts with ompF mRNA to prevent translation ( 4 , 18 ) .	5	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
MarA	gene	ompF	repressor	15073288	12	ver/dev	Studies in E. coli indicate that MarA indirectly represses ompF .	313	Studies in E. coli indicate that MarA indirectly represses ompF , reducing the number of porins in the outer membrane and activates transcription of acrAB to increase the number of efflux pumps in the membrane ( Alekshun & Levy , 1997 ) .	12	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	New	Level 1
CsrA	gene	csrA	activator	16413221	2	att	Of 93 CsrA-induced genes identified in-vitro , we found that 88 % were downregulated during infection of J774A .1 macrophages by S. typhimurium ; consistent with this , csrA was also downregulated threefold ( Figure 1 ) [ 19,30 ] .	203	Of 93 CsrA-induced genes identified in vitro , we found that 88 % were downregulated during infection of J774A .1 macrophages by S. typhimurium ; consistent with this , csrA was also downregulated threefold ( Figure 1 ) [ 19,30 ] .	8	NEW INSIGHTS FROM TRANSCRIPTOMIC DATA COMPARISONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	15703297	18	att	The experimental verification that the PhoP protein binds to different classes of promoters in-vivo ( Fig. 1 A ) and in-vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	149	The experimental verification that the PhoP protein binds to different classes of promoters in vivo ( Fig. 1 A ) and in vitro ( Fig. 2C ) , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation ( data not shown ) , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly ( 15 ) .	4	RESULTS	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtC	activator	15703297	7	att	Furthermore , we conducted site-directed mutagenesis of the hexameric repeat sequences that makes up the PhoP box in the mgtC promoter ( see Supporting Text ) and demonstrated that , despite its orientation , the PhoP box is essential for the low-Mg2 PhoP-dependent expression of the mgtC gene ( data not shown ) .	112	Furthermore , we conducted site-directed mutagenesis of the hexameric repeat sequences that makes up the PhoP box in the mgtC promoter ( see Supporting Text ) and demonstrated that , despite its orientation , the PhoP box is essential for the low-Mg2 PhoP-dependent expression of the mgtC gene ( data not shown ) .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	mgtC	activator	15703297	7	att	Furthermore , we conducted site-directed mutagenesis of the hexameric repeat sequences that makes up the PhoP box in the mgtC promoter ( see Supporting Text ) and demonstrated that , despite its orientation , the PhoP box is essential for the low-Mg2 PhoP-dependent expression of the mgtC gene ( data not shown ) .	112	Furthermore , we conducted site-directed mutagenesis of the hexameric repeat sequences that makes up the PhoP box in the mgtC promoter ( see Supporting Text ) and demonstrated that , despite its orientation , the PhoP box is essential for the low-Mg2 PhoP-dependent expression of the mgtC gene ( data not shown ) .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	mgtC	activator	18248433	0	att	To characterize the physiological role of the Mg ribos-21 witch present in mgtA , the expression of both mgtA and mgtC was determined in the presence of increasing Mg 21 concentrations in the culture medium and compared them with that obtained for other PhoP-activated genes .	169	To characterize the physiological role of the Mg ribos-21 witch present in mgtA , the expression of both mgtA and mgtC was determined in the presence of increasing Mg 21 concentrations in the culture medium and compared them with that obtained for other PhoP-activated genes .	10	RESULTS	Glyptocephalus cynoglossus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	18248433	2	att	PhoP overexpression from the pPB1019 plasmid results in a Mg - and PhoQ-indepen-21 dent expression of the PhoP-activated genes ( Lejona et al. , 2004 ) , with the notable exception of mgtA and mgtC , whose expression was still modulated by Mg ( Fig. 1c ) .	309	PhoP overexpression from the pPB1019 plasmid results in a Mg - and PhoQ-indepen-21 dent expression of the PhoP-activated genes ( Lejona et al. , 2004 ) , with the notable exception of mgtA and mgtC , whose expression was still modulated by Mg ( Fig. 1c ) .	10	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	18620040	0	att	The mgtC and pagC genes are both PhoP-activated genes required for intramacrophage growth [ 2,5 -- 7 ] .	28	The mgtC and pagC genes are both PhoP-activated genes required for intramacrophage growth [ 2,5 -- 7 ] .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	19436747	0	ver/dev	In addition , by using genes we determined that PhoP regulator induce mgtC expression in Typhi .	11	In addition , by using reporter 2 + genes we determined that the low-Mg concentration , acidic media and PhoP regulator induce mgtC expression in S. 2 + Typhi .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtC	activator	19436747	0	ver/dev	In addition , by using genes we determined that PhoP regulator induce mgtC expression in S. 2 .	11	In addition , by using reporter 2 + genes we determined that the low-Mg concentration , acidic media and PhoP regulator induce mgtC expression in S. 2 + Typhi .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtC	activator	19436747	0	ver/dev	In addition , by using reporter 2 we determined that PhoP regulator induce mgtC expression in Typhi .	11	In addition , by using reporter 2 + genes we determined that the low-Mg concentration , acidic media and PhoP regulator induce mgtC expression in S. 2 + Typhi .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtC	activator	19436747	0	ver/dev	In addition , by using reporter 2 we determined that PhoP regulator induce mgtC expression in S. 2 .	11	In addition , by using reporter 2 + genes we determined that the low-Mg concentration , acidic media and PhoP regulator induce mgtC expression in S. 2 + Typhi .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtC	activator	19436747	1	ver/dev	In addition , the PhoP regulator participates in inducing the expression of mgtC in S. Typhi .	40	In addition , the PhoP regulator participates in inducing the expression of mgtC in S. Typhi .	5	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtC	activator	25624475	4	att	This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 's own F1Fo ATPase , and a small protein of unknown function , respectively .	20	This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 's own F1Fo ATPase , and a small protein of unknown function , respectively .	4	MAIN	Salmonella;unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	mgtC	activator	25624475	8	att	The PhoP-activated mgtA , mgtC , and pagM genes are required for motility on 0.3 % agarose low Mg2 + media .	116	The PhoP-activated mgtA , mgtC , and pagM genes are required for motility on 0.3 % agarose low Mg2 + media .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	25848006	0	ver/dev	This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to recruiting RNA polymerase .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	25848006	0	ver/dev	This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	25848006	0	ver/dev	This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	25848006	0	ver/dev	This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to recruiting RNA polymerase .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	25848006	0	ver/dev	This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	25848006	0	ver/dev	This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .	192	This is because the PhoP protein , a major regulator of Salmonella virulence ( 41 ) , activates mgtC transcription directly by binding to the mgtC promoter and recruiting RNA polymerase ( 42 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	26231375	1	ver/dev	Although PhoP activates mgtC transcription initiation from a single promoter located in front of the mgtC gene , a computational approach found two other PhoP-binding sites .	31	Although PhoP activates mgtC transcription initiation from a single promoter located in front of the mgtC gene , a computational approach found two other PhoP-binding sites , which are located downstream of the experimentally determined mgtC promoter ( Zwir et al. , 2014 ) .	5	REGULATION AT THE LEVEL OF TRANSCRIPTION INITIATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	28181542	1	att	Indeed , when grown in media containing 500 μM Mg2 + for 1 h to initiate transcription from the PhoP-dependent promoter , the efp mutant increased mRNA levels of both the mgtC and mgtB genes by ~ 100 fold ( Fig .	61	Indeed , when grown in media containing 500 μM Mg2 + for 1 h to initiate transcription from the PhoP-dependent promoter , the efp mutant increased mRNA levels of both the mgtC and mgtB genes by ~ 100 fold ( Fig .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtC	activator	28874555	0	att	Previous Northern blot analysis using a DNA probe corresponding to the leader region of the mgtCBR operon detected multiple short transcripts in RNA samples prepared from Salmonella grown in low Mg2 + , which activates transcription from the PhoP-dependent mgtC promoter ( 22 ) .	58	Previous Northern blot analysis using a DNA probe corresponding to the leader region of the mgtCBR operon detected multiple short transcripts in RNA samples prepared from Salmonella grown in low Mg2 + , which activates transcription from the PhoP-dependent mgtC promoter ( 22 ) .	6	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtC	activator	29802740	1	att	In addition , the accumulation of the mgtCBR mRNA is subject to regulation by turnover by a 1.2 kb-long antisense RNA , AmgR , that is generated from a PhoP-dependent promoter located between mgtC and mgtB and can hybridize to the sense mRNA across the mgtM , mgtP and mgtC coding sequences ( Lee and Groisman , 2010 ) .	49	In addition , the accumulation of the mgtCBR mRNA is subject to regulation by turnover by a 1.2 kb-long antisense RNA , AmgR , that is generated from a PhoP-dependent promoter located between mgtC and mgtB and can hybridize to the sense mRNA across the mgtM , mgtP and mgtC coding sequences ( Lee and Groisman , 2010 ) .	3	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	mgtC	activator	31346161	12	att	PhoQ senses low Mg2 + , acidic pH , or antimicrobial peptides20 -- 22 that could be encountered within a macrophage phagosome and phosphorylates PhoP to promote transcription of the PhoP-dependent genes , including mgtC ( Fig. 6 ) 19,39 .	522	PhoQ senses low Mg2 + , acidic pH , or antimicrobial peptides20 -- 22 that could be encountered within a macrophage phagosome and phosphorylates PhoP to promote transcription of the PhoP-dependent genes , including mgtC ( Fig. 6 ) 19,39 .	4	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	mgtC	activator	31346161	14	att	However , PhoP-dependent transcription is not influenced by the PhoB/PhoR-activating signal because low phosphate does not affect mgtC transcription ( Fig. 4 ) .	526	However , PhoP-dependent transcription is not influenced by the PhoB/PhoR-activating signal because low phosphate does not affect mgtC transcription ( Fig. 4 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtC	activator	31866990	3	att	The resulting strain ( 1LD ) still possessed PhoP-dependent Mg2 + regulation of mgtC expression .	192	The resulting strain ( 1LD ) still possessed PhoP-dependent Mg2 + regulation of mgtC expression .	13	A SALMONELLA STRAIN DESIGNED TO PRODUCE LEADERLESS MGTCBR MRNA IS SEVERELY	Ancylobacter plantiphilus;Rhodopirellula baltica;Calidifontibacillus azotoformans;Vibrio diazotrophicus	0	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtC	activator	33849981	0	att	Because both plasmids harbor a 1.2-kb DNA fragment containing the PhoP-dependent promoter ( pmgtC ) , as well as the mgtC and mgtQ genes upstream of the mgtB-fused gfp gene , we grew Salmonella strains harboring the mgtB-fused gfp plasmids in PhoP-inducing ( 0.01 mM Mg21 ) or PhoP-repressing ( 10 mM Mg21 ) conditions .	70	Because both plasmids harbor a 1.2-kb DNA fragment containing the PhoP-dependent promoter ( pmgtC ) , as well as the mgtC and mgtQ genes upstream of the mgtB-fused gfp gene , we grew Salmonella strains harboring the mgtB-fused gfp plasmids in PhoP-inducing ( 0.01 mM Mg21 ) or PhoP-repressing ( 10 mM Mg21 ) conditions .	3	KEYWORDS UORF, TRANSLATION-INHIBITORY STEM-LOOP STRUCTURE, INTERGENIC REGION, RIBOSOME DESTABILIZATION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	nadD	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA rfbJ .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	nadD	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA biosynthetic genes abe .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	nadD	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA rfbA .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM1674	gene	nadD	repressor	31560731	2	ver/dev	Inactivation of six D23580 genes increased nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 -LRB- -RRB- , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA rmlA .	243	Inactivation of six D23580 genes increased fitness in the macrophage infection model ( log2 fold-change > 1 , P-value < 0.05 ) : nadD , encoding a nicotinate-nucleotide adenylyltransferase ; STM1674 ( STMMW_16691 ) , encoding a transcriptional regulator ; barA , encoding the sensor of the two-component regulatory system SirA/BarA that controls carbon metabolism via the CsrA/CsrB regulatory system ; the pSLT-BT plasmid gene repC ; and the LPS O-antigen biosynthetic genes abe ( rfbJ ) and rmlA ( rfbA ) .	11	INTRA-MACROPHAGE INFECTION WITH THE TRANSPOSON LIBRARY SUGGESTS THE ABSENCE OF NOVEL VIRULENCE FACTORS IN S. TYPHIMURIUM D23580	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	tcfA	activator	28922626	2	ver/dev	Lrp where in its absence the expression of tcfA increased by four to sixteen-fold compared to the S. Infantis wild-type background	106	Interestingly , the most prominent regulatory affect was found for Lrp , where in its absence the expression of tcfA increased by four to sixteen-fold compared to the S. Infantis wild-type background ( Fig. 5 ) .	6	TCF CONTAINS INTERCHANGING ALLELES OF THE FIMBRIA ADHESIN TCFD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	tsr	regulator	16949866	38	ver/dev	Of these genes , a master regulator of the flagellar operon , tsr are known to bind CRP .	501	Of these genes , flhD ( a master regulator of the flagellar operon ) , aer and tsr ( chemotaxis genes ) , the malB region , and the phs operon are known to bind CRP or are predicted to have CRP -- cAMP-binding sites in their regulatory regions ( Brown and Callan , 2004 ; Heinzinger et al. , 1995 ; Yanagihara et al. , 1999 ) .	19	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CRP	gene	tsr	regulator	16949866	38	ver/dev	Of these genes , flhD , tsr are known to bind CRP .	501	Of these genes , flhD ( a master regulator of the flagellar operon ) , aer and tsr ( chemotaxis genes ) , the malB region , and the phs operon are known to bind CRP or are predicted to have CRP -- cAMP-binding sites in their regulatory regions ( Brown and Callan , 2004 ; Heinzinger et al. , 1995 ; Yanagihara et al. , 1999 ) .	19	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CRP	gene	tsr	regulator	16949866	38	ver/dev	Of these genes , a master regulator of the flagellar operon , tsr are predicted to have CRP .	501	Of these genes , flhD ( a master regulator of the flagellar operon ) , aer and tsr ( chemotaxis genes ) , the malB region , and the phs operon are known to bind CRP or are predicted to have CRP -- cAMP-binding sites in their regulatory regions ( Brown and Callan , 2004 ; Heinzinger et al. , 1995 ; Yanagihara et al. , 1999 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sigD	activator	10692170	5	att	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	92	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	sigD	activator	10692170	5	att	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	92	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	sigD	activator	10692170	8	ver/dev	AraC requires arabinose for the expression of AraC-activated promoters , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD .	207	AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA .	8	INVF AND SICA ARE SUFFICIENT TO ACTIVATE TRANSCRIPTION OF SICA- AND SIGD±LACZYA IN E:COLI CC118LPIR.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MarA	gene	acrB	repressor	32468234	10	ver/dev	The study also reports suppression of acrB expression along with downregulation of MarA regulators .	146	The study also reports suppression of acrB expression along with downregulation of SoxS and MarA regulators ( Huang et al. 2016 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
DksA	TU	flhDC	repressor	26553464	11	ver/dev	E. coli strains increased motility , possibly due to the inhibition of flhDC promoters by DksA -LRB- 14 , on 19 October 2021 by 132.24	215	E. coli strains lacking dksA were shown to express higher levels of che-motaxis and flagellum genes , resulting in overproduction of flagellin , hyperflagellated cells , and increased motility , possibly due to the inhibition of flhDC and fliA promoters by DksA ( 14 , loaded from https://journals.asm.org/journal/iai on 19 October 2021 by 132.24	6	DISCUSSION	Escherichia coli	0	L1	SPEC	Other	OTHER	New	Level 1
DksA	TU	flhDC	repressor	26553464	11	ver/dev	the inhibition of flhDC promoters by DksA ( 14 , _ loaded from https://journals.asm.org/journal/iai	215	E. coli strains lacking dksA were shown to express higher levels of che-motaxis and flagellum genes , resulting in overproduction of flagellin , hyperflagellated cells , and increased motility , possibly due to the inhibition of flhDC and fliA promoters by DksA ( 14 , loaded from https://journals.asm.org/journal/iai on 19 October 2021 by 132.24	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrG	regulator	18467098	6	att	PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid-A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .	136	PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .	10	PMRAB-MEDIATED LPS MODIFICATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	csgA	repressor	11489123	15	ver/dev	Olsén , A. , Arnqvist , A. , Normar , S. The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	484	Olsén , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , and Normark , S. ( 1993 ) The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	11489123	15	ver/dev	Olsén , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , S. The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	484	Olsén , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , and Normark , S. ( 1993 ) The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	11518527	0	ver/dev	The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .	504	The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of ® bronectin-binding curli in Escherichia coli .	35	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	14503792	3	ver/dev	Olsen , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , Normark , S. : The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .	277	Olsen , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , Normark , S. : The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Esche-richia coli .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	14643403	34	ver/dev	A. Olsen , A. Arnqvist , M. Hammar , S. Sukupolvi , S. Normark , The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli , Mol .	314	[ 29 ] A. Olsen , A. Arnqvist , M. Hammar , S. Sukupolvi , S. Normark , The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli , Mol .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	16707690	39	ver/dev	The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .	665	The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	25	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	18195033	2	ver/dev	The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .	554	The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgA	repressor	23159630	1	ver/dev	A. Olsen , A. Arnqvist , M. Hammar , S. Sukupolvi , S. Normark , The RpoS sigma factor relieves HNS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli , Mol .	280	[ 10 ] A. Olsen , A. Arnqvist , M. Hammar , S. Sukupolvi , S. Normark , The RpoS sigma factor relieves HNS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli , Mol .	20	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by Lrp .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by cooperative interactions between Lrp The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	TU	flhDC	activator	32032766	4	ver/dev	The results showed that Fis , activated the transcription of flhDC , whereas RpoS suppressed their expression .	195	The results showed that the regulators , OmpR and Fis , activated the transcription of AsfD and flhDC , whereas RpoS suppressed their expression .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	bcsA	regulator	16707690	35	ver/dev	We did not expect regulation of bcsA by RpoS , as Zogaj et al. found in an RpoS-independent manner .	438	We did not expect regulation of bcsA by RpoS , as Zogaj et al. ( 58 ) found that a bcsA-lacZ gene fusion ( we used the same gene fusion [ Table 1 ] ) was indeed partially induced in the stationary phase , but in an RpoS-independent manner .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	bcsA	regulator	16707690	35	ver/dev	We did not expect regulation of bcsA by RpoS , as Zogaj et al. found that a bcsA-lacZ gene fusion was indeed partially induced in the stationary-phase .	438	We did not expect regulation of bcsA by RpoS , as Zogaj et al. ( 58 ) found that a bcsA-lacZ gene fusion ( we used the same gene fusion [ Table 1 ] ) was indeed partially induced in the stationary phase , but in an RpoS-independent manner .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	stiA	regulator	8045891	0	ver/dev	The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiA , has been characterized .	9	The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiA , stiB , and stiC , has been characterized .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiA	regulator	8045891	8	ver/dev	Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during P starvation .	92	Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during C , N , and P starvation .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiA	regulator	8045891	8	ver/dev	Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during N .	92	Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during C , N , and P starvation .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiA	regulator	8045891	8	ver/dev	Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during C .	92	Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during C , N , and P starvation .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiA	regulator	8045891	13	ver/dev	Since the stiA are regulated by RpoS , we wanted to examine the combined effects of sti mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiA	regulator	8045891	13	ver/dev	Since the stiA are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiA	regulator	8045891	14	ver/dev	Role of the altermative a factor RpoS , in the the regulation of starvation survival genes stiA .	145	Role of the altermative a factor RpoS , ovra , in the the regulation of starvation survival genes stiA and stiC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	stiA	regulator	8045891	15	ver/dev	Role of the altermative a factor RpoS , in the the regulation of starvation survival genes stiA .	160	Role of the altermative a factor RpoS , ovra , in the the regulation of starvation survival genes stiA and stiC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	stiA	regulator	8045891	24	ver/dev	On the basis of the fact that stiA are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	225	On the basis of the fact that stiA , stiB , and stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA and stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RpoS	gene	stiA	regulator	8045891	24	ver/dev	On the basis of the fact that stiA are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA are not induced and/or because stiB is overexpressed in an rpoS mutant .	225	On the basis of the fact that stiA , stiB , and stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA and stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RcsA	gene	rcsC	activator	15469511	0	att	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	14	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilC	repressor	17074910	20	ver/dev	Given that both the csrB/C genes are required , we hypothesize that hilC gene expression requires the csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilC	repressor	17074910	20	ver/dev	Given that both sirA are required , we hypothesize that hilC gene expression requires the csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	stiB	activator	8045891	10	ver/dev	The rpoS mutation resulted in a two - to threefoldhigher level of induction of stiB during P starvation during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	99	The rpoS mutation resulted in a two - to threefoldhigher level of induction of stiB during P starvation and a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	virK	regulator	17379730	5	ver/dev	SlyA is also involved in the regulation of virK	362	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA , which is also involved in the regulation of virulence genes such as mig-14 , sopD2 and virK ( Brumell et al. , 2003 ; Ho et al. , 2002 ; Navarre et al. , 2005 ) .	14	GIFSY-1 AND GIFSY-2 PROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	ssaG	regulator	27601571	47	ver/dev	ssaG are regulated by HilC	422	ssaG and ssaJ are regulated by HilC , and sifB is regulated by SprB .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	regulator	29473025	2	ver/dev	FliZ regulates expression of class 2 genes through a non-flagellar gene ydiV	414	One such feedback loop corresponds to a positive feedback from FliZ that regulates expression of class 2 genes through a non-flagellar gene ydiV and the master regulator FlhD4C2 ( Ohnishi et al. , 1990 ) .	13	ROLES OF FLIZ AND FLIT FEEDBACK LOOPS ON CONTROLLING FLAGELLAR GENE EXPRESSION AT A	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	STM1485	regulator	30763640	31	ver/dev	In order to confirm the binding of RstA on the STM1485 promoter sequence we performed an EMSA .	174	In order to confirm the binding of RstA on the STM1485 promoter sequence we performed an EMSA .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RstA	gene	STM1485	regulator	30763640	34	ver/dev	Taken together , these results demonstrated that RstA could bind to the predicted regulatory sites on the STM1485 promoter region .	177	Taken together , these results demonstrated that RstA could bind to the predicted regulatory sites on the STM1485 promoter region .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
RstA	gene	STM1485	regulator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RstA	gene	STM1485	regulator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RstA	gene	STM1485	regulator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression under PhoP-dependent RstA activation was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RstA	gene	STM1485	regulator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression under magnesium starvation conditions was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
RstA	gene	STM1485	regulator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression under PhoP-dependent RstA activation was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RstA	gene	STM1485	regulator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression under magnesium starvation conditions was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	NEG	Other	Level 1
DksA	gene	sufA	activator	27065993	1	att	To validate • NO - and DksA-dependent regulatory control in aspects of iron homeostasis , we used quantitative real-time PCR ( qPCR ) to measure the mRNA levels of feoB , sitA , and sufA in wild-type and 1dksA Salmonella treated ± dNO ( Figure 3 ) .	173	To validate • NO - and DksA-dependent regulatory control in aspects of iron homeostasis , we used quantitative real-time PCR ( qPCR ) to measure the mRNA levels of feoB , sitA , and sufA in wild-type and 1dksA Salmonella treated ± dNO ( Figure 3 ) .	12	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	12453229	7	ver/dev	The expression of hilA is itself controlled by two additional SPI-1 regulators : HilC .	68	The expression of hilA is itself controlled by two additional SPI-1 regulators : HilC and HilD ( Eichelberg et al. , 1999 ; Schechter et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	12535071	9	ver/dev	HilC bind the same regions upstream of hilA .	53	In vitro , HilD and HilC bind the same regions upstream of hilA ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	12535071	87	ver/dev	In addition to binding upstream of hilA , HilC also bind to sites upstream of hilC .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	12535071	87	ver/dev	In addition to binding upstream of hilA , HilC also bind within S. Akbar , unpublished results .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	12535071	87	ver/dev	In addition to binding upstream of hilA , HilC also bind within the prgH-hilD intergenic region .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	15661008	0	ver/dev	HilC are positive regulators of hilA expression	19	We found that HilC and HilD , which are positive regulators of hilA expression , accumulate in Lon-depleted cells , and that the enhancement of SPI1 expression that occurs in a lon-disrupted mutant is not observed in the lon hilC hilD triple null mutant .	4	SUMMARY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	15661008	2	ver/dev	HilC have been shown to bind to URS of hilA .	48	HilC and HilD have been shown to bind to the upstream repressing sequence ( URS ) of hilA and counteract the repression ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilA	regulator	15661008	2	ver/dev	HilC have been shown to bind to the upstream repressing sequence of hilA .	48	HilC and HilD have been shown to bind to the upstream repressing sequence ( URS ) of hilA and counteract the repression ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilA	regulator	15661008	8	ver/dev	HilC bind directly to the upstream sequence of hilA .	84	HilC and HilD bind directly to the upstream sequence of hilA and derepress the transcription of PhilA .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	15661008	23	ver/dev	HilC can independently bind the hilA promoter .	267	HilC and HilD can independently bind and activate the hilA promoter ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilA	regulator	15765064	35	ver/dev	HilC , directly bind the Salmonella typhimurium hilA promoter .	410	HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	26	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	16045614	19	ver/dev	a model in which expression of hilA is controlled by the combined action of HilC	81	Based on our genetic analyses , and taking into account the published results outlined above , we present a model in which expression of hilA is controlled by the combined action of HilC , HilD and RtsA , each of which can independently bind upstream of hilA to induce its expression ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	16045614	19	ver/dev	a model in which expression of hilA is controlled by the combined action of HilC	81	Based on our genetic analyses , and taking into account the published results outlined above , we present a model in which expression of hilA is controlled by the combined action of HilC , HilD and RtsA , each of which can independently bind upstream of hilA to induce its expression ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	16045614	63	ver/dev	This is consistent with the feedforward loop model ; when neither HilC are present , regulation of hilA is dampened , even though the primary signal is mediated through HilD .	409	This is consistent with the feedforward loop model ; when neither RtsA nor HilC are present , regulation of hilA is dampened , even though the primary signal is mediated through HilD .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilC	gene	hilA	regulator	16045614	72	ver/dev	HilC bind to overlapping sites in the hilA promoter .	470	HilC and HilD bind to overlapping sites in the hilA promoter ( Olekhnovich and Kadner , 2002 ) .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	16045614	95	ver/dev	Lee , C.A. Roles of HilC in regulation of hilA expression in Salmonella enterica sero-var Typhimurium .	742	Lucas , R.L. , and Lee , C.A. ( 2001 ) Roles of HilC and HilD in regulation of hilA expression in Salmonella enterica sero-var Typhimurium .	27	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	17208038	1	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC .	51	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD and RtsA [ 23 -- 25 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	17208038	2	ver/dev	Studies have shown PheU that HilC can each individually bind to the hilA promoter	55	Studies have shown PheU that HilC , HilD and RtsA can each individually bind to the hilA promoter , and deletions of hilC , hilD or rtsA cause a decrease in expression of hilA [ 19 ,23 -- 25 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HilC	gene	hilA	regulator	17208038	6	ver/dev	HilC , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by the sic/sip operon -- in a fashion independent of HilA .	67	HilC , HilD and RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through , the sic/sip operon -- in a fashion independent of HilA [ 15,16,25,27 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	17208038	6	ver/dev	HilC , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through -- in a fashion independent of HilA .	67	HilC , HilD and RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through , the sic/sip operon -- in a fashion independent of HilA [ 15,16,25,27 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilA by HilC .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilA	regulator	17208038	36	ver/dev	Schechter LM , Lee CA : HilC , directly bind the Salmonella typhimurium hilA promoter .	237	Schechter LM , Lee CA : AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	17575908	0	ver/dev	HilC were described to influence the expression of hilA .	34	HilD and HilC were described to influence the expression of hilA ( Rakeman et al. 1999 ) .	2	ABBREVIATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilA	regulator	17575908	4	ver/dev	SCHECHTER L.M. , LEE C.A. : HilC , directly bind the Salmonella typhimurium hilA promoter .	261	SCHECHTER L.M. , LEE C.A. : AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	14	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	17993530	3	ver/dev	Expression of hilA is directly controlled by three AraC-like activators : HilC .	35	Expression of hilA is directly controlled by three AraC-like activators : HilC , HilD , and RtsA ( 18 , 42 , 47 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	19003447	0	ver/dev	Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilC .	38	Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilD , HilC and RtsA , which in a complex arrangement of feedback and feedforward loops bring about maximal induction of HilA ( Altier 2005 ; Jones 2005 ; Ellermeier and Slauch 2007 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	19537165	3	ver/dev	Earlier work on mathematical modeling of regulation of expression of hilA by HilC was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .	44	Earlier work on mathematical modeling of regulation of expression of hilA by HilC , HilD and RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop [ Maithreye and Mande , 2007 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	20008574	4	ver/dev	The results of these surveys can be summarized as follows : i. Dam-dependent regulation of hilA was not abolished in the absence of HilC .	150	The results of these surveys are shown in Figure 3 and can be summarized as follows : i. Dam-dependent regulation of hilA was not abolished in the absence of HilC .	4	RESULTS	nan	1	L2	OTHER	Other	NEG	Other	Level 1
HilC	gene	hilA	regulator	20008574	4	ver/dev	The results of these surveys are shown in Figure 3 : i. Dam-dependent regulation of hilA was not abolished in the absence of HilC .	150	The results of these surveys are shown in Figure 3 and can be summarized as follows : i. Dam-dependent regulation of hilA was not abolished in the absence of HilC .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilC	gene	hilA	regulator	21168230	4	ver/dev	In turn , hilA is regulated by HilC .	343	In turn , hilA is regulated by HilD and HilC ( Schechter and Lee , 2001 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	22479568	0	ver/dev	HilC can activate expression of rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilA	regulator	23442379	0	ver/dev	Schechter LM , Lee CA : HilC , directly bind the Salmonella typhimurium hilA promoter .	568	Schechter LM , Lee CA : AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhimurium hilA promoter .	30	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	23504014	3	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC .	24	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD , and RtsA ( 14 -- 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	24929817	1	ver/dev	HilC mutually regulate the hilA gene expression	166	HilC and HilD mutually regulate the hilA gene expression	9	SURVIVAL AND PROPHAGE INDUCTION OF LYSOGENIC S. TYPHIMURIUM EXPOSED TO GASTROINTESTINAL JUICES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	25182488	2	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC .	19	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD , and RtsA ( 8 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	25991823	26	ver/dev	Schechter , L. M. , and C. A. Lee , 2001 AraC/XylS family members , HilC , directly bind the Salmonella typhi-murium hilA promoter .	633	Schechter , L. M. , and C. A. Lee , 2001 AraC/XylS family members , HilC and HilD , directly bind and derepress the Salmonella typhi-murium hilA promoter .	44	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	regulator	27565525	0	ver/dev	Differential expression of hilA , is influenced by HilC	361	Differential expression of hilA , that encodes the transcriptional activator of the SPI1 structural genes , is influenced by three AraC-like regulators ( HilD , HilC , and RtsA ) and each of them can activate the hilD , hilC , rtsA , and hilA genes that form a complex feed-forward regulatory loop ( Golubeva et al. , 2012 ; Lim et al. , 2012 ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	28575106	0	ver/dev	Expression of hilA is directly controlled by SPI-1-encoded HilC and HilD	84	Expression of hilA is directly controlled by three AraC-like transcriptional regulators , including SPI-1-encoded HilC and HilD , and RtsA encoded outside of SPI-1 , which constitute a feed-forward regulatory loop [ 29 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	28575106	6	ver/dev	As the expression of hilA is directly controlled by HilC , we tested whether LoiA regulates HilA through any of these three regulators .	177	As the expression of hilA is directly controlled by HilD , HilC and RtsA , we tested whether LoiA regulates HilA through any of these three regulators .	9	LOIA ACTIVATES EXPRESSION OF HILA GENE THROUGH ACTIVATING HILD	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilC	gene	hilA	regulator	30716090	46	ver/dev	Transcription of hilA is controlled by HilC .	464	Transcription of hilA is controlled by a complex feed-forward loop including RtsA , HilC and HilD [ 46 ] .	25	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	31182495	3	ver/dev	electrophoretic-mobility-shift assays suggest that PhoP specifically binds the hilA promoter to block binding of HilC as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	regulator	31182495	3	ver/dev	Genetic analyses suggest that PhoP specifically binds the hilA promoter to block binding of HilC as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	regulator	31428589	15	ver/dev	a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression through the degradation of HilC .	202	Lon protease , a negative regulator of SPI-1 genes , is important for the downregulation of hilA expression and intracellular survival after the invasion of epithelial cells through the degradation of HilC and HilD ( Boddicker and Jones , 2004 ; Takaya et al. , 2005 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	32041797	0	ver/dev	Expression of hilA is positively regulated by three homologous transcriptional regulators , HilC , .	9	Expression of hilA is positively regulated by three homologous transcriptional regulators , HilD , HilC , and RtsA , belonging to the AraC/XylS family .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	32041797	2	ver/dev	Expression of hilA is regulated by the combined actions of three AraC-like transcriptional activators , HilC , .	30	Expression of hilA is regulated by the combined actions of three AraC-like transcriptional activators , HilD , HilC , and RtsA ( 17 -- 19 ) , each of which is capable of inducing transcription of the hilD , hilC , and rtsA genes .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	regulator	34202800	14	ver/dev	PhoP specifically binds the hilA promoter to block the binding of HilC as a repression mechanism	329	PhoP specifically binds the hilA promoter to block the binding of HilD , HilC , and RtsA activators as a repression mechanism [ 126 ]	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	rpsD	regulator	30941426	3	ver/dev	To further test whether a HilD deficiency causes down-regulation of SPI-1 genes in the rpsD * , we overexpressed HilD on a plasmid under the control of a lac promoter .	240	To further test whether a HilD deficiency causes down-regulation of SPI-1 genes in the rpsD * and rpsL * strains , we overexpressed HilD on a plasmid under the control of a lac promoter .	24	NON-OPTIMAL TRANSLATIONAL FIDELITY IMPAIRS HOST-CELL INTERAC- TIONS AND ANIMAL INFECTION	unidentified plasmid	1	L3	SPEC	Other	OTHER	New	Level 1
Mlc	gene	mtfA	regulator	29417056	1	ver/dev	The mtfA gene encodes the Mlc titration factor ; Mlc is a global regulator of sugar metabolism .	335	The mtfA gene encodes the Mlc titration factor ; Mlc is a global regulator of sugar metabolism .	5	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	metE	activator	19447191	20	att	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	200	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MetR	gene	metE	activator	19447191	14	ver/dev	In the pres-using oriented RNAP indicated that a single CTD the ′ - associated subunit is sufficient for the MetR activation of metE , while MetR interacts preferentially with the C on the - associated subunit at metH .	150	In the pres-using oriented RNAP indicated that a single CTD on either the or the ′ - associated subunit is sufficient for the MetR activation of metE , while MetR interacts preferentially with the CTD on the - associated subunit at metH ( Fritsch et al. , 2000 ) .	8	4.5. CYSB AND METR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MetR	gene	metE	activator	19447191	14	ver/dev	In the pres-using oriented RNAP indicated that a single CTD the ′ - associated subunit is sufficient for the MetR activation of metE , while MetR interacts preferentially with the C on the - associated subunit at metH .	150	In the pres-using oriented RNAP indicated that a single CTD on either the or the ′ - associated subunit is sufficient for the MetR activation of metE , while MetR interacts preferentially with the CTD on the - associated subunit at metH ( Fritsch et al. , 2000 ) .	8	4.5. CYSB AND METR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MetR	gene	metE	activator	19447191	20	ver/dev	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE : orientation requirements within RNA polymerase .	200	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MetR	gene	metE	activator	19447191	20	ver/dev	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE : important residues in the C-terminal domain .	200	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MetR	gene	metE	activator	21768276	2	ver/dev	The MetR protein acts as an activator for the transcription of metE .	727	The MetR protein acts as an activator for the transcription of metE , metA , metF , and metH ( 93 ) .	8	TRANSCRIPTION STM3773 PUTATIVE TRANSCRIPTIONAL REGULATOR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	slrP	regulator	25182488	0	ver/dev	A search for genetic factors unveiled LeuO as novel regulators of slrP .	7	A search for genetic factors involved in controlling the expression of slrP unveiled LeuO , Lon , and the two-component system PhoQ/PhoP as novel regulators of slrP .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	slrP	regulator	25182488	8	ver/dev	Results support the model that LeuO regulate slrP in a manner dependent .	238	Results shown in Fig. 4C support the model that Lon and LeuO regulate slrP in a manner that is mostly HilD dependent .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LuxS	gene	metE	activator	11722742	0	ver/dev	We reason that metE is not a true target of AI-2 regulation but , instead , metE transcription is induced in the wild-type luxS strain relative to the luxS null strain because homocysteine is produced during the generation of AI-2 in the LuxS strain .	95	We reason that metE is not a true target of AI-2 regulation but , instead , metE transcription is induced in the wild-type luxS strain relative to the luxS null strain because homocysteine is produced during the generation of AI-2 in the LuxS strain .	5	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
AraC	gene	srgC	regulator	29276700	0	ver/dev	The last two ORFs of srgC , encode a transcriptional regulator of the AraC family respectively .	110	The last two ORFs of the operon , srgB and srgC , encode a putative lipoprotein and a transcriptional regulator of the AraC family respectively .	3	FROM THE PEFI-SRGC OPERON TO THE REGULATION OF RCK EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tag	regulator	21625519	72	ver/dev	full-length S. Typhimurium PhoP _ fused to a His6 tag on the N terminus , with a predicted molecular mass of 27.8 kDa , under the control of the T7 promoter	435	This plasmid expresses full-length S. Typhimurium PhoP fused to a His6 tag on the N terminus , with a predicted molecular mass of 27.8 kDa , under the control of the T7 promoter .	14	CONSTRUCTION OF S. TYPHIMURIUM HIS TAGGED PHOP	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfN	regulator	22418438	1	att	In accord with these data , another group showed that dalS/STM1633 clustered into an SsrB-controlled regulatory network enriched in virulence genes including genes in SPI-2 and with srfN ( 19 ) , the latter of which we previously showed was required for in-vivo fitness ( 20 ) .	164	In accord with these data , another group showed that dalS/STM1633 clustered into an SsrB-controlled regulatory network enriched in virulence genes including genes in SPI-2 and with srfN ( 19 ) , the latter of which we previously showed was required for in vivo fitness ( 20 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	srfN	regulator	28674150	26	ver/dev	SsrB controls srfN directly through binding to the srfN cis-regulatory element	302	The mRNA level of srfN was reduced 8-fold in ssrB cells compared with the wild-type bacteria under SPI-2-inducing conditions and SsrB controls srfN directly through binding to the srfN cis-regulatory element .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfN	regulator	28674150	26	ver/dev	SsrB controls srfN directly through binding to the srfN cis-regulatory element	302	The mRNA level of srfN was reduced 8-fold in ssrB cells compared with the wild-type bacteria under SPI-2-inducing conditions and SsrB controls srfN directly through binding to the srfN cis-regulatory element .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfN	regulator	28674150	26	ver/dev	SsrB controls srfN directly through binding to the srfN cis-regulatory element	302	The mRNA level of srfN was reduced 8-fold in ssrB cells compared with the wild-type bacteria under SPI-2-inducing conditions and SsrB controls srfN directly through binding to the srfN cis-regulatory element .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	sodA	repressor	31479952	3	ver/dev	FNR negatively regulates sodA + , sodB +	59	Accordingly , it was demonstrated that FNR negatively regulates genes such as sodA + , sodB + , cycD + C + and metE + and thereby FnrS functions to adjust gene expression for adaptation to anaerobic growth ( Boysen et al. , 2010 ; Durand and Storz , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	rho	activator	30201777	26	att	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	259	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	rho	activator	30201777	26	att	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	259	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CueR	gene	cueR	regulator	23645605	4	att	( B ) - Galactosidase activity from GolS - or CueR-regulated transcriptional-fusions golB : : lacZ ( PgolB ) or copA-lacZ ( PcopA ) , respectively , on cells carrying either wild-type golS and cueR , or golSL , golSsL , or golSC111S , replacing the wild-type copy of golS , or cueRL , replacing cueR .	140	( B ) - Galactosidase activity from GolS - or CueR-regulated transcriptional fusions golB : : lacZ ( PgolB ) or copA-lacZ ( PcopA ) , respectively , on cells carrying either wild-type golS and cueR , or golSL , golSsL , or golSC111S , replacing the wild-type copy of golS , or cueRL , replacing cueR .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
InvF	gene	tnpA	regulator	28335027	6	ver/dev	Notably , our observation that deletion of all of the IS200 copies in S. Typhimurium impacted on the expression of an SPI-1 gene not under the control of InvF is consistent with tnpA producing either a multi-functional regulatory RNA or , as in the case of IS1341 , multiple regulatory sRNAs .	737	Notably , our observation that deletion of all of the IS200 copies in S. Typhimurium impacted on the expression of an SPI-1 gene ( prgH ) not under the control of InvF is consistent with tnpA producing either a multi-functional regulatory RNA or , as in the case of IS1341 , multiple regulatory sRNAs .	22	RIBONUCLEOLYTIC PROCESSING OF TNPA MRNA GENERATES SRNA REGULATORS OF INVF EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26056383	2	ver/dev	RflM functions as a transcriptional repressor in the autogenous control of the Salmonella Flagellar master operon flhDC .	579	RflM functions as a transcriptional repressor in the autogenous control of the Salmonella Flagellar master operon flhDC .	17	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26209134	1	ver/dev	Hughes , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	475	Singer , H.M. , Erhardt , M. and Hughes , K.T. ( 2013 ) RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	28	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26209134	1	ver/dev	M. , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	475	Singer , H.M. , Erhardt , M. and Hughes , K.T. ( 2013 ) RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	28	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26209134	1	ver/dev	Erhardt , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	475	Singer , H.M. , Erhardt , M. and Hughes , K.T. ( 2013 ) RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	28	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26209134	1	ver/dev	H.M. , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	475	Singer , H.M. , Erhardt , M. and Hughes , K.T. ( 2013 ) RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	28	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26209134	1	ver/dev	Singer , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	475	Singer , H.M. , Erhardt , M. and Hughes , K.T. ( 2013 ) RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .	28	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	26441883	17	ver/dev	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / the Spi-1-encoded regulator RtsB .	361	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / EcnR , the Spi-1-encoded regulator RtsB , the LysR-type regulator LrhA ( RovM in Yersinia ) , and SlyA ( RovA in Yersinia ) with the P1 and P5 promoters being the main regulatory targets ( Yanagihara et al. , 1999 ; Wang et al. , 2007 ; Singer et al. , 2013 ; Mouslim and Hughes , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RflM	TU	flhDC	regulator	26441883	17	ver/dev	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / EcnR .	361	Moreover , flhDC gene expression is also under negative control of the phosphorelay system RcsCDB , the LysR-family protein RflM / EcnR , the Spi-1-encoded regulator RtsB , the LysR-type regulator LrhA ( RovM in Yersinia ) , and SlyA ( RovA in Yersinia ) with the P1 and P5 promoters being the main regulatory targets ( Yanagihara et al. , 1999 ; Wang et al. , 2007 ; Singer et al. , 2013 ; Mouslim and Hughes , 2014 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RflM	TU	flhDC	regulator	26441883	48	ver/dev	RflM functions as a transcriptional repressor in the autogenous control of the Salmonella flagellar master operon flhDC .	1379	RflM functions as a transcriptional repressor in the autogenous control of the Salmonella flagellar master operon flhDC .	93	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	27206164	3	ver/dev	We propose that RflM stabilizes binding of unphosphorylated RcsB to the flhDC promoter in absence of environmental cues .	31	We propose that RflM stabilizes binding of unphosphorylated RcsB to the flhDC promoter in absence of environmental cues .	3	SUMMARY	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
RflM	TU	flhDC	regulator	27206164	36	ver/dev	We determined which flhDC promoter is regulated via RflM using luxCDABE fusions to flhDC promoter mutants -LRB- Fig. 4C -RRB- .	204	We determined which flhDC promoter is regulated via RcsB and RflM using luxCDABE fusions to flhDC promoter mutants that retained either a functional P1 or P5 promoter , respectively ( Fig. 4C ) .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	27206164	51	ver/dev	In the present study , we elucidated the mode-of-action of RflM in regulation of flhDC .	281	In the present study , we elucidated the mode-of-action of RcsB and RflM in regulation of flhDC .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	27206164	59	ver/dev	We further demonstrated that efficient binding of the RcsB-RflM complex to the flhDC promoter required the DNA-binding domain of RflM .	305	We further demonstrated that efficient binding of the RcsB-RflM complex to the flhDC promoter required the DNA-binding domain of RflM .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RflM	TU	flhDC	regulator	27206164	68	ver/dev	Hughes , K.T. RflM functions as a transcriptional repressor on the autogenous control of the Salmonella flagellar master operon flhDC .	523	Singer , H.M. , Erhardt , M. , and Hughes , K.T. ( 2013 ) RflM functions as a transcriptional repressor on the autogenous control of the Salmonella flagellar master operon flhDC .	41	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RflM	TU	flhDC	regulator	27601574	0	ver/dev	RflM functions as a transcriptional repressor in the autogenous control of the Salmonella flagellar master operon flhDC .	717	RflM functions as a transcriptional repressor in the autogenous control of the Salmonella flagellar master operon flhDC .	43	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	TU	flhDC	regulator	15256548	20	ver/dev	Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon .	678	Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon ( Ellermeier & Slauch , 2003 ) .	15	STRESS RESPONSE GENES AND GLOBAL REGULATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	TU	flhDC	regulator	16988271	0	ver/dev	RtsA have also been shown to regulate SPI-1 genes and flhDC , respectively .	357	RtsA and RtsB have also been shown to regulate SPI-1 genes and flhDC ( which direct flagellum biosynthesis ) , respectively ( 16 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HdfR	gene	hdfR	regulator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of Fig 1A , upregulation of hdfR transcription by StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	regulator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of Fig 1A , upregulation of hdfR transcription by StdE may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	regulator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of std expression , upregulation of hdfR transcription by StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	hdfR	regulator	30252837	0	ver/dev	Because the HdfR gene product is a transcriptional activator of std expression , upregulation of hdfR transcription by StdE may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	102	Because the HdfR gene product is a transcriptional activator of std expression [ 31 ] ( Fig 1A ) , upregulation of hdfR transcription by StdE and StdF may suggest the existence of a positive feedback loop for autogenous regulation of the std operon .	8	GENOME-WIDE CONSEQUENCES OF STD EXPRESSION: TRANSCRIPTOMIC ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LysR	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , i.e. missense SNP in ilvC is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-valine .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , i.e. missense SNP in ilvC is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , i.e. missense SNP in ilvC is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to p.Glu206Lys .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , i.e. missense SNP in ilvC is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to avian .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , i.e. missense SNP in ilvC is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to p.Leu106Gln sources .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , i.e. missense SNP in ilvC is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to swine sources .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	Sus scrofa	0	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	prgH	regulator	10672185	7	ver/dev	The pattern of hilA-dependent regulation of prgH by BarA together with partially hilA-indepen-dent regulation of invF by BarA parallels the pattern recently reported for SirA .	155	The pattern of hilA-dependent regulation of prgH by BarA together with partially hilA-indepen-dent regulation of invF by BarA parallels the pattern recently reported for SirA ( Rakeman et al. , 1999 ) , which we have con ® rmed under our culture conditions ( Table 3 ) .	8	INTEGRATION OF MULTIPLE INVASION REGULATORS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	prgH	regulator	28439039	9	ver/dev	It is known that prgH is under the regulation of SirA .	327	It is known that prgH is under the regulation of many global regulators , such as HilA , InvF , PhoP , and SirA .	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilA	gene	gtgE	regulator	27886269	3	ver/dev	HilA , regulates the expression of gtgE .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ptsN	activator	30967459	7	att	We further verified the EIIANtr 's regulatory effects on PhoP-activated genes using quantitative reverse transcription-PCR ( qRT-PCR ) : the ptsN mutant displayed 3 - to 7-fold-higher transcript levels of PhoP-regulated genes than the wild type ( Fig. 3A ) .	132	We further verified the EIIANtr 's regulatory effects on PhoP-activated genes using quantitative reverse transcription-PCR ( qRT-PCR ) : the ptsN mutant displayed 3 - to 7-fold-higher transcript levels of PhoP-regulated genes than the wild type ( Fig. 3A ) .	3	RESULTS	Terfezia eliocrocae	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ptsN	activator	30967459	9	att	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	144	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	3	RESULTS	Salmonella;unidentified plasmid;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ptsN	activator	30967459	4	ver/dev	Furthermore , the lack of PhoP increased Fig. 2B even when transcription of ptsN was induced by isopropyl - - IPTG , further .	79	Furthermore , the lack of PhoP increased EIIANtr abundance ( Fig. 2B ) even when transcription of ptsN was induced by isopropyl - - D-thiogalactopyranoside ( IPTG ) , further supporting the notion that PhoP modulates the abundance of EIIANtr posttranscriptionally .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ptsN	activator	30967459	4	ver/dev	Furthermore , the lack of PhoP increased Fig. 2B even when transcription of ptsN was induced by isopropyl - - D-thiogalactopyranoside , further .	79	Furthermore , the lack of PhoP increased EIIANtr abundance ( Fig. 2B ) even when transcription of ptsN was induced by isopropyl - - D-thiogalactopyranoside ( IPTG ) , further supporting the notion that PhoP modulates the abundance of EIIANtr posttranscriptionally .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ptsN	activator	30967459	4	ver/dev	Furthermore , the lack of PhoP increased EIIANtr abundance even when transcription of ptsN was induced by isopropyl - - IPTG , further .	79	Furthermore , the lack of PhoP increased EIIANtr abundance ( Fig. 2B ) even when transcription of ptsN was induced by isopropyl - - D-thiogalactopyranoside ( IPTG ) , further supporting the notion that PhoP modulates the abundance of EIIANtr posttranscriptionally .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ptsN	activator	30967459	4	ver/dev	Furthermore , the lack of PhoP increased EIIANtr abundance even when transcription of ptsN was induced by isopropyl - - D-thiogalactopyranoside , further .	79	Furthermore , the lack of PhoP increased EIIANtr abundance ( Fig. 2B ) even when transcription of ptsN was induced by isopropyl - - D-thiogalactopyranoside ( IPTG ) , further supporting the notion that PhoP modulates the abundance of EIIANtr posttranscriptionally .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ompC	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-2 genes by SsrB resembles the reciprocal control of ompC transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ompC	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-1 genes by SsrB resembles the reciprocal control of ompC transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	pstS	regulator	26386064	0	ver/dev	the former _ being regulated by a promoter located upstream of the pstS gene regulated by CRP	148	Both operons have been shown to be induced under phosphate starvation conditions , with the former being regulated by a promoter located upstream of the pstS gene and the latter regulated by RpoS , PhoB , and CRP ( 16 , 17 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	pstS	regulator	26386064	0	ver/dev	the former _ being regulated by a promoter located upstream of the pstS gene regulated by CRP	148	Both operons have been shown to be induced under phosphate starvation conditions , with the former being regulated by a promoter located upstream of the pstS gene and the latter regulated by RpoS , PhoB , and CRP ( 16 , 17 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	csrA	regulator	16949866	4	ver/dev	Although SirA does not regulate csrA , this gene was also under crp/cya control .	18	Although SirA does not regulate csrA , this gene was also under crp/cya control .	2	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SirA	gene	csrA	regulator	16949866	17	ver/dev	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA .	301	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	nan	1	L3	OTHER	Other	NEG	New	Level 1
RpoS	gene	rho	activator	11673423	3	att	With plasmid pHYD373 ( S. enterica P1 ) , lac expression was absent in the wild-type strain , as expected ; in the rho mutant , however , there was a marked ( at least 12-fold-induced ) level of RpoS-dependent lac expression which was further elevated moderately in cultures grown with 0.3 M NaCl supplementation ( Table 2 ) .	99	With plasmid pHYD373 ( S. enterica P1 ) , lac expression was absent in the wild-type strain , as expected ; in the rho mutant , however , there was a marked ( at least 12-fold-induced ) level of RpoS-dependent lac expression which was further elevated moderately in cultures grown with 0.3 M NaCl supplementation ( Table 2 ) .	6	RESULTS	unidentified plasmid;Salmonella;Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rho	activator	11673423	5	att	With the deletion-bearing plasmid pHYD374 , growth at 10 °C resulted in a remarkably high level of RpoS-dependent lac expression ( nearly 200-fold more than that for the cryptic wild-type promoter at 30 °C ) in the rho strain , which was again only marginally elevated by introduction of the rho mutation ( Table 2 ) .	144	With the deletion-bearing plasmid pHYD374 , growth at 10 °C resulted in a remarkably high level of RpoS-dependent lac expression ( nearly 200-fold more than that for the cryptic wild-type promoter at 30 °C ) in the rho strain , which was again only marginally elevated by introduction of the rho mutation ( Table 2 ) .	6	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rho	activator	11673423	7	att	At 10 °C , there was a 30 - to100-fold induction of RpoS-dependent expression in the rho mutant but none in the wild-type strain ( Table 2 ) .	156	At 10 °C , there was a 30 - to100-fold induction of RpoS-dependent expression in the rho mutant but none in the wild-type strain ( Table 2 ) .	6	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	rho	activator	11673423	8	att	RpoS-dependent expression of osmY-lac in LBON medium was unaffected by rho but was increased around 6-fold by hns ( comparable to that reported earlier [ 5 ] ) and around 25-fold by growth at 10 °C ( Table 3 ) .	160	RpoS-dependent expression of osmY-lac in LBON medium was unaffected by rho but was increased around 6-fold by hns ( comparable to that reported earlier [ 5 ] ) and around 25-fold by growth at 10 °C ( Table 3 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	rho	activator	11673423	9	att	RpoS-dependent expression of csiD-lac was not affected by any of the conditions , that is , by rho or hns mutations or growth at low-temperature ( Table 3 ) .	164	RpoS-dependent expression of csiD-lac was not affected by any of the conditions , that is , by rho or hns mutations or growth at low temperature ( Table 3 ) .	6	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	rho	activator	11673423	7	ver/dev	At 10 °C , there was a 30 - to100-fold induction of RpoS-dependent expression in the rho mutan .	156	At 10 °C , there was a 30 - to100-fold induction of RpoS-dependent expression in the rho mutant but none in the wild-type strain ( Table 2 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rho	activator	33939833	0	att	The here-observed strong association of this RpoS-dependent stationary-phase specific sRNA ( 54,55 ) lends support to a previously proposed activity of SraL as a ProQ dependent regulator of rho mRNA ( 56 ) .	241	The here-observed strong association of this RpoS-dependent stationary-phase specific sRNA ( 54,55 ) lends support to a previously proposed activity of SraL as a ProQ dependent regulator of rho mRNA ( 56 ) .	20	FINP AND REPX ARE THE MAJOR LIGANDS OF FINO INDEPENDENT OF GROWTH STAGE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	umuC	activator	21102598	0	ver/dev	DNA damage has been shown to be sufficient to stimulate umuC transcription and the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes .2,3 -LRB- In Escherichia .	78	DNA damage created by quinolone antibiotics has been shown to be sufficient to stimulate umuC transcription and the SOS response .4,5 The initial response to DNA damage is the reduction in LexA protein levels and induction of LexA repressed genes , which include lexA , umuDC and dinP .2,3 ( In Escherichia .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hyaB	activator	10692151	4	ver/dev	J.W. Cyclic-AMP-receptor-protein are required for anaerobic induction of hyaB in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hyaB	activator	10692151	4	ver/dev	J.W. Cyclic-AMP-receptor-protein are required for acid-pH induction of hyaB in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hyaB	activator	17906148	9	ver/dev	Cyclic-AMP-receptor-protein are required for anaerobic induction of hyaB in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hyaB	activator	17906148	9	ver/dev	Cyclic-AMP-receptor-protein are required for acid-pH induction of hyaB in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sicA	activator	11918812	0	att	As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	116	As a first application of the two-colour flow cytometric technique , the in vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	6	IN VITRO CHARACTERIZATION OF TRANSCRIPTIONAL FUSIONS TO VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	argR	regulator	26944792	0	ver/dev	Putative regulation by the global regulators RcsB was evaluated by generating three isogenic S. Typhi deletion mutants of argR .	261	Putative regulation by the global regulators RcsB , Fur and ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of rcsDBC , fur and argR .	8	REGULATION OF TCF EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	gogB	regulator	15843015	0	ver/dev	The genetic regulation of gogB in Salmonella is influenced by SsrB , under SPI-2-inducing conditions	20	The genetic regulation of gogB in Salmonella is influenced by the transcriptional activator , SsrB , under SPI-2-inducing conditions , but the modular nature of the gogB gene allows for autonomous expression and type III secretion following horizontal gene transfer into a heterologous pathogen .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	gogB	regulator	15843015	0	ver/dev	The genetic regulation of gogB in Salmonella is influenced by SsrB , under SPI-2-inducing conditions	20	The genetic regulation of gogB in Salmonella is influenced by the transcriptional activator , SsrB , under SPI-2-inducing conditions , but the modular nature of the gogB gene allows for autonomous expression and type III secretion following horizontal gene transfer into a heterologous pathogen .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	hilA	activator	27564394	6	att	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
BaeR	gene	zraP	repressor	23651595	9	ver/dev	Significant transcriptional repression of zraP is observed during overexpression of BaeR .	362	Significant transcriptional repression of zraP is observed during overexpression of BaeR ( Appia-Ayme et al. , 2011 ) .	19	2.3.3. ZRASRP	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CspC	gene	cspB	activator	24056458	0	ver/dev	this effect was reflected by induction of cspB and proteins ( CspC ) in response to preadaptation to cold-stress	146	Cold stress genes and proteins regulate membrane fluidity and resume protein synthesis ( 18 ) , and this effect was reflected by induction of cold stress genes ( cspB and cspD ) and proteins ( CspA , CspE , and CspC ) in response to preadaptation to cold stress .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LrhA	gene	rpoS	regulator	21657791	3	ver/dev	Peterson , C. N. ; Carabetta , V. J. ; Chowdhury , T. ; Silhavy , T. J. LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli .	490	( 28 ) Peterson , C. N. ; Carabetta , V. J. ; Chowdhury , T. ; Silhavy , T. J. LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli .	19	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	10692170	0	ver/dev	HilA , is believed to directly activate expression from the prgH promoters in SPI1 .	59	HilA , encoded within SPI1 , is a ToxR/OmpR-type regulator and is believed to directly activate expression from the invF and prgH promoters in SPI1 .	4	MAIN	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilA	gene	prgH	activator	11466291	12	att	Changing the ( 229 to 18 ) sequences in PprgH ( 257 to 18 ) to PinvF-1 ( 229 to 110 ) allows the prgH HilA box to serve as a HilA-dependent upstream activating site , even in the absence of the half-site-like hexamers ( Fig. 5 ) .	344	Changing the ( 229 to 18 ) sequences in PprgH ( 257 to 18 ) to PinvF-1 ( 229 to 110 ) allows the prgH HilA box to serve as a HilA-dependent upstream activating site , even in the absence of the half-site-like hexamers ( Fig. 5 ) .	7	2	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	12396235	9	att	These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .	106	These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	prgH	activator	12396235	6	ver/dev	HilA directly activates the prgH promoter .	80	HilA binds upstream of and directly activates the prgH promoter [ 4 ] .	5	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	12535071	96	att	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	280	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	prgH	activator	12535071	6	ver/dev	By binding upstream of prgH , HilA directly activates expression of the prgH operons that encode the components of the TTS apparatus .	34	By binding upstream of invF and prgH , HilA directly activates expression of the invF and prgH operons that encode the components of the TTS apparatus ( Lostroh et al. , 2000 ; Lostroh and Lee , 2001 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	12535071	96	ver/dev	Thus , by the time HilA-dependent activation of prgH leads to the expression and formation of a functional TTS apparatus , effector proteins would already be ready to be secreted .	280	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	prgH	activator	12535071	96	ver/dev	Thus , by the time HilA-dependent activation of prgH leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed .	280	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	prgH	activator	17208038	38	att	Lostroh CP , Lee CA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	261	Lostroh CP , Lee CA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	17208038	38	ver/dev	sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	261	Lostroh CP , Lee CA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	17208038	38	ver/dev	The HilA box outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	261	Lostroh CP , Lee CA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	17208038	38	ver/dev	Lee CA outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	261	Lostroh CP , Lee CA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	17208038	38	ver/dev	Lostroh CP outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	261	Lostroh CP , Lee CA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	21320585	4	att	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella patho-genicity island 1 .	626	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella patho-genicity island 1 .	35	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	21320585	4	ver/dev	sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella patho-genicity island 1 .	626	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella patho-genicity island 1 .	35	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	21320585	4	ver/dev	The HilA box determine the magnitude of HilA-dependent activation of prgH from Salmonella patho-genicity island 1 .	626	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella patho-genicity island 1 .	35	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	21573071	1	ver/dev	HilA , directly activates the expression of the prgH operons .	32	The main regulator of SPI1 , HilA , directly activates the expression of the invF and prgH operons , which encode the components of the T3SS apparatus [ 6,7 ] .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	22004521	16	att	Lostroh C.P. , Lee C.A. ( 2001 ) The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	517	Lostroh C.P. , Lee C.A. ( 2001 ) The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	37	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	23040276	7	att	[ 64 ] C.P. Lostroh , C.A. Lee , The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella patho-genicity island 1 , J. Bacteriol .	569	[ 64 ] C.P. Lostroh , C.A. Lee , The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella patho-genicity island 1 , J. Bacteriol .	35	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	26300871	40	att	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	699	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	19	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	26300871	40	ver/dev	sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	699	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	19	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	26300871	40	ver/dev	The HilA box determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	699	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	19	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	27886269	39	att	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	366	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	9	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	27886269	39	ver/dev	sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	366	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	9	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	27886269	39	ver/dev	The HilA box determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	366	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	9	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	29555922	20	att	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P prgH from Salmonella pathogenicity island 1 .	496	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P prgH from Salmonella pathogenicity island 1 .	11	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	29555922	20	ver/dev	sequences outside it determine the magnitude of HilA-dependent activation of P prgH from Salmonella pathogenicity island 1 .	496	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P prgH from Salmonella pathogenicity island 1 .	11	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	29555922	20	ver/dev	The HilA box determine the magnitude of HilA-dependent activation of P prgH from Salmonella pathogenicity island 1 .	496	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P prgH from Salmonella pathogenicity island 1 .	11	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	32316180	4	ver/dev	HilA binds to the prgH promoters , triggering the activation of T3SE genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	32316180	4	ver/dev	HilA binds to the prgH promoters , triggering the activation of T3SS genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	prgH	activator	32323733	3	att	Lostroh cP and Lee cA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	565	Lostroh cP and Lee cA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	30	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	32323733	3	ver/dev	The HilA sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1	565	Lostroh cP and Lee cA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	30	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	32323733	3	ver/dev	The HilA box outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1	565	Lostroh cP and Lee cA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	30	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	32323733	3	ver/dev	The HilA sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1	565	Lostroh cP and Lee cA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	30	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	32323733	3	ver/dev	The HilA box outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1	565	Lostroh cP and Lee cA : The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	30	REFERENCES	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	33101243	9	att	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	414	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	29	SUPPLEMENTARY MATERIAL	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	33101243	9	ver/dev	sequences outside it determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	414	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	29	SUPPLEMENTARY MATERIAL	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	33101243	9	ver/dev	The HilA box determine the magnitude of HilA-dependent activation of prgH from Salmonella pathogenicity island 1 .	414	The HilA box and sequences outside it determine the magnitude of HilA-dependent activation of P ( prgH ) from Salmonella pathogenicity island 1 .	29	SUPPLEMENTARY MATERIAL	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	activator	34424033	19	ver/dev	Since the prgH gene is directly activated by HilA , for a control , we created a prgH-lacZ fusion containing nucleotides corresponding to -265 to +116 relative to expressing HilA from a plasmid .	218	Since the prgH gene is directly activated by HilA ( 41 ) , for a control , we created a prgH-lacZ fusion containing nucleotides corresponding to -265 to +116 relative to expressing HilA from a plasmid .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	prgH	activator	34424033	37	ver/dev	The prgH promoter is transcriptionally activated by HilA .	441	The prgH promoter is transcriptionally activated by HilA ( 41 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	prgH	activator	34424033	44	ver/dev	Likewise , activation of the prgH promoter is strictly dependent on HilA ,	549	Likewise , activation of the prgH promoter is strictly dependent on HilA ,	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM3611	activator	25437188	50	ver/dev	In addition , CsrA stimulates expression of STM3611 tenfold .	560	In addition , CsrA stimulates expression of STM3611 tenfold ( Figure 2 ) [ 134 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Zur	gene	znuA	activator	24858080	6	att	Using semiquantitative RT-PCR we verified not only the repression by Zn and the Zur-dependent expression of znuA , zinT and , but also their induction by Cu ( Fig. 3 ) .	271	Using semiquantitative RT-PCR we verified not only the repression by Zn and the Zur-dependent expression of znuA , zinT and rpmE2-rpmJ_1 , but also their induction by Cu ( Fig. 3 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	NEG	New	Level 1
Zur	gene	znuA	activator	24858080	6	ver/dev	Using semiquantitative RT-PCR we verified not the Zur-dependent expression of znuA their induction by Cu .	271	Using semiquantitative RT-PCR we verified not only the repression by Zn and the Zur-dependent expression of znuA , zinT and rpmE2-rpmJ_1 , but also their induction by Cu ( Fig. 3 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	sipB	activator	33617591	7	ver/dev	All of the hilD mutants retained their full capacity to induce sipB in the absence of c2-HDA , demonstrating that the point mutations did not reduce transcriptional activation by HilD .	97	All of the hilD mutants retained their full capacity to induce sipB in the absence of c2-HDA , complementing the chromosomal hilD null mutant , and demonstrating that the point mutations did not reduce transcriptional activation by HilD ( Fig 2A ) .	10	SPECIFIC AMINO ACID RESIDUES OF HILD ARE ESSENTIAL FOR REPRESSION BY C2-HDA	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
OxyR	gene	dps	activator	10618525	1	ver/dev	The dps promoter is activated by OxyR during-growth in stationary-phase .	303	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	dps	activator	10874730	6	ver/dev	1994 The dps promoter is activated by OxyR during-growth in stationary-phase .	375	1994 The dps promoter is activated by OxyR during growth and by IHF and ss in stationary phase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	dps	activator	14742565	1	ver/dev	The dps promoter is activated by OxyR during-growth in stationary-phase .	133	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase .	4	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	dps	activator	15790293	15	ver/dev	The dps promoter is activated by OxyR during-growth in stationary-phase .	385	The dps promoter is activated by OxyR during growth and by IHF and ss in stationary phase .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	dps	activator	18166161	0	ver/dev	Moreover , while in E. coli the expression of dps in logarithmic phase is modulated by the exposition to sources of hydrogen-peroxide -LRB- mediated by OxyR -RRB- , in the stationary-phase its expression is not induced by this reactive oxygen specie .	155	Moreover , while in E. coli the expression of dps in logarithmic phase is modulated by the exposition to sources of hydrogen peroxide ( mediated by OxyR ) , in the stationary phase its expression is regulated by σs and is not induced by this reactive oxygen species [ 34 ] .	13	3.2. SUSCEPTIBILITY OF S. TYPHIMURIUM TO SUPEROXIDE	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
OxyR	gene	dps	activator	19223478	2	ver/dev	The dps promoter is activated by OxyR during-growth in stationary-phase .	427	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase .	8	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	dps	activator	23651595	1	ver/dev	Activated OxyR induces H2O2 breakdown , dps lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	dps	activator	25028458	48	ver/dev	The dps promoter is activated by OxyR during-growth in stationary-phase .	415	The dps promoter is activated by OxyR during growth and by IHF and s in stationary phase .	11	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tlpA	repressor	16782389	0	ver/dev	The response regulator PhoP was found to play a key role in the repression of tlpA in conjunction with two other regulators , TlpA itself .	13	The response regulator PhoP was found to play a key role in the repression of tlpA in conjunction with two other regulators , RpoS and TlpA itself .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tlpA	repressor	16782389	0	ver/dev	The response regulator PhoP was found to play a key role in the repression of tlpA in conjunction with two other regulators , RpoS itself .	13	The response regulator PhoP was found to play a key role in the repression of tlpA in conjunction with two other regulators , RpoS and TlpA itself .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tlpA	repressor	16782389	1	ver/dev	The response regulator PhoP represses the expression of tlpA	138	3.4. The response regulator PhoP represses the expression of tlpA	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tlpA	repressor	16782389	6	ver/dev	Consistent with that , a putative PhoP binding motif was identified in the upstream region of tlpA , suggesting that PhoP may directly repress tlpA expression .	163	Consistent with that , a putative PhoP binding motif was identified in the upstream region of tlpA , suggesting that PhoP may directly repress tlpA expression ( see Section 4 ) .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	tlpA	repressor	16782389	12	ver/dev	The presence of a PhoP binding sequence in the promoter region would indicate that the repression of tlpA by PhoP is direct ; however , further studies are needed in order to confirm this .	381	The presence of a PhoP binding sequence in the promoter region would indicate that the repression of tlpA by PhoP is direct ; however , further studies are needed in order to confirm this .	23	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sinR	regulator	27886269	3	ver/dev	InvF , regulates the expression of sinR .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
ArcA	gene	lldP	repressor	32392214	31	att	This is because similar fluorescence was displayed by wild-type and barA mutant Salmonella harboring transcriptional-fusions between a promoterless gfp gene and the promoter of the ArcA-repressed lldP gene ( S16 Fig ) .	327	This is because similar fluorescence was displayed by wild-type and barA mutant Salmonella harboring transcriptional fusions between a promoterless gfp gene and the promoter of the ArcA-repressed lldP gene ( S16 Fig ) .	17	BARA IS DISPENSABLE FOR ACTIVATION OF THE REGULATORS ARCA, OMPR, AND PHOP UNDER CONDITIONS IN WHICH IT ACTIVATES RCSB	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	araH	regulator	24272778	6	att	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	88	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	2	MAIN	Escherichia coli;Iris germanica;Escherichia coli;Iris germanica;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	repressor	28704543	1	ver/dev	The mechanism of this SPI-1 repression by SsrB acts upon the hilD .	42	The mechanism of this SPI-1 repression by SsrB was direct and acts upon the hilD and hilA regulatory genes .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	hilD	repressor	28704543	6	ver/dev	Together , these results demonstrate that SsrB represses the transcription of the SPI-1 regulatory genes hilD .	126	Together , these results demonstrate that SsrB represses the transcription of the SPI-1 regulatory genes hilD , hilA and invF .	7	SSRB REPRESSES THE SPI-1 REGULATORY CASCADE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	hilD	repressor	28704543	7	ver/dev	SsrB directly represses hilD	127	SsrB directly represses hilD and hilA	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	repressor	28704543	8	ver/dev	To determine whether SsrB indirectly represses the expression of hilD , we analyzed the interaction of SsrB with the regulatory regions of these genes by EMSAs .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	repressor	28704543	8	ver/dev	To determine whether SsrB indirectly represses the expression of hilD , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility-shift assays .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	repressor	28704543	8	ver/dev	To determine whether SsrB directly represses the expression of hilD , we analyzed the interaction of SsrB with the regulatory regions of these genes by EMSAs .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	repressor	28704543	8	ver/dev	To determine whether SsrB directly represses the expression of hilD , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility-shift assays .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	repressor	28704543	12	ver/dev	To determine whether SsrB represses hilD through these two putative SsrB-binding sites , three different cat transcriptional-fusions were constructed , each with distinct 5 ' and 3 ' deletions of the hilD-cat-364 +88 fusion .	147	To determine whether SsrB represses hilD through these two putative SsrB-binding sites , three different cat transcriptional fusions were constructed , each with distinct 5 ' and 3 ' deletions of the hilD-cat-364 +88 fusion that showed repression by SsrB ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	hilD	repressor	28704543	18	ver/dev	SsrB directly represses the hilD SPI-1 regulatory genes .	158	SsrB directly represses the hilD and hilA SPI-1 regulatory genes .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	repressor	28704543	23	ver/dev	The SsrB-binding sites _ involved in repression of hilD	181	The SsrB-binding sites involved in repression of hilD or hilA are displayed as blue boxes below or above the respective regulatory region , which indicates the sense and anti-sense strand of DNA , respectively ; their respective 18-bp sequence is shown .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	repressor	28704543	24	ver/dev	SsrB represses hilD by directly acting on its promoter .	188	SsrB represses hilD by directly acting on its promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	repressor	28704543	46	ver/dev	a mechanism whereby SsrB represses the SPI-1 genes by directly acting on the hilD	293	Our data strongly support a mechanism whereby SsrB represses the SPI-1 genes by directly acting on the hilD and hilA regulatory genes .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	hilD	repressor	30355489	16	ver/dev	For example , SsrB has been shown to directly repress the hilD .	195	For example , SsrB has been shown to directly repress the hilD and hilA regulatory genes that activate SPI-1 gene expression involved in assembling the T3SS-1 ( Pérez - Morales et al. , 2017 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	ssrB	repressor	26300871	18	ver/dev	Taken together , these results show that CpxR represses the autoregulation of ssrB located in SPI-2 .	390	Taken together , these results show that CpxR represses the autoregulation of HilD , which in turn affects the expression of hilA and thus the SPI-1 genes , as well as of other virulence genes regulated by HilD , such as ssrB and sseB located in SPI-2 .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	sufA	activator	23651595	1	ver/dev	Activated OxyR induces sufA ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	sufA	activator	23651595	1	ver/dev	Activated OxyR induces sufA lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hilD	repressor	32213244	2	att	Interestingly , in S. enterica , CRP-repressed Spot 42 acquired an additional function of positively regulating hilD encoding the master regulator of virulence ( 187 ) , providing an example of a conserved sRNA influencing species-specific regulons .	468	Interestingly , in S. enterica , CRP-repressed Spot 42 acquired an additional function of positively regulating hilD encoding the master regulator of virulence ( 187 ) , providing an example of a conserved sRNA influencing species-specific regulons .	27	CONTROLLING PATHOGENESIS	Salmonella;Salmonella;Leiostomus xanthurus	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hilD	repressor	33162952	3	ver/dev	In agreement , Spot 42 might be responsible to fine-tune the expression of CsrC in conditions where the CRP-cAMP activity is downregulated similarly as it occurs for the Spot 42-regulated hilD mRNA .	198	In agreement , Spot 42 might be responsible to fine-tune the expression of CsrC in conditions where the CRP-cAMP activity is downregulated similarly as it occurs for the Spot 42-regulated hilD mRNA ( El Mouali et al. , 2018 ) .	9	DISCUSSION	Leiostomus xanthurus;Leiostomus xanthurus	0	L1	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	narJ	regulator	29857034	19	ver/dev	narJ are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	csgD	regulator	32604994	4	ver/dev	In high-osmolarity , transcription is repressed through binding of phosphorylated CpxR to multiple sites on the csgD promoter .	50	In high osmolarity , transcription is repressed through binding of phosphorylated CpxR to multiple sites on the csgD promoter [ 36 ] , as well as phosphorylated OmpR binding to a low-afinity site in the csgD promoter [ 38 ] .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
ArcA	gene	arcA	activator	30038032	1	att	Next we focus our attention on the ArcA-activated proteins ( i.e. those proteins of lower levels in the arcA mutant , Fig. 1B ) .	194	Next we focus our attention on the ArcA-activated proteins ( i.e. those proteins of lower levels in the arcA mutant , Fig. 1B ) .	6	COMPARATIVE PROTEOMICS ANALYSIS OF S. TYPHIMURIUM AND ITS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	sdiA	activator	19820103	2	ver/dev	those bacteria in which SdiA becomes activated stay in the Peyer 's patch while the sdiA mutant bacteria	383	Therefore , we hypothesize that those bacteria in which SdiA becomes activated stay in the Peyer 's patch while the sdiA mutant bacteria or the sdiA bacteria that are not activated continue to the MLN and spleen .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	sdiA	activator	19820103	2	ver/dev	those bacteria in which SdiA becomes activated stay in the sdiA bacteria	383	Therefore , we hypothesize that those bacteria in which SdiA becomes activated stay in the Peyer 's patch while the sdiA mutant bacteria or the sdiA bacteria that are not activated continue to the MLN and spleen .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	sdiA	activator	22149171	12	ver/dev	However , activation of SdiA did not appear to confer a fitness advantage when compared with a sdiA -- strain .	61	However , activation of SdiA did not appear to confer a fitness advantage when compared with a sdiA -- strain .	5	INTRODUCTION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
SdiA	gene	sdiA	activator	25080967	19	att	However , when we measured Rck protein expression at 37 °C in S. Enteritidis LA5rck : :3 xFLAG strain constitutively expressing sdiA from S. Typhimurium , only a weak SdiA-dependent expression of Rck was observed for S. Enteritidis compared to S. Typhimurium 14028 and this Rck expression was independent on the presence of AHLs ( Fig. 6C ) .	190	However , when we measured Rck protein expression at 37 °C in S. Enteritidis LA5rck : :3 xFLAG strain constitutively expressing sdiA from S. Typhimurium , only a weak SdiA-dependent expression of Rck was observed for S. Enteritidis compared to S. Typhimurium 14028 and this Rck expression was independent on the presence of AHLs ( Fig. 6C ) .	11	DIFFERENT RCK REGULATION BY SDIA BETWEEN S. ENTERITIDIS AND S. TYPHIMURIUM IS DUE TO DIFFERENCES IN THE PROMOTER REGION OF THE PEFI-SRGC OPERON	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	sdiA	activator	27565088	0	ver/dev	However , the activation of SdiA from EHEC by AHLs conferred greater stability and affinity to DNA , albeit not affecting sdiA gene transcription .	43	However , the activation of SdiA from EHEC by AHLs conferred greater stability and affinity to DNA , albeit not affecting sdiA gene transcription [ 16 ] .	4	MAIN	nan	1	L2	OTHER	Other	OTHER	New	Level 1
MarR	TU	acrAB	activator	19120970	6	ver/dev	This means that a strong induction of and a sequential induction of acrAB is expected only when MarR is inactivated as , indeed , occurs with SAL .	193	This means that a strong induction of MarA ( and a sequential induction of acrAB ) is expected only when MarR is inactivated as , indeed , occurs with SAL which binds MarR and inactivates it ( 52 ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	acrAB	activator	19120970	6	ver/dev	This means that a strong induction of and a sequential induction of acrAB is expected only when MarR is inactivated as , indeed , occurs with SAL .	193	This means that a strong induction of MarA ( and a sequential induction of acrAB ) is expected only when MarR is inactivated as , indeed , occurs with SAL which binds MarR and inactivates it ( 52 ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	invF	repressor	28335027	12	ver/dev	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	770	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	flgI	activator	9765570	0	att	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	sifB	regulator	33045730	48	ver/dev	The xenogeneic silencer H-NS binds to AT-rich horizontally acquired sifB .	246	The xenogeneic silencer H-NS binds to AT-rich horizontally acquired DNA , preventing expression of the corresponding genes ( 50,51 ) , including ugtL and sifB .	27	SSRB ANTAGONIZES THE GENE SILENCER H-NS IN THE UGTL PRO- MOTER REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	sifB	regulator	33045730	60	ver/dev	In vivo binding of H-NS to the promoter regions of he sifB were determined in ns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	274	( F ) In vivo binding of H-NS to the promoter regions of the sifB , ugtL , STM14 3310 and mgtA genes were determined in hns-FLAG ( JC805 ) and hns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	Iris germanica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	sifB	regulator	33045730	60	ver/dev	In vivo binding of H-NS to the promoter regions of he sifB were determined in ns-FLAG ( JC805 ) .	274	( F ) In vivo binding of H-NS to the promoter regions of the sifB , ugtL , STM14 3310 and mgtA genes were determined in hns-FLAG ( JC805 ) and hns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	Iris germanica	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SprB	gene	sifB	regulator	27601571	47	ver/dev	sifB is regulated by SprB	422	ssaG and ssaJ are regulated by HilC , and sifB is regulated by SprB .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	15256548	20	ver/dev	Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon .	678	Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon ( Ellermeier & Slauch , 2003 ) .	15	STRESS RESPONSE GENES AND GLOBAL REGULATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	regulator	15661008	25	ver/dev	RtsA can directly bind the hilA promoter .	324	RtsA belongs to the AraC/XylS family of regulators , and can directly bind the hilA promoter and induce the hilA expression independent of HilC and HilD .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilA	regulator	16045614	19	ver/dev	a model in which expression of hilA is controlled by the combined action of RtsA	81	Based on our genetic analyses , and taking into account the published results outlined above , we present a model in which expression of hilA is controlled by the combined action of HilC , HilD and RtsA , each of which can independently bind upstream of hilA to induce its expression ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	16045614	19	ver/dev	a model in which expression of hilA is controlled by the combined action of RtsA	81	Based on our genetic analyses , and taking into account the published results outlined above , we present a model in which expression of hilA is controlled by the combined action of HilC , HilD and RtsA , each of which can independently bind upstream of hilA to induce its expression ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	16045614	63	ver/dev	This is consistent with the feedforward loop model ; when neither RtsA are present , regulation of hilA is dampened , even though the primary signal is mediated through HilD .	409	This is consistent with the feedforward loop model ; when neither RtsA nor HilC are present , regulation of hilA is dampened , even though the primary signal is mediated through HilD .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RtsA	gene	hilA	regulator	17208038	1	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : RtsA .	51	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD and RtsA [ 23 -- 25 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	17208038	2	ver/dev	Studies have shown PheU that RtsA can each individually bind to the hilA promoter	55	Studies have shown PheU that HilC , HilD and RtsA can each individually bind to the hilA promoter , and deletions of hilC , hilD or rtsA cause a decrease in expression of hilA [ 19 ,23 -- 25 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
RtsA	gene	hilA	regulator	17208038	6	ver/dev	RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by the sic/sip operon -- in a fashion independent of HilA .	67	HilC , HilD and RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through , the sic/sip operon -- in a fashion independent of HilA [ 15,16,25,27 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	17208038	6	ver/dev	RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through -- in a fashion independent of HilA .	67	HilC , HilD and RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through , the sic/sip operon -- in a fashion independent of HilA [ 15,16,25,27 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilA by RtsA .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	17675384	18	ver/dev	In agreement with genetic data , we show that the purified RtsA protein , like HilD , binds to hilA promoters .	302	In agreement with genetic data , we show that the purified RtsA protein , like HilC and HilD , binds to the hilC , hilD , rtsA , and hilA promoters .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	regulator	17675384	18	ver/dev	In agreement with genetic data , we show that the purified RtsA protein , like HilC , binds to hilA promoters .	302	In agreement with genetic data , we show that the purified RtsA protein , like HilC and HilD , binds to the hilC , hilD , rtsA , and hilA promoters .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	regulator	17993530	3	ver/dev	Expression of hilA is directly controlled by three AraC-like activators : RtsA .	35	Expression of hilA is directly controlled by three AraC-like activators : HilC , HilD , and RtsA ( 18 , 42 , 47 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	19003447	0	ver/dev	Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; RtsA .	38	Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilD , HilC and RtsA , which in a complex arrangement of feedback and feedforward loops bring about maximal induction of HilA ( Altier 2005 ; Jones 2005 ; Ellermeier and Slauch 2007 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	19537165	3	ver/dev	Earlier work on mathematical modeling of regulation of expression of hilA by RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .	44	Earlier work on mathematical modeling of regulation of expression of hilA by HilC , HilD and RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop [ Maithreye and Mande , 2007 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	22479568	0	ver/dev	RtsA can activate expression of rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilA	regulator	23504014	3	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : RtsA .	24	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD , and RtsA ( 14 -- 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	25182488	2	ver/dev	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : RtsA .	19	Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC , HilD , and RtsA ( 8 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	26039089	8	ver/dev	RtsA is a major regulator of both hilA of a feed-forward loop for activation of SPI1 expression .	181	RtsA is a major regulator of both hilA and hilD expression and forms part of a feed-forward loop for activation of SPI1 expression [ 53 ] .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	27565525	0	ver/dev	Differential expression of hilA , is influenced by RtsA	361	Differential expression of hilA , that encodes the transcriptional activator of the SPI1 structural genes , is influenced by three AraC-like regulators ( HilD , HilC , and RtsA ) and each of them can activate the hilD , hilC , rtsA , and hilA genes that form a complex feed-forward regulatory loop ( Golubeva et al. , 2012 ; Lim et al. , 2012 ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	28575106	6	ver/dev	As the expression of hilA is directly controlled by RtsA , we tested whether LoiA regulates HilA through any of these three regulators .	177	As the expression of hilA is directly controlled by HilD , HilC and RtsA , we tested whether LoiA regulates HilA through any of these three regulators .	9	LOIA ACTIVATES EXPRESSION OF HILA GENE THROUGH ACTIVATING HILD	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RtsA	gene	hilA	regulator	30716090	46	ver/dev	Transcription of hilA is controlled by RtsA .	464	Transcription of hilA is controlled by a complex feed-forward loop including RtsA , HilC and HilD [ 46 ] .	25	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	31182495	3	ver/dev	electrophoretic-mobility-shift assays suggest that PhoP specifically binds the hilA promoter to block binding of RtsA as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	regulator	31182495	3	ver/dev	Genetic analyses suggest that PhoP specifically binds the hilA promoter to block binding of RtsA as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	regulator	31182495	44	ver/dev	PhoP represses hilA expression primarily by blocking binding of HilD/HilC / RtsA .	206	PhoP represses hilA expression primarily by blocking binding of HilD/HilC / RtsA .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	regulator	31262841	10	ver/dev	In the absence of this degradation , regulation of hilA results from only the direct effect of PinT on hilA translation , explaining the fact that RtsA plays no role in hilA expression in the strain .	145	In the absence of this degradation , regulation of hilA results from only the direct effect of PinT on hilA translation , explaining the fact that RtsA plays no role in hilA expression in the strain lacking a functional degradosome ( Fig. 4B ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	32041797	0	ver/dev	Expression of hilA is positively regulated by three homologous transcriptional regulators , RtsA , .	9	Expression of hilA is positively regulated by three homologous transcriptional regulators , HilD , HilC , and RtsA , belonging to the AraC/XylS family .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	32041797	2	ver/dev	Expression of hilA is regulated by the combined actions of three AraC-like transcriptional activators , RtsA , .	30	Expression of hilA is regulated by the combined actions of three AraC-like transcriptional activators , HilD , HilC , and RtsA ( 17 -- 19 ) , each of which is capable of inducing transcription of the hilD , hilC , and rtsA genes .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	regulator	34202800	14	ver/dev	PhoP specifically binds the hilA promoter to block the binding of RtsA activators as a repression mechanism	329	PhoP specifically binds the hilA promoter to block the binding of HilD , HilC , and RtsA activators as a repression mechanism [ 126 ]	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FruR	gene	rpoS	repressor	21388802	4	ver/dev	FruR represses rpoS genes .	170	FruR activates crp expression and represses rpoS and SPI2 genes .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	rpoS	activator	19843227	28	ver/dev	However , there are indications that CRP-cAMP also plays a different role as an activator of rpoS expression during the late stages of growth .	147	However , there are indications that CRP-cAMP also plays a different role as an activator of rpoS expression during the late stages of growth ( Hengge-Aronis , 2002 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	rpoS	activator	20075614	2	ver/dev	further _ suggesting that cAMP-CRP upregulated rpoS expression	10	rpoS expression increased in cpdA ( cAMP phosphodiesterase coding gene ) mutant , further suggesting that cAMP-CRP upregulated rpoS expression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	rpoS	activator	20075614	2	ver/dev	further _ suggesting that cAMP-CRP upregulated rpoS expression	10	rpoS expression increased in cpdA ( cAMP phosphodiesterase coding gene ) mutant , further suggesting that cAMP-CRP upregulated rpoS expression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	rpoS	activator	20075614	28	ver/dev	Interestingly , in the stationary-phase , we still observed a slight increase of rpoS transcription in the ppk mutant compared with WT , although both of the cAMP-CRP-binding sites were mutated ( Fig. 6B ) .	255	Interestingly , in the stationary phase , we still observed a slight increase of rpoS transcription in the ppk mutant compared with WT , although both of the cAMP-CRP-binding sites were mutated ( Fig. 6B ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	19835951	14	att	In this work , we showed that hlyE and taiA genes found in SPI-18 present RpoS-dependent induction at low pH or high-osmolarity .	194	In this work , we showed that hlyE and taiA genes found in SPI-18 present RpoS-dependent induction at low pH or high osmolarity .	17	4. DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	hlyE	activator	19835951	16	att	hlyE gene transcription is induced by low pH in an RpoS-dependent manner .	207	hlyE gene transcription is induced by low pH in an RpoS-dependent manner .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	19835951	7	att	These results show that hlyE transcription is increased by low pH and high-osmolarity in an RpoS-dependent manner .	161	These results show that hlyE transcription is increased by low pH and high osmolarity in an RpoS-dependent manner .	15	3.1. THE EXPRESSION OF SPI-18 GENES IS INCREASED AT LOW PH AND HIGH OSMOLARITY IN AN RPOS-DEPENDENT MANNER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	19835951	6	ver/dev	Nevertheless , this effect was abolished in the rpoS mutant , indicating that induction of hlyE transcription is dependent on RpoS under these conditions .	150	Nevertheless , this effect was abolished in the rpoS mutant , indicating that induction of hlyE transcription is dependent on RpoS under these conditions .	15	3.1. THE EXPRESSION OF SPI-18 GENES IS INCREASED AT LOW PH AND HIGH OSMOLARITY IN AN RPOS-DEPENDENT MANNER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	hlyE	activator	19835951	7	ver/dev	These results show that hlyE transcription is increased by low pH and high-osmolarity in an RpoS-dependent manner .	161	These results show that hlyE transcription is increased by low pH and high osmolarity in an RpoS-dependent manner .	15	3.1. THE EXPRESSION OF SPI-18 GENES IS INCREASED AT LOW PH AND HIGH OSMOLARITY IN AN RPOS-DEPENDENT MANNER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	19835951	14	ver/dev	In this work , we showed that hlyE genes found in SPI-18 present RpoS-dependent induction at low pH or high-osmolarity .	194	In this work , we showed that hlyE and taiA genes found in SPI-18 present RpoS-dependent induction at low pH or high osmolarity .	17	4. DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	hlyE	activator	19835951	16	ver/dev	hlyE gene transcription is induced by low pH in an RpoS-dependent manner .	207	hlyE gene transcription is induced by low pH in an RpoS-dependent manner .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	24885225	38	ver/dev	Finally , rpoS is epistatic over phoPQ , reinforcing the fact that the induction of the hlyE expression under low concentration of Mg2 + occurs via RpoS .	145	Finally , rpoS is epistatic over phoPQ , reinforcing the fact that the induction of the hlyE expression under low concentration of Mg2 + depends on PhoPQ and occurs via RpoS .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	24885225	60	ver/dev	In this paper we showed that RpoS is the most import-ant activator of hlyE expression .	229	In this paper we showed that RpoS is the most import-ant activator of hlyE expression .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hlyE	activator	24885225	62	ver/dev	Furthermore , hlyE induction by high-osmolarity is RpoS dependent .	242	Furthermore , hlyE induction by high osmolarity is RpoS dependent [ 14 ] , reinforcing the fact that this sigma factor is an integrator of different signaling pathways .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	sbp	activator	18957594	7	ver/dev	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources .	329	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ( Kredich , 1996 ; Stec et al. , 2006 ; Van Der Ploeg et al. , 1997 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	cpxR	regulator	27199934	16	ver/dev	CpxR also can bind to the cpxR box located in the promoter region of target genes .	377	CpxR also can bind to the cpxR box located in the promoter region of target genes .	16	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CpxR	gene	cpxR	regulator	31627387	4	ver/dev	In the ∆ cpxR genetic background during planktonic growth , , the gen were significantly up-regulated , showing their constitutive regulation by CpxR .	223	In the ∆ cpxR genetic background during planktonic growth , the genes encoding the T3SS apparatus ( invG , prgHIJK , orgA ) , T3SS specific ATPase ( invC ) , translocons ( invABCEFIJH , spaOPQRS ) , SPI1 effectors ( sipABCD , sicAP , sopBDEE2 , hilACD , iagB ) and SPI2 effectors ( pipBC , ssaBDGHIJKL , srfABC , sseA , avrA ) were significantly up-regulated , showing their constitutive regulation by CpxR .	9	2.5. EFFECT OF CPXR DELETION ON THE TRANSCRIPTOME OF PLANKTONIC CELLS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
Rho	gene	ribB	repressor	22431636	15	ver/dev	a Rho-dependent terminator inhibits transcription elongation into the ribB coding region in the presence of FMN	141	Taken together , these data establish that the ribB leader contains a Rho-dependent terminator that inhibits transcription elongation into the ribB coding region in the presence of FMN .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	fur	activator	27242152	0	ver/dev	However , in the presence of H2O2 , transcription of fur is also activated by OxyR in E. coli , resulting in repression of target mRNAs for iron-uptake proteins .	136	However , in the presence of H2O2 , transcription of fur is also activated by OxyR in E. coli ( Zheng et al. , 1999 ) , resulting in repression of target mRNAs for iron-uptake proteins .	11	3.3. POSSIBLE MODEL OF RYHB(S)-MEDIATED REGULATION IN SALMONELLA	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	hmp	activator	17024490	5	ver/dev	IHF , known to aVect hmp expression , apparently are not involved in the hmpEc induction by NO .	43	Other regulators such as RpoS and IHF , known to aVect hmp expression , apparently are not involved in the hmpEc induction by NO ( Memb-rillo-Hernández et al. 1996 , 1997a ) .	4	INTRODUCTION	nan	1	L2	OTHER	Fact	NEG	Other	Level 1
SprB	gene	STM1841	regulator	27601571	24	att	S1E ) as an SprB-regulated gene , ( STM1841 ) , is shown in additional gene that is positively regulated by InvF .	231	S1E ) as an SprB-regulated gene , STM14_2227 ( STM1841 ) , is shown in additional gene that is positively regulated by InvF .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssaB	regulator	17630976	0	att	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	14	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	2	SUMMARY	synthetic construct	0	L3	OTHER	Analysis	OTHER	New	Level 2
FNR	gene	hilA	activator	28575106	14	ver/dev	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in-vitro SPI-1-inducing conditions .	306	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in vitro SPI-1-inducing conditions ( low O2 and high salt ) [ 46,55 ] .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	activator	28575106	14	ver/dev	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in-vitro high salt .	306	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in vitro SPI-1-inducing conditions ( low O2 and high salt ) [ 46,55 ] .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	activator	28575106	14	ver/dev	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in-vitro low O2 .	306	Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5 - to 2-fold increase of hilA expression under in vitro SPI-1-inducing conditions ( low O2 and high salt ) [ 46,55 ] .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	activator	28575106	15	ver/dev	However , whether the repression of hilA by Fnr was induced by low O2 was not clarified in those studies .	307	However , whether the repression of hilA by Fnr was induced by low O2 was not clarified in those studies .	13	DISCUSSION	nan	1	L3	SPEC	Investigation	NEG	Other	Level 1
HNS	gene	ssrB	activator	27564394	7	ver/dev	HilD also mediates regulatory cross-talk between SPI2 , resulting in the activation of the SPI2 T3SS through counter-silencing of H-NS at the ssrB promoter .	263	HilD is the primary regulator of all components of the SPI1 T3SS and also mediates regulatory cross-talk between SPI1 and SPI2 , resulting in the activation of the SPI2 T3SS through counter-silencing of H-NS at the ssrB promoter [ 30 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ssrB	activator	27564394	7	ver/dev	HilD also mediates regulatory cross-talk between SPI1 , resulting in the activation of the SPI2 T3SS through counter-silencing of H-NS at the ssrB promoter .	263	HilD is the primary regulator of all components of the SPI1 T3SS and also mediates regulatory cross-talk between SPI1 and SPI2 , resulting in the activation of the SPI2 T3SS through counter-silencing of H-NS at the ssrB promoter [ 30 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	14563863	10	att	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	125	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	14563863	21	ver/dev	The fact that mgtA was PhoP controlled led us to understand its physiological role .	183	The fact that mgtA was PhoP controlled led us to define the inducing signal of the regulon and to understand its physiological role ( 10 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	14563863	21	ver/dev	The fact that mgtA was PhoP controlled led us to define the inducing signal of the regulon .	183	The fact that mgtA was PhoP controlled led us to define the inducing signal of the regulon and to understand its physiological role ( 10 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	15703297	0	att	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5-7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8-10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in-vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	12	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5–7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8–10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Shigella flexneri;Yersinia pestis;Pectobacterium carotovorum;Neisseria meningitidis;Photorhabdus luminescens;Escherichia coli;Escherichia coli	0.5	L3	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	mgtA	regulator	15703297	12	att	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	15703297	3	att	For example , one of the profiles encompassed promoters that belong to the same expression ( E1 ) , PhoP box submotif ( M2 ) , and promoter class ( P1 ) ( Fig. 1H ) and harbored not only the prototypical PhoP-regulated phoP and mgtA promoters ( 13 , 14 ) but also the yhiW promoter , which was not known to be under PhoP control .	97	For example , one of the profiles encompassed promoters that belong to the same expression ( E1 ) , PhoP box submotif ( M2 ) , and promoter class ( P1 ) ( Fig. 1H ) and harbored not only the prototypical PhoP-regulated phoP and mgtA promoters ( 13 , 14 ) but also the yhiW promoter , which was not known to be under PhoP control .	4	RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PhoP	gene	mgtA	regulator	15703297	5	att	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	105	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtA	regulator	15703297	6	ver/dev	We established that when Salmonella experiences the PhoP protein binds to both the archetypal mgtA promoter as well as the mig-14 , mgtC , and pagC promoters .	110	We established that when Salmonella experiences low Mg2 , the PhoP protein binds to both the archetypal mgtA promoter as well as the mig-14 , mgtC , and pagC promoters ( Fig. 1 A ) .	4	RESULTS	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	15703297	12	ver/dev	hIP of hoP-regulated promoters demonstrates binding of the PhoP-HA protein to he PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	15703297	12	ver/dev	hromatin immunoprecipitation of hoP-regulated promoters demonstrates binding of the PhoP-HA protein to he PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	16339942	3	att	Although some genes regulated by PhoP do not display a consensus DNA recognition sequence for PhoP , other PhoP-regulated genes , such as the mgtA gene , contain a single conserved PhoP box in their promoter region ( Lejona et al. , 2003 ) .	45	Although some genes regulated by PhoP do not display a consensus DNA recognition sequence for PhoP , other PhoP-regulated genes , such as the mgtA gene , contain a single conserved PhoP box in their promoter region ( Lejona et al. , 2003 ) .	4	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtA	regulator	16339942	12	ver/dev	A BIAcore biosensor was used to examine , in the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .	303	A BIAcore biosensor was used to examine , in real-time , the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .	10	DNA BINDING OF PHOP PROTEINS BY SPR	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	16339942	20	ver/dev	The graph shows the binding of PhoP to biotinylated oligonucleotide duplexes containing the PhoP box of the mgtA promoter .	353	The graph shows the binding of PhoP ( i ) to biotinylated oligonucleotide duplexes containing the PhoP box of the mgtA promoter , and ( ii ) to biotinylated oligonucleotide duplexes containing a rando-mized PhoP box .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	16339942	21	ver/dev	Our SPR experiments clearly showed that both PhoP ~ P bind to the PhoP box of the mgtA promoter .	360	Our SPR experiments ( Fig. 6 ) clearly showed that both PhoP and PhoP ~ P bind to the PhoP box of the mgtA promoter .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	16339942	21	ver/dev	Our SPR experiments clearly showed that both PhoP bind to the PhoP box of the mgtA promoter .	360	Our SPR experiments ( Fig. 6 ) clearly showed that both PhoP and PhoP ~ P bind to the PhoP box of the mgtA promoter .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	16339942	22	ver/dev	Overall , this study clearly showed that the S. enterica PhoP protein binds to the mgtA promoter regardless of its phosphorylation state .	364	Overall , this study clearly showed that the S. enterica PhoP protein dimerizes and binds to the mgtA promoter regardless of its phosphorylation state .	11	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	16339942	25	ver/dev	Specific binding of the various PhoP proteins to the PhoP box of the mgtA promoter .	405	Specific binding of the various PhoP proteins to the PhoP box of the mgtA promoter .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	16359323	2	ver/dev	The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .	308	The existence of a pair of divergently transcribed genes , one being activated and the other repressed by PhoP ( Fig. 4D ) , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA and treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ( Yamamoto et al. , 2002 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	mgtA	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the mgtA promoters increased during the first 10 min .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the mgtA promoters increased during the first 10 min .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the mgtA promoters then asymptotically reached the steady-state levels .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	17158330	7	ver/dev	When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the mgtA promoters then asymptotically reached the steady-state levels .	36	When the strain expressing the PhoP protein constitutively was shifted from repressing ( 10 mM ) to inducing ( 50 mM ) Mg2 + concentrations , binding of PhoP to the mgtA and pmrD promoters ( Fig. 3C ) and transcription of the respective genes ( Fig. 3D ) increased during the first 10 min and then asymptotically reached the steady-state levels displayed by the strain with the wild-type phoPQ promoter ( 15 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	18270203	10	att	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	151	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	2	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtA	regulator	18792679	3	ver/dev	the PhoP protein binds to the promoters of the mgtA gene to stimulate gene transcription	131	Model illustrating direct transcriptional control where low Mg2 + detected by the PhoQ protein promotes phosphorylation of the PhoP protein , which binds to the promoters of the mgtA gene and the phoPphoQ operon to stimulate gene transcription	6	THE HOW AND WHY OFPHOQLPHOP POSITIVE AUTOREGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	19091955	32	att	This motif in such promoters depends functionally on its orientation , probably because the reverse sequence in this box would change the interaction of PhoP and RNA polymerase , thereby nullifying PhoP-regulated mgtA transcription ( unpublished data ) .	196	This motif in such promoters depends functionally on its orientation , probably because the reverse sequence in this box would change the interaction of PhoP and RNA polymerase , thereby nullifying PhoP-regulated mgtA transcription ( unpublished data ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	mgtA	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	22431636	1	ver/dev	In both strains , transcription initiation from the mgtA promoter is controlled by the transcription factor PhoP in response to extracytoplasmic Mg2 .	48	In both strains , transcription initiation from the mgtA promoter is controlled by the transcription factor PhoP in response to extracytoplasmic Mg2 + sensed by the PhoQ sensor kinase ( 15 ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtA	regulator	26943369	4	att	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	mgtA	regulator	26943369	4	ver/dev	To determine whether acetylation affects the activity of PhoP as a transcription factor , mgtA were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgtA	regulator	27849575	1	ver/dev	Transcription of mgtA is regulated at activation of the promoter by PhoP .	62	Transcription of mgtA is regulated at two steps : activation of the promoter by PhoP , which is phosphorylated by PhoQ in response to low [ Mg2 + ] and other periplasmic signals ( inset 1 ) ( 4 ) , and translation of mgtL ( encoded by nucleotides 71 -- 124 ) ( 12 ) , which governs folding of the 5 ′ LR mRNA and Rho-dependent termination .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtA	regulator	29324231	11	att	We also compared the expression of other PhoP-regulated genes in the wild-type and Δhns / ΔphoPQ strains , including genes whose expression in S. Typhimurium is dependent ( pagC ) or independent ( slyB and mgtA ) of H-NS ( Perez et al. , 2008 ) .	161	We also compared the expression of other PhoP-regulated genes in the wild-type and Δhns / ΔphoPQ strains , including genes whose expression in S. Typhimurium is dependent ( pagC ) or independent ( slyB and mgtA ) of H-NS ( Perez et al. , 2008 ) .	5	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	fhuF	activator	18790861	40	att	We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .	219	We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	tviA	activator	16842356	4	ver/dev	It is known that RcsB also interacts with TviA protein , to activate viaB transcription from the tviA promoter .	122	It is known that RcsB also interacts with TviA protein , encoded by the first gene of the viaB locus , to activate viaB transcription from the tviA promoter ( Virlo-geux et al. , 1996 ) .	12	GROWTH PHASE, OSMOTIC, AND GENETIC REGULATION OF PIL TRANSCRIPTION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
Fur	gene	foxA	regulator	21573071	5	att	The activity of purified S. enterica Fur was confirmed by electrophoretic-mobility-shift assays ( EMSAs ) , which tested the ability of the protein to bind the promoter region of a confirmed Fur-regulated gene , foxA [ 56 ] .	87	The activity of purified S. enterica Fur was confirmed by electrophoretic mobility shift assays ( EMSAs ) , which tested the ability of the protein to bind the promoter region of a confirmed Fur-regulated gene , foxA [ 56 ] .	8	PROTEIN PURIFICATION	Salmonella;Salmonella	1	L2	OTHER	Analysis	OTHER	Other	Level 1
YgaE	gene	ompF	regulator	24592164	4	ver/dev	whether the regulation of YgaE to ompF is direct	216	However , whether the regulation of YgaE to ompC and ompF is direct and the concrete regulation mechanism still need further experiments to explore .	8	3.2. YGAE REPRESSES THE EXPRESSION OF OMPF/OMPC AT THE	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
YgaE	gene	ompF	regulator	24592164	6	ver/dev	This result suggested that YgaE does not influence the growth of S. Typhi by the regulation of ompF .	230	This result suggested that YgaE does not influence the growth of S. Typhi by the regulation of ompC and ompF .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
FliZ	gene	rpsL	activator	30941426	24	ver/dev	It appears that FliZ only modestly contribute to the down-regulation of SPI-1 genes in rpsL * .	287	It appears that Lon and FliZ only modestly contribute to the down-regulation of SPI-1 genes in rpsL * .	25	NON-OPTIMAL TRANSLATIONAL FIDELITY PROMOTES DEGRADATION OF HILD BY LON	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CspE	gene	yciF	activator	30992363	16	att	Increased transcript levels of yciF in a bile-salts-supplemented milieu were detected ( Fig. 3A ) in a CspE-dependent manner ( Fig. 2A ) .	249	Increased transcript levels of yciF in a bile salts-supplemented milieu were detected ( Fig. 3A ) in a CspE-dependent manner ( Fig. 2A ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CspE	gene	yciF	activator	30992363	6	ver/dev	CspE increases the stability of yciF mRNA	142	CspE increases the stability of yciF mRNA	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CspE	gene	yciF	activator	30992363	10	ver/dev	qRT-PCR revealed the induction of yciF transcripts upon the F30V mutant of CspE , in the bile-salts -- treated cspE ( Fig. 2B ) .	188	qRT-PCR revealed the induction of yciF transcripts upon complementation of WT cspE , but not the F30V mutant of CspE ( pcspE-F30V ) , in the bile salts -- treated cspE ( Fig. 2B ) .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CspE	gene	yciF	activator	30992363	13	ver/dev	S. Typhimurium -- encoded CspE increases the stability of yciF mRNA .	198	S. Typhimurium -- encoded CspE increases the stability of yciF mRNA .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
CspE	gene	yciF	activator	30992363	21	ver/dev	In the present context , it is possible that CspE increases the half-life of the yciF mRNA by preventing subsequent degradation .	296	In the present context , it is possible that CspE increases the half-life of the yciF mRNA by binding to it , unwinding its secondary structure , and preventing subsequent degradation .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CspE	gene	yciF	activator	30992363	21	ver/dev	In the present context , it is possible that CspE increases the half-life of the yciF mRNA by unwinding its secondary structure .	296	In the present context , it is possible that CspE increases the half-life of the yciF mRNA by binding to it , unwinding its secondary structure , and preventing subsequent degradation .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CspE	gene	yciF	activator	30992363	21	ver/dev	In the present context , it is possible that CspE increases the half-life of the yciF mRNA by binding to it .	296	In the present context , it is possible that CspE increases the half-life of the yciF mRNA by binding to it , unwinding its secondary structure , and preventing subsequent degradation .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CspE	gene	yciF	activator	30992363	25	ver/dev	CspE increases yciF mRNA stability , thereby enabling further functions of YciF .	379	CspE increases yciF mRNA stability , thereby enabling translation and further functions of YciF .	9	CLONING OF GENES FOR TRANS-COMPLEMENTATION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CspE	gene	yciF	activator	30992363	25	ver/dev	CspE increases yciF mRNA stability , thereby enabling translation functions of YciF .	379	CspE increases yciF mRNA stability , thereby enabling translation and further functions of YciF .	9	CLONING OF GENES FOR TRANS-COMPLEMENTATION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
FliA	gene	ycgO	activator	33257526	12	att	ycgO is also likely not FliA transcribed , although FliA-dependent expression could be masked by substantially higher levels of transcription involving a different s factor .	114	ycgO is also likely not FliA transcribed , although FliA-dependent expression could be masked by substantially higher levels of transcription involving a different s factor .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
FliA	gene	ycgO	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	acrD	regulator	30448437	3	ver/dev	As BaeR can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as positive controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L2	OTHER	Other	OTHER	New	Level 1
BaeR	gene	acrD	regulator	30448437	3	ver/dev	As BaeR can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as positive controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L2	OTHER	Other	OTHER	New	Level 1
BaeR	gene	acrD	regulator	30448437	3	ver/dev	As BaeR can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
BaeR	gene	acrD	regulator	30448437	3	ver/dev	As BaeR can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
BaeR	gene	acrD	regulator	30448437	5	ver/dev	Binding of BaeR to the promoter regions of acrD was performed to serve as positive controls , respectively .	191	Binding of BaeR to the promoter regions of acrA and acrD was performed to serve as negative and positive controls , respectively .	16	STM3030 AND STM3031 INTERACT WITH EACH OTHER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	acrD	regulator	30448437	5	ver/dev	Binding of BaeR to the promoter regions of acrD was performed to serve as negative controls , respectively .	191	Binding of BaeR to the promoter regions of acrA and acrD was performed to serve as negative and positive controls , respectively .	16	STM3030 AND STM3031 INTERACT WITH EACH OTHER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	nin	activator	33561243	0	att	Transcription termination signals in the nin region of bacteriophage lambda : identification of Rho-dependent termination regions .	401	Transcription termination signals in the nin region of bacteriophage lambda : identification of Rho-dependent termination regions .	35	REFERENCES	Bacteriophage sp.;Escherichia virus Lambda	0	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ydeI	regulator	33106344	10	att	Deletion of ydeI differentially regulates expression of several PhoP-regulated genes .	207	Deletion of ydeI differentially regulates expression of several PhoP-regulated genes .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ydeI	regulator	33106344	12	att	So , we hypothesized that deletion of ydeI could be altering the expression of several PhoP-regulated genes associated with stress resistance and virulence .	210	So , we hypothesized that deletion of ydeI could be altering the expression of several PhoP-regulated genes associated with stress resistance and virulence .	4	BACKGROUND	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ydeI	regulator	33106344	13	att	FIG 3 Deletion of ydeI differentially regulates expression of PhoP-regulated genes .	244	FIG 3 Deletion of ydeI differentially regulates expression of PhoP-regulated genes .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ydeI	regulator	33106344	15	att	Moreover , there were significant changes in the expression of various PhoP-regulated genes in the ydeI mutant cultured under different stress conditions .	411	Moreover , there were significant changes in the expression of various PhoP-regulated genes in the ydeI mutant cultured under different stress conditions .	5	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	ydeI	regulator	33106344	0	ver/dev	GFP reporter showed ydeI was transcriptionally regulated by PhoP .	11	Green fluorescent protein ( GFP ) reporter and quantitative real-time PCR ( qRT-PCR ) assays showed ydeI was transcriptionally regulated by PhoP , which is a major regulator of stress and virulence .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	0	ver/dev	Green fluorescent protein reporter showed ydeI was transcriptionally regulated by PhoP .	11	Green fluorescent protein ( GFP ) reporter and quantitative real-time PCR ( qRT-PCR ) assays showed ydeI was transcriptionally regulated by PhoP , which is a major regulator of stress and virulence .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	0	ver/dev	qRT-PCR assays showed ydeI was transcriptionally regulated by PhoP .	11	Green fluorescent protein ( GFP ) reporter and quantitative real-time PCR ( qRT-PCR ) assays showed ydeI was transcriptionally regulated by PhoP , which is a major regulator of stress and virulence .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	0	ver/dev	quantitative real-time PCR assays showed ydeI was transcriptionally regulated by PhoP .	11	Green fluorescent protein ( GFP ) reporter and quantitative real-time PCR ( qRT-PCR ) assays showed ydeI was transcriptionally regulated by PhoP , which is a major regulator of stress and virulence .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	1	ver/dev	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of PydeI .	56	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of its promoter ( PydeI ) .	2	MAIN	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	1	ver/dev	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of its promoter .	56	Our study showed that ydeI is transcriptionally regulated by PhoP under different stress conditions through differential activation of its promoter ( PydeI ) .	2	MAIN	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	2	ver/dev	PhoP regulates the expression of ydeI .	155	PhoP regulates the expression of ydeI .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ydeI	regulator	33106344	3	ver/dev	Previous reports have shown that ydeI was regulated by PhoP in S. Typhimurium .	156	Previous reports have shown that ydeI was regulated by PhoP in S. Typhimurium ( 11 , 13 ) .	4	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	4	ver/dev	So , we investigated the role of PhoP in regulation of ydeI in S. Enteritidis through qRT-PCR analysis .	157	So , we investigated the role of PhoP in regulation of ydeI in S. Enteritidis through quantitative real-time PCR ( qRT-PCR ) analysis .	4	BACKGROUND	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	4	ver/dev	So , we investigated the role of PhoP in regulation of ydeI in S. Enteritidis through quantitative real-time PCR analysis .	157	So , we investigated the role of PhoP in regulation of ydeI in S. Enteritidis through quantitative real-time PCR ( qRT-PCR ) analysis .	4	BACKGROUND	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	5	ver/dev	FIG 2 PhoP regulates the expression of ydeI .	175	FIG 2 PhoP regulates the expression of ydeI .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ydeI	regulator	33106344	7	ver/dev	The absence of the PhoP box in the upstream portion of ydeI implied ydeI was possibly indirectly regulated by PhoP .	191	The absence of the PhoP box in the upstream portion of ydeI implied ydeI was possibly indirectly regulated by PhoP .	4	BACKGROUND	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ydeI	regulator	33106344	7	ver/dev	The absence of the PhoP box in the upstream portion of ydeI implied ydeI was possibly indirectly regulated by PhoP .	191	The absence of the PhoP box in the upstream portion of ydeI implied ydeI was possibly indirectly regulated by PhoP .	4	BACKGROUND	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ydeI	regulator	33106344	8	ver/dev	PydeI was subsequently cloned into promoterless gfp-mut2 pM968 vector to further validate the role of PhoP regulation of ydeI by GFP reporter assays .	192	PydeI was subsequently cloned into promoterless gfp-mut2 pM968 vector ( Table 1 ) to further validate the role of PydeI and PhoP regulation of ydeI by flow cytometric green fluorescent protein ( GFP ) reporter assays .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	8	ver/dev	PydeI was subsequently cloned into promoterless gfp-mut2 pM968 vector to further validate the role of PhoP regulation of ydeI by flow cytometric green fluorescent protein reporter assays .	192	PydeI was subsequently cloned into promoterless gfp-mut2 pM968 vector ( Table 1 ) to further validate the role of PydeI and PhoP regulation of ydeI by flow cytometric green fluorescent protein ( GFP ) reporter assays .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	9	ver/dev	This suggested a pertinent role of PhoP in regulation of ydeI under various growth-conditions .	206	This suggested a pertinent role of PhoP in regulation of ydeI under various growth conditions .	4	BACKGROUND	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ydeI	regulator	33106344	11	ver/dev	According to previously reported findings , ydeI was regulated by PhoP .	209	According to the current and previously reported findings , ydeI was regulated by PhoP .	4	BACKGROUND	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	11	ver/dev	According to the current , ydeI was regulated by PhoP .	209	According to the current and previously reported findings , ydeI was regulated by PhoP .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	14	ver/dev	Additionally , GFP reporter assays also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	410	Additionally , our qRTPCR and GFP reporter assays also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ydeI	regulator	33106344	14	ver/dev	Additionally , our qRTPCR also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	410	Additionally , our qRTPCR and GFP reporter assays also showed ydeI was regulated by PhoP through activation of PydeI under different stress conditions .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	acnA	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , acnA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	acnA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , acnA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Hha	gene	pefB	repressor	31661351	8	ver/dev	Hha negatively regulate PefA expression by acting on the pefB promoter .	210	Hha and YdgT negatively regulate PefA expression by acting on the pefB promoter .	8	H-NS EXERTS ITS REPRESSION ACTIVITY MOSTLY ON THE PPEFB PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	mcpC	regulator	33441540	11	ver/dev	FliA _ purified H-NS bound to the region upstream of mcpC	76	Reporter expression was independent of HilD but still dependent on FliA purified H-NS bound to the region upstream of mcpC ( PmcpC-387 ) but not to the promoter of mcpB ( PmcpB-333 ) ( Fig. 3a , compare lanes 1 and 3 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	mcpC	regulator	33441540	11	ver/dev	FliA _ purified H-NS bound to the region upstream of mcpC	76	Reporter expression was independent of HilD but still dependent on FliA purified H-NS bound to the region upstream of mcpC ( PmcpC-387 ) but not to the promoter of mcpB ( PmcpB-333 ) ( Fig. 3a , compare lanes 1 and 3 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	dps	regulator	14742565	0	ver/dev	Expression of dps in E. coli has been shown to be regulated by the stationary-phase sigma factor RpoS .	15	Expression of dps in E. coli has been shown to be regulated by the stationary-phase sigma factor RpoS ( 38 ) , OxyR , and IHF ( 3 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	dps	regulator	16597989	0	att	In E. coli , a decrease in RpoS-regulated transcripts was observed in a pnp mutant ( 8 ) , including the dps gene involved in acid resistance ( 12 ) .	294	In E. coli , a decrease in RpoS-regulated transcripts was observed in a pnp mutant ( 8 ) , including the dps gene involved in acid resistance ( 12 ) .	3	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dps	regulator	25028458	0	ver/dev	It has been reported that in Salmonella dps expression is controlled by RpoS .	10	It has been reported that in Salmonella dps expression is controlled by RpoS and Fur proteins .	0	Unknown	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	dps	regulator	25028458	1	ver/dev	Almiron et al. reported that expression of the dps gene is induced by the cessation of bacterial growth under S control of RpoS .	33	Almiron et al. ( 1992 ) reported that expression of the dps gene is induced by the cessation of bacterial growth under S control of RpoS , the s factor .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	dps	regulator	27246569	0	ver/dev	The dps gene is regulated by RpoS .	200	The dps gene is regulated by RpoS and encodes a nonspecific DNA-binding protein that acts to protect bacterial cells against oxidative stress ( 40 , 41 ) .	7	4	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	tufB	regulator	26934594	3	ver/dev	Rho-dependent transcriptional termination regulates tufB expression	163	Rho-dependent transcriptional termination regulates tufB expression	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	tufB	regulator	26934594	4	ver/dev	Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	168	Using this experimental system we tested two hypotheses : ( i ) that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; ( ii ) that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	regulator	26934594	4	ver/dev	Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	168	Using this experimental system we tested two hypotheses : ( i ) that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; ( ii ) that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	regulator	26934594	4	ver/dev	Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	168	Using this experimental system we tested two hypotheses : ( i ) that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; ( ii ) that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	regulator	26934594	4	ver/dev	Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	168	Using this experimental system we tested two hypotheses : ( i ) that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; ( ii ) that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	regulator	26934594	6	ver/dev	that Rho-dependent transcriptional termination is involved in the regulation of tufB gene expression	193	Taken together our results support the hypothesis that Rho-dependent transcriptional termination is involved in the regulation of tufB gene expression and that there might be factors , addi -	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	tufB	regulator	26934594	8	ver/dev	that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination	265	In this paper , we have shown that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination , modulated by the rate of translation elongation in the early part of the coding sequence , and that the mechanism depends on the nucleotide sequence in the early part of the tufB mRNA having the ability to form a closed secondary structure that hides the ribosome binding site .	13	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	12519186	27	att	C. Alignment of the RcsB-dependent regulatory sequences of S. enterica ( Se ) ugd , P. stewartii ( Ps ) cps , Erwinia amylovora ( Ea ) ams , E. coli ( Ec ) cps and E. coli ( Ec ) fts genes .	91	C. Alignment of the RcsB-dependent regulatory sequences of S. enterica ( Se ) ugd , P. stewartii ( Ps ) cps , Erwinia amylovora ( Ea ) ams , E. coli ( Ec ) cps and E. coli ( Ec ) fts genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	Salmonella;Salmonella;Erwinia amylovora;Escherichia coli;Escherichia coli	0.5	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes promoted by various signals -- RcsB systems .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	12519186	37	ver/dev	Role of the RcsB binding sites for activation of ugd transcription promoted by different signals .	110	Role of the PhoP , PmrA and RcsB binding sites for activation of ugd transcription promoted by different signals .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	12519186	41	ver/dev	Likewise , ugd transcription is co-ordinately induced with that of the cps genes by RcsB system , possibly because of its role in col-anic acid capsule synthesis .	125	Likewise , ugd transcription is co-ordinately induced with that of the cps genes by the RcsC -- YojN -- RcsB system and the RcsA protein ( Fig. 3 ) , possibly because of its role in col-anic acid capsule synthesis .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	ugd	activator	12519186	42	ver/dev	Transcriptional activation of the ugd gene by the RcsC -- YojN -- RcsB system	130	Transcriptional activation of the ugd gene by the RcsC -- YojN -- RcsB system and RcsA protein	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	12519186	43	ver/dev	We have established that the tolB-promoted expression of the ugd gene occurs by activation of the RcsB proteins	131	We have established that the tolB-promoted expression of the ugd gene occurs by activation of the RcsB and RcsA proteins and is independent of the PhoP -- PhoQ and	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	ugd	activator	12519186	49	ver/dev	The rcsA dependence of the tolB-promoted activation of ugd places this RcsB-regulated gene in the first group .	137	The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	ugd	activator	18792679	12	ver/dev	The Salmonella ugd promoter harbors RcsB .70 The PmrA protein stimulates ugd transcription in strains .	182	The Salmonella ugd promoter harbors binding sites for three different response regulators : Phol ' , PmrA and RcsB .70 The PmrA protein stimulates ugd transcription in strains deleted for both the phoPand rcsB genes from one promoter .	9	PHOP AS A CO-ACTIVATOR PROTEIN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	25028458	20	att	( b ) Alignment of the RcsB-dependent regulatory sequences of dps S. enterica ( Se ) , ugd S. enterica ( Se ) and fts E. coli ( Ec ) genes .	175	( b ) Alignment of the RcsB-dependent regulatory sequences of dps S. enterica ( Se ) , ugd S. enterica ( Se ) and fts E. coli ( Ec ) genes .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	Salmonella;Salmonella;Salmonella;Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	activator	27206164	8	ver/dev	The ugd gene are positively regulated under RcsB activating conditions .	63	The ugd gene encoding UDP-glucose dehydrogenase , which enables colonic acid and lipopoly-saccharide ( LPS ) 4-aminoarabinose production , and the capsule synthesis operon cps are positively regulated under RcsB activating conditions ( Mouslim et al. , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	ugd	activator	30763640	17	att	B ) The putative RcsB binding site on STM1485 was identified by alignment of the conserved RcsB box identified in other RcsB-dependent genes : ugd S. enterica ( Se ) and ams E. amylovora ( Ea ) genes .	146	B ) The putative RcsB binding site on STM1485 was identified by alignment of the conserved RcsB box identified in other RcsB-dependent genes : ugd S. enterica ( Se ) and ams E. amylovora ( Ea ) genes .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	STM1697	regulator	25437188	45	ver/dev	Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .	552	STM1344 ( YdiV ) and Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis [ 168,174 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	STM1697	regulator	25437188	45	ver/dev	Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .	552	STM1344 ( YdiV ) and Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis [ 168,174 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	STM1697	regulator	25437188	49	ver/dev	Besides positive regulation of FlhDC , CsrA indirectly inhibits the expression of several GGDEF and/or EAL domain proteins STM1697 .	559	Besides positive regulation of FlhDC , CsrA directly or indirectly inhibits the expression of several GGDEF and/or EAL domain proteins involved in motility repression including the DGCs STM4551 and STM1987 and the degenerated EAL proteins STM1344 and STM1697 .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	NEG	New	Level 1
FlhDC	gene	STM1697	regulator	25437188	49	ver/dev	Besides positive regulation of FlhDC , CsrA directly inhibits the expression of several GGDEF and/or EAL domain proteins STM1697 .	559	Besides positive regulation of FlhDC , CsrA directly or indirectly inhibits the expression of several GGDEF and/or EAL domain proteins involved in motility repression including the DGCs STM4551 and STM1987 and the degenerated EAL proteins STM1344 and STM1697 .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	STM1697	regulator	28973452	57	ver/dev	These data support our hypothesis that the binding of STM1697 to the periphery of the FlhDC complex prevents RNA polymerase from binding to the promoter .	248	These data support our hypothesis that the binding of anti-factors ( YdiV or STM1697 ) to the periphery of the FlhDC complex prevents RNA polymerase from binding to the promoter .	26	THE BINDING OF STM1697 TO FLHD4C2 RESTRAINS RNA POLY- MERASE RECRUITMENT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	sopE2	repressor	33563986	9	ver/dev	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence-factors .	346	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , as well as SPI-2 genes when STM is inside macrophages65 , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence factors .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	avrA	repressor	19042154	10	ver/dev	CsrA in turn affects an inhibition of the AvrA protein production of chromo-somal-encoded avrA	257	We suggest that csrB mutations enable an overproduction of CsrA which in turn affects an inhibition of the AvrA protein production of chromo-somal-encoded avrA , but not of plasmidal-encoded avrA due to an increased avrA-mRNA copy number in such strains ( Table 3 ; see also Altier et al. , 2000a , b ; Lawhon et al. , 2003 ) .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	invJ	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	kbl	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	rpoS	repressor	25566242	4	ver/dev	Later , LeuO was determined to reduce rpoS translation ( which encodes S sigma factor ) by repression of the small regulatory DsrA-RNA .	67	Later , LeuO was determined to reduce rpoS translation ( which encodes S sigma factor ) by repression of the small regulatory DsrA-RNA , who positively regulates rpoS translation , mainly at low temperature ( 54 ) .	4	LEUO HISTORY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	osmC	regulator	19389776	1	ver/dev	Interplay between global regulators of Escherichia coli : effect of Lrp on the transcription of the gene osmC .	493	Interplay between global regulators of Escherichia coli : effect of RpoS , Lrp and H-NS on the transcription of the gene osmC .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	osmC	regulator	19843227	46	ver/dev	Gutierrez , C. Interplay between global regulators of Escherichia coli : effect of Lrp on transcription of the gene osmC .	469	Bouvier , J. , Gordia , S. , Kampmann , G. , Lange , R. , Hengge-Aronis , R. , and Gutierrez , C. ( 1998 ) Interplay between global regulators of Escherichia coli : effect of RpoS , Lrp and H-NS on transcription of the gene osmC .	32	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	sipB	repressor	17178790	15	ver/dev	In contrast , RcsB under low-osmolarity conditions , acting in association with the viaB locus-encoded TviA protein , negatively controls the transcription of sipB .	345	In contrast , RcsB under low-osmolarity conditions , acting in association with the viaB locus-encoded TviA protein , negatively controls the transcription of iagA , invF , and sipB ( encoding proteins involved in cell invasion ) ( 1 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AcrR	gene	acrB	repressor	28380031	0	ver/dev	the local repressor AcrR inhibits the transcription of acrB	340	AcrAB is also regulated by the local repressor AcrR , which inhibits the transcription of acrA and acrB , and the mutation of acrR contributes to the overexpression of AcrAB and increases bacterial resistance to multiple drugs [ 21 , 22 ] .	27	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HdfR	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the master biofilm regulator CsgD on fliF operons ; .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HdfR	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the master biofilm regulator CsgD on fliE ; .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HdfR	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the master biofilm regulator CsgD on fliA ; .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HdfR	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of motor-binding protein YcgR on motor rotation and switching .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HdfR	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the second messenger c-di-GMP on motor rotation and switching .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	dam	regulator	21984608	0	ver/dev	It is interesting to note that several regulators of InvF , were found in significantly lower levels in the dam mutant .	135	It is interesting to note that several regulators of T3SS1 , such as HilA , HilC , HilD , and InvF , were found in significantly lower levels in the dam mutant .	5	TRANSCRIPTIONAL AND TRANSLATIONAL REGULATION DURING INVASION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
InvF	gene	dam	regulator	24947562	0	ver/dev	However , it is important to mention that sopB , is cooperatively regulated by InvF dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control .	232	However , it is important to mention that sopB , is cooperatively regulated by InvF and HilA [ 30 ] and lowered levels of all SPI-1-encoded transcriptional regulators ( HilA , HilC , HilD , and InvF ) were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control [ 24 ] .	19	4. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LexA	gene	yebG	activator	33921732	7	att	When we analyzed yebG : : GFP expression by flow cytometry , the ON subpopulation was higher in ST4/74 ON , thus strengthening the unsuspected observation that genes with LexA-dependent bistability produce larger ON subpopulations in the absence of DNA damage if the LexA box has a low HI ( Figure 6B ) .	316	When we analyzed yebG : : GFP expression by flow cytometry , the ON subpopulation was higher in ST4/74 ON , thus strengthening the unsuspected observation that genes with LexA-dependent bistability produce larger ON subpopulations in the absence of DNA damage if the LexA box has a low HI ( Figure 6B ) .	15	3.4. INFLUENCE OF THE DISTANCE AND THE NUCLEOTIDE SEQUENCE OF THE LEXA BOX ON THE EXPRESSION PATTERNS OF SOS GENES	Salmonella enterica subsp. enterica serovar Typhimurium ST4/74	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	cas2	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas2 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
SsrB	gene	ugtL	regulator	27601571	48	ver/dev	Strikingly , ugtL , is also regulated by SsrB , .	425	Strikingly , ugtL , a target of SprB , is also regulated by SsrB , the master regulator of SPI-1 ( 74 ) , reinforcing the idea of a role of this gene in cross talk between the two T3SSs .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	regulator	33045730	6	ver/dev	Non-pathogenic S. bongori fails to activate PhoQ in mildly acidic pH because it lacks both the ssrB gene and the SsrB binding site in the ugtL promoter .	44	Non-pathogenic S. bongori fails to activate PhoQ in mildly acidic pH because it lacks both the ssrB gene and the SsrB binding site in the ugtL promoter .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	aldB	activator	15256548	26	att	aldB , an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp .	865	aldB , an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp .	18	MCCLELLAND, M. & ALTIER, C. (2003). GLOBAL REGULATION BY CSRA IN OBERTO, J., DRLICA, K. & ROUVIÈRE-YANIV, J. (1994). HISTONES, HMG, SALMONELLA TYPHIMURIUM. MOL MICROBIOL 48, 1633–1645. HU, IHF: MÊME COMBAT. BIOCHIMIE 76, 901–908.	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	aldB	activator	16777370	39	att	aldB , and RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp .	330	aldB , and RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp .	35	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoB	activator	18790861	43	att	Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels which are simply accomplished by iron .	230	Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels which are simply accomplished by iron .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	feoB	activator	18790861	54	att	We propose that the RstA-induced feoB expression allows Salmonella cells to take up more Fe ( II ) , thereby promoting Fur activity [ as evidenced by Fur-Fe ( II ) levels ] based on the following .	269	We propose that the RstA-induced feoB expression allows Salmonella cells to take up more Fe ( II ) , thereby promoting Fur activity [ as evidenced by Fur-Fe ( II ) levels ] based on the following .	5	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	feoB	activator	18790861	55	att	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoB	activator	18790861	38	ver/dev	Activation of feoB transcription by the RstA protein is necessary for repression of iron-responsive genes .	215	Activation of feoB transcription by the RstA protein is necessary for repression of iron-responsive genes .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoB	activator	18790861	43	ver/dev	Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels .	230	Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels which are simply accomplished by iron .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	feoB	activator	18790861	56	ver/dev	This emphasizes that , in the presence of iron , the feoB gene should be induced by the RstA protein to repress iron-responsive genes .	274	This emphasizes that , in the presence of iron , the feoB gene should be induced by the RstA protein to repress iron-responsive genes and differs from the finding that iron chelator inactivated the Fur protein to abolish the regulatory effect of RstA on its regulated genes ( Fig. 1B ) .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FliZ	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
FliZ	gene	hilA	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
SoxR	TU	acrAB	regulator	26446080	0	ver/dev	Mutations in AcrR have been shown to impair its repressive effect , hence leading to derepression of the acrAB genes .16 -- 18 the activator SoxR are regulators of transcriptional factors MarA , RamA and SoxS , respectively .	257	Mutations in AcrR have been shown to impair its repressive effect , hence leading to derepression of the acrAB genes .16 -- 18 The repressors MarR and RamR and the activator SoxR are regulators of transcriptional factors MarA , RamA and SoxS , respectively .	22	EFFLUX AND PERMEABILITY ARE ALTERED IN TY_C2	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MetR	gene	metH	activator	19447191	20	att	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	200	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MetR	gene	metH	activator	19447191	20	ver/dev	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metH : orientation requirements within RNA polymerase .	200	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MetR	gene	metH	activator	19447191	20	ver/dev	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metH : important residues in the C-terminal domain .	200	Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH : important residues in the C-terminal domain and orientation requirements within RNA polymerase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MetR	gene	metH	activator	21768276	2	ver/dev	The MetR protein acts as an activator for the transcription of metH .	727	The MetR protein acts as an activator for the transcription of metE , metA , metF , and metH ( 93 ) .	8	TRANSCRIPTION STM3773 PUTATIVE TRANSCRIPTIONAL REGULATOR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	topA	repressor	21276095	4	ver/dev	Transcription of E. coli topA is driven by the interplay of at least four transcription start sites , allowing FIS to be both a repressor of E. coli topA expression .	42	Transcription of E. coli topA is driven by the interplay of at least four transcription start sites , allowing FIS to be both an activator and a repressor of E. coli topA expression ( WeinsteinFischer and Altuvia , 2007 ) .	3	INTRODUCTION	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	topA	repressor	21276095	14	ver/dev	Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare 4A -RRB- .	219	Although topA promoter function has routinely been studied using plasmid-based systems ( Tse-Dinh , 1985 ; Tse-Dinh and Beran , 1988 ; Lesley et al. , 1990 ; Marshall et al. , 2000 ; Weinstein-Fischer and Altuvia , 2007 ) , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS ( compare Figs 3A and 4A ) .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	unidentified plasmid;Escherichia coli;unidentified plasmid	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	topA	repressor	21276095	14	ver/dev	Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare Figs 3A -RRB- .	219	Although topA promoter function has routinely been studied using plasmid-based systems ( Tse-Dinh , 1985 ; Tse-Dinh and Beran , 1988 ; Lesley et al. , 1990 ; Marshall et al. , 2000 ; Weinstein-Fischer and Altuvia , 2007 ) , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS ( compare Figs 3A and 4A ) .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	unidentified plasmid;Escherichia coli;unidentified plasmid	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , d t occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in + background on , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhC	gene	cheA	repressor	30252837	4	ver/dev	Quantitative RT-PCR in FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , , ch occurred in n an Flh , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	208	Quantitative RT-PCR in FlhC and FlhC backgrounds revealed that StdEF-mediated + − repression of cheA , cheM , cheB , and trg occurred in an FlhDC + background only ( Fig 4 , panel E ) , suggesting that downregulation of chemotaxis genes by StdEF is mediated by repression of the flagellar master operon flhDC .	10	CHIP-SEQ ANALYSIS OF STDE AND STDF DNA BINDING ABILITY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	pefB	regulator	31661351	19	ver/dev	After binding of H-NS , the high AT richness of these regions , especially the one upstream of pefB , will then favor the oligomerization of H-NS along this DNA segment .	347	After binding of H-NS , the high AT richness of these regions , especially the one upstream of pefB , will then favor the oligomerization of H-NS along this DNA segment .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugd	regulator	12519186	5	att	On the one hand , ugd expression is promoted in low Mg2 + in a process that requires the Mg2 + - responsive PhoP -- PhoQ two-component system , the PhoP-regulated shunt protein PmrD and the PmrA -- PmrB two-component system ( Kox et al. , 2000 ) .	26	On the one hand , ugd expression is promoted in low Mg2 + in a process that requires the Mg2 + - responsive PhoP -- PhoQ two-component system , the PhoP-regulated shunt protein PmrD and the PmrA -- PmrB two-component system ( Kox et al. , 2000 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugd	regulator	12519186	53	att	The PhoP -- PhoQ -- PmrA -- PmrB pathway of ugd activation in macrophages may be the same as that taking 2 + place in low Mg , where the PhoP -- PhoQ system activates the PmrA -- PmrB system via the PhoP-regulated protein PmrD ( Fig. 1 ; Kox et al. , 2000 ) .	145	The PhoP -- PhoQ -- PmrA -- PmrB pathway of ugd activation in macrophages may be the same as that taking 2 + place in low Mg , where the PhoP -- PhoQ system activates the PmrA -- PmrB system via the PhoP-regulated protein PmrD ( Fig. 1 ; Kox et al. , 2000 ) .	7	THE HOST SIGNALS CONTROLLING UGD EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugd	regulator	12519186	17	ver/dev	Boxed region indicates what was previously known about the regulation of ugd transcription by the PhoP -- PmrA -- PmrB systems before the studies .	55	Boxed region indicates what was previously known about the regulation of ugd transcription by the PhoP -- PhoQ and PmrA -- PmrB systems before the studies described in this paper .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	ugd	regulator	12519186	17	ver/dev	Boxed region indicates what was previously known about the regulation of ugd transcription by the PhoP -- PhoQ -- PmrB systems before the studies .	55	Boxed region indicates what was previously known about the regulation of ugd transcription by the PhoP -- PhoQ and PmrA -- PmrB systems before the studies described in this paper .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	ugd	regulator	15703297	12	att	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugd	regulator	15703297	21	att	For example , the ugd promoter of Salmonella ( Fig. 1B ) , but not of Escherichia coli , harbors a PhoP box that is located much further upstream from an RNA polymerase binding site than in other PhoP-regulated promoters ( Table 3 ) .	166	For example , the ugd promoter of Salmonella ( Fig. 1B ) , but not of Escherichia coli , harbors a PhoP box that is located much further upstream from an RNA polymerase binding site than in other PhoP-regulated promoters ( Table 3 ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli	0.5	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	regulator	15703297	22	ver/dev	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
AraC	gene	araB	regulator	24272778	14	att	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	201	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
AraC	gene	araB	regulator	24272778	6	att	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	88	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	2	MAIN	Escherichia coli;Iris germanica;Escherichia coli;Iris germanica;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
FliZ	gene	hilD	activator	30755273	0	ver/dev	FliZ upregulates the transcription factor hilD .	77	FliZ controls both flagellar hook assembly and upregulates the transcription factor hilD [ 39 -- 41 ] .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	ppa	regulator	24272778	15	ver/dev	We did not detect significant regulation of ppa by AraC in the transcription profiling experiment ; however , ytfQ encodes a transporter .	204	We did not detect significant regulation of ytfQ or ppa by AraC or arabinose in the transcription profiling experiment ; however , ytfQ encodes a transporter that binds arabinose and galactose ( 39 ) , consistent with ytfQ being a regulatory target of AraC .	4	RESULTS	nan	1	L2	OTHER	Other	NEG	New	Level 1
AraC	gene	ppa	regulator	24272778	19	ver/dev	The ChIP-chip analysis identified binding of AraC upthe genes are not associated stream of ppa ( divergently transcribed genes ) .	231	The ChIP-chip analysis identified binding of AraC upthe genes regulated by AraC/arabinose ( Table 2 ) are not associated stream of ytfQ and ppa ( divergently transcribed genes ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	ssaU	activator	23690578	8	att	Thus , we investigated expression of the SsrB-activated ssaG gene , which is the first gene of a large operon ( from ssaG to ssaU ) and encodes a component of the Spi/Ssa T3SS ( 22 ) .	51	Thus , we investigated expression of the SsrB-activated ssaG gene , which is the first gene of a large operon ( from ssaG to ssaU ) and encodes a component of the Spi/Ssa T3SS ( 22 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
TviA	gene	fliC	activator	24992093	5	att	To determine whether reduced motility or diminished flagellin production could account for the TviA-dependent reduction in NF-kB activation , we inactivated the fliC gene encoding the sole flagellin of the monophasic serovar Typhi , thereby rendering strains carrying these mutations aflagellate and non-motile .	126	To determine whether reduced motility or diminished flagellin production could account for the TviA-dependent reduction in NF-kB activation , we inactivated the fliC gene encoding the sole flagellin of the monophasic serovar Typhi , thereby rendering strains carrying these mutations aflagellate and non-motile .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	yibD	regulator	12438352	0	att	PmrA-regulated loci identified included dgoA and yibD and demonstrated 500 - and 2,500-fold activation by PmrA , respectively .	13	PmrA-regulated loci identified included dgoA and yibD and demonstrated 500 - and 2,500-fold activation by PmrA , respectively .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	yibD	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	yibD	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	yibD	regulator	12438352	10	att	PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .	183	PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal medium supplemented with 100 M FeSO4 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	yibD	regulator	12438352	12	att	For further characterization of the PmrA-regulated gene mutants , the promoter regions of yibD and dgoA were analyzed for the presence of a putative PmrA-binding site , which was defined by the occurrence of the consensus binding sequence for PmrA , YTTAAK-N5-YTTAAK ( 1 ) .	190	For further characterization of the PmrA-regulated gene mutants , the promoter regions of yibD and dgoA were analyzed for the presence of a putative PmrA-binding site , which was defined by the occurrence of the consensus binding sequence for PmrA , YTTAAK-N5-YTTAAK ( 1 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	yibD	regulator	12438352	18	att	JSG897 and JSG899 , with mutations in PmrA-regulated genes yibD and dgoA , respectively , also still possessed Ara4N modification of lipid-A in similar amounts to the parental PmrAc strain .	257	JSG897 and JSG899 , with mutations in PmrA-regulated genes yibD and dgoA , respectively , also still possessed Ara4N modification of lipid A in similar amounts to the parental PmrAc strain .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	yibD	regulator	12438352	19	att	PmrA-regulated gene mutants JSG1525 ( yibD ) and JSG1526 ( dgoA ) were as virulent as wild-type Salmonella serovar Typhimurium , so the genes interrupted have no essential role in the infection process ( Table 4 ) .	264	PmrA-regulated gene mutants JSG1525 ( yibD ) and JSG1526 ( dgoA ) were as virulent as wild-type Salmonella serovar Typhimurium , so the genes interrupted have no essential role in the infection process ( Table 4 ) .	4	RESULTS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	yibD	regulator	12438352	2	att	All PMs mutants identified in this study demonstrated a defect in virulence compared to wild-type Salmonella serovar Typhimurium when administered orally to mice , while the PmrA-regulated gene ( yibD and dgoA ) mutants showed normal virulence in mice .	17	All PMs mutants identified in this study demonstrated a defect in virulence compared to wild-type Salmonella serovar Typhimurium when administered orally to mice , while the PmrA-regulated gene ( yibD and dgoA ) mutants showed normal virulence in mice .	1	ABSTRACT	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Mus sp.	0.5	L3	OTHER	Investigation	OTHER	Other	Level 2
PmrA	gene	yibD	regulator	12438352	23	att	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	331	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	5	DISCUSSION	nan	1	L1	SPEC	Fact	NEG	Other	Level 1
PmrA	gene	yibD	regulator	12438352	9	att	The PmrA-regulated gene mutants JSG897 ( yibD ) and JSG899 ( dgoA ) were also analyzed for sensitivity to PM by MIC assay .	179	The PmrA-regulated gene mutants JSG897 ( yibD ) and JSG899 ( dgoA ) were also analyzed for sensitivity to PM by MIC assay .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	yibD	regulator	12438352	24	ver/dev	A strong match to the consensus PmrA-binding site was identified upstream of yibD , indicating direct regulation by PmrA .	332	A strong match to the consensus PmrA-binding site was identified upstream of yibD , indicating direct regulation by PmrA .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	yibD	regulator	15681155	17	att	To determine whether PmrA can bind directly to promoter fragments of PmrA-regulated loci that lack the published PmrA consensus binding site , gel mobility-shift assays were performed to compare the ability of purified PmrA to bind the promoters of yibD and dgoR-KAT [ 34 ] .	264	To determine whether PmrA can bind directly to promoter fragments of PmrA-regulated loci that lack the published PmrA consensus binding site , gel mobility shift assays were performed to compare the ability of purified PmrA to bind the promoters of yibD and dgoR-KAT [ 34 ] .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	yibD	regulator	15681155	21	ver/dev	PmrA was able to bind the yibD promoter .	291	PmrA was able to bind the yibD promoter , which contains the consensus site ( lane 1 , yibDp alone ; lane 2 , yibDp plus 300 ng PmrA ) .	13	3.4. SURVIVAL OF MUTANTS IN THE MURINE MODEL	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	yibD	regulator	20227482	0	att	In S. Typhimurium , the QseBC ( PreAB ) two-component system was initially described by Merighi et al. as modulating a subset of PmrA-regulated genes including pmrCAB and yibD [ 12 ] .	37	In S. Typhimurium , the QseBC ( PreAB ) two-component system was initially described by Merighi et al. as modulating a subset of PmrA-regulated genes including pmrCAB and yibD [ 12 ] .	6	1. INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	lrp	repressor	21398529	4	ver/dev	the double hns/lrp mutant showed 5,002 activity units , hence demonstrating the role of both H-NS in the repression of casA	253	The pKK-375 fusion in the wild-type strain showed a value of 34 activity units ; in the single H-NS mutant , an activity of 1,907 activity units was observed ; in the lrp single mutant , a value of 78 activity units was detected ; and the double hns/lrp mutant showed 5,002 activity units , hence demonstrating the role of both LRP and H-NS in the repression of casA ( see Fig. 4 for standard deviation values ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	lrp	repressor	21398529	6	ver/dev	In the wild type and the hns , lrp , and the activity values for the pKK-51 / 49 fusion ( which contains the promoter region without cis-acting negative elements ) were around 14,000 to 15,000 , supporting the conclusion that H-NS are the main repressors of casA expression .	292	In the wild type and the hns , lrp , and double hns/lrp mutants , the activity values for the pKK-51 / 49 fusion ( which contains the promoter region without cis-acting negative elements ) were around 14,000 to 15,000 ( Fig. 6 ) , supporting the conclusion that H-NS and LRP are the main repressors of casA expression .	4	RESULTS	Terfezia albida	0	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	gene	lrp	repressor	21398529	6	ver/dev	In the wild type and the hns , lrp , and double hns/lrp mutants / 49 fusion ( which contains the promoter region without cis-acting negative elements ) were around 14,000 to 15,000 , supporting the conclusion that H-NS are the main repressors of casA expression .	292	In the wild type and the hns , lrp , and double hns/lrp mutants , the activity values for the pKK-51 / 49 fusion ( which contains the promoter region without cis-acting negative elements ) were around 14,000 to 15,000 ( Fig. 6 ) , supporting the conclusion that H-NS and LRP are the main repressors of casA expression .	4	RESULTS	Terfezia albida	0	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	gene	lrp	repressor	32284321	5	ver/dev	lrp mutant strains _ supporting the notion that ltrR1 is repressed by both H-NS at its coding region	148	However , the transcriptional expression of pKK8/ltrR1 -35 616 , pKK8/ltrR1 -35 678 , pKK8/ltrR1 -35 836 , and pKK8/ltrR1 -35 887 increased to 432 , 264 , 529 , and 432 CAT units in the hns lrp double mutant compared with the values observed for the wild type ( 167 , 105 , 27 , and 35 CAT units , respectively ) or for the individual hns ( 199 , 107 , 224 , and 272 CAT units , respectively ) and lrp ( 219 , 51 , 40 , and 21 CAT units , respectively ) mutant strains ( Fig. 4B ) , supporting the notion that ltrR1 is repressed by both H-NS and Lrp at its coding region .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	lrp	repressor	32284321	5	ver/dev	lrp mutant strains _ supporting the notion that ltrR1 is repressed by both H-NS at its coding region	148	However , the transcriptional expression of pKK8/ltrR1 -35 616 , pKK8/ltrR1 -35 678 , pKK8/ltrR1 -35 836 , and pKK8/ltrR1 -35 887 increased to 432 , 264 , 529 , and 432 CAT units in the hns lrp double mutant compared with the values observed for the wild type ( 167 , 105 , 27 , and 35 CAT units , respectively ) or for the individual hns ( 199 , 107 , 224 , and 272 CAT units , respectively ) and lrp ( 219 , 51 , 40 , and 21 CAT units , respectively ) mutant strains ( Fig. 4B ) , supporting the notion that ltrR1 is repressed by both H-NS and Lrp at its coding region .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	lrp	repressor	32284321	5	ver/dev	lrp mutant strains _ supporting the notion that ltrR1 is repressed by both H-NS at its coding region	148	However , the transcriptional expression of pKK8/ltrR1 -35 616 , pKK8/ltrR1 -35 678 , pKK8/ltrR1 -35 836 , and pKK8/ltrR1 -35 887 increased to 432 , 264 , 529 , and 432 CAT units in the hns lrp double mutant compared with the values observed for the wild type ( 167 , 105 , 27 , and 35 CAT units , respectively ) or for the individual hns ( 199 , 107 , 224 , and 272 CAT units , respectively ) and lrp ( 219 , 51 , 40 , and 21 CAT units , respectively ) mutant strains ( Fig. 4B ) , supporting the notion that ltrR1 is repressed by both H-NS and Lrp at its coding region .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CspE	gene	cspD	activator	24056458	0	ver/dev	this effect was reflected by induction of cspD and proteins ( CspE ) in response to preadaptation to cold-stress	146	Cold stress genes and proteins regulate membrane fluidity and resume protein synthesis ( 18 ) , and this effect was reflected by induction of cold stress genes ( cspB and cspD ) and proteins ( CspA , CspE , and CspC ) in response to preadaptation to cold stress .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	rpoD	regulator	17158330	6	ver/dev	The values of PhoP binding were obtained from normalization of ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein of the target promoter to that of the endogenous control rpoD promoter .	30	The values of PhoP binding were obtained from normalization of PhoP occupancy ( ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein ) of the target promoter to that of the endogenous control rpoD promoter .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rpoD	regulator	17158330	6	ver/dev	The values of PhoP binding were obtained from normalization of ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein of the target promoter to that of the endogenous control rpoD promoter .	30	The values of PhoP binding were obtained from normalization of PhoP occupancy ( ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein ) of the target promoter to that of the endogenous control rpoD promoter .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rpoD	regulator	17158330	10	ver/dev	The values of PhoP binding were obtained from normalization of ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein of the target promoter to that of the endogenous control rpoD promoter .	48	The values of PhoP binding were obtained from normalization of PhoP occupancy ( ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein ) of the target promoter to that of the endogenous control rpoD promoter .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rpoD	regulator	17158330	10	ver/dev	The values of PhoP binding were obtained from normalization of ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein of the target promoter to that of the endogenous control rpoD promoter .	48	The values of PhoP binding were obtained from normalization of PhoP occupancy ( ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein ) of the target promoter to that of the endogenous control rpoD promoter .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	rpoD	regulator	18270203	9	ver/dev	The rpoD promoter neither is regulated by the PhoP protein .	123	The rpoD promoter neither binds to nor is regulated by the PhoP protein .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJ	activator	18957594	3	ver/dev	To test whether environmental sulfur availability affected induction of the CysB regulon in swarm cells , cysJ expression was used to represent CysB regulon activity , as the cells swim media with sulfur sources added .	245	To test whether environmental sulfur availability affected induction of the CysB regulon in swarm cells , cysJ expression was used to represent CysB regulon activity , as the cells were grown in NBG swarm and swim media with sulfur sources added .	7	CYSTEINE AUXOTROPHS HAVE ALTERED SWARM COLONY MORPHOLOGY	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CysB	gene	cysJ	activator	18957594	3	ver/dev	To test whether environmental sulfur availability affected induction of the CysB regulon in swarm cells , cysJ expression was used to represent CysB regulon activity , as the cells were grown in NBG swarm .	245	To test whether environmental sulfur availability affected induction of the CysB regulon in swarm cells , cysJ expression was used to represent CysB regulon activity , as the cells were grown in NBG swarm and swim media with sulfur sources added .	7	CYSTEINE AUXOTROPHS HAVE ALTERED SWARM COLONY MORPHOLOGY	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
FimZ	TU	flhDC	repressor	27777572	3	ver/dev	Furthermore , the type-1 fimbrial regulator FimZ can control Salmonella motility by inactivating the flhDC flagellar operon .	392	Furthermore , the type-1 fimbrial regulator FimZ can control Salmonella motility by inactivating the flhDC flagellar operon ( Clegg and Hughes , 2002 ) .	21	MENAQUINONE REVERSES THE EFFECT OF YQIC DELETION ON EXPRESSION OF TYPE-1	Salmonella	1	L2	OTHER	Other	OTHER	New	Level 1
FimZ	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliT , FimZ .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	repressor	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	18270203	2	ver/dev	In vivo , H-NS remained bound to the ugtL promoters under inducing conditions that promoted RNA polymerase recruitment and transcription of the ugtL genes .	14	In vivo , H-NS remained bound to the ugtL and pagC promoters under inducing conditions that promoted RNA polymerase recruitment and transcription of the ugtL and pagC genes .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ugtL	regulator	18270203	3	ver/dev	SlyA-dependent ugtL are normally bound by the H-NS protein	37	Thus , to understand this process , we investigated the expression of the PhoP - and SlyA-dependent ugtL and pagC genes , which are normally bound by the H-NS protein ( 4 , 5 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	18270203	6	ver/dev	Model _ depicting transcriptional control of ugtL genes by the regulatory proteins H-NS	59	Model depicting transcriptional control of the horizontally acquired pagC and ugtL genes by the regulatory proteins H-NS , PhoP , and SlyA .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ugtL	regulator	18270203	56	ver/dev	the pagC promoter els for the ugtL mRNAs are probably due to the less are bound by the H-NS proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HNS	gene	ugtL	regulator	18270203	74	ver/dev	The apparent simultaneous occupancy of ugtL promoter regions by the H-NS , SlyA , and PhoP proteins and even RNA polymerase is not unprecedented , since many regions of the E. coli genome can also associate with binding of H-NS to various promoters is not mutually exclusive , at least in-vitro ( Fig .	304	The apparent simultaneous occupancy of the pagC and ugtL promoter regions by the H-NS , SlyA , and PhoP proteins and even RNA polymerase is not unprecedented , since many regions of the E. coli genome bound by H-NS can also associate with RNA polymerase ( 6 , 39 ) , and binding of H-NS and of SlyA to various promoters is not mutually exclusive , at least in vitro ( 40 , 41 ) ( Fig .	4	DISCUSSION	Escherichia coli	0	L2	OTHER	Other	NEG	Other	Level 1
HNS	gene	ugtL	regulator	33045730	48	ver/dev	The xenogeneic silencer H-NS binds to AT-rich horizontally acquired ugtL .	246	The xenogeneic silencer H-NS binds to AT-rich horizontally acquired DNA , preventing expression of the corresponding genes ( 50,51 ) , including ugtL and sifB .	27	SSRB ANTAGONIZES THE GENE SILENCER H-NS IN THE UGTL PRO- MOTER REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ugtL	regulator	33045730	49	ver/dev	the ugtL-sifB intergenic region is bound by H-NS	247	Given that SsrB overcomes the silencing effects of H-NS at certain horizontally acquired genes ( 52 ) , we wondered whether SsrB promotes ugtL transcription by binding to the SsrB binding site in the ugtL-sifB intergenic region that is bound by H-NS .	27	SSRB ANTAGONIZES THE GENE SILENCER H-NS IN THE UGTL PRO- MOTER REGION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	33045730	60	ver/dev	In vivo binding of H-NS to the promoter regions of gtA genes were determined in ns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	274	( F ) In vivo binding of H-NS to the promoter regions of the sifB , ugtL , STM14 3310 and mgtA genes were determined in hns-FLAG ( JC805 ) and hns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	Iris germanica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	33045730	60	ver/dev	In vivo binding of H-NS to the promoter regions of TM14 3310 were determined in ns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	274	( F ) In vivo binding of H-NS to the promoter regions of the sifB , ugtL , STM14 3310 and mgtA genes were determined in hns-FLAG ( JC805 ) and hns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	Iris germanica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	33045730	60	ver/dev	In vivo binding of H-NS to the promoter regions of gtL were determined in ns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	274	( F ) In vivo binding of H-NS to the promoter regions of the sifB , ugtL , STM14 3310 and mgtA genes were determined in hns-FLAG ( JC805 ) and hns-FLAG ugtL-sifBmu ( JC1625 ) S. Typhimurium strains grown to mid-log phase in N-minimal media with 1 mM of Mg2 + at pH 4.9 using chromatin immunoprecipitation .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	Iris germanica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	33201432	5	ver/dev	Among these genes , ugtL are bound by H-NS proteins in Salmonella .	185	Among these genes , pagC and ugtL are bound by H-NS proteins in Salmonella .	7	POST-TRANSLATIONAL MODIFICATION OF H-NS GENE-SILENCING FACTOR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ugtL	regulator	34202800	30	ver/dev	In Salmonella , ugtL are bound by H-NS proteins .	472	In Salmonella , pagC and ugtL are bound by H-NS proteins .	15	3.6. THE HISTONE-LIKE PROTEIN FAMILY (H-NS)	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	dsbA	regulator	23504014	13	att	A very recent report has shown that DsbA acts as a periplasmic oxidant and that deletion of dsbA leads to increased transcription of PhoP-regulated genes in E. coli .	254	A very recent report has shown that DsbA acts as a periplasmic oxidant and that deletion of dsbA leads to increased transcription of PhoP-regulated genes in E. coli .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	leuABCD	repressor	17908208	6	ver/dev	also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region	44	Furthermore , expression of LeuO has been found to affect the expression of several genes influenced by mutations in hns : LeuO relieved silencing of the bgl operon , the operon involved in the utilization of certain b-glucosides ( Ueguchi et al. , 1998 ) ; suppressed the effect of an hns mutation on cadC , which codes for the activator of the acid-inducible lysine decarboxylase ( Shi and Bennet , 1995 ) ; and also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene and the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region ( Chen et al. , 2001 ; 2003 ) .	3	B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	uspB	activator	22275872	0	att	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	125	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	9	ADAPTATION OF S. ENTERICA TO LETHAL CONCENTRATIONS OF SODIUM DEOXYCHOLATE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopA	regulator	31428589	0	ver/dev	sopA are regulated cooperatively by InvF .	125	sopA , sopB , and sopE are regulated cooperatively by HilA and InvF ( Thijs et al. , 2007 ) .	3	THE ROLE OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	ssrA	activator	31838175	3	ver/dev	These observations suggested that SoxS induced the expression of SPI-2 genes through ssrA .	154	These observations suggested that SoxS induced the expression of SPI-2 genes through ssrA and ssrB .	17	3.1. RNA-SEQ DATA ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
AraC	TU	araBAD	regulator	21871930	1	ver/dev	Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter .	274	Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	TU	araBAD	regulator	24272778	54	ver/dev	Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter .	697	Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter .	42	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	TU	araBAD	regulator	28332591	0	ver/dev	the arabinose-inducible araBAD promoter _ regulated by the AraC protein	183	The resultant plasmid was designated as pJHL350 where the subcloned 1433-bp R ghost cassette was placed between upstream of the arabinose-inducible araBAD promoter regulated by the AraC protein and downstream of E gene .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rcsB	activator	30763640	60	att	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	NEG	Other	Level 1
FhlA	gene	hypO	activator	28373272	4	ver/dev	However , since operon is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO .	331	However , since the hydrogenase 2 ( hypO-hybABCDE ) operon is differentially expressed under conditions that favor fermentation ( 60 , 61 ) , we hypothesized that FhlA , a bEBP that is activated by the fermentation product formate ( 62 ) , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO and yghW ( Pinter-hypO-yghW ) and thereby modulates expression of the hydrogenase 2 operon ( Fig. 3B ) .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FhlA	gene	hypO	activator	28373272	4	ver/dev	However , since the hydrogenase 2 -LRB- hypO-hybABCDE -RRB- is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO .	331	However , since the hydrogenase 2 ( hypO-hybABCDE ) operon is differentially expressed under conditions that favor fermentation ( 60 , 61 ) , we hypothesized that FhlA , a bEBP that is activated by the fermentation product formate ( 62 ) , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO and yghW ( Pinter-hypO-yghW ) and thereby modulates expression of the hydrogenase 2 operon ( Fig. 3B ) .	4	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	hilC	regulator	17208038	11	ver/dev	The interpretation of these data was that OmpR controls hilC transcription .	98	The interpretation of these data was that OmpR controls hilC transcription , a logical conclusion [ 35 ] .	7	ENVZ/OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	hilC	regulator	23370732	2	ver/dev	Increased OmpR can be recruited to bind to hilC promoters , in a process .	154	Increased OmpR can be recruited to bind to hilC and hilD promoters ( PhilC and PhilD ) , in a process that stimulates hilC transcription but restrains hilD [ 9 ] .	8	REGULATORS OF THE EXPRESSION OF SPI-1 PROTEINS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
OmpR	gene	hilC	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilC , the main regulators of pathogenicity islands 2 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilC	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilC , the main regulators of pathogenicity islands 2 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilC	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilC , the main regulators of pathogenicity islands 1 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilC	regulator	33854491	17	ver/dev	OmpR regulates the expression of hilC , the main regulators of pathogenicity islands 1 of Salmonella Typhimurium	309	In this sense , OmpR regulates the expression of hilC , hilD , and ssrAB , the main regulators of pathogenicity islands 1 and 2 of Salmonella Typhimurium , and it also controls the expression of the viaB locus that encodes Vi polysaccharide biosynthesis genes in S. Typhi ( Pickard et al. , 1994 ; Lee et al. , 2000 ; Feng et al. , 2003 ; Cameron and Dorman , 2012 ) .	20	B	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	cspH	regulator	15235764	11	ver/dev	These results suggest that Fis from S. typhimurium influences the expression of cspH by binding to its promoter , although a direct interaction between the cspH promoter was not shown in this study .	161	These results suggest that Fis from S. typhimurium influences the expression of cspH by binding to its promoter , although a direct interaction between Fis and the cspH promoter was not shown in this study .	16	FIS AFFECTS THE EXPRESSION OF CSPH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
Fis	gene	cspH	regulator	15235764	11	ver/dev	These results suggest that Fis from S. typhimurium influences the expression of cspH by binding to its promoter , although a direct interaction between Fis was not shown in this study .	161	These results suggest that Fis from S. typhimurium influences the expression of cspH by binding to its promoter , although a direct interaction between Fis and the cspH promoter was not shown in this study .	16	FIS AFFECTS THE EXPRESSION OF CSPH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
Fis	gene	cspH	regulator	15235764	22	ver/dev	However , based on these results we could not conclude that Fis directly interacts with the cspH promoter , since this might also be due to the pleio-tropic effect of Fis , coordinating the expression of a large set of genes both by direct control at the level of transcription initiation .	191	However , based on these results we could not conclude that Fis directly interacts with the cspH promoter , since this might also be due to the pleio-tropic effect of Fis , coordinating the expression of a large set of genes both by direct control at the level of transcription initiation and by possible indirect effects ( Drlica and Rouviere-Yaniv 1987 ; Finkel and Johnson 1992 ; McLeod et al. 2002 ; Schmid 1990 ) .	17	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FliZ	gene	fliZ	regulator	18469103	4	ver/dev	To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid .	210	To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the wild type ( strain 14028 ) , an isogenic fliZ mutant , and the fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid ( 41 ) .	5	RESULTS	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
FliZ	gene	fliZ	regulator	18469103	4	ver/dev	To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in an isogenic fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid .	210	To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the wild type ( strain 14028 ) , an isogenic fliZ mutant , and the fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid ( 41 ) .	5	RESULTS	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
FliZ	gene	fliZ	regulator	18469103	4	ver/dev	To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the wild type constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid .	210	To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the wild type ( strain 14028 ) , an isogenic fliZ mutant , and the fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid ( 41 ) .	5	RESULTS	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	sseB	activator	20221735	0	ver/dev	Most of these genes were induced at a higher level in the RpoS - sseB .	167	Most of these genes were induced at a higher level in the RpoS - mutant background with a few exceptions , such as sptP , sscB , sseB , and mgtC .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	csgD	activator	14643403	4	ver/dev	OmpR binding to D1 is responsible for transcriptional activation of csgD since in-vivo transcription studies showed high activity for transcriptional-fusion constructs .	136	OmpR binding to D1 is responsible for transcriptional activation of csgD since in vivo transcription studies showed high activity for transcriptional fusion constructs containing only the D1 site in the wild type and almost no activity in the respective ompR deletion mutant ( our unpublished data ) [ 13 ] .	16	6.1. OMPR	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	csgD	activator	14643403	4	ver/dev	OmpR binding to D1 is responsible for transcriptional activation of csgD since in-vivo transcription studies showed high no activity in our unpublished data .	136	OmpR binding to D1 is responsible for transcriptional activation of csgD since in vivo transcription studies showed high activity for transcriptional fusion constructs containing only the D1 site in the wild type and almost no activity in the respective ompR deletion mutant ( our unpublished data ) [ 13 ] .	16	6.1. OMPR	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	csgD	activator	14643403	4	ver/dev	OmpR binding to D1 is responsible for transcriptional activation of csgD since in-vivo transcription studies showed high no activity in the respective ompR deletion mutant .	136	OmpR binding to D1 is responsible for transcriptional activation of csgD since in vivo transcription studies showed high activity for transcriptional fusion constructs containing only the D1 site in the wild type and almost no activity in the respective ompR deletion mutant ( our unpublished data ) [ 13 ] .	16	6.1. OMPR	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	csgD	activator	14643403	5	ver/dev	The precise mechanism of activation of the csgD promoter by OmpR remains to be elucidated .	137	The precise mechanism of activation of the csgD promoter by OmpR remains to be elucidated .	16	6.1. OMPR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	csgD	activator	30663891	1	ver/dev	csgD expression is controlled by the response regulator OmpR is also required for transcriptional activation of the csgD promoter	159	csgD expression is controlled by the alternative sigma factor rS and the response regulator OmpR is also required for transcriptional activation of the csgD promoter ( Ro $ mling et al. , 1998 )	8	4.1.1. SALMONELLA PROTECTIVE SURFACE STRUCTURES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	glyA	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	glyA	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	glyA	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser ' : nitrosation of modulation of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	glyA	activator	20829289	3	ver/dev	A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser ' : nitrosation of homocysteine of MetR binding to the glyA -- hmp intergenic region .	367	A novel mechanism for upregulation of the Escherichia coli K-12 hmp ( flavohaemoglobin ) gene by the ` NO releaser ' , S-nitrosoglutathione : nitrosation of homocysteine and modulation of MetR binding to the glyA -- hmp intergenic region .	61	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	hilA	activator	31262841	15	att	Given the effect on flagellar gene expression , we then hypothesized that PinT could also control hilA by affecting expression of the FlhDC-activated flagellar gene fliZ , encoding a major regulator of HilD protein activity ( 72 , 73 , 77 ) .	192	Given the effect on flagellar gene expression , we then hypothesized that PinT could also control hilA by affecting expression of the FlhDC-activated flagellar gene fliZ , encoding a major regulator of HilD protein activity ( 72 , 73 , 77 ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
FliA	gene	fliN	regulator	29061704	2	ver/dev	However , no significant differences were observed in fliN mRNA levels between isolates , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected .	48	However , no significant differences were observed in fliN and flgB mRNA levels between the two classes of isolates , suggesting that class 3 genes ( controlled by FliA sigma factor ) , but not class 2 genes , were affected .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
FliA	gene	fliN	regulator	29061704	2	ver/dev	However , no significant differences were observed in fliN mRNA levels between the two classes , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected .	48	However , no significant differences were observed in fliN and flgB mRNA levels between the two classes of isolates , suggesting that class 3 genes ( controlled by FliA sigma factor ) , but not class 2 genes , were affected .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	xthA	activator	22275872	7	att	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	326	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	10	VALIDATION OF MICROARRAY ANALYSIS USING LAC FUSIONS	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	pagM	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
DksA	gene	gnd	regulator	20851888	6	ver/dev	gnd , , do not appear to be regulated by DksA .	179	Several other genes of the pentose phosphate pathway , glycolysis , and tricarboxylic acid cycle such as gnd , aceEF , and mdh , which are also associated with production of reductive power , do not appear to be regulated by DksA .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
CpxR	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of CpxR to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of CpxR to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CusR	gene	copA	regulator	34125582	5	ver/dev	detoxification genes copA _ regulated by CusR	249	As expected , the known copper efflux and detoxification genes copA , cueO , and cusCFBA , regulated by CueR and CusR , are upregulated in E. coli during growth in copper-supplemented media .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PreA	gene	pmrCAB	activator	18467098	2	ver/dev	PreA activated the transcription of pmrCAB indirectly in PmrA RR-independent fashion .	79	PreA activated the transcription of pmrCAB indirectly in a PhoP and PmrA RR-independent fashion .	8	INDIRECT ACTIVATION OF PMRAB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PreA	gene	pmrCAB	activator	18467098	2	ver/dev	PreA activated the transcription of pmrCAB indirectly in a PhoP .	79	PreA activated the transcription of pmrCAB indirectly in a PhoP and PmrA RR-independent fashion .	8	INDIRECT ACTIVATION OF PMRAB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	nfo	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates Mn-containing superoxide dismutase , nfo .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	nfo	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , nfo .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	nfo	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , nfo .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	nfo	activator	12886427	0	ver/dev	SoxS protein , activates sodA , nfo .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NadR	gene	nadB	repressor	15968063	0	ver/dev	The NadR function represses transcription of the nadB genes .	37	The NadR ( R ) function represses transcription of the nadB and pncB genes and the nadA-pnuC operon when NAD levels are high ( 7 , 37 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NtrC	gene	glnK	activator	30201777	9	ver/dev	To ensure that NtrC was activated by the nitrogen-limiting conditions , expression of NtrC-regulated glnK was measured by qRT-PCR -LRB- see Fig .	118	To ensure that NtrC was activated by the nitrogen-limiting conditions , expression of NtrC-regulated glnK ( 41 ) was measured by qRT-PCR ( see Fig .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NtrC	gene	glnK	activator	30201777	10	ver/dev	this induction of glnK expression was NtrC dependent , as indicated by the 1,336-fold-lower expression of glnK in the ΔntrC strain versus the WT under nitrogen-limiting conditions ( Fi	120	Expression of glnK was significantly increased by the treatment in WT cells ( 28-fold , P 0.0001 ) , and this induction of glnK expression was NtrC dependent , as indicated by the 1,336-fold-lower expression of glnK in the ΔntrC strain versus the WT under nitrogen-limiting conditions ( P 0.0001 ) ( Fig .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	TU	acrAB	activator	18577510	2	ver/dev	Other regulators of SdiA did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by EnvZ through SsrA -- both protein pairs being two-component regulators -- and not by PhoP .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by EnvZ through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	steA	regulator	23504014	0	ver/dev	These screens identified the response regulator PhoP as positive regulators of steA .	6	These screens identified the histidine kinase PhoQ and the response regulator PhoP as positive regulators of steA .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	steA	regulator	23504014	5	ver/dev	FIG 1 PhoP are regulators of steA expression .	191	FIG 1 PhoP , PhoQ , and MgrB are regulators of steA expression .	5	AATGCGTGTCAGTCAGGCAC TTAGCTACGATCAGTGGTAG	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	steA	regulator	23504014	6	ver/dev	In summary , our T-POP-based screens detected PhoP as positive regulators and MgrB as a negative regulator of steA .	229	In summary , our T-POP-based screens detected PhoP and PhoQ as positive regulators and MgrB as a negative regulator of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	steA	regulator	23504014	7	ver/dev	These results establish that regulation of steA by PhoQ/PhoP suggest that PhoP could be a direct activator of steA .	243	These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system and suggest that PhoP could be a direct activator of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	steA	regulator	23504014	7	ver/dev	These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system .	243	These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system and suggest that PhoP could be a direct activator of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
PhoP	gene	steA	regulator	23504014	17	ver/dev	Direct binding of PhoP to the steA promoter .	294	Direct binding of PhoP to the steA promoter .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steA	regulator	23504014	18	ver/dev	A slot blot method was used to analyze the binding of PhoP to the promoter of steA .	295	A slot blot method was used to analyze the binding of PhoP to the promoter of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	steA	regulator	23504014	20	ver/dev	As seen in Fig. 5 , phosphorylated PhoP was able to bind to the promoter of steA with similar kinetics , whereas no binding was detected to the promoter of phoN .	299	As seen in Fig. 5 , phosphorylated PhoP was able to bind to the promoter of steA and slyB with similar kinetics , whereas no binding was detected to the promoter of phoN .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	steA	regulator	23504014	23	ver/dev	Finally , slot blot analysis was carried out to test the effect of these mutations in the binding of PhoP to steA promoter .	311	Finally , slot blot analysis was carried out to test the effect of these mutations in the binding of PhoP to steA promoter .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	steA	regulator	23504014	25	ver/dev	FIG 5 PhoP binds directly to the promoter of steA .	325	FIG 5 PhoP binds directly to the promoter of steA .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	steA	regulator	23504014	29	ver/dev	FIG 6 The integrity of a putative PhoP box is essential for binding of regulation of steA expression by PhoP .	363	FIG 6 The integrity of a putative PhoP box is essential for binding of PhoP and regulation of steA expression by PhoP .	7	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	steA	regulator	23504014	29	ver/dev	FIG 6 The integrity of a putative PhoP box is essential for binding of regulation of steA expression by PhoP .	363	FIG 6 The integrity of a putative PhoP box is essential for binding of PhoP and regulation of steA expression by PhoP .	7	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	steA	regulator	23504014	29	ver/dev	FIG 6 The integrity of a putative PhoP box is essential for binding of PhoP of steA expression by PhoP .	363	FIG 6 The integrity of a putative PhoP box is essential for binding of PhoP and regulation of steA expression by PhoP .	7	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	steA	regulator	23504014	34	ver/dev	phosphorylated PhoP binds then to the steA promoter to directly activate transcription of this gene	397	Our data , together with previous data in E. coli , suggest a model in which DsbA is a negative regulator of the PhoQ/PhoP system probably through disul-fide bond formation in MgrB : reducing conditions disrupting di-sulfide bonds increase PhoQ/PhoP activity , and phosphorylated PhoP binds then to the steA promoter to directly activate transcription of this gene .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	ytfE	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
NsrR	gene	ytfE	regulator	33024855	11	att	A role in virulence has been identified for the NsrR-regulated STM1808 and ytfE ( Karlinsey et al. , 2012 ) .	452	A role in virulence has been identified for the NsrR-regulated STM1808 and ytfE ( Karlinsey et al. , 2012 ) .	12	3.3. NITROSATIVE AND OXIDATIVE STRESS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	csgDEFG	activator	15790293	13	att	While CsgD activates the two divergent csg promoters for csgABC and csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	319	While CsgD activates the two divergent csg promoters for csgABC and csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	18	THE LUXR FAMILY OF GENE REGULATORS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgDEFG	activator	15790293	13	ver/dev	While CsgD activates the two divergent csg promoters for csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	319	While CsgD activates the two divergent csg promoters for csgABC and csgDEFG transcription , the effect on bcs expression is achieved through CsgD-dependent activation of the adrA gene .	18	THE LUXR FAMILY OF GENE REGULATORS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgDEFG	activator	25101984	3	ver/dev	The transcription factor CsgD is known to be the activator of the csgBAC operon but to do not participate in the activation of the genes in the csgDEFG operon .	339	The transcription factor CsgD is known to be the activator of the csgBAC operon but to do not participate in the activation of the genes in the csgDEFG operon [ 29 ] .	17	EXPRESSION COMPARISON OF GENES INVOLVED IN QUORUM SENSING AND PATHOGENICITY	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CsgD	TU	csgDEFG	activator	25101984	3	ver/dev	The transcription factor CsgD is known to be the activator of the csgBAC operon but to do not participate in the activation of the genes in the csgDEFG operon .	339	The transcription factor CsgD is known to be the activator of the csgBAC operon but to do not participate in the activation of the genes in the csgDEFG operon [ 29 ] .	17	EXPRESSION COMPARISON OF GENES INVOLVED IN QUORUM SENSING AND PATHOGENICITY	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	sefA	repressor	25217722	0	ver/dev	It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sefA	repressor	25217722	0	ver/dev	It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	15205413	12	att	These results indicate that the pbg operon and the pmrC genes are solely responsible for PmrA-regulated polymyxin B resistance .	198	These results indicate that the pbg operon and the pmrC genes are solely responsible for PmrA-regulated polymyxin B resistance .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	15205413	18	att	Whereas the PmrA-regulated promoter has been defined by S1-mapping experiments ( 47 ) , evidence for the constitutive promoter is based on the ability of a 346-bp fragment from the pmrC coding region to promote transcription from a plasmid-linked promoterless reporter gene ( 14 ) and the fact that pmrC-lac fusions generated with the MudJ transposon near the 3 end , but within the pmrC coding region , exhibit normal PmrA-dependent transcription ( 41 ) .	272	Whereas the PmrA-regulated promoter has been defined by S1 mapping experiments ( 47 ) , evidence for the constitutive promoter is based on the ability of a 346-bp fragment from the pmrC coding region to promote transcription from a plasmid-linked promoterless reporter gene ( 14 ) and the fact that pmrC-lac fusions generated with the MudJ transposon near the 3 end , but within the pmrC coding region , exhibit normal PmrA-dependent transcription ( 41 ) .	5	DISCUSSION	unidentified plasmid	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	15205413	19	att	We have now provided genetic evidence for the presence of a promoter within the pmrC gene by establishing that the deletion of the complete pmrC open reading frame abolished PmrA-mediated transcription , whereas a strain retaining 360 bp at the 3 of the pmrC gene exhibited normal PmrA-controlled transcription ( Fig. 1B ) .	273	We have now provided genetic evidence for the presence of a promoter within the pmrC gene by establishing that the deletion of the complete pmrC open reading frame abolished PmrA-mediated transcription , whereas a strain retaining 360 bp at the 3 of the pmrC gene exhibited normal PmrA-controlled transcription ( Fig. 1B ) .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	15205413	2	att	A pbgP pmrC double mutant resembled a pmrA mutant both in its lipid-A profile and in its susceptibility to polymyxin B , indicating that the PmrA-dependent modification of lipid-A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance .	11	A pbgP pmrC double mutant resembled a pmrA mutant both in its lipid A profile and in its susceptibility to polymyxin B , indicating that the PmrA-dependent modification of lipid A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	15205413	7	att	This analysis suggested that the PmrA-regulated pmrC gene might be involved in the phosphoethano-lamine modification of the LPS .	144	This analysis suggested that the PmrA-regulated pmrC gene might be involved in the phosphoethano-lamine modification of the LPS .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	15659161	5	att	Lee , H. , Hsu , F.F. , Turk , J. , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanola-mine modification of lipid-A and polymyxin resistance in Salmonella enterica .	549	Lee , H. , Hsu , F.F. , Turk , J. , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanola-mine modification of lipid A and polymyxin resistance in Salmonella enterica .	30	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	15681155	32	att	PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	432	PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	30	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	15774888	2	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .	464	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and poly-myxin resistance in Salmonella enterica .	6	CS283 WILD TYPE 10 MM 26.4 6.5 WILD TYPE 10 M 424.9 53.6 KCS040 PMRA::TN10D 10 M 388.5 81.0	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	15866924	1	att	pmrC , a PmrA-regulated gene necessary for the addition of pEtN to lipid-A , did not affect core pEtN addition .	8	pmrC , a PmrA-regulated gene necessary for the addition of pEtN to lipid A , did not affect core pEtN addition .	1	ABSTRACT	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	pmrC	regulator	15866924	14	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid a and poly-myxin resistance in Salmonella enterica .	423	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid a and poly-myxin resistance in Salmonella enterica .	16	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	15866924	2	att	Recently , the PmrA-regulated pmrC gene product was shown to mediate the addition of pEtN to the 1-position of lipid-A and affect resistance to PM ( 22 ) .	27	Recently , the PmrA-regulated pmrC gene product was shown to mediate the addition of pEtN to the 1-position of lipid A and affect resistance to PM ( 22 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	17483225	1	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .	421	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and poly-myxin resistance in Salmonella enterica .	23	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	18467098	6	att	PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid-A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .	136	PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .	10	PMRAB-MEDIATED LPS MODIFICATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	18467098	8	att	68 , 6139 -- 6146 58 Lee , H. et al. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	325	68 , 6139 -- 6146 58 Lee , H. et al. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	39	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	19076233	12	att	Lee H , Hsu FF , Turk J & Groisman EA ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	218	Lee H , Hsu FF , Turk J & Groisman EA ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	29	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	19076233	6	att	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	138	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	14	INACTIVATION OF RPON INDUCES PM RESISTANCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	19332669	1	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .	354	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and poly-myxin resistance in Salmonella enterica .	19	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	19332669	0	ver/dev	After being phosphorylated by PmrB , PmrA can effectively bind to the transcriptional sites of pmrC .	37	After being phosphorylated by PmrB , PmrA can effectively bind to the transcriptional sites of other genes ( pmrE , pmrHFIJKLM , and pmrC ) and activate their transcription .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	20593264	5	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	423	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	37	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrC	regulator	20833808	3	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .	206	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and poly-myxin resistance in Salmonella enterica .	10	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	22921935	10	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	341	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrC	regulator	23690578	19	att	Importantly , the enrichment in ssrB promoter DNA was comparable to that of other known PmrA-regulated genes , including pmrC ( Fig. 4C ) .	86	Importantly , the enrichment in ssrB promoter DNA was comparable to that of other known PmrA-regulated genes , including pmrC ( Fig. 4C ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrC	regulator	24021902	7	att	Lee H , Hsu FF , Turk J , Groisman EA : The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	472	Lee H , Hsu FF , Turk J , Groisman EA : The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	9	REFERENCES AND RECOMMENDED READING	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	27381382	2	att	Lee , H. , Hsu , F.F. , Turk , J , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanol-amine modification of lipid a and polymyxin resistance in Salmonella enterica .	681	Lee , H. , Hsu , F.F. , Turk , J , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanol-amine modification of lipid a and polymyxin resistance in Salmonella enterica .	46	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	28875943	1	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	1141	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	24	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrC	regulator	29739882	18	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	368	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrC	regulator	30017920	1	att	[ 75 ] H. Lee , F.F. Hsu , J. Turk , E.A. Groisman , The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica , J. Bacteriol .	821	[ 75 ] H. Lee , F.F. Hsu , J. Turk , E.A. Groisman , The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica , J. Bacteriol .	79	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrC	regulator	33932721	2	att	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .	361	The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica .	35	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	STM2585	regulator	27564394	11	ver/dev	Furthermore , STM2585 are regulated by PhoP .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IlvY	gene	ilvC	activator	29791499	5	ver/dev	IlvY variants increase expression of ilvC	240	IlvY variants increase expression of ilvC	14	ILVY VARIANTS INCREASE EXPRESSION OF ILVC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	activator	29791499	6	ver/dev	The IlvY variants activate expression of ilvC , enhancing ketopantoate reductase activity in the cell , leading to increased CoA levels .	294	The IlvY variants described here activate expression of ilvC , enhancing ketopantoate reductase activity in the cell , leading to increased CoA levels that improve ThiC-variant activity to restore thiamine production .	16	SUPPRESSED STRAINS HAVE INCREASED COA POOL SIZE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	activator	11101680	1	ver/dev	the expression of luxCDABE results from the activation of the spvA promoter by SpvR	105	Expression of the SpvR protein requires an active RpoS protein ( Guiney et al. , 1995 ) and the expression of luxCDABE results from the activation of the spvA promoter by SpvR and RpoS .	4	METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvA	activator	12011028	0	ver/dev	The SpvR protein functions as a transcriptional activator for the spvA promoter	11	The SpvR protein functions as a transcriptional activator for the spvA promoter , and SpvB and SpvC are highly conserved .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SpvR	gene	spvA	activator	12011028	2	ver/dev	Therefore , we determined whether the SpvR protein from serovar Arizona was able to activate transcription from the spvA promoter of serovar Dublin .	73	Therefore , we determined whether the SpvR protein from serovar Arizona was able to activate transcription from the spvA promoter of serovar Dublin .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SpvR	gene	spvA	activator	12011028	4	ver/dev	We also demonstrated that the serovar Arizona SpvR protein is a functional activator of the spvA promoter .	118	We also demonstrated that the serovar Arizona SpvR protein is a functional activator of the spvA promoter .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SpvR	gene	spvA	activator	23936152	13	ver/dev	Increased levels of spvR would then lead to increased expression of the spvABCD operon as SpvR is essential for activation of the spvA promoter .	439	Increased levels of spvR would then lead to increased expression of the spvABCD operon as SpvR is essential for activation of the spvA promoter and is known to be able to induce RpoS-independent expression from the spvA promoter [ 31 ] .	25	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	pagN	activator	14742517	3	ver/dev	in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagN	activator	14742517	3	ver/dev	in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagN	activator	14742517	3	ver/dev	Interestingly we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagN	activator	14742517	3	ver/dev	Interestingly we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	137	Interestingly , and in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 and 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagN	activator	20368731	0	ver/dev	The pagN gene is activated by PhoP	353	The pagN gene is activated by PhoP and the corresponding protein shares identities with the Hek and Tia invasins / adhesins of pathogenic E. coli [ 7 ] .	13	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	spvR	regulator	15790293	3	ver/dev	Genetic evidence has implicated HU in the control of SPI-1 virulence gene expression while IHF has been shown to bind to the promoter region of the spvR regulatory virulence gene on the 96-kb plasmid of S. Typhimurium where it has a positive effect in stationary-phase .	214	Genetic evidence has implicated HU in the control of SPI-1 virulence gene expression ( Schechter et al. , 2003 ) while IHF has been shown to bind to the promoter region of the spvR regulatory virulence gene on the 96-kb plasmid of S. Typhimurium where it has a positive effect in stationary phase ( Marshall et al. , 1999 ) .	13	NUCLEOID-ASSOCIATED PROTEINS	unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
IHF	gene	spvR	regulator	19447191	2	ver/dev	IHF binds to DNA sequences upstream of the spvR regulatory region	82	Integration host factor ( IHF ) binds to DNA sequences upstream of the spvR regulatory region , and the leucine-responsive regulatory protein ( Lrp ) binds to sequences upstream of the spvABCD operon and regulate spv expression ( Marshall et al. , 1999 ) .	5	4.1. SPVR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IscR	gene	iscR	regulator	27704705	31	ver/dev	Conversely , the iscR mutant was shown to be less virulent in mice compared to the wild‐type , consistent with a possible regulation of other genes involved in Salmonella pathogenesis by IscR .	304	Conversely , the iscR mutant was shown to be more invasive in HeLa cells and less virulent in mice compared to the wild‐type , consistent with a possible regulation of other genes involved in Salmonella pathogenesis by IscR .	12	2.7 | ISCR REDUCES THE INVASION OF HELA CELLS BY SALMONELLA	Mus sp.;Salmonella	0.5	L1	SPEC	Analysis	OTHER	Other	Level 1
IscR	gene	iscR	regulator	27704705	31	ver/dev	Conversely , the iscR mutant was shown to be more invasive in HeLa cells virulent in mice compared to the wild‐type , consistent with a possible regulation of other genes involved in Salmonella pathogenesis by IscR .	304	Conversely , the iscR mutant was shown to be more invasive in HeLa cells and less virulent in mice compared to the wild‐type , consistent with a possible regulation of other genes involved in Salmonella pathogenesis by IscR .	12	2.7 | ISCR REDUCES THE INVASION OF HELA CELLS BY SALMONELLA	Mus sp.;Salmonella	0.5	L1	SPEC	Analysis	OTHER	Other	Level 1
IscR	gene	iscR	regulator	29213059	2	ver/dev	In E. coli , this operon is regulated by IscR , iron sulfur cluster regulator58 ; in Salmonella the gene iscR is named yfhP .	348	In E. coli , this operon is regulated by IscR , iron sulfur cluster regulator58 ; in Salmonella the gene iscR encoding this transcription regulator is named yfhP .	3	RESULTS AND DISCUSSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
TviA	gene	tviA	regulator	20808848	0	att	To determine how TviA affects gene expression in a non-typhoidal serotype , the tviA gene was introduced into the S. Typhimurium chromosome and the gene expression profile compared to a published gene expression profile of TviA-regulated genes in S. Typhi [ 8 ] .	47	To determine how TviA affects gene expression in a non-typhoidal serotype , the tviA gene was introduced into the S. Typhimurium chromosome and the gene expression profile compared to a published gene expression profile of TviA-regulated genes in S. Typhi [ 8 ] .	6	CHANGES IN S. TYPHIMURIUM GENE EXPRESSION AFTER CHROMOSOMAL INSERTION OF TVIA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
TviA	gene	tviA	regulator	33651854	5	att	In addition , the tviA-REP mutant and the TviA-deficient S. Typhi strains induced similar increases in the levels of cell death and IL-1β release compared to WT S. Typhi ( Fig 7A , 7B and 7C ) , consistent with the role of the tviA RNAT controlling expression of TviA-regulated genes , such as flagellin .	330	In addition , the tviA-REP mutant and the TviA-deficient S. Typhi strains induced similar increases in the levels of cell death and IL-1β release compared to WT S. Typhi ( Fig 7A , 7B and 7C ) , consistent with the role of the tviA RNAT controlling expression of TviA-regulated genes , such as flagellin .	14	S. TYPHI EVASION OF INNATE IMMUNE SIGNALING IN INTESTINAL EPITHELIAL CELLS REQUIRES THE TVIA RNAT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	gene	tviA	regulator	33651854	6	ver/dev	tviA exerts post-transcriptional control of TviA protein production	360	Our work shows that one mechanism dictating temperature-dependent control of virulence factor expression is mediated by an RNAT in the 5 ' UTR of tviA that exerts post-transcriptional control of TviA protein production .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	yciE	regulator	34149657	1	att	yciE is in an operon with catalase katN and yciGF that contains a putative RpoS-regulated promoter ( Robbe-Saule et al. , 2001 ) .	418	yciE is in an operon with catalase katN and yciGF that contains a putative RpoS-regulated promoter ( Robbe-Saule et al. , 2001 ) .	24	TIME: 11:13 # 10	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	yciE	regulator	34149657	3	ver/dev	The regulation of yciE has been partially attributed to RpoS , respectively .	432	The regulation of yciE , yjbE , and ASPP has been partially attributed to RpoS , Rcs phosphorelay , and RpoN , respectively .	25	TIME: 11:13 # 11	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	yciE	regulator	34149657	5	ver/dev	the regulation of yciE in response to bile-salts is likely independent of RpoS	436	Interestingly , the regulation of yciE , yjbE , and ASPP has only been partially attributed to the above-mentioned regulators , and the regulation of yciE in response to bile salts is likely independent of RpoS ( Prouty et al. , 2004b ) .	25	TIME: 11:13 # 11	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CpxR	gene	hilA	regulator	26300871	14	ver/dev	To confirm that CpxR regulates hilA through not directly , we analyzed the effect of CpxR on the expression of hilA in the presence or not of HilD .	376	To confirm that CpxR regulates hilA through HilD and not directly , we analyzed the effect of CpxR on the expression of hilA in the presence or not of HilD .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
CpxR	gene	hilA	regulator	26300871	14	ver/dev	To confirm that CpxR regulates hilA through HilD , we analyzed the effect of CpxR on the expression of hilA in the presence or not of HilD .	376	To confirm that CpxR regulates hilA through HilD and not directly , we analyzed the effect of CpxR on the expression of hilA in the presence or not of HilD .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
CpxR	gene	hilA	regulator	26300871	16	ver/dev	mutant _ indicating that CpxR regulates hilA through not directly	381	The overexpression of CpxR , from plasmid pK3-CpxR , reduced five-fold the expression of a hilA-cat transcriptional fusion in the WT strain ( Figure 4C ) , but did not affect the high levels of expression showed by this fusion in the 1hilD 1Cthns mutant ( Figure 4D ) , indicating that CpxR regulates hilA through HilD and not directly .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilA	regulator	26300871	16	ver/dev	mutant _ indicating that CpxR regulates hilA through HilD	381	The overexpression of CpxR , from plasmid pK3-CpxR , reduced five-fold the expression of a hilA-cat transcriptional fusion in the WT strain ( Figure 4C ) , but did not affect the high levels of expression showed by this fusion in the 1hilD 1Cthns mutant ( Figure 4D ) , indicating that CpxR regulates hilA through HilD and not directly .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilA	regulator	26300871	16	ver/dev	mutant _ indicating that CpxR regulates hilA through not directly	381	The overexpression of CpxR , from plasmid pK3-CpxR , reduced five-fold the expression of a hilA-cat transcriptional fusion in the WT strain ( Figure 4C ) , but did not affect the high levels of expression showed by this fusion in the 1hilD 1Cthns mutant ( Figure 4D ) , indicating that CpxR regulates hilA through HilD and not directly .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilA	regulator	26300871	16	ver/dev	mutant _ indicating that CpxR regulates hilA through HilD	381	The overexpression of CpxR , from plasmid pK3-CpxR , reduced five-fold the expression of a hilA-cat transcriptional fusion in the WT strain ( Figure 4C ) , but did not affect the high levels of expression showed by this fusion in the 1hilD 1Cthns mutant ( Figure 4D ) , indicating that CpxR regulates hilA through HilD and not directly .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	hilA	regulator	30716090	41	ver/dev	tatABC are involved in the expression of hilA to be under direct control of CpxR ( Fig	417	Here , we identified 1,2-propanediol degradation system ( pocR ) and the Tat-system ( tatABC ) which are involved in the expression of hilA to be under direct control of CpxR ( Fig	25	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	hilA	regulator	30716090	41	ver/dev	the Tat-system are involved in the expression of hilA to be under direct control of CpxR ( Fig	417	Here , we identified 1,2-propanediol degradation system ( pocR ) and the Tat-system ( tatABC ) which are involved in the expression of hilA to be under direct control of CpxR ( Fig	25	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	otsA	regulator	11101680	5	ver/dev	The trehalose synthesis gene otsA is regulated by RpoS in S. typhimurium	345	The trehalose synthesis gene otsA is regulated by RpoS in S. typhimurium ( Fang et al. , 1996 ) and trehalose is known to protect cells from drying by stabilizing membranes and enzymes , and this may explain the observation ( Potts , 1994 ) .	8	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	otsA	regulator	12160319	0	ver/dev	Previous workers have shown that the otsA gene is regulated by RpoS to the stationary-phase of growth .	167	Previous workers have shown that the otsA gene is regulated by RpoS , a master regulator of the bacterial response to stresses such as nutrient deprivation or to the stationary phase of growth [ 7,11 ] .	20	3.5. VIRULENCE OF S. ENTERICA SEROVAR TYPHIMURIUM SL1344 OTSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	otsA	regulator	12160319	0	ver/dev	Previous workers have shown that the otsA gene is regulated by RpoS to nutrient deprivation .	167	Previous workers have shown that the otsA gene is regulated by RpoS , a master regulator of the bacterial response to stresses such as nutrient deprivation or to the stationary phase of growth [ 7,11 ] .	20	3.5. VIRULENCE OF S. ENTERICA SEROVAR TYPHIMURIUM SL1344 OTSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	otsA	regulator	12160319	0	ver/dev	Previous workers have shown that the otsA gene is regulated by RpoS to stresses .	167	Previous workers have shown that the otsA gene is regulated by RpoS , a master regulator of the bacterial response to stresses such as nutrient deprivation or to the stationary phase of growth [ 7,11 ] .	20	3.5. VIRULENCE OF S. ENTERICA SEROVAR TYPHIMURIUM SL1344 OTSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoR	gene	phoE	activator	31346161	7	ver/dev	It is interesting to note that the phoRL421G substitution showed a defect in the increase of phoE mRNA levels in low phosphate , suggesting that it might compromise the ability of PhoR-P to transfer its phosphate to PhoB .	279	It is interesting to note that the phoRL421G substitution had no effect on PhoR autophosphorylation but showed a defect in the increase of phoE mRNA levels in low phosphate ( Supplementary Fig. 6 and Fig. 4k ) , suggesting that it might compromise the ability of PhoR-P to transfer its phosphate to PhoB .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoR	gene	phoE	activator	31346161	10	ver/dev	These data suggest that the interaction between PhoR is required for a full induction of the mRNA levels of the phoE genes inside macrophages .	294	These data suggest that the interaction between MgtC and PhoR is required for a full induction of the mRNA levels of the phoE and phoB genes inside macrophages .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	12535071	88	ver/dev	HilD do not seem to regulate expression of hilD .	251	HilD and HilC do not seem to regulate expression of hilD or prgH ( Olekhnovich and Kadner , 2002 ) ( Figs 1 and 2B ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Other	NEG	New	Level 1
HilD	gene	hilD	regulator	15661008	15	ver/dev	These results indicate that Lon is involved in the autoregulation of hilD transcription by modulating amounts of HilD .	181	These results indicate that Lon is involved in the autoregulation of hilC and hilD transcription by modulating amounts of HilC and HilD .	7	LEVEL OF HILC AND HILD TRANSCRIPTION IN WILD-TYPE AND LON-DISRUPTED MUTANT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilD by HilD .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	regulator	17993530	19	ver/dev	Fur regulation of hilD requires the HilD protein .	200	Fur regulation of hilD requires the HilD protein .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	regulator	17993530	31	ver/dev	Fur regulation of hilD requires the HilD protein .	224	Fur regulation of hilD requires the HilD protein .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	regulator	19003447	1	ver/dev	Of these regulators , HilD can be considered as the most important single regulator of PhilA since the hilD knockout strain shows nearly basal levels of HilA under inducing conditions .	39	Of these regulators , HilD can be considered as the most important single regulator of the hilA promoter ( PhilA ) since the hilD knockout strain shows nearly basal levels of HilA under inducing conditions ( Lucas and Lee 2001 ; Boddicker et al. 2003 ; Ellermeier et al. 2005 ) .	5	INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	20008574	9	ver/dev	Transcription of hilD is under the control of an autogenous , positive feedback loop by the HilD product ( Ellermeier et al. 2005 ; Slauch	163	Transcription of hilD is under the control of an autogenous , positive feedback loop by the HilD product ( Ellermeier et al. 2005 ; Ellermeier and Slauch	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	regulator	20008574	9	ver/dev	Transcription of hilD is under the control of an autogenous , positive feedback loop by the HilD product ( Ellermeier et al. 2005 ; Ellermeier	163	Transcription of hilD is under the control of an autogenous , positive feedback loop by the HilD product ( Ellermeier et al. 2005 ; Ellermeier and Slauch	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	regulator	21680637	7	ver/dev	Interestingly , hilD mRNA levels have been found to be dependent upon Dam activity , thus suggesting posttranscriptional control of HilD expression .	53	Interestingly , hilD mRNA levels have been found to be dependent upon DNA adenine methylation ( Dam ) activity , thus suggesting posttranscriptional control of HilD expression ( López - Garrido & Casadesús , 2010 ) .	3	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	21680637	7	ver/dev	Interestingly , hilD mRNA levels have been found to be dependent upon DNA adenine methylation activity , thus suggesting posttranscriptional control of HilD expression .	53	Interestingly , hilD mRNA levels have been found to be dependent upon DNA adenine methylation ( Dam ) activity , thus suggesting posttranscriptional control of HilD expression ( López - Garrido & Casadesús , 2010 ) .	3	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	22479568	0	ver/dev	HilD can activate expression of hilD of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilD	regulator	24018968	14	ver/dev	In addition , P hilD expression decreased in Fig. 3B because HilD is the positive regulator for hilD promoter activation .	237	In addition , P hilD expression decreased in hfq mutants ( Fig. 3B ) because HilD is the positive regulator for hilD promoter activation [ 6 , 15 ] .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	regulator	24018968	14	ver/dev	In addition , P hilD expression decreased in hfq mutants because HilD is the positive regulator for hilD promoter activation .	237	In addition , P hilD expression decreased in hfq mutants ( Fig. 3B ) because HilD is the positive regulator for hilD promoter activation [ 6 , 15 ] .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	regulator	25135218	6	ver/dev	HilD also directly controls the expression of the SPI-1 genes hilD .	23	HilD also directly controls the expression of the SPI-1 genes hilD , hilC , and invF , as well as other acquired and ancestral genes located outside SPI-1 , such as rtsA , flhDC , siiA , lpxR , ytfK , STM14_1282 , and STM14_2342 ( 2 , 25 -- 31 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	regulator	25991823	16	ver/dev	The evidence that L-arabinose regulates SPI-1 expression through HilD suggested that hilD expression itself might be controlled by L-arabinose .	262	The evidence that L-arabinose regulates SPI-1 expression through HilD suggested that hilD expression itself might be controlled by L-arabinose .	14	L-ARABINOSE-DEPENDENT REPRESSION OF SPI-1 IS TRANSMITTED VIA HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	26300871	5	att	CpxR Represses hilD and thus Indirectly Affects HilD-regulated Genes Several global regulators control the expression of the SPI-1 genes by directly affecting the expression , activity or concentration of	349	CpxR Represses hilD and thus Indirectly Affects HilD-regulated Genes Several global regulators control the expression of the SPI-1 genes by directly affecting the expression , activity or concentration of	15	NLPE FROM THE T5-LAC PROMOTER OF PLASMID PCA-NLPE WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	hilD	regulator	27341691	18	att	The C-terminal domain of RNAPa has been shown to be important for transcription of HilD-regulated genes in-vivo , as the mutation of leucine 289 to phenylalanine within this domain fails to induced hilA expression , similarly to a hilD null mutant	292	The C-terminal domain of RNAPa has been shown to be important for transcription of HilD-regulated genes in vivo , as the mutation of leucine 289 to phenylalanine within this domain fails to induced hilA expression , similarly to a hilD null mutant	11	SALMONELLA TO MAXIMIZE ITS VIRULENCE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	regulator	27341691	0	ver/dev	The control of HilD by Pat was through post-transcriptional mechanisms , moderately repressing hilD translation while significantly reducing HilD stability .	15	The control of HilD by Pat was through post-transcriptional mechanisms , moderately repressing hilD translation while significantly reducing HilD stability .	2	SUMMARY	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilD	regulator	28329249	18	ver/dev	HilD DNA-Binding Ability and Stability At the transcriptional level , the expression of hilD is positively autoregulated by a feed-forward loop	195	Acetylation of K297 Regulating HilD DNA-Binding Ability and Stability At the transcriptional level , the expression of hilD is positively autoregulated and modulated by a feed-forward loop involving HilD itself and regulators HilC and RtsA [ 3 , 28 ] .	15	MODULATION BY PAT ON HILD K297 ACETYLATION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilD	regulator	28575106	1	ver/dev	HilD is the dominant regulator of the system , as a hilD mutant had almost no hilA expression , whereas deletion of either rtsA decreased hilA expression less significantly .	85	HilD is the dominant regulator of the system , as a hilD mutant had almost no hilA expression , whereas deletion of either hilC or rtsA decreased hilA expression less significantly [ 29,30 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilD	regulator	28575106	1	ver/dev	HilD is the dominant regulator of the system , as a hilD mutant had almost no hilA expression , whereas deletion of either hilC decreased hilA expression less significantly .	85	HilD is the dominant regulator of the system , as a hilD mutant had almost no hilA expression , whereas deletion of either hilC or rtsA decreased hilA expression less significantly [ 29,30 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilD	regulator	28704543	13	ver/dev	Positive autoregulation of hilD is not essential for hilD-cat-37 +6 fusions that lack the HilD-binding site upstream of hilD , were expected to be expressed .	149	Positive autoregulation of hilD is not essential for its expression [ 26 ] , therefore , the hilD-cat-48 +88 and hilD-cat-37 +6 fusions that lack the HilD-binding site upstream of hilD , were expected to be expressed .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilD	regulator	28704543	13	ver/dev	Positive autoregulation of hilD is not essential for the hilD-cat-48 +88 that lack the HilD-binding site upstream of hilD , were expected to be expressed .	149	Positive autoregulation of hilD is not essential for its expression [ 26 ] , therefore , the hilD-cat-48 +88 and hilD-cat-37 +6 fusions that lack the HilD-binding site upstream of hilD , were expected to be expressed .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	hilD	regulator	28704543	13	ver/dev	Positive autoregulation of hilD is not essential for its expression , therefore that lack the HilD-binding site upstream of hilD , were expected to be expressed .	149	Positive autoregulation of hilD is not essential for its expression [ 26 ] , therefore , the hilD-cat-48 +88 and hilD-cat-37 +6 fusions that lack the HilD-binding site upstream of hilD , were expected to be expressed .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilD	gene	hilD	regulator	29378886	22	ver/dev	Although the actual mechanism is known in only a few cases , we have shown that regulation is primarily through either translation of the hilD message or control of HilD protein activity .	239	Although the actual mechanism is known in only a few cases , we have shown that regulation is primarily through either translation of the hilD message or control of HilD protein activity ( 14 , 16 , 19 , 27 ) .	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	hilD	regulator	29555922	2	ver/dev	to confirm whether its expression is controlled by HilD , the chromosomal gene was tagged in its isogenic ∆ hilD muta , with h the sequen .	60	To determine whether SL1344_1872 indeed codes for a protein and to confirm whether its expression is controlled by HilD , the SL1344_1872 chromosomal gene was tagged in the wild-type ( WT ) S. Typhimurium SL1344 strain and its isogenic ∆ hilD mutant , with the sequence encoding a 3XFLAG epitope .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	30077369	1	ver/dev	HilD is the dominant regulator of this system , as a hilD mutant had almost no hilA expression .	44	HilD is the dominant regulator of this system , as a hilD mutant had almost no hilA expression .	6	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	hilD	regulator	31017982	1	auto	The hilD message employs alternative secondary structures , with mRNA stability enhanced by binding to CsrA , to control the production of HilD , and HilD in turn amplifies induction through the control of its own transcription .	65	The hilD message employs alternative secondary structures , with mRNA stability enhanced by binding to CsrA , to control the production of HilD , and HilD in turn amplifies induction through the control of its own transcription .	5	HOW THEN IS THIS FINE LEVEL OF CONTROL ACHIEVED? THE EXISTENCE OF TWO SUB-POPULATIONS,	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilD	regulator	31017982	1	ver/dev	The hilD message employs alternative secondary structures , with mRNA stability , to control the production of HilD	65	The hilD message employs alternative secondary structures , with mRNA stability enhanced by binding to CsrA , to control the production of HilD , and HilD in turn amplifies induction through the control of its own transcription .	5	HOW THEN IS THIS FINE LEVEL OF CONTROL ACHIEVED? THE EXISTENCE OF TWO SUB-POPULATIONS,	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilD	regulator	31017982	26	ver/dev	The fine control of the hilD message level may thus provide a threshold for induction : The small proportion of the population with sufficient hilD message to produce HilD are invasive , while those .	251	The fine control of the hilD message level may thus provide a threshold for induction : The small proportion of the population with sufficient hilD message to produce HilD and induce subsequent autoinduction are invasive , while those that do not reach that threshold are not .	12	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	regulator	31182495	13	ver/dev	Many regulators of SPI1 function by controlling HilD protein activity , including the flagellar regulator FliZ , while other factors function by controlling hilD translation .	88	Many regulators of SPI1 function by controlling HilD protein activity , including HilE ( 53 , 54 ) and the flagellar regulator FliZ ( 10 ) , while other factors function by controlling hilD translation ( 8 , 9 , 44 , 59 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	regulator	31182495	13	ver/dev	Many regulators of SPI1 function by controlling HilD protein activity , including HilE , while other factors function by controlling hilD translation .	88	Many regulators of SPI1 function by controlling HilD protein activity , including HilE ( 53 , 54 ) and the flagellar regulator FliZ ( 10 ) , while other factors function by controlling hilD translation ( 8 , 9 , 44 , 59 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	regulator	31484980	8	ver/dev	To investigate if yobH indeed codes to further confirm the positive regulation of yobH by HilD , we tested the expression of the YobH-FLAG putative protein ( YobH ) in its derivative ∆ hilD muta .	53	To investigate if yobH indeed codes for a protein and to further confirm the positive regulation of yobH by HilD , we tested the expression of the YobH-FLAG putative protein ( YobH tagged with a 3XFLAG epitope ) in the WT S. Typhimurium strain and its derivative ∆ hilD mutant .	3	RESULTS	Iris germanica	0	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	hilD	regulator	34424033	4	ver/dev	NS-mediated repression of the hilA promoter , downstream of hilD , is through its control of HilD .	41	NS-mediated repression of the hilA promoter , downstream of hilD , is through its control of HilD , which directly activates hilA transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopB	activator	22291596	2	ver/dev	InvF activates expression of sopB .	597	InvF activates expression of effector genes inside SPI1 and also effector genes outside SPI-1 such as sopB and sopE [ 47 ] .	27	EXPRESSION OF SPI-1 AND SPI-2 TYPE 3 SECRETION SYSTEM REGULATORY GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopB	activator	23419780	7	ver/dev	InvF are transcription activators of effectors downregulates sopB .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopB	activator	25128737	0	ver/dev	Along with InvF , SicA is required for transcription activation of several virulence genes like sopB , pipC .	187	Along with InvF , SicA is required for transcription activation of several virulence genes like sigDE ( sopB , pipC ) , sipBCDA , and sopE ( Darwin et al. , 2001 ) .	19	3.3. THE FIVE INDIVIDUAL SPI AND COMBINED INTERACTOMES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopB	activator	27601571	26	ver/dev	Our RNA - explaining how SPI-4 gene expression is coordinated with that of seq data show strong upregulation of sopB by InvF ( see SPI-1 .	239	Our RNA - explaining how SPI-4 gene expression is coordinated with that of seq data show strong upregulation of sopB and sicA by InvF ( see SPI-1 .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sopB	activator	31991172	0	ver/dev	InvF itself is a transcriptional activator of the sopB gene , located outside of SPI1 , secreted effector .	153	InvF itself is a transcriptional activator of the sic/sip operon of SPI1 and of the sopB gene , located outside of SPI1 , encoding a TTSS1 secreted effector [ 37 ] .	14	3.2. POLYAMINE DEPLETION AFFECTS VIRULENCE GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopB	activator	33119619	13	att	These results confirm previous reports made in Salmonella indicating that both InvF and the chaperon SicA are required in-vivo for expression of InvF-dependent genes and that both proteins are necessary for expression of sopB even in the absence of the global repressor H-NS when using an E. coli surrogate system .	193	These results confirm previous reports made in Salmonella indicating that both InvF and the chaperon SicA are required in vivo for expression of InvF-dependent genes and that both proteins are necessary for expression of sopB even in the absence of the global repressor H-NS when using an E. coli surrogate system .	21	THE INVF/SICA COMPLEX DOES NOT ACT AS AN ANTI-HNS FACTOR ON SOPB	Salmonella;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sopB	activator	33119619	9	ver/dev	However , those previously reported indicate that transcriptional activation of sopB requires both InvF .	74	However , our results and those previously reported indicate that transcriptional activation of sopB requires both InvF and SicA .	11	HERE WE SHOW THAT, IN CONTRAST TO HILD AND OTHER SALMONELLA TRANSCRIPTIONAL REGULATORS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sopB	activator	33119619	9	ver/dev	However , our results indicate that transcriptional activation of sopB requires both InvF .	74	However , our results and those previously reported indicate that transcriptional activation of sopB requires both InvF and SicA .	11	HERE WE SHOW THAT, IN CONTRAST TO HILD AND OTHER SALMONELLA TRANSCRIPTIONAL REGULATORS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	purB	activator	33045730	108	ver/dev	SsrB also increases phoP transcription by directly binding to the purB .	451	SsrB also increases phoP transcription by directly binding to the purB coding region upstream of the phoP promoter region .	37	DIFFERENT HORIZONTALLY ACQUIRED GENES ENABLE ESCHERICHIA COLI TO ACTIVATE PHOP/PHOQ IN MILDLY ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RflM	TU	flhDC	activator	27206164	0	att	In this study , we elucidated the molecular mechanism of RflM-dependent repression of flhDC .	23	In this study , we elucidated the molecular mechanism of RflM-dependent repression of flhDC .	3	SUMMARY	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RflM	TU	flhDC	activator	27206164	45	ver/dev	RflM enhances binding affinity of RcsB to the flhDC target promoter DNA	252	RflM enhances binding affinity of RcsB to the flhDC target promoter DNA	10	RFLM ENHANCES BINDING AFFINITY OF RCSB TO THE FLHDC TARGET PROMOTER DNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RflM	TU	flhDC	activator	27206164	56	ver/dev	We propose that RflM enhances target specific-ity of the RcsB-RflM complex to the binding site within the flhDC promoter independent of the phosphorylation state of RcsB .	295	We propose that RflM stabilizes RcsB binding to the flhDC promoter leading to formation of a stable RcsB-RflM heterodimer and thereby enhances target specific-ity of the RcsB-RflM complex to the binding site within the flhDC promoter independent of the phosphorylation state of RcsB .	11	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
Crl	gene	csgB	activator	16707690	15	ver/dev	The in-vivo studies showed that Crl played a role in the transcriptional activation of the S-regulated genes csgB , bcsA .	324	The in vivo studies showed that Crl played a role in the transcriptional activation of the S-regulated genes csgB , csgD , adrA , and bcsA .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
Crl	gene	csgB	activator	16707690	15	ver/dev	The in-vivo studies showed that Crl played a role in the transcriptional activation of the S-regulated genes csgB , adrA .	324	The in vivo studies showed that Crl played a role in the transcriptional activation of the S-regulated genes csgB , csgD , adrA , and bcsA .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
Crl	gene	csgB	activator	16707690	15	ver/dev	The in-vivo studies showed that Crl played a role in the transcriptional activation of the S-regulated genes csgB , csgD .	324	The in vivo studies showed that Crl played a role in the transcriptional activation of the S-regulated genes csgB , csgD , adrA , and bcsA .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	sopE2	activator	33563986	9	att	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , as well as SPI-2 genes when STM is inside macrophages65 , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence-factors .	346	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , as well as SPI-2 genes when STM is inside macrophages65 , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence factors .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	phoN	regulator	19348639	0	ver/dev	phoN are known to be regulated by SlyA	254	The SPI-2 cluster is closely associated with three virulence-related genes ( pagJ , pagK , and phoN ) , which are known to be regulated by two virulenceassociated regulators , SlyA and PhoP ,56 that also regulate a number of SPI-2 genes .	14	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	prgH	regulator	12535071	88	ver/dev	HilD do not seem to regulate expression of prgH .	251	HilD and HilC do not seem to regulate expression of hilD or prgH ( Olekhnovich and Kadner , 2002 ) ( Figs 1 and 2B ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Other	NEG	New	Level 1
SlyA	gene	glpA	activator	29857034	11	ver/dev	This is consistent with RNA-seq analysis results , where , in the presence of NaOCl , glpA expression in WT showed a log2 fold-change of 3.6 compared to the mutant , suggesting that glpA is upregulated by SlyA .	294	This is consistent with RNA-seq analysis results , where , in the presence of NaOCl , glpA expression in WT showed a log2 fold-change of 3.6 compared to the mutant , suggesting that glpA is upregulated by SlyA .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	glpA	activator	29857034	29	ver/dev	These results suggest that SlyA upregulates the glpA gene .	362	These results suggest that SlyA upregulates the glpA gene .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	yciG	activator	11260470	5	att	The position of the putative RpoS-dependent transcriptional start site of yciG is indicated by asterisks ( 11 ) .	258	The position of the putative RpoS-dependent transcriptional start site of yciG is indicated by asterisks ( 11 ) .	9	IDENTIFICATION OF A PUTATIVE RPOS-DEPENDENT PROMOTER UPSTREAM OF THE YCIGFEKATN OPERON	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yciG	activator	11260470	7	att	Consistent with this finding and with our Northern blotting results ( Fig. 6 ) , a putative RpoS-dependent promoter ( yciGp1 ) was identified upstream of the yciG gene in Salmonella ( Fig. 7 ) .	306	Consistent with this finding and with our Northern blotting results ( Fig. 6 ) , a putative RpoS-dependent promoter ( yciGp1 ) was identified upstream of the yciG gene in Salmonella ( Fig. 7 ) .	11	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yciG	activator	15145463	2	att	yciF was initially identified by a screen for RpoSregulated genes and a putative RpoS-dependent promoter has been located upstream of yciG [ 39 ] .	210	yciF was initially identified by a screen for RpoSregulated genes and a putative RpoS-dependent promoter has been located upstream of yciG [ 39 ] .	12	3.2. BILE ACTIVATES YCIF INDEPENDENTLY OF RPOS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yciG	activator	15145463	3	ver/dev	Because yciF was identified in a screen for RpoSregulated genes , we examined transcription of yciG : : luc without RpoS to determine if activation of yciGFE-katN by bile was dependent upon RpoS .	215	Because yciF was identified in a screen for RpoSregulated genes , we examined transcription of yciG : : luc with and without RpoS to determine if activation of yciGFE-katN by bile was dependent upon RpoS .	12	3.2. BILE ACTIVATES YCIF INDEPENDENTLY OF RPOS	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RpoS	gene	yciG	activator	15145463	4	ver/dev	These data show that bile-mediated activation of yciG still occurred in the absence of RpoS .	216	These data show that bile-mediated activation of yciG still occurred in the absence of RpoS ( Fig. 4 ) .	12	3.2. BILE ACTIVATES YCIF INDEPENDENTLY OF RPOS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	yciG	activator	25281378	1	att	Finally , yciG of the yciGFE-katN operon is transcribed as a polycistronic messenger and harbors a putative RpoS-dependent promoter upstream of yciG , directing the transcription of genes essential for the general stress response ( 42 ) .	208	Finally , yciG of the yciGFE-katN operon is transcribed as a polycistronic messenger and harbors a putative RpoS-dependent promoter upstream of yciG , directing the transcription of genes essential for the general stress response ( 42 ) .	3	MAIN	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	yciG	activator	25281378	1	att	Finally , yciG of the yciGFE-katN operon is transcribed as a polycistronic messenger and harbors a putative RpoS-dependent promoter upstream of yciG , directing the transcription of genes essential for the general stress response ( 42 ) .	208	Finally , yciG of the yciGFE-katN operon is transcribed as a polycistronic messenger and harbors a putative RpoS-dependent promoter upstream of yciG , directing the transcription of genes essential for the general stress response ( 42 ) .	3	MAIN	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RcsB	TU	flhDC	regulator	27206164	12	ver/dev	In E. coli flagellar motility is negatively regulated by RcsB binding to the RcsAB box of the promoter of the flagellar master regulator flhDC .	71	In E. coli flagellar motility is negatively regulated by RcsB and RcsA binding to the RcsAB box of the promoter of the flagellar master regulator flhDC ( Francez-Charlot et al. , 2003 ) .	4	INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	regulator	27206164	19	ver/dev	RcsB is a previously described negative regulator of flhDC	86	RcsB is a previously described negative regulator of flhDC , and together with the LuxR-type auxiliary protein RcsA represses flhDC transcription in E. coli ( Francez-Charlot et al. , 2003 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
RcsB	TU	flhDC	regulator	27206164	36	ver/dev	We determined which flhDC promoter is regulated via RcsB using luxCDABE fusions to flhDC promoter mutants -LRB- Fig. 4C -RRB- .	204	We determined which flhDC promoter is regulated via RcsB and RflM using luxCDABE fusions to flhDC promoter mutants that retained either a functional P1 or P5 promoter , respectively ( Fig. 4C ) .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	regulator	27206164	39	ver/dev	gyrA was not shifted , indicating specific binding of RcsB to the flhDC promoter .	213	A control DNA fragment ( gyrA ) was not shifted , indicating specific binding of RcsB to the flhDC promoter .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsB	TU	flhDC	regulator	27206164	39	ver/dev	A control DNA fragment was not shifted , indicating specific binding of RcsB to the flhDC promoter .	213	A control DNA fragment ( gyrA ) was not shifted , indicating specific binding of RcsB to the flhDC promoter .	8	RCSB-RFLM PROTEIN COMPLEX BINDS TO A RCSB BOX DOWNSTREAM OF THE P1 TRANSCRIPTIONAL START SITE OF FLHDC	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsB	TU	flhDC	regulator	27206164	47	ver/dev	A. Dose response curve of the binding of gray and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using MST .	259	A. Dose response curve of the binding of RcsB protein ( gray ) and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis ( MST ) .	10	RFLM ENHANCES BINDING AFFINITY OF RCSB TO THE FLHDC TARGET PROMOTER DNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	TU	flhDC	regulator	27206164	47	ver/dev	A. Dose response curve of the binding of gray and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis .	259	A. Dose response curve of the binding of RcsB protein ( gray ) and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis ( MST ) .	10	RFLM ENHANCES BINDING AFFINITY OF RCSB TO THE FLHDC TARGET PROMOTER DNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	TU	flhDC	regulator	27206164	47	ver/dev	A. Dose response curve of the binding of RcsB protein and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using MST .	259	A. Dose response curve of the binding of RcsB protein ( gray ) and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis ( MST ) .	10	RFLM ENHANCES BINDING AFFINITY OF RCSB TO THE FLHDC TARGET PROMOTER DNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	TU	flhDC	regulator	27206164	47	ver/dev	A. Dose response curve of the binding of RcsB protein and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis .	259	A. Dose response curve of the binding of RcsB protein ( gray ) and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis ( MST ) .	10	RFLM ENHANCES BINDING AFFINITY OF RCSB TO THE FLHDC TARGET PROMOTER DNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	TU	flhDC	regulator	27206164	51	ver/dev	In the present study , we elucidated the mode-of-action of RcsB in regulation of flhDC .	281	In the present study , we elucidated the mode-of-action of RcsB and RflM in regulation of flhDC .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	regulator	27206164	60	ver/dev	We thus propose that RflM enables a stable binding of a RcsB-RflM heterodimer to the flhDC promoter .	306	We thus propose that RflM modulates binding affinity of RcsB for its target DNA and enables a fast and stable binding of a RcsB-RflM heterodimer to the flhDC promoter .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	TU	flhDC	regulator	27206164	60	ver/dev	We thus propose that RflM enables a fast binding of a RcsB-RflM heterodimer to the flhDC promoter .	306	We thus propose that RflM modulates binding affinity of RcsB for its target DNA and enables a fast and stable binding of a RcsB-RflM heterodimer to the flhDC promoter .	11	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RcsB	TU	flhDC	regulator	27206164	63	ver/dev	the P1flhDC promoter _ resulting in high affinity binding of a RcsB-RflM heterodimer and repression of flhDC operon transcription	316	RflM would then be able to subsequently direct an existing pool of unphosphorylated RcsB to its target DNA downstream of the P1flhDC promoter resulting in high affinity binding of a RcsB-RflM heterodimer and repression of flhDC operon transcription .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	regulator	27206164	64	ver/dev	Phosphorylated RcsB is able to bind as homodimer with low affinity to the RcsB box in the flhDC promoter region .	338	Phosphorylated RcsB is able to bind as homodimer with low affinity to the RcsB box in the flhDC promoter region .	13	BACTERIAL STRAINS, PLASMIDS AND MEDIA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RcsB	TU	flhDC	regulator	28973452	3	ver/dev	RcsB also regulate cell motility by interacting with the flhDC promoter .	29	RcsB , H-NS and RtsB also regulate cell motility by interacting with the flhDC promoter ( 11 -- 13 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	regulator	33638994	0	ver/dev	Our structural data reveal that RcsB binds promoters of flhDC in a dimeric active conformation .	17	Our structural data reveal that RcsB binds promoters of target genes such as rprA and flhDC in a dimeric active conformation .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	rck	repressor	25080967	36	ver/dev	The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS .	315	The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS ( Ono et al. , 2005 ; Navarre et al. , 2006 ) .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	rck	repressor	25080967	36	ver/dev	The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS .	315	The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS ( Ono et al. , 2005 ; Navarre et al. , 2006 ) .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	dsbA	regulator	11254626	1	att	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	208	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	6	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	ssrA	activator	27564394	6	att	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	virB	activator	11577150	2	ver/dev	Site of transcriptional activation of virB on the large plasmid of Shigella flexneri 2a by a member of the AraC family of transcriptional activators .	430	Site of transcriptional activation of virB on the large plasmid of Shigella flexneri 2a by VirF , a member of the AraC family of transcriptional activators .	15	GUZMAN, L. M., BELIN, D., CARSON, M. J. & BECKWITH, J. (1995).	unidentified plasmid;Shigella flexneri	0.5	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilE	repressor	27564394	6	ver/dev	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliA	repressor	11237608	0	ver/dev	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by ¯ iA * mutan .	50	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino acid residues of s28 that interact with FlgM , we carried out a selection for ¯ iA mutants defective for negative regulation by FlgM ( ¯ iA * mutants ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	fliA	repressor	11237608	0	ver/dev	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by Flg .	50	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino acid residues of s28 that interact with FlgM , we carried out a selection for ¯ iA mutants defective for negative regulation by FlgM ( ¯ iA * mutants ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	invF	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	avrA	activator	19042154	5	ver/dev	The results confirm the findings of Table 3 that only a effective concentration of CsrA allows the post-transcriptional activation of avrA mRNA to be translated into the AvrA protein .	187	The results summarised in Table 4 confirm the findings of Table 3 that only a critical or effective concentration of CsrA allows the post-transcriptional activation of avrA mRNA to be translated into the AvrA protein which is achieved by the counteracting ncRNA CsrB .	13	THE POST-TRANSCRIPTIONAL CONTROL FACTOR IS THE CSRA PROTEIN TOGETHER WITH THE NCRNA CSRB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	avrA	activator	19042154	5	ver/dev	The results confirm the findings of Table 3 that only a critical concentration of CsrA allows the post-transcriptional activation of avrA mRNA to be translated into the AvrA protein .	187	The results summarised in Table 4 confirm the findings of Table 3 that only a critical or effective concentration of CsrA allows the post-transcriptional activation of avrA mRNA to be translated into the AvrA protein which is achieved by the counteracting ncRNA CsrB .	13	THE POST-TRANSCRIPTIONAL CONTROL FACTOR IS THE CSRA PROTEIN TOGETHER WITH THE NCRNA CSRB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	stiC	regulator	8045891	0	ver/dev	The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiC , has been characterized .	9	The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiA , stiB , and stiC , has been characterized .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiC	regulator	8045891	13	ver/dev	Since stiC loci are regulated by RpoS , we wanted to examine the combined effects of sti mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiC	regulator	8045891	13	ver/dev	Since stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .	115	Since the stiA , stiB , and stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS and sti mutations on starvation survival .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	stiC	regulator	8045891	14	ver/dev	Role of the altermative a factor RpoS , in the the regulation of stiC .	145	Role of the altermative a factor RpoS , ovra , in the the regulation of starvation survival genes stiA and stiC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	stiC	regulator	8045891	15	ver/dev	Role of the altermative a factor RpoS , in the the regulation of stiC .	160	Role of the altermative a factor RpoS , ovra , in the the regulation of starvation survival genes stiA and stiC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	stiC	regulator	8045891	24	ver/dev	On the basis of the fact that stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	225	On the basis of the fact that stiA , stiB , and stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA and stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RpoS	gene	stiC	regulator	8045891	24	ver/dev	On the basis of the fact that stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA are not induced and/or because stiB is overexpressed in an rpoS mutant .	225	On the basis of the fact that stiA , stiB , and stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA and stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , stationary-phase , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , stationary-phase , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , stationary-phase , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , stationary-phase , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , stationary-phase , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , stationary-phase , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , stationary-phase , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , stationary-phase , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	12675803	1	ver/dev	Transcription of the flhDC operon is known to be regulated by signals from a network of OmpR .	44	Transcription of the flhDC operon is known to be regulated by signals from a network of cell components including CRP , OmpR , H-NS and the DnaK-DnaJ-GrpE system ( Yokota and Gots , 1970 ; Shi et al. , 1992 ; Bertin et al. , 1994 ; Kutsukake , 1997 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	TU	flhDC	regulator	12753201	1	ver/dev	Emerging evidence indicates that OmpR regulates regulation of the flagellar operon flhDC .	29	Emerging evidence indicates that OmpR regulates many additional genes outside the porin repertoire ( Oshima et al. , 2002 ) , including regulation of the flagellar operon flhDC ( Shin and Park , 1995 ) , curli fimbrial expression ( Vidal et al. , 1998 ) and cryptic porins ompS1 and ompS2 in S. typhi ( Fernandez-Mora et al. , 1995 ; Oropeza et al. , 1999 ) .	3	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	TU	flhDC	regulator	12753201	1	ver/dev	Emerging evidence indicates that OmpR regulates regulation of the flagellar operon flhDC .	29	Emerging evidence indicates that OmpR regulates many additional genes outside the porin repertoire ( Oshima et al. , 2002 ) , including regulation of the flagellar operon flhDC ( Shin and Park , 1995 ) , curli fimbrial expression ( Vidal et al. , 1998 ) and cryptic porins ompS1 and ompS2 in S. typhi ( Fernandez-Mora et al. , 1995 ; Oropeza et al. , 1999 ) .	3	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	TU	flhDC	regulator	24031550	8	ver/dev	fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC by OmpR .	268	fljB : z66 at low osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC and fliA by OmpR .	5	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
OmpR	TU	flhDC	regulator	26441883	4	ver/dev	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of flagellation by activation of the flagellar operon flhDC .	207	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility and flagellation by activation of the flagellar operon flhDC ( Hu et al. , 2009 ; Raczkowska et al. , 2011b ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	26441883	4	ver/dev	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility by activation of the flagellar operon flhDC .	207	Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility and flagellation by activation of the flagellar operon flhDC ( Hu et al. , 2009 ; Raczkowska et al. , 2011b ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	26441883	42	ver/dev	Positive regulation of flhDC expression by OmpR in Yersinia pseudotuberculosis .	990	Positive regulation of flhDC expression by OmpR in Yersinia pseudotuberculosis .	53	REFERENCES	Yersinia pseudotuberculosis	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	flhDC	regulator	26441883	46	ver/dev	OmpR controls Yersinia enterocolitica motility by positive regulation of flhDC expression .	1311	OmpR controls Yersinia enterocolitica motility by positive regulation of flhDC expression .	81	REFERENCES	Yersinia enterocolitica	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	flhDC	regulator	32032766	0	ver/dev	Furthermore , the flhDC operon was reported to be regulated by RpoS , OmpR .	151	Furthermore , the flhDC operon was reported to be activated during the stationary phase under high osmolarity stress and regulated by several regulators ( such as , RpoS , OmpR , and Fis ) [ 17,24 ] .	17	3.2. EXPRESSION AND REGULATION OF ASFD IN S. TYPHI	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	TU	flhDC	regulator	32032766	3	ver/dev	Furthermore , we utilized qRT-PCR to investigate the regulation of OmpR on the flhDC operon .	194	Furthermore , we utilized qRT-PCR to investigate the regulation of RpoS , OmpR , Fis , and Hfq on AsfD and the flhDC operon .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	gyrA	repressor	12898222	2	ver/dev	Fis represses transcription of the gyrA genes in E. coli .	18	Fis represses transcription of the gyrA and gyrB genes in E. coli ( Schneider et al. 1999 ) .	3	INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	gyrA	repressor	12898222	26	ver/dev	Thus , Fis has the potential to act as a repressor at the S. enterica gyrA promoter by interfering with RNA polymerase binding , as it does in E. coli .	214	Thus , Fis has the potential to act as a repressor at the S. enterica gyrA promoter by interfering with RNA polymerase binding , as it does in E. coli .	18	DISCUSSION	Salmonella;Salmonella;Escherichia coli	0.5	L1	OTHER	Analysis	OTHER	Other	Level 1
Fis	gene	gyrA	repressor	12898222	28	ver/dev	The retention of Fis-mediated repression of gyrA in S. enterica despite the radically different nucleotide sequence found immediately upstream of the Pribnow box is indicative of the physiological importance for the cell of regulation of gyrase expression by Fis .	217	The retention of Fis-mediated repression of gyrA in S. enterica despite the radically different nucleotide sequence found immediately upstream of the Pribnow box is indicative of the physiological importance for the cell of regulation of gyrase expression by Fis .	18	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrA	repressor	16999831	1	ver/dev	the Fis protein is a repressor of gyrA transcription	44	Second , the Fis protein is a repressor of gyrA and gyrB transcription ( Schneider et al. , 1999 ; Keane and Dorman , 2003 ) and it is an activator of topA , at least under certain conditions ( Weinstein-Fischer et al. , 2000 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrA	repressor	21276095	2	ver/dev	In E. coli , FIS binds the gyrA promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrA .	40	In E. coli , FIS binds the gyrA and gyrB promoters to repress their expression ( Schneider et al. , 1999 ) ; similarly , FIS has been found to repress S. enterica gyrA and gyrB ( Keane and Dorman , 2003 ) .	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
UhpA	gene	uhpT	activator	16443238	37	ver/dev	Separate contributions of UhpA to activation of transcription of the uhpT promoter of Escherichia coli .	684	Separate contributions of UhpA and CAP to activation of transcription of the uhpT promoter of Escherichia coli .	61	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
UhpA	gene	uhpT	activator	19727945	1	ver/dev	Upon phosphoryl transfer , the response regulator UhpA -LRB- presumably phosphorylated on the conserved Asp-54 -RRB- shows enhanced affinity for the uhpT promoter , initiates uhpT transcription .	40	Upon phosphoryl transfer , the response regulator UhpA ( presumably phosphorylated on the conserved Asp-54 ) shows enhanced affinity for the uhpT promoter , and toge-ther with the catabolite gene activator protein , initiates uhpT transcription [ 26 ] .	2	INTRODUCTION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
FNR	gene	rnc	regulator	33524062	9	ver/dev	Analysis of binding of FNR to rnc .	595	Analysis of binding of FNR and ArcA to rnc , rng , and hns promoters .	33	ENO LEVELS WERE SET TO 1. FOR (B) AND (C), M; SIZE MARKER. (TIF)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	macA	repressor	16359323	3	ver/dev	In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	repressor	16359323	3	ver/dev	In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	repressor	16359323	3	ver/dev	In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	repressor	16359323	3	ver/dev	In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	repressor	24169575	0	ver/dev	macA transcript levels are elevated in 12 h postinfection , consistent with potential rapid inactivation of PhoP .	211	macA and macB transcript levels are elevated in mRNA isolated from Salmonella-infected J774 macrophage-like cells at later time points , including 4 , 8 , and 12 h postinfection ( 73 , 74 ) , consistent with potential rapid inactivation of PhoP and with our data .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	macA	repressor	24169575	0	ver/dev	macA transcript levels are elevated in 8 h postinfection , consistent with potential rapid inactivation of PhoP .	211	macA and macB transcript levels are elevated in mRNA isolated from Salmonella-infected J774 macrophage-like cells at later time points , including 4 , 8 , and 12 h postinfection ( 73 , 74 ) , consistent with potential rapid inactivation of PhoP and with our data .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	macA	repressor	24169575	0	ver/dev	macA transcript levels are elevated in 4 h postinfection , consistent with potential rapid inactivation of PhoP .	211	macA and macB transcript levels are elevated in mRNA isolated from Salmonella-infected J774 macrophage-like cells at later time points , including 4 , 8 , and 12 h postinfection ( 73 , 74 ) , consistent with potential rapid inactivation of PhoP and with our data .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	araE	activator	24272778	21	att	To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .	251	To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	araE	activator	25991823	5	ver/dev	an allosteric change enables AraC to activate the expression of araE	211	In the bacterial cytoplasm , L-arabinose binds AraC and causes an allosteric change that enables AraC to activate the expression of genes involved in L-arabinose catabolism , including araE ( Schleif 2010 ) .	13	SPI-1 REPRESSION BY L-ARABINOSE IS INDEPENDENT OF ARAC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	araE	activator	25991823	8	ver/dev	As AraC activates araE transcription , suppression in an AraCˉ background might be caused by a decrease of intracellular L-arabinose due to lack of AraE permease .	216	As AraC activates araE transcription , suppression in an AraCˉ background might be caused by a decrease of intracellular L-arabinose due to lack of AraE permease .	13	SPI-1 REPRESSION BY L-ARABINOSE IS INDEPENDENT OF ARAC	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	yqjB	regulator	15225317	18	ver/dev	This raised the possibility that the yqjA and/or yqjB genes might be regulated by the PhoP protein .	174	This raised the possibility that the yqjA and/or yqjB genes might be required for magainin 2 resistance and regulated by the PhoP protein .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
TyrR	gene	aroP	regulator	32111072	0	ver/dev	the divergent TyrR _ regulated P3 promoter of the aroP gene	13	We show that , in both E. coli and S. bongori , the divergent TyrR regulated P3 promoter of the aroP gene , encoding an aromatic amino acid membrane transporter , drives usp transcription while H-NS acts antagonistically repressing expression .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TyrR	gene	aroP	regulator	32111072	9	ver/dev	To ascertain whether the TyrR transcription regulator is also involved in urea mediated regulation of aroP P3 , β-galactosidase activity was also investigated in the tyrR-defective strain .	299	To ascertain whether the TyrR transcription regulator is also involved in urea mediated regulation of aroP P3 , β-galactosidase activity was also investigated in the tyrR-defective strain .	16	3.7. UREA MEDIATED ACTIVATION OF PROMOTER P3	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
TyrR	gene	aroP	regulator	32111072	10	ver/dev	the divergent TyrR _ regulated aroP P3 promoter	336	Here we demonstrated that PAIusp usurped the divergent TyrR regulated aroP P3 promoter resulting in adjustment of PAIusp gene expression with amino acid availability in the environment .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	pagC	regulator	19843227	36	ver/dev	Two StpA-repressed PhoP-dependent genes _ bound by pagC	262	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MltC	gene	csgD	activator	25437188	39	att	Therefore , the MltE MltC-dependent regulation of csgD expression and rdar morphotype development occurs independently of major signaling pathways sensing cell wall disturbance and turnover , and regulating biofilm formation , suggesting the existence of a novel signaling pathway .	384	Therefore , the MltE MltC-dependent regulation of csgD expression and rdar morphotype development occurs independently of major signaling pathways sensing cell wall disturbance and turnover , and regulating biofilm formation , suggesting the existence of a novel signaling pathway .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	1	ver/dev	The mechanism of this SPI-1 repression by SsrB acts upon hilA regulatory genes .	42	The mechanism of this SPI-1 repression by SsrB was direct and acts upon the hilD and hilA regulatory genes .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	6	ver/dev	Together , these results demonstrate that SsrB represses the transcription of hilA .	126	Together , these results demonstrate that SsrB represses the transcription of the SPI-1 regulatory genes hilD , hilA and invF .	7	SSRB REPRESSES THE SPI-1 REGULATORY CASCADE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	7	ver/dev	SsrB directly represses hilA	127	SsrB directly represses hilD and hilA	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	8	ver/dev	To determine whether SsrB indirectly represses the expression of hilA , we analyzed the interaction of SsrB with the regulatory regions of these genes by EMSAs .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	8	ver/dev	To determine whether SsrB indirectly represses the expression of hilA , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility-shift assays .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	8	ver/dev	To determine whether SsrB directly represses the expression of hilA , we analyzed the interaction of SsrB with the regulatory regions of these genes by EMSAs .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	8	ver/dev	To determine whether SsrB directly represses the expression of hilA , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility-shift assays .	128	To determine whether SsrB directly or indirectly represses the expression of hilD , hilA , and invF , we analyzed the interaction of SsrB with the regulatory regions of these genes by electro-phoretic mobility shift assays ( EMSAs ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	18	ver/dev	SsrB directly represses the hilA SPI-1 regulatory genes .	158	SsrB directly represses the hilD and hilA SPI-1 regulatory genes .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	19	ver/dev	To determine whether SsrB mediates repression of hilA at any of the SsrB-binding sites we predicted bioinformatically , four different hilA-cat transcriptional-fusions were constructed that have 5 ' or 3 ' deletions ( or both ) with respect to the hilA-cat-410 +446 fusion ( Fig 4B ) .	167	To determine whether SsrB mediates repression of hilA at any of the SsrB-binding sites we predicted bioinformatically , four different hilA-cat transcriptional fusions were constructed that have 5 ' or 3 ' deletions ( or both ) with respect to the hilA-cat-410 +446 fusion that showed repression by SsrB ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	hilA	repressor	28704543	19	ver/dev	the hilA-cat-410 +446 fusion showed repression by SsrB	167	To determine whether SsrB mediates repression of hilA at any of the SsrB-binding sites we predicted bioinformatically , four different hilA-cat transcriptional fusions were constructed that have 5 ' or 3 ' deletions ( or both ) with respect to the hilA-cat-410 +446 fusion that showed repression by SsrB ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	22	ver/dev	the activity of hilA-cat-35 +446 _ suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35	174	Notably , the presence of pK3-SsrB reduced the expression of hilA-cat-410 +66 and hilA-cat-100 +6 , but it did not affect the activity of hilA-cat-35 +6 and hilA-cat-35 +446 ( Fig 6A , 6B , 6C and 6D ) , suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35 .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	22	ver/dev	the activity of hilA-cat-35 +6 _ suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35	174	Notably , the presence of pK3-SsrB reduced the expression of hilA-cat-410 +66 and hilA-cat-100 +6 , but it did not affect the activity of hilA-cat-35 +6 and hilA-cat-35 +446 ( Fig 6A , 6B , 6C and 6D ) , suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35 .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	22	ver/dev	the activity of Fig 6A , 6D _ suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35	174	Notably , the presence of pK3-SsrB reduced the expression of hilA-cat-410 +66 and hilA-cat-100 +6 , but it did not affect the activity of hilA-cat-35 +6 and hilA-cat-35 +446 ( Fig 6A , 6B , 6C and 6D ) , suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35 .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	22	ver/dev	the activity of Fig 6A , 6C _ suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35	174	Notably , the presence of pK3-SsrB reduced the expression of hilA-cat-410 +66 and hilA-cat-100 +6 , but it did not affect the activity of hilA-cat-35 +6 and hilA-cat-35 +446 ( Fig 6A , 6B , 6C and 6D ) , suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35 .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	22	ver/dev	the activity of Fig 6A , 6B _ suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35	174	Notably , the presence of pK3-SsrB reduced the expression of hilA-cat-410 +66 and hilA-cat-100 +6 , but it did not affect the activity of hilA-cat-35 +6 and hilA-cat-35 +446 ( Fig 6A , 6B , 6C and 6D ) , suggesting that SsrB mediates repression of hilA by acting on the region between -100 to -35 .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	23	ver/dev	The SsrB-binding sites _ involved in repression of hilA	181	The SsrB-binding sites involved in repression of hilD or hilA are displayed as blue boxes below or above the respective regulatory region , which indicates the sense and anti-sense strand of DNA , respectively ; their respective 18-bp sequence is shown .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	27	ver/dev	To determine whether SsrB mediates direct repression of hilA at this site , we mutated this site in the hilA-cat-100 +6 fusion by substituting five nucleotides within the predicted SsrB-binding site .	202	To determine whether SsrB mediates direct repression of hilA at this site , we mutated this site in the hilA-cat-100 +6 fusion by substituting five nucleotides within the predicted SsrB-binding site ( Fig 7 ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	hilA	repressor	28704543	30	ver/dev	These results show that SsrB represses hilA by binding to the site .	207	These results show that SsrB represses hilA by binding to the site centered at position -70 that overlaps a HilD-binding site , which suggested that SsrB inhibits the HilD-mediated expression of hilA .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	30	ver/dev	position -70 overlaps a HilD-binding site , which suggested SsrB inhibits the HilD-mediated expression of hilA	207	These results show that SsrB represses hilA by binding to the site centered at position -70 that overlaps a HilD-binding site , which suggested that SsrB inhibits the HilD-mediated expression of hilA .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	32	ver/dev	SsrB represses hilA by binding to the regulatory region between positions -100 to -35 .	213	SsrB represses hilA by binding to the regulatory region between positions -100 to -35 .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	34	ver/dev	SsrB represses HilD-mediated expression of hilA by binding to a sequence .	223	SsrB represses HilD-mediated expression of hilA by binding to a sequence overlapping the HilD-binding sequence upstream of the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	36	ver/dev	100 +6 fusions in the ΔSPI-1 ΔrtsA ΔCthns ns mut , which further indicates that SsrB inhibits the HilD-mediated expression of hilA .	233	100 +6 fusions in the ΔSPI-1 ΔrtsA ΔCthns mutant ( Fig 7B and 7D ) , which further indicates that SsrB inhibits the HilD-mediated expression of hilA .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilA	repressor	28704543	37	ver/dev	Taken together , these results strongly support that SsrB represses the expression of hilA by preventing HilD from binding .	234	Taken together , these results strongly support that SsrB represses the expression of hilA by preventing HilD from binding .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	38	ver/dev	SsrB can also repress hilA through an indirect mechanism by negatively regulating the expression of hilD .	235	SsrB can also repress hilA through an indirect mechanism by negatively regulating the expression of hilD .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	46	ver/dev	a mechanism whereby SsrB represses the SPI-1 genes by directly acting on hilA regulatory genes	293	Our data strongly support a mechanism whereby SsrB represses the SPI-1 genes by directly acting on the hilD and hilA regulatory genes .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	hilA	repressor	28704543	49	ver/dev	SsrB represses hilA in-vivo .	302	SsrB represses hilA in vivo .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	28704543	58	ver/dev	hilA _ affecting repression by SsrB	657	Mutations in hilA affecting repression by SsrB also affect activation by HilD .	25	SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	repressor	30355489	16	ver/dev	For example , SsrB has been shown to directly repress hilA regulatory genes .	195	For example , SsrB has been shown to directly repress the hilD and hilA regulatory genes that activate SPI-1 gene expression involved in assembling the T3SS-1 ( Pérez - Morales et al. , 2017 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	tlpA	regulator	16782389	2	ver/dev	In agreement with that , at logarithmic phase , higher expression of tlpA : : lacZ was found in the rpoS background vs. the wild-type , suggesting a possible role for RpoS in the regulation of tlpA .	146	In agreement with that , during stationary phase , but not at logarithmic phase , higher expression of tlpA : : lacZ was found in the rpoS background vs. the wild-type ( Fig. 3B , P < 0.0001 ) , suggesting a possible role for RpoS in the regulation of tlpA .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	tlpA	regulator	16782389	2	ver/dev	In agreement with that , during stationary-phase , higher expression of tlpA : : lacZ was found in the rpoS background vs. the wild-type , suggesting a possible role for RpoS in the regulation of tlpA .	146	In agreement with that , during stationary phase , but not at logarithmic phase , higher expression of tlpA : : lacZ was found in the rpoS background vs. the wild-type ( Fig. 3B , P < 0.0001 ) , suggesting a possible role for RpoS in the regulation of tlpA .	19	3.4. THE RESPONSE REGULATOR PHOP REPRESSES THE EXPRESSION OF TLPA	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	tlpA	regulator	16782389	7	ver/dev	In agreement with this , higher expression levels of tlpA : : lacZ were found in stationary-phased culture , in the absence of the alternative stationary-phase sigma factor RpoS , indicating that RpoS plays a role in the regulation of tlpA .	310	In agreement with this , higher expression levels of tlpA : : lacZ were found in stationary phased culture , in the absence of the alternative stationary phase sigma factor RpoS , indicating that RpoS plays a role in the regulation of tlpA .	23	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompX	regulator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	acrA	regulator	21148208	20	ver/dev	Therefore , SoxS is proposed to bind to the upstream region of acrA .	262	Therefore , SoxS is proposed to bind to the upstream region of acrA and directly induce acrAB .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SoxS	gene	acrA	regulator	21148208	21	ver/dev	This suggests that SoxS competitively bind to the upstream region of acrA .	263	This suggests that RamA and SoxS competitively bind to the upstream region of acrA .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NagC	gene	chiP	regulator	24450479	7	ver/dev	ChbR only binds in Salmonella DNase I footprinting confirmed that NagC bound to a site upstream of chiP as well as in E.	66	NagC binds upstream of chiP in E. coli and Salmonella but ChbR only binds in Salmonella DNase I footprinting confirmed that NagC bound to a site upstream of chiP overlapping the − 10 and − 35 regions of the chiP promoter ( site NagC1 ) in S. enterica serovar Typhimurium LT2 ( henceforth referred to as Salmonella ) as well as in E. coli ( Fig. 2 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
NagC	gene	chiP	regulator	24450479	19	ver/dev	The chiP gene is under the transcriptional control of the NagC repressor	90	The chiP gene is under the transcriptional control of the NagC repressor	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	regulator	24450479	32	ver/dev	We have shown that the chiP gene , is under the control of GlcNAc operon repressor , NagC , in Salmonella .	154	We have shown that the chiP gene , encoding a specialized porin for chitobiose and chitotriose , is under the control of the N-acetylglucosamine ( GlcNAc ) operon repressor , NagC , in both E. coli and Salmonella .	8	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	regulator	24450479	32	ver/dev	We have shown that the chiP gene , is under the control of GlcNAc operon repressor , NagC , in both E. coli .	154	We have shown that the chiP gene , encoding a specialized porin for chitobiose and chitotriose , is under the control of the N-acetylglucosamine ( GlcNAc ) operon repressor , NagC , in both E. coli and Salmonella .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	regulator	24450479	32	ver/dev	We have shown that the chiP gene , is under the control of the N-acetylglucosamine operon repressor , NagC , in Salmonella .	154	We have shown that the chiP gene , encoding a specialized porin for chitobiose and chitotriose , is under the control of the N-acetylglucosamine ( GlcNAc ) operon repressor , NagC , in both E. coli and Salmonella .	8	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	regulator	24450479	32	ver/dev	We have shown that the chiP gene , is under the control of the N-acetylglucosamine operon repressor , NagC , in both E. coli .	154	We have shown that the chiP gene , encoding a specialized porin for chitobiose and chitotriose , is under the control of the N-acetylglucosamine ( GlcNAc ) operon repressor , NagC , in both E. coli and Salmonella .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	chiP	regulator	24450479	33	ver/dev	NagC binds to two sites upstream of the chiP gene , one .	155	NagC binds to two sites upstream of the chiP gene , one spanning the interval between the − 35 and − 10 hexamers of the promoter , the other more than 200 bp upstream from the promoter .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	chiP	regulator	24450479	43	ver/dev	The strong conservation of the NagC1 site clearly implies that NagC regulation of chiP is important for these bacteria .	193	The strong conservation of the NagC1 site clearly implies that NagC regulation of chiP is important for these bacteria .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LrhA	TU	flhDC	repressor	24706743	1	ver/dev	The known posttranscriptional inhibitors of flhDC expression included in this study were LrhA .	126	The known transcriptional and posttranscriptional inhibitors of flhDC expression included in this study were EcnR , RscB , LrhA , FliT , DskA , and YdiV .	4	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
LrhA	TU	flhDC	repressor	24706743	1	ver/dev	The known transcriptional inhibitors of flhDC expression included in this study were LrhA .	126	The known transcriptional and posttranscriptional inhibitors of flhDC expression included in this study were EcnR , RscB , LrhA , FliT , DskA , and YdiV .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
NsrR	gene	ygbA	repressor	24021902	0	att	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	77	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrA	regulator	15208313	69	ver/dev	Although full resist-ance to polymyxin B requires pmrA , these genes appear to be differentially regulated by PhoP in that transcription of Fig. 1A	232	Although full resist-ance to polymyxin B requires ugtL and pmrA , these genes appear to be differentially regulated by PhoP in that transcription of the former ( Fig. 1A ) , but not the latter ,1 is dependent on the SlyA protein .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pmrA	regulator	15208313	69	ver/dev	Although full resist-ance to polymyxin B requires pmrA , these genes appear to be differentially regulated by PhoP in that transcription of the former	232	Although full resist-ance to polymyxin B requires ugtL and pmrA , these genes appear to be differentially regulated by PhoP in that transcription of the former ( Fig. 1A ) , but not the latter ,1 is dependent on the SlyA protein .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pmrA	regulator	15225317	22	att	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	192	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	8	UGTL IS AN INNER MEMBRANE PROTEIN THAT PROMOTES THE FORMATION OF MONOPHOSPHORYLATED LIPID A	Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrA	regulator	15225317	4	att	A phoP mutant is > 20 times more polymyxin B sensitive than a pmrA mutant when bacteria are grown in low Mg2 + and > 20 times more sensitive than wild-type Salmonella when bacteria are grown in the presence of Fe3 + ( Wosten et al. , 2000 ) , indicating that a PhoP-regulated PmrA-independent gene ( s ) participate ( s ) in polymyxin B resistance .	34	A phoP mutant is > 20 times more polymyxin B sensitive than a pmrA mutant when bacteria are grown in low Mg2 + and > 20 times more sensitive than wild-type Salmonella when bacteria are grown in the presence of Fe3 + ( Wosten et al. , 2000 ) , indicating that a PhoP-regulated PmrA-independent gene ( s ) participate ( s ) in polymyxin B resistance .	3	2 ND POLYMYXIN B	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pmrA	regulator	26943369	4	att	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	pmrA	regulator	26943369	4	ver/dev	To determine whether acetylation affects the activity of PhoP as a transcription factor , pmrA were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pmrA	regulator	29739882	23	ver/dev	PhoP promotes lpxT transcription directly by binding to the lpxT promoter Quantification of lpxT transcripts by qRT-PCR before pmrA mutant Salmonella high Mg2 ; normalized to the 16S ribosomal RNA transcript .	647	PhoP promotes lpxT transcription directly by binding to the lpxT promoter ( A ) Quantification of lpxT transcripts by qRT-PCR before and 60 min after switching wildtype ( WT , 14028s ) and pmrA ( EG7139 ) , phoP ( MS7953s ) , and phoP pmrA ( EG12443 ) mutant Salmonella high Mg2 + medium ( 10 mM MgCl2 ) to low Mg2 + medium ( 10 µM MgCl2 ) at pH 7.7 ; normalized to the rrs ( 16S ribosomal RNA ) transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrA	regulator	29739882	23	ver/dev	PhoP promotes lpxT transcription directly by binding to the lpxT promoter Quantification of lpxT transcripts by qRT-PCR before pmrA mutant Salmonella high Mg2 ; normalized to the rrs transcript .	647	PhoP promotes lpxT transcription directly by binding to the lpxT promoter ( A ) Quantification of lpxT transcripts by qRT-PCR before and 60 min after switching wildtype ( WT , 14028s ) and pmrA ( EG7139 ) , phoP ( MS7953s ) , and phoP pmrA ( EG12443 ) mutant Salmonella high Mg2 + medium ( 10 mM MgCl2 ) to low Mg2 + medium ( 10 µM MgCl2 ) at pH 7.7 ; normalized to the rrs ( 16S ribosomal RNA ) transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipC	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of orgA remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipC	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgK remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipC	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgH remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipC	activator	21168230	5	ver/dev	In addition , HilD directly activate sipC in non-HilA dependent manner .	344	In addition , HilD and HilC directly activate invF , sipA and sipC in non-HilA dependent manner ( Akbar et al. , 2003 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	tviA	regulator	23982073	0	ver/dev	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of CD11c dendritic cells in the lamina .	309	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR and RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes and CD11c dendritic cells in the lamina ( 37 -- 39 ) .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	tviA	regulator	23982073	0	ver/dev	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes dendritic cells in the lamina .	309	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR and RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes and CD11c dendritic cells in the lamina ( 37 -- 39 ) .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	tviA	regulator	29417203	1	ver/dev	RcsB interacts with TviA to bind to the tviA promoter to activate the Vi antigen expression .	25	RcsB interacts with TviA to bind to the tviA promoter to activate the Vi antigen expression [ 16 -- 18 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	zwf	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates Mn-containing superoxide dismutase , zwf .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	zwf	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , zwf .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	zwf	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , zwf .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	zwf	activator	12886427	0	ver/dev	SoxS protein , activates sodA , zwf .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	lptA	regulator	15866924	3	att	We recently identified a number of new Salmonella PmrA-regulated genes , including one locus with homology to both lpt-3 and lptA of N. meningitidis ( 34 ) .	32	We recently identified a number of new Salmonella PmrA-regulated genes , including one locus with homology to both lpt-3 and lptA of N. meningitidis ( 34 ) .	2	MAIN	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hilA	repressor	28575106	15	ver/dev	However , whether the repression of hilA by Fnr was induced by low O2 was not clarified in those studies .	307	However , whether the repression of hilA by Fnr was induced by low O2 was not clarified in those studies .	13	DISCUSSION	nan	1	L3	SPEC	Investigation	NEG	Other	Level 1
RpoS	gene	mlrA	regulator	24735176	7	ver/dev	mlrA expression itself is positively regulated by RpoS .	410	mlrA expression itself is positively regulated by RpoS , the stationary phase and stress response sigma-factor ( Hengge-Aronis 2002 ) .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	cueO	activator	17768242	1	ver/dev	CueR directly stimulates the transcription of cueO .	29	CueR directly stimulates the transcription of copA and cueO , coding for a P-type ATPase and a multicopper oxidase , respectively .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	cueO	activator	34125582	3	ver/dev	CueR also activates the transcription of cueO during copper-stress in S. enterica .	86	CueR also activates the transcription of cueO , copA , and cueP genes during copper stress in S. enterica ( 40 ) .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	cueO	activator	34125582	4	ver/dev	Cu - bound CueR is the transcriptional activator for cueO genes .	106	Cu ( I ) - bound CueR is the transcriptional activator for copA and cueO genes .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilD	repressor	34048498	25	ver/dev	It is reasonable to suggest that when SirA counteracts the CsrA-mediated repression of hilD , higher levels of HilE would be required to negatively control the activity of HilD .	179	It is reasonable to suggest that when SirA counteracts the CsrA-mediated repression of hilD , higher levels of HilE would be required to negatively control the activity of HilD , which can be reached with the positive regulation of the hilE expression by SirA .	9	HILE REPRESSES HILD-MEDIATED EXPRESSION OF SPI-1, SPI-2 AND SPI-5 GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxS	gene	lpxC	regulator	19917752	0	ver/dev	SoxS _ regulated , including lpxC	266	Among the genes that were upregulated in 104-cip , a number were SoxS regulated , including acnA , fpr , ribA , sodA , lpxC , and soxS itself .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	16585772	10	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .	408	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .	19	REFERENCES	Salmonella;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	17060472	11	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .	698	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .	22	REFERENCES	Salmonella;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	19074398	49	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .	1001	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .	39	REFERENCES	Salmonella;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	23651595	22	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	1190	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	77	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	26300871	41	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	750	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	19	ACKNOWLEDGMENTS	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	30716090	51	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmo-nella enterica serovar Typhimurium .	721	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Salmo-nella enterica serovar Typhimurium .	33	2	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	33613478	17	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	647	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	20	SUPPLEMENTARY TABLE 1 | PRIMERS USED IN THIS STUDY.	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	hilA	activator	33751923	30	ver/dev	Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	1895	Activation of hilA expression at low pH requires the signal sensor CpxA , but not the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .	141	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	kgtP	repressor	29857034	12	ver/dev	These results suggest that kgtP is downregulated by SlyA under evaluated conditions .	298	These results suggest that kgtP is downregulated by SlyA under evaluated conditions .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	kgtP	repressor	29857034	31	ver/dev	SlyA thus seems to downregulate kgtP expression by direct binding to the promoter region .	365	SlyA thus seems to downregulate kgtP expression by direct binding to the promoter region .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SpvR	gene	spvABC	regulator	11443102	2	ver/dev	SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	316	phase and SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	3	0	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABC	regulator	12902215	0	ver/dev	SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	305	Growth phase and SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	10	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABC	regulator	17060472	9	ver/dev	SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	539	Growth phase and SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	12	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABC	regulator	24720747	21	ver/dev	Norel , F. Growth SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	476	Coynault , C. , Robbe-Saule , V. , Popoff , M.Y. , and Norel , F. ( 1992 ) Growth phase and SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	28	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABC	regulator	24720747	21	ver/dev	Coynault , C. , Robbe-Saule , V. , Popoff , M.Y. , SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	476	Coynault , C. , Robbe-Saule , V. , Popoff , M.Y. , and Norel , F. ( 1992 ) Growth phase and SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .	28	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrCAB	regulator	11755422	1	att	PmrE/PmrF operon is involved in lipid-A and core glycosylation The PhoP-regulated locus , pmrCAB , mediates the addition of aminoarabinose and ethanolamine to lipid-A and the changes in core polysaccharide structure [ 26 , 38 , 39 ] .	112	PmrE/PmrF operon is involved in lipid A and core glycosylation The PhoP-regulated locus , pmrCAB , mediates the addition of aminoarabinose and ethanolamine to lipid A and the changes in core polysaccharide structure [ 26 , 38 , 39 ] .	8	6.1. PAGP IS AN OUTER MEMBRANE PALMITOYL TRANSFERASE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompC	regulator	18156266	14	ver/dev	As we expected , no regulation of ompC by LeuO was observed since no differences in CAT activity were detected in the presence or absence of LeuO ( data not shown ) .	244	As we expected , no regulation of ompC by LeuO was observed since no differences in CAT activity were detected in the presence or absence of LeuO ( data not shown ) .	5	FIG. 2	Felis catus;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pqaA	activator	18350168	4	att	The suppressive effects of spermine NONOate on PhoP-dependent gene transcription appear to be directly related to the production of RNS because the polyamine base spermine did not suppress the acid-induced expression of the PhoP-activated loci lpxO , pqaA , and pcgE ( fig. 6B -- D ) .	301	The suppressive effects of spermine NONOate on PhoP-dependent gene transcription appear to be directly related to the production of RNS because the polyamine base spermine did not suppress the acid-induced expression of the PhoP-activated loci lpxO , pqaA , and pcgE ( fig. 6B -- D ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	pqaA	activator	18350168	6	att	The acid-inducible expression of the PhoP-activated loci lpxO , pqaA and pcgE were monitored in the presence or absence of 250 mM spermine , 250 mM spermine NONOate or 500 mM NaNO2 ( B -- D ) .	343	The acid-inducible expression of the PhoP-activated loci lpxO , pqaA and pcgE were monitored in the presence or absence of 250 mM spermine , 250 mM spermine NONOate or 500 mM NaNO2 ( B -- D ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	flhDC	repressor	30355489	3	ver/dev	For example , SlyA is a repressor of flhDC ; however SsrB was able to repress motility in a DslyA mutant equivalently to wild-type , thus ruling out contributions by SlyA .	95	For example , SlyA is a repressor of flhDC that is activated by SsrB ; however SsrB was able to repress motility in a DslyA mutant equivalently to wild-type , thus ruling out contributions by SlyA ( Figure S3A ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SlyA	TU	flhDC	repressor	30355489	3	ver/dev	For example , SlyA is a repressor of flhDC ; however SsrB was able to repress motility in a DslyA mutant equivalently to wild-type , thus ruling out contributions by SlyA .	95	For example , SlyA is a repressor of flhDC that is activated by SsrB ; however SsrB was able to repress motility in a DslyA mutant equivalently to wild-type , thus ruling out contributions by SlyA ( Figure S3A ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
OmpR-P	gene	ssrA	regulator	12753201	16	ver/dev	Phosphorylation of OmpR stimulates DNA binding to ssrA We next measured equilibrium binding of OmpR-P to the ssrA-1 binding site .	137	Phosphorylation of OmpR stimulates DNA binding to ssrA We next measured equilibrium binding of OmpR and OmpR-P to the ssrA-1 binding site ( Fig. 5 ) .	6	PRIMER EXTENSION OF SSRA AND SSRB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ssrA	regulator	12753201	34	ver/dev	The effect of OmpR appears to be direct , based on our observation that OmpR-P binds to the intergenic region between ssrA .	218	The effect of OmpR appears to be direct , based on our observation that OmpR-P binds upstream of ssrA and to the intergenic region between ssrA and ssrB ( Fig. 6 ) .	11	THE SSRA/B REGION CONTAINS TWO PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR-P	gene	ssrA	regulator	12753201	45	ver/dev	Altogether , our data indicate that OmpR-P binds to the upstream region of ssrA .	242	Altogether , our data indicate that OmpR-P binds to the upstream region of ssrA and around the intergenic region between ssrA and ssrB ( Fig. 6 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR-P	gene	ssrA	regulator	12753201	45	ver/dev	Altogether , our data indicate that OmpR-P binds around the intergenic region between ssrA .	242	Altogether , our data indicate that OmpR-P binds to the upstream region of ssrA and around the intergenic region between ssrA and ssrB ( Fig. 6 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR-P	gene	ssrA	regulator	15491370	7	ver/dev	OmpR-P binds to sites downstream of the ssrA transcriptional start site , activating ssrA .	85	OmpR-P binds to sites upstream and downstream of the ssrA transcriptional start site , activating ssrA .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ssrA	regulator	15491370	7	ver/dev	OmpR-P binds to sites upstream of the ssrA transcriptional start site , activating ssrA .	85	OmpR-P binds to sites upstream and downstream of the ssrA transcriptional start site , activating ssrA .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ssrA	regulator	24079299	3	ver/dev	In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrA genes .	123	In low osmolarity conditions , OmpR and/or OmpR-P ( phosphorylayted OmpR present in low levels ) can bind to the upstream regions of ssrA and ssrB genes .	5	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
HilD	TU	flhDC	repressor	24706743	9	ver/dev	One HilD-activated gene product , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon .	255	One HilD-activated gene product , RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon ( 49 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	flhDC	repressor	27206164	7	ver/dev	Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV .	48	Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV ( Chubiz et al. , 2010 ; Wada et al. , 2011 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EmrR	gene	emrB	repressor	30992361	8	ver/dev	The RNA-Seq data were first validated by increased RNA levels of the emrB genes in the ΔemrR mutant , since transcription of these genes was shown to be repressed by EmrR previously .	81	The RNA-Seq data were first validated by increased RNA levels of the emrA and emrB genes in the ΔemrR mutant ( 5.7 - and 5.9-fold , respectively ; Table S3 ) , since transcription of these genes was shown to be repressed by EmrR previously ( 9 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	polB	regulator	24272778	37	att	Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .	377	Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
AraC	gene	polB	regulator	24272778	39	att	We also identified AraC-regulated genes that are transcribed due to read-through of inefficient Rho-independent terminators ( ygeA and polB ) .	384	We also identified AraC-regulated genes that are transcribed due to read-through of inefficient Rho-independent terminators ( ygeA and polB ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	polB	regulator	24272778	48	att	It is possible that some or all of the novel AraC-regulated genes have as-yet-unidentified connections to arabinose metabolism , although this seems especially unlikely for polB , which encodes a well-characterized DNA polymerase .	440	It is possible that some or all of the novel AraC-regulated genes have as-yet-unidentified connections to arabinose metabolism , although this seems especially unlikely for polB , which encodes a well-characterized DNA polymerase .	5	DISCUSSION	unidentified	1	L1	SPEC	Other	OTHER	Other	Level 1
AraC	gene	polB	regulator	24272778	46	ver/dev	polB are positively regulated by AraC due to partial read-through of Rho-independent terminators .	423	ygeA and polB are positively regulated by AraC and arabinose due to partial read-through of Rho-independent terminators ( Fig. 2 , 4 , and 5 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	polB	regulator	24272778	51	ver/dev	We did not detect regulation of polB by AraC in S. enterica .	455	We did not detect regulation of polB by AraC in S. enterica .	5	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
AraC	gene	polB	regulator	24272778	52	ver/dev	Hence , polB regulation by AraC may be widely conserved .	458	Hence , polB regulation by AraC may be widely conserved .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	invF	regulator	20008574	6	ver/dev	Dam-dependent regulation of invF was still observed in RtsA backgrounds	152	In an analogous fashion , Dam-dependent regulation of invF was still observed in HilA , HilC , and RtsA backgrounds , and no information was obtained in a HilD background ( Figure 3 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CspC	gene	uspA	activator	17081727	1	ver/dev	The CspC proteins increase stability of uspA mRNA facilitating steady-state expression .	37	The CspC and CspE proteins increase stability of uspA mRNA facilitating steady-state expression but are not involved in uspA induction during physiological stress [ 16 ] .	3	1. INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HNS	gene	ompR	repressor	12068808	35	ver/dev	The next question addressed was whether acid shock might control ompR expression by changing the phosphorylation level of OmpR or , perhaps , by modulating ompR P2 repression by H-NS .	202	The next question addressed was whether acid shock might control ompR expression by changing the phosphorylation level of OmpR or , perhaps , by modulating ompR P2 repression by H-NS .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HNS	gene	ompR	repressor	12068808	37	ver/dev	H-NS represses ompR expression .	205	H-NS represses ompR expression .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12068808	39	ver/dev	An alternative model states acid regulates ompR by modulating repression by H-NS	214	An alternative model states that acid regulates ompR by modulating repression by H-NS .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12068808	48	ver/dev	that H-NS represses ompR	254	The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12068808	55	ver/dev	autoinduction in which OmpR-P overcomes H-NS repression of ompR on OmpR-P-dependent ATR gene promoters	282	These include ( i ) increasing OmpR levels through autoinduction in which OmpR-P overcomes H-NS repression of ompR ; ( ii ) binding of OmpR-P to specific ATR genes ; and ( iii ) an undefined effect of acid pH on OmpR-P-dependent ATR gene promoters .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12080060	35	ver/dev	The next question addressed was whether acid shock might control ompR expression by changing the phosphorylation level of OmpR or , perhaps , by modulating ompR P2 repression by H-NS .	202	The next question addressed was whether acid shock might control ompR expression by changing the phosphorylation level of OmpR or , perhaps , by modulating ompR P2 repression by H-NS .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HNS	gene	ompR	repressor	12080060	37	ver/dev	H-NS represses ompR expression .	205	H-NS represses ompR expression .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12080060	39	ver/dev	An alternative model states acid regulates ompR by modulating repression by H-NS	214	An alternative model states that acid regulates ompR by modulating repression by H-NS .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12080060	48	ver/dev	that H-NS represses ompR	254	The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	repressor	12080060	55	ver/dev	autoinduction in which OmpR-P overcomes H-NS repression of ompR on OmpR-P-dependent ATR gene promoters	282	These include ( i ) increasing OmpR levels through autoinduction in which OmpR-P overcomes H-NS repression of ompR ; ( ii ) binding of OmpR-P to specific ATR genes ; and ( iii ) an undefined effect of acid pH on OmpR-P-dependent ATR gene promoters .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	fimA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp emphasize the regulatory linkage between ancestral metabolic pathways .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of the papBA operon by Lrp demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimA	repressor	31139165	11	ver/dev	More recent studies revealed that direct binding of Lrp to the fimA promoter is indispensable for repression of T1F expression .	125	More recent studies revealed that direct binding of Lrp to the fimA promoter is indispensable for activation as well as repression of T1F expression ( Baek et al. , 2011 ) .	5	GLOBAL REGULATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	osmY	activator	19843227	29	att	This was exemplified by the expression profile of the s38-dependent gene osmY ; the expression of osmY is StpA-dependent ( i.e. altered in the stpA deletion strain ) during mid-exponential-growth ( Fig. 7C ) .	188	This was exemplified by the expression profile of the s38-dependent gene osmY ; the expression of osmY is StpA-dependent ( i.e. altered in the stpA deletion strain ) during mid-exponential growth ( Fig. 7C ) .	13	STPA MODULATES S38 STABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PrpR	gene	prpBCDE	regulator	12700259	0	ver/dev	These redundant systems of propionyl-CoA synthesis are needed because the prpE gene is part of the prpBCDE operon under the control of the PrpR regulatory protein .	11	These redundant systems of propionyl-CoA synthesis are needed because the prpE gene encoding the propionyl-CoA synthetase enzyme is part of the prpBCDE operon under the control of the PrpR regulatory protein , which needs 2-meth-ylcitrate as a coactivator .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PrpR	gene	prpBCDE	regulator	12700259	2	ver/dev	the PrpR regulatory protein controls the expression of the prpBCDE operon	274	PrpC catalyzes the condensation of Pro-CoA and oxaloacetate to yield 2-methylcitrate , the coactivator molecule sensed by the PrpR regulatory protein that controls the expression of the prpBCDE operon encoding propionate catabolic enzymes ( 31 , 42 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpBCDE	regulator	12700259	2	ver/dev	the PrpR regulatory protein controls the expression of the prpBCDE operon	274	PrpC catalyzes the condensation of Pro-CoA and oxaloacetate to yield 2-methylcitrate , the coactivator molecule sensed by the PrpR regulatory protein that controls the expression of the prpBCDE operon encoding propionate catabolic enzymes ( 31 , 42 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PrpR	gene	prpBCDE	regulator	15528672	14	ver/dev	PrpR protein bound to the DNA region between the prpBCDE operon and prpR .	404	PrpR protein bound to the DNA region between the prpBCDE operon and prpR ( Figs 1a and 4a ) .	13	THE PRPR BINDING SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	crl	repressor	20008066	11	ver/dev	crl transcription in E. coli W3110 is repressed by Crl -LRB- by more than 10-fold -RRB- .	417	crl transcription in E. coli W3110 is repressed by Fur ( by 100-fold ) and by Crl ( by more than 10-fold ) ( 28 ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	crl	repressor	20008066	16	ver/dev	These results suggested that crl transcription is not repressed by Crl in ATCC 14028 .	423	These results suggested that crl transcription is not repressed by Fur and Crl in ATCC 14028 .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
SoxS	gene	acrB	activator	34202800	6	ver/dev	SoxS , , are involved in activating acrB expression .	254	Three homologous transcriptional activators , RamA , SoxS , and MarA , controlled by RamR , SoxR , and MarR , are involved in activating acrB and tolC expression [ 68 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	sprB	repressor	31484980	28	ver/dev	To know whether HilD induces expression of sprB by a similar way , we analyzed if inactivation of H-NS leads to HilD-independent expression of this gene .	157	To know whether HilD induces expression of sprB by a similar way , we analyzed if inactivation of H-NS leads to HilD-independent expression of this gene .	3	RESULTS	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
HNS	gene	sprB	repressor	31484980	33	ver/dev	These results show that H-NS directly represses expression of sprB	167	These results show that H-NS directly represses expression of sprB , but not of yobH , and that when the activity of H-NS is inactivated , or when H-NS is absent , expression of sprB becomes independent of HilD , which supports that HilD acts on this gene as an anti-H-NS factor .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	sprB	repressor	31484980	55	ver/dev	H-NS represses expression of sprB by binding the two promoter regions .	294	H-NS represses expression of sprB by binding the two promoter regions transcribing this gene .	4	METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimW	gene	fimA	repressor	22654583	3	ver/dev	These results demonstrate that the fimZ gene encodes a positive regulator for fimA , while FimW is a repressor for fimA .	363	These results demonstrate that the fimZ gene encodes a positive regulator for fimA , while FimW is a repressor for fimA [ 6 , 7 ] .	5	4. DISCUSSIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseJ	regulator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sseJ by both relief of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	sseJ	regulator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sseJ by both direct activation of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	hns	activator	16763111	3	att	This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS - and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .	60	This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS - and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	hns	activator	16763111	3	att	This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS - and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .	60	This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS - and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	dinB	repressor	20421601	14	ver/dev	Escherichia coli where inactivation of RpoS reduced Pol IV protein levels three - to fivefold in the wild-type background , indicating that regulation of dinB expression is different in these two species	163	These results are different from those observed in Escherichia coli ( Layton and Foster 2003 ) , where inactivation of RpoS reduced Pol IV protein levels three - to fivefold in the wild-type background , indicating that regulation of dinB expression is different in these two species .	4	RESULTS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	ssaH	regulator	19126220	0	ver/dev	HilA binds the promoter of ssaH	32	These include HilA that binds and represses the promoter of ssaH [ 24 ] , and HilD that binds and activates the promoter of the ssrAB operon [ 25 ] .	3	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagD	activator	10816543	3	ver/dev	Upon analysis of alkaline phosphatase activity , it was shown that both mutations resulted in activation of the pagD : , with PhoP S93N .	97	Upon analysis of alkaline phosphatase activity , it was shown that both mutations resulted in activation of the pagD : : TnphoA fusion , with PhoP S93N resulting in 65-fold activation and PhoP Q203R resulting in 15-fold activation .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	activator	19091955	13	att	The pagD and pagC genes are PhoP-activated genes ( 9 ) located next to each other in the Salmonella chromosome but transcribed in opposite directions from a shared intergenic region .	86	The pagD and pagC genes are PhoP-activated genes ( 9 ) located next to each other in the Salmonella chromosome but transcribed in opposite directions from a shared intergenic region .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	activator	19091955	16	ver/dev	Fig. 2B _ suggesting that a single PhoP box box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	19091955	16	ver/dev	low-Mg conditions _ suggesting that a single PhoP box box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	19091955	16	ver/dev	Fig. 2B _ suggesting that a single PhoP box box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	19091955	16	ver/dev	low-Mg conditions _ suggesting that a single PhoP box box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	19091955	16	ver/dev	Fig. 2B _ suggesting that a single PhoP box box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	19091955	16	ver/dev	low-Mg conditions _ suggesting that a single PhoP box box control transcriptional activation of both pagD and pagC	92	2 or SlyA box ( SB ) is zero when bacteria are grown in low-Mg conditions ( Fig. 2B ) , suggesting that a single PhoP box and a single SlyA box control transcriptional activation of both pagD and pagC .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	30373755	12	att	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	221	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	activator	30967459	18	att	To evaluate this , macrophages were infected with wild-type and mutant Salmonella strains harboring a gfp fusion with the promoter of the PhoP-activated gene pagD , and fluorescence was measured .	181	To evaluate this , macrophages were infected with wild-type and mutant Salmonella strains harboring a gfp fusion with the promoter of the PhoP-activated gene pagD , and fluorescence was measured .	3	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	activator	30967459	9	att	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	144	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	3	RESULTS	Salmonella;unidentified plasmid;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pagD	activator	30967459	20	ver/dev	The ptsN mutant showed earlier activation of pagD expression than Fig. 5A , indicating that EIIANtr inhibits PhoP activation inside macrophages .	183	The ptsN mutant showed higher and earlier activation of pagD expression than the wild type ( Fig. 5A ) , indicating that EIIANtr inhibits PhoP activation inside macrophages .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagD	activator	30967459	20	ver/dev	The ptsN mutant showed earlier activation of pagD expression than the wild type , indicating that EIIANtr inhibits PhoP activation inside macrophages .	183	The ptsN mutant showed higher and earlier activation of pagD expression than the wild type ( Fig. 5A ) , indicating that EIIANtr inhibits PhoP activation inside macrophages .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagD	activator	30967459	20	ver/dev	The ptsN mutant showed higher activation of pagD expression than Fig. 5A , indicating that EIIANtr inhibits PhoP activation inside macrophages .	183	The ptsN mutant showed higher and earlier activation of pagD expression than the wild type ( Fig. 5A ) , indicating that EIIANtr inhibits PhoP activation inside macrophages .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	pagD	activator	30967459	20	ver/dev	The ptsN mutant showed higher activation of pagD expression than the wild type , indicating that EIIANtr inhibits PhoP activation inside macrophages .	183	The ptsN mutant showed higher and earlier activation of pagD expression than the wild type ( Fig. 5A ) , indicating that EIIANtr inhibits PhoP activation inside macrophages .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagD	activator	31370702	0	att	SPI-11 includes the PhoP-activated genes pagD and pagC , which are involved in intramacrophage survival [ 40 ] ; pagD and pagC were downregulated 2.5 - and 2.6-fold in the lon mutant , respectively ( Supplementary Table 2 ) .	219	SPI-11 includes the PhoP-activated genes pagD and pagC , which are involved in intramacrophage survival [ 40 ] ; pagD and pagC were downregulated 2.5 - and 2.6-fold in the lon mutant , respectively ( Supplementary Table 2 ) .	15	LON REGULATES THE EXPRESSION OF SEVERAL SPIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagD	activator	33045730	18	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	pagD	activator	33045730	28	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
Lrp	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of one main regulator while switching of pap is controlled by Lrp .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of one main regulator while switching of pap is controlled by Lrp .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of OxyR while switching of pap is controlled by Lrp .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of OxyR while switching of pap is controlled by Lrp .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of Fur while switching of pap is controlled by Lrp .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	agn43	regulator	31216025	6	ver/dev	Switching of agn43 is under the control of Fur while switching of pap is controlled by Lrp .	351	Switching of sci1 , agn43 , gtr and opvAB is under the control of one main regulator ( Fur or OxyR ) while switching of pap is controlled by two main regulators , Lrp and PapI ( 40,29 -- 30 ) .	31	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyA	regulator	15208313	34	att	The PhoP Protein Binds to the Promoter of the slyA Gene -- Investigation of PhoP-controlled slyA transcription has been carried out using plasmid-borne constructs harboring the slyA promoter region ( 20 ) .	147	The PhoP Protein Binds to the Promoter of the slyA Gene -- Investigation of PhoP-controlled slyA transcription has been carried out using plasmid-borne constructs harboring the slyA promoter region ( 20 ) .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyA	regulator	15208313	34	att	The PhoP Protein Binds to the Promoter of the slyA Gene -- Investigation of PhoP-controlled slyA transcription has been carried out using plasmid-borne constructs harboring the slyA promoter region ( 20 ) .	147	The PhoP Protein Binds to the Promoter of the slyA Gene -- Investigation of PhoP-controlled slyA transcription has been carried out using plasmid-borne constructs harboring the slyA promoter region ( 20 ) .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyA	regulator	15208313	7	att	The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .	30	The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	slyA	regulator	15208313	8	ver/dev	Although the mechanism remains unknown , it has been suggested that the PhoP protein regulates slyA expression indirectly because a PhoP box could not be identified in the slyA promoter region .	31	Although the mechanism by which the PhoP/PhoQ system controls slyA transcription remains unknown , it has been suggested that the PhoP protein regulates slyA expression indirectly because a PhoP box could not be identified in the slyA promoter region ( 20 ) .	2	MAIN	unidentified	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	slyA	regulator	15208313	11	ver/dev	that the PhoP protein binds to the slyA promoter	35	We establish that the PhoP protein binds to the slyA promoter and that both the PhoP and SlyA proteins bind to the ugtL promoter , suggesting that these two proteins use a feed-forward loop to control ugtL expression .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slyA	regulator	15208313	36	ver/dev	It has been suggested that the PhoP protein regulates the slyA gene indirectly because a PhoP box could not be identified in the slyA promoter .	151	It has been suggested that the PhoP protein regulates the slyA gene indirectly because a PhoP box could not be identified in the slyA promoter ( 20 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	slyA	regulator	15208313	42	ver/dev	These results indicate that the PhoP protein controls slyA transcription directly .	164	These results indicate that the PhoP protein controls slyA transcription directly .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	slyA	regulator	15208313	49	ver/dev	The PhoP protein binds to the slyA promoter .	181	The PhoP protein is required for slyA transcription and binds to the slyA promoter .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slyA	regulator	15208313	62	ver/dev	Although others have proposed that the PhoP protein regulates slyA transcription indirectly -LRB- i.e. by modulating the expression of another regulatory protein -RRB- , our results argue that PhoP controls slyA transcription directly -LRB- i.e. by binding to the slyA promoter . -RRB-	207	Although others have proposed that the PhoP protein regulates slyA transcription indirectly ( i.e. by modulating the expression of another regulatory protein ) , our results argue that PhoP controls slyA transcription directly ( i.e. by binding to the slyA promoter . )	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	slyA	regulator	15208313	62	ver/dev	Although others have proposed that the PhoP protein regulates slyA transcription indirectly -LRB- i.e. by modulating the expression of another regulatory protein -RRB- , our results argue that PhoP controls slyA transcription directly -LRB- i.e. by binding to the slyA promoter . -RRB-	207	Although others have proposed that the PhoP protein regulates slyA transcription indirectly ( i.e. by modulating the expression of another regulatory protein ) , our results argue that PhoP controls slyA transcription directly ( i.e. by binding to the slyA promoter . )	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	slyA	regulator	18270203	10	att	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	151	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	2	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	slyA	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
MqsA	gene	rpoS	regulator	31832871	3	ver/dev	the Escherichia coli antitoxin MqsA regulates the expression of rpoS	267	TA systems are also involved in the transcriptional regulation of some other genes ( Goeders and Van Melderen 2014 ) , e.g. , the Escherichia coli antitoxin MqsA , which regulates the expression of rpoS ( Wang et al. 2011 ) , and biofilm formation gene csgD ( Soo and Wood 2013 ) .	16	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	3	ver/dev	Furthermore , electrophoretic-mobility-shift assays showed that both H-NS bind to the ssrAB region containing the repressing sequences .	10	Furthermore , electrophoretic mobility shift assays showed that both HilD and H-NS bind to the ssrAB region containing the repressing sequences .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	17	ver/dev	the mechanism by which H-NS regulate the expression of ssrAB for the first time that HilD is able to displace H-NS from one of its target genes	47	Our results elucidate the mechanism by which HilD and H-NS regulate the expression of ssrAB and show for the first time that HilD is able to displace H-NS from one of its target genes .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	TU	ssrAB	regulator	25135218	35	ver/dev	Our data from the expression analysis showed that H-NS regulate the expression of ssrAB mainly by acting on the 55 / 119 / 336 regions , respectively .	134	Our data from the expression analysis showed that HilD and H-NS regulate the expression of ssrAB mainly by acting on the 55 / 240 and 119 / 336 regions , respectively .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	regulator	25135218	35	ver/dev	Our data from the expression analysis showed that H-NS regulate the expression of ssrAB mainly by acting on the 55 / 240 / 336 regions , respectively .	134	Our data from the expression analysis showed that HilD and H-NS regulate the expression of ssrAB mainly by acting on the 55 / 240 and 119 / 336 regions , respectively .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	regulator	25135218	36	ver/dev	To further dissect ated regulation of ssrAB , we analyzed the interaction of H-NS to different segments of EMSAs .	135	To further dissect the cis sequences required for the HilD/H-NS-medi - ated regulation of ssrAB , we analyzed the interaction of HilD and H-NS to different segments of the 302 / 478 region by electro-phoretic mobility shift assays ( EMSAs ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	36	ver/dev	To further dissect ated regulation of ssrAB , we analyzed the interaction of H-NS to different segments of the 302 / 478 region by electro-phoretic mobility-shift assays .	135	To further dissect the cis sequences required for the HilD/H-NS-medi - ated regulation of ssrAB , we analyzed the interaction of HilD and H-NS to different segments of the 302 / 478 region by electro-phoretic mobility shift assays ( EMSAs ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	48	ver/dev	In this study , we elucidated the mechanism by which H-NS regulate the expression of ssrAB .	162	In this study , we elucidated the mechanism by which HilD and H-NS regulate the expression of ssrAB and thus the SPI-2 genes ( Fig. 7 ) .	5	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HNS	TU	ssrAB	regulator	25135218	50	ver/dev	H-NS bind to the same regions of ssrAB .	165	FIG 5 HilD and H-NS bind to the same regions of ssrAB .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	55	ver/dev	Furthermore , we showed that H-NS binds to the region 111 to 287 of ssrAB .	183	Furthermore , we showed that H-NS binds to the region spanning positions 111 to 287 of ssrAB ( Fig. 5 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	57	ver/dev	Furthermore , our EMSAs revealed that H-NS binds to at least two different sites along the 111 / 287 region of ssrAB .	190	Furthermore , our EMSAs revealed that H-NS binds to at least two different sites along the 111 / 287 region of ssrAB ( Fig. 5 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	58	ver/dev	the model in which H-NS represses the expression of ssrAB initially by binding by forming a nucleoprotein filament on the promoter	191	Taken together , these results favor the model in which H-NS represses the expression of ssrAB initially by binding to two nucleation sites and then by forming a nucleoprotein filament on the promoter ( Fig. 7 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	25135218	63	ver/dev	The regions _ required for the regulation of ssrAB by H-NS	203	The regions required for the regulation of ssrAB by HilD and H-NS , defined in this study by expression and binding assays , are shown .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	regulator	30718301	10	ver/dev	On the other hand , the expression of ssrAB is also controlled by the nucleoid-associated protein H-NS .	48	On the other hand , the expression of ssrAB is also controlled by negative regulators , such as the nucleoid-associated protein H-NS ( 18 , 19 , 52 -- 54 ) , which acts as a global transcriptional factor in many bacteria ( 55 , 56 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	regulator	30718301	69	ver/dev	FIG 8 Model for the regulation of ssrAB by H-NS .	211	FIG 8 Model for the regulation of ssrAB by SlyA , HilD , OmpR , and H-NS .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DksA	gene	hmp	regulator	22311927	3	ver/dev	250 M Fig. 4A _ suggesting that DksA is not involved in the regulation of hmp transcription	155	Transcription of the hmp gene was induced 20-fold in both wild-type and dksA-de-ficient Salmonella strains 1.5 h after treatment with 250 M the NO-donor spermine NONOate ( Fig. 4A ) , suggesting that DksA is not involved in the regulation of hmp transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
DksA	gene	hmp	regulator	22311927	3	ver/dev	250 M the NO-donor spermine NONOate _ suggesting that DksA is not involved in the regulation of hmp transcription	155	Transcription of the hmp gene was induced 20-fold in both wild-type and dksA-de-ficient Salmonella strains 1.5 h after treatment with 250 M the NO-donor spermine NONOate ( Fig. 4A ) , suggesting that DksA is not involved in the regulation of hmp transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
DksA	gene	hmp	regulator	22311927	3	ver/dev	250 M Fig. 4A _ suggesting that DksA is not involved in the regulation of hmp transcription	155	Transcription of the hmp gene was induced 20-fold in both wild-type and dksA-de-ficient Salmonella strains 1.5 h after treatment with 250 M the NO-donor spermine NONOate ( Fig. 4A ) , suggesting that DksA is not involved in the regulation of hmp transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
DksA	gene	hmp	regulator	22311927	3	ver/dev	250 M the NO-donor spermine NONOate _ suggesting that DksA is not involved in the regulation of hmp transcription	155	Transcription of the hmp gene was induced 20-fold in both wild-type and dksA-de-ficient Salmonella strains 1.5 h after treatment with 250 M the NO-donor spermine NONOate ( Fig. 4A ) , suggesting that DksA is not involved in the regulation of hmp transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Hu	gene	STM1530	regulator	24055826	1	ver/dev	S. Hu , H.W. Chen , R.Y. Zhang , C.Y. Huang , C.F. Shen , The expression levels of outer membrane proteins STM1530 and OmpD are influenced by aeSR two-component systems	237	[ 21 ] W.S. Hu , H.W. Chen , R.Y. Zhang , C.Y. Huang , C.F. Shen , The expression levels of outer membrane proteins STM1530 and OmpD , which are influenced by the CpxAR and BaeSR two-component systems , play important roles in the ceftriaxone resistance of Salmonella enterica	28	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Hu	gene	STM1530	regulator	24055826	1	ver/dev	S. Hu , H.W. Chen , R.Y. Zhang , C.Y. Huang , C.F. Shen , The expression levels of outer membrane proteins STM1530 and OmpD are influenced by he CpxAR	237	[ 21 ] W.S. Hu , H.W. Chen , R.Y. Zhang , C.Y. Huang , C.F. Shen , The expression levels of outer membrane proteins STM1530 and OmpD , which are influenced by the CpxAR and BaeSR two-component systems , play important roles in the ceftriaxone resistance of Salmonella enterica	28	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	uvrB	regulator	19525399	5	att	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	175	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	3	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	uvrB	regulator	20421601	6	att	To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .	121	To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .	4	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
LexA	gene	uvrB	regulator	20421601	7	att	The levels of uvrB mRNA were increased 3.5 - to 6-fold in both strains as compared to a lexA1 strain ( Figure S1 a ) , implying that LexA-regulated genes were expressed as normal in the multiple polymerase mutant .	122	The levels of uvrB mRNA were increased 3.5 - to 6-fold in both strains as compared to a lexA1 strain ( Figure S1 a ) , implying that LexA-regulated genes were expressed as normal in the multiple polymerase mutant .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	regulator	12753201	39	ver/dev	that OmpR binds directly to ssrB regulatory regions to affect their expression	228	In the present work , we have demonstrated that OmpR binds directly to the ssrA and ssrB regulatory regions to affect their expression and that regulation requires the sensor kinase EnvZ .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	regulator	15491370	5	ver/dev	Previous results from gene fusions suggest that regulation of ssrB by OmpR is distinct .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	regulator	15491370	5	ver/dev	Previous results from gene fusions suggest that regulation of ssrB by OmpR is uncoupled .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	regulator	15491370	5	ver/dev	Previous results from primer-extension analysis suggest that regulation of ssrB by OmpR is distinct .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	synthetic construct	0	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	regulator	15491370	5	ver/dev	Previous results from primer-extension analysis suggest that regulation of ssrB by OmpR is uncoupled .	40	Previous results from primer extension analysis and gene fusions suggest that regulation of ssrA and ssrB by OmpR is uncoupled and distinct ( Feng et al. , 2003 ) .	4	INTRODUCTION	synthetic construct	0	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrB	regulator	17259627	3	ver/dev	OmpR binds to ssrB promoters in-vitro	41	OmpR binds to both ssrA and ssrB promoters in vitro ( Feng et al. , 2003 , 2004 ; Lee et al. , 2000 ) , and PhoP is directly involved in ssrB transcription and the protein levels of SsrA posttranscriptionally ( Bijlsma & Groisman , 2005 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
OmpR	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
OmpR	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by ofthe sensor SpiR at a posttranscriptionallevel .64 The PhoP protein appears to control translation of the spiR message ' UTR with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrB	regulator	18792679	6	ver/dev	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB , PhoP governs expression ofthe regulator SsrB at a transcriptional level by ofthe sensor SpiR at a posttranscriptionallevel .64 The PhoP protein appears to control translation of the spiR message ' untranslated region with the potential to adopt a secondary structure .	162	Whereas the regulator OmpR controls the initiation of transcription from the separate ssrB and spiR promoters , PhoP governs expression ofthe regulator SsrB at a transcriptional level by binding to the ssrB promoter , and ofthe sensor SpiR at a posttranscriptionallevel ( Fig. 4 ) .64 The PhoP protein appears to control translation of the spiR message , which includes a long 5 ' untranslated region ( UTR ) with the potential to adopt a secondary structure occluding the ribosome-binding site .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrB	regulator	19609351	4	ver/dev	Other examples of genes include ssrB known regulators of SPI-2 previously reported to be influenced by OmpR	320	Other examples of genes identified by ssRNA-seq include ssrA and ssrB ( expression ratios of 0.09 and 0.31 respectively ) known regulators of SPI-2 previously reported to be influenced by OmpR	6	NON-CODING (NC) RNA SEQUENCES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssrB	regulator	19609351	4	ver/dev	Other examples of genes include ssrB known regulators of SPI-2 previously reported to be influenced by OmpR	320	Other examples of genes identified by ssRNA-seq include ssrA and ssrB ( expression ratios of 0.09 and 0.31 respectively ) known regulators of SPI-2 previously reported to be influenced by OmpR	6	NON-CODING (NC) RNA SEQUENCES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssrB	regulator	19759044	2	ver/dev	previous work in Salmonella has shown that phosphorylated OmpR can bind to either ssrB within SPI-2	390	Furthermore , the 56 local activator for SPI-2 , ssrA , was increased in expression after triclosan exposure , and previous work in Salmonella has shown that phosphorylated OmpR can bind to either sensor kinase gene ssrA or ssrB within SPI-2 and activate expression .	23	DISCUSSION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
OmpR	gene	ssrB	regulator	24079299	3	ver/dev	In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrB genes .	123	In low osmolarity conditions , OmpR and/or OmpR-P ( phosphorylayted OmpR present in low levels ) can bind to the upstream regions of ssrA and ssrB genes .	5	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	New	Level 1
OmpR	gene	ssrB	regulator	26880544	1	ver/dev	Under low osmolality , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrB	regulator	26880544	1	ver/dev	Under acidic pH , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrB	regulator	29751061	1	ver/dev	For example , OmpR promotes SPI-2 expression by directly binding to both ssrB promoters .	235	For example , OmpR promotes SPI-2 expression by directly binding to both the ssrA and ssrB promoters [ 16 ] ; PhoP activates SPI-2 transcription by directly binding to the ssrB promoter and controls SsrA levels post-transcriptionally [ 15 ] ; SlyA , HilD and Fis proteins can bind to the ssrA promoter to regulate SPI-2 genes [ 19,20,22 ] , and PmrA represses SPI-2 gene transcription through directly binding to the ssrB promoter [ 18 ] .	19	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrB	regulator	33045730	4	ver/dev	Transcription of the horizontally acquired ssrB is regulated by OmpR .	29	Transcription of the horizontally acquired ssrB and spiR genes is regulated by several ancestral regulators , including SlyA ( 20 ) , OmpR ( 6 ) , and PhoP ( 7 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrB	regulator	33751923	7	ver/dev	OmpR also regulates the transcription of ssrB , genes .	385	OmpR also regulates the transcription of ssrA and ssrB , genes encoding another TCS that is also required for the expression of SPI-2 genes and Salmonella survival inside host cells , by direct binding to the promoter of ssrA ( Lee , Detweiler , et al. 2000 ) ( Lee , Detweiler , et al. 2000 ; Leonhartsberger et al. 2001 ) .	9	ENVZ-OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	treA	activator	21563813	1	att	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	fliC	regulator	33799446	12	ver/dev	that , given the complexity of regulatory controls , it can not be determined whether the positive regulation of fliC accounts for the effect of RpoS on motility	341	These authors nevertheless also indicated that , given the complexity of regulatory controls affecting motility , it can not be determined whether the positive regulation of fliC accounts for the effect of RpoS on motility , or if RpoS would be acting by other means as well .	16	4. IMPACT OF STRESS RESISTANCE RESPONSES ON OTHER ASPECTS OF SALMONELLA PHYSIOLOGY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FruR	gene	crp	regulator	2203752	7	ver/dev	With regard to transcriptional regulation of thefru operon , the results summarized here and previously , as well as unpublished results -LRB- Cao and Saier -RRB- suggest that the fru regulon in S. typhimurium is complex ; that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru -LRB- Cao and Saier , unpublished results -RRB- ; that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; that it may be regulated at the transcriptional level by two or more distinct mechanisms -LRB- possibly involving two distinct inducers , fructose-i-phos-phate and fructose -RRB- which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .	452	With regard to transcriptional regulation of thefru operon , the results summarized here and previously ( 6 ) , as well as unpublished results ( Cao and Saier ) suggest ( i ) that the fru regulon in S. typhimurium is complex ; ( ii ) that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru ( Cao and Saier , unpublished results ) ; ( iii ) that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; ( iv ) that it may be regulated at the transcriptional level by two or more distinct mechanisms ( possibly involving two distinct inducers , fructose-i-phos-phate and fructose ) which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and ( v ) that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FruR	gene	crp	regulator	2203752	7	ver/dev	With regard to transcriptional regulation of thefru operon , the results summarized here and previously , as well as unpublished results -LRB- Cao and Saier -RRB- suggest that the fru regulon in S. typhimurium is complex ; that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru -LRB- Cao and Saier , unpublished results -RRB- ; that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; that it may be regulated at the transcriptional level by two or more distinct mechanisms -LRB- possibly involving two distinct inducers , fructose-i-phos-phate and fructose -RRB- which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .	452	With regard to transcriptional regulation of thefru operon , the results summarized here and previously ( 6 ) , as well as unpublished results ( Cao and Saier ) suggest ( i ) that the fru regulon in S. typhimurium is complex ; ( ii ) that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru ( Cao and Saier , unpublished results ) ; ( iii ) that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; ( iv ) that it may be regulated at the transcriptional level by two or more distinct mechanisms ( possibly involving two distinct inducers , fructose-i-phos-phate and fructose ) which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and ( v ) that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	flhDC	repressor	16763111	6	ver/dev	For example , the apparent activation of flagellar genes by H-NS most likely occurs by a repressor of the flagellar regulators flhDC .	91	For example , the apparent activation of flagellar genes by H-NS most likely occurs by means of H-NS -- mediated repression of hdfR , a repressor of the flagellar regulators flhDC ( 1 ) .	4	6 FEBRUARY 2006; ACCEPTED 30 MAY 2006 10.1126/SCIENCE.1125878	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HNS	TU	flhDC	repressor	25375226	20	ver/dev	H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly .	349	H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly [ 22,74 ] .	9	INACTIVATION OF SALMONELLA PATHOGENICITY ISLAND 1 IMPROVES GROWTH OF HNS MUTANTS	nan	1	L3	OTHER	Fact	OTHER	New	Level 3
HNS	TU	flhDC	repressor	25375226	20	ver/dev	H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly .	349	H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly [ 22,74 ] .	9	INACTIVATION OF SALMONELLA PATHOGENICITY ISLAND 1 IMPROVES GROWTH OF HNS MUTANTS	nan	1	L3	OTHER	Fact	OTHER	New	Level 3
FimY	gene	fimA	regulator	31139165	1	ver/dev	three major regulatory proteins , FimY ( each ) control fim operon expression primarily through regulation of the fimA promotor	84	In Salmonella , there are three major regulatory proteins , FimZ , FimY , and FimW ( each expressed under its own promoter ) , that control fim operon expression primarily through regulation of the fimA promotor ( PfimA ; Yeh et al. , 1995 , 2002b ; Tinker and Clegg , 2000 , 2001 ) .	4	DIRECT REGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	ftsQ	activator	11544237	1	ver/dev	It was later demonstrated that E. coli SdiA activates ftsQ in response to AHL .	64	It was later demonstrated that E. coli SdiA activates ftsQ in response to AHL ( 43 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
FimZ	gene	pstS	activator	25547794	23	ver/dev	One possible explanation of this finding is that the pstS mutation increases protein levels of FimZ , potentially activating transcription of its own gene , consistent with previous work by Yeh et al. .	240	One possible explanation of this finding is that the pstS mutation increases protein levels of FimZ , potentially activating transcription of its own gene , consistent with previous work by Yeh et al. ( 43 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	micF	regulator	19120970	0	ver/dev	In E. coli , the transcription of micF is controlled by the homologous proteins MarA .	23	In E. coli , the transcription of acrAB and micF is controlled by the homologous proteins MarA , SoxS and Rob ( 9 , 10 ) , but may be affected by other proteins such as AcrR ( 11 ) .	4	ABSTRACT	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	activator	11036033	1	ver/dev	Like marRAB , acrAB are positively regulated by SoxS .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates Mn-containing superoxide dismutase , acrAB .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , acrAB .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , acrAB .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	activator	12886427	0	ver/dev	SoxS protein , activates sodA , acrAB .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	activator	15047514	0	ver/dev	both MarA and SoxS can activate acrAB expression	21	In E. coli , the acrRAB locus is a member of the mar and sox regulons , and both MarA and SoxS can activate acrAB expression ( 33 ) .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SoxS	TU	acrAB	activator	16842216	0	ver/dev	SoxS are primarily responsible for activation of acrAB transcription .	343	The global regulatory proteins MarA , SoxS and Rob are primarily responsible for activation of acrAB and tolC transcription .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	activator	18577510	2	ver/dev	Other regulators of SoxS did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
SoxS	TU	acrAB	activator	18984645	1	ver/dev	8 -- 13 _ shown that SoxS , play a role in antimicrobial resistance by activating acrAB	21	Studies in Escherichia coli have 8 -- 13 shown that transcriptional activators , such as MarA , SoxS and Rob , play a role in antimicrobial resistance by activating transcription of efflux pumps , including acrAB and tolC .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	activator	21148208	16	att	There are at least two independent pathways of acrAB expression in response to extracellular signals , the RamR/RamA-dependent pathway and the SoxS-dependent pathway .	252	There are at least two independent pathways of acrAB expression in response to extracellular signals , the RamR/RamA-dependent pathway and the SoxS-dependent pathway .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	acrAB	activator	21148208	20	ver/dev	Therefore , SoxS is proposed to directly induce acrAB .	262	Therefore , SoxS is proposed to bind to the upstream region of acrA and directly induce acrAB .	9	PARAQUAT INDUCES ACRAB VIA THE SOXS REGULATOR AND NOT VIA THE RAMA REGULATOR	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SoxS	TU	acrAB	activator	23453941	0	ver/dev	The SoxS proteins can activate acrAB expression .	39	The MarA and SoxS proteins can activate acrAB expression .	1	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SoxS	TU	acrAB	activator	32468234	6	ver/dev	SoxS induces acrAB expression in response to SoxR activation by a superoxide generating agent .	126	SoxS induces acrAB expression in response to SoxR activation by methyl viologen , a superoxide generating agent ( Nikaido et al. 2011 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	acrAB	activator	32468234	6	ver/dev	SoxS induces acrAB expression in response to SoxR activation by methyl viologen .	126	SoxS induces acrAB expression in response to SoxR activation by methyl viologen , a superoxide generating agent ( Nikaido et al. 2011 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	TU	flhDC	regulator	22291596	0	ver/dev	The class I flhDC operon is the master regulator , with FlhC .	538	The class I flhDC operon is the master regulator , with FlhD and FlhC forming a hetero-tetramer that is required for transcriptional activation of the class II genes , which encode the hook-basal body complexes and the alternative sigma factor FliA ( sigma28 ) .	25	EXPRESSION OF FLAGELLA GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhD	gene	dnaK	activator	16430704	8	ver/dev	Therefore , the slower increasing of FlhD proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of s ClpAP , HslVU and L .	175	Therefore , the slower increasing of FlhD and FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of protease ( s ) such as ClpAP , HslVU and Lon .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FlhD	gene	dnaK	activator	16430704	8	ver/dev	Therefore , the slower increasing of FlhD proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of f protea .	175	Therefore , the slower increasing of FlhD and FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of protease ( s ) such as ClpAP , HslVU and Lon .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	lpxO	regulator	15659161	2	ver/dev	Partial transcriptional regulation of the lpxO gene by and PhoP in Salmonella .	245	Partial transcriptional regulation of the lpxO gene by low Mg2 + and PhoP in Salmonella .	6	SUPPRESSION OF ALL LIPID A MODIFICATIONS EXCEPT FOR 2-HYDROXYLATION AT HIGH PH	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	lpxO	regulator	18467098	5	att	The PhoP-regulated genes described and the modifications their products mediate are : pagP , palmitoyl transferase ; lpxO , formation of 2-hydroxy myristate ; pagL , 3-O-deacylase .	135	The PhoP-regulated genes described and the modifications their products mediate are : pagP , palmitoyl transferase ; lpxO , formation of 2-hydroxy myristate ; pagL , 3-O-deacylase .	10	PMRAB-MEDIATED LPS MODIFICATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YqhC	gene	yqhD	activator	22004521	10	ver/dev	Further , this study showed that yqhD activation was induced by direct binding of YqhC to the promoter region of the yqhD gene .	310	Further , this study showed that yqhD activation was induced by direct binding of YqhC to the promoter region of the yqhD gene ( 32 ) .	25	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HNS	gene	yaeB	activator	31487966	12	ver/dev	Ja.tMthleSecx.p20re19s , s2io0 , nxof yaeB was not induced by acidic pH in ind9icoafti1n6g that acidic pH activated yaeB expression through H-NS .	245	Ja.tMthleSecx.p20re19s , s2io0 , nxof yaeB was not induced by acidic pH in an hns mutant strain ( Figure 5E ) , ind9icoafti1n6g that acidic pH activated yaeB expression through H-NS .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	bolA	activator	25123657	9	att	This is due to an increase in the expression of the untranslated mRNA dsrA , which activates RpoS translation and cause induced expression of RpoS-dependent genes such as bolA [ 19 ] .	94	This is due to an increase in the expression of the untranslated mRNA dsrA , which activates RpoS translation and cause induced expression of RpoS-dependent genes such as bolA [ 19 ] .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	bolA	activator	25123657	9	ver/dev	the untranslated mRNA dsrA activates RpoS translation induced expression of bolA	94	This is due to an increase in the expression of the untranslated mRNA dsrA , which activates RpoS translation and cause induced expression of RpoS-dependent genes such as bolA [ 19 ] .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	STM2589	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	araC	activator	19103774	1	ver/dev	Since Crp positively enhances transcription from PBAD TT araC	133	Since Crp positively enhances transcription from PBAD such that transcription is reduced 10-fold in the absence of Crp ( 45 ) , the inclusion of the Pcrp527 : : TT araC	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FabR	gene	fabB	regulator	27004424	14	ver/dev	In S. Typhimurium , this represents the first evidence for direct in-vivo binding of FabR to the fabB promoters .	196	In S. Typhimurium , this represents the first evidence for direct in vivo binding of FabR to the fabB , fabA and yqfA promoters .	11	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
NsrR	gene	trpE	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Cra	TU	cydAB	regulator	11238977	7	ver/dev	Cooperative interaction between Cra in the regulation of the cydAB operon of Escherichia coli .	370	Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli .	14	O’NEAL, C. R., GABRIEL, W. M., TURK, A. K., LIBBY, S. J., FANG, F. C. &	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Cra	TU	cydAB	regulator	19136587	9	ver/dev	Cra is known to bind to at least one nonconsensus binding site within the cydAB promoter .	347	Cra is known to bind to at least one nonconsensus binding site within the cydAB promoter ( 29 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
Cra	TU	cydAB	regulator	19136587	14	ver/dev	For example , Cra binds to a nonconsensus site in the cydAB promoter region .	356	For example , Cra binds to a nonconsensus site in the cydAB promoter region only when high ( 278 nM ) concentrations of Cra and Fnr are both present ( 29 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cra	TU	cydAB	regulator	19136587	15	ver/dev	Cooperative interaction between Cra in the regulation of the cydAB operon of Escherichia coli .	545	Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli .	20	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	gap	activator	30845912	0	att	Conclusions : Our analysis shows that RhoTermPredict is a powerful tool for Rho-dependent terminators search in the three analyzed genomes and could fill this gap in computational genomics .	23	Conclusions : Our analysis shows that RhoTermPredict is a powerful tool for Rho-dependent terminators search in the three analyzed genomes and could fill this gap in computational genomics .	2	ABSTRACT	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
s-32	gene	htrA	regulator	19246758	2	ver/dev	Sequence analysis and regulation of the htrA gene of Escherichia coli : a s-32 independent mechanism of heat-inducible transcription .	376	Sequence analysis and regulation of the htrA gene of Escherichia coli : a s-32 independent mechanism of heat-inducible transcription .	29	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	invA	activator	26441883	15	ver/dev	In addition , FliA was found to induce expression of the primary invasin gene invA .	356	In addition , FliA was found to induce expression of the primary invasin gene invA , which is encoded between two flagellar operons ( Badger and Miller , 1998 ; Horne and Pruss , 2006 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	ftnA	regulator	17302823	0	ver/dev	Thus , ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM4264	regulator	17322315	29	ver/dev	Overcoming the temperature regulation of Salmonella serovar Typhimurium UMR1 by mutations in STM4264 demonstrated that both gene products act as suppressors of the rdar morphotype expression upstream of CsgD at 37 °C .	284	Overcoming the temperature regulation of Salmonella serovar Typhimurium UMR1 by mutations in STM1703 and STM4264 demonstrated that both gene products act as suppressors of the rdar morphotype expression upstream of CsgD at 37 °C .	4	RESULTS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM4264	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	STM4264	regulator	19376870	23	ver/dev	Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 .	298	Consequently , STM1344 acts upstream of STM1703 and STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 and STM1827 or is part of an independent pathway overriding CsgD regulation by STM4264 and STM1827 .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	STM4264	regulator	22164276	10	ver/dev	Deletion of he gene encoding transcription regulator of rdar biofilm formation CsgD restored invasion to wild type levels in the STM4264 mutant .	261	( A ) Deletion of the gene encoding transcription regulator of rdar biofilm formation CsgD and the gene encoding the cellulose synthase BcsA restored invasion to wild type levels in the STM4264 mutant .	10	SCREENING OF GG(D/E)EF/EAL DOMAIN PROTEINS FOR THE CYTOKINE INDUCTION PHENOTYPE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilA	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
RstA	gene	fur	repressor	18790861	0	ver/dev	The RstA protein controlled iron-responsive genes through the Fur-Fe protein because deletion of the fur gene abrogated RstA-mediated repression of these genes .	10	The RstA protein controlled iron-responsive genes through the Fur-Fe ( II ) protein because deletion of the fur gene or iron depletion abrogated RstA-mediated repression of these genes .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	fur	repressor	18790861	51	ver/dev	The regulatory effect of the RstA protein occurred through the Fur protein because the RstA protein failed to repress transcription of the iron-regu-lated genes in a fur deletion strain .	261	The regulatory effect of the RstA protein occurred through the Fur protein because the RstA protein failed to repress transcription of the iron-regu-lated genes ( i.e. , fhuA and fhuF ) in a fur deletion strain ( Fig. 1B ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sipBCDA	activator	11918812	0	att	As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	116	As a first application of the two-colour flow cytometric technique , the in vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	6	IN VITRO CHARACTERIZATION OF TRANSCRIPTIONAL FUSIONS TO VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	repressor	10856650	1	ver/dev	While normally repressed by MarR , a mutation within the marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance .	29	While normally repressed by MarR , a mutation within the marR or marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance that can be overcome by overexpression of wild-type MarR [ 5 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	repressor	10856650	1	ver/dev	While normally repressed by MarR , a mutation within the marR genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance .	29	While normally repressed by MarR , a mutation within the marR or marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance that can be overcome by overexpression of wild-type MarR [ 5 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	repressor	11229910	2	ver/dev	The repressor MarR , binds to the marO operator region to negatively regulate expression of marRAB .	28	The repressor MarR ( 43 ) , encoded by marR , binds to the marO operator region ( 39 ) to negatively regulate expression of marRAB .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	repressor	15073288	2	ver/dev	MarR inhibits binding of MarR to the marRAB promoter	41	The mechanism of induction by phenolic compounds , specifically salicylate , is by the binding of salicylate to MarR , which inhibits binding of MarR to the marRAB promoter ( Martin & Rosner , 1995 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	repressor	15336432	1	ver/dev	MarR negatively regulates expression of marRAB by binding to the marO operator region .	44	MarR negatively regulates expression of marRAB by binding to the marO operator region [ 13,15 ] .	3	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	repressor	16201927	1	ver/dev	MarR negatively regulates the expression of marRAB by binding to the marO operator region .	165	MarR negatively regulates the expression of marRAB by binding to the marO operator region .17 On the other hand , proteins encoded by the soxRS locus include the transcriptional activator , SoxS , and another protein , SoxR , the oxidized form of which can activate soxS expression .	13	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	repressor	19120970	7	ver/dev	Thus induction of marRAB by DEC without inhibition of the repression activity of MarR is expected to be less effective than induction with SAL .	195	Thus induction of marRAB by DEC without inhibition of the repression activity of MarR is expected to be less effective than induction with SAL .	18	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarR	TU	marRAB	repressor	31501286	8	ver/dev	For instance , MarR2-dependent transcriptional repression of the marRAB operon is relieved via copper-mediated disulfide bond formation between MarR monomers .	130	For instance , MarR2-dependent transcriptional repression of the marRAB operon is relieved via MarR2 binding to aromatic acids or copper-mediated disulfide bond formation between MarR monomers ( 51 -- 56 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	repressor	33024855	7	ver/dev	MarR represses expression of marRAB	316	Salicylates , found in abundance in tomato , are known inducers of the marRAB operon by binding to MarR which represses expression of marRAB .	11	3.2. STRESS RESPONSE AND PLANT HOST ADAPTATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarR	TU	marRAB	repressor	34202800	11	ver/dev	For example , the MarR2-dependent transcriptional repression of the marRAB operon is moderated by the formation of disulfide bonds between MarR monomers via copper .	290	For example , the MarR2-dependent transcriptional repression of the marRAB operon ( discussed in Section 3.5 ) is moderated by MarR2 binding with aromatic acids or the formation of disulfide bonds between MarR monomers via copper [ 107 ] .	7	3.2. THE ARAC/XYLS FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	marRAB	repressor	34202800	26	ver/dev	MarR represses the expression of the marRAB operon .	440	MarR represses the expression of the marRAB operon , which encodes MarR ( MarR family ) and MarA ( AraC/XylS family , discussed in Section 3.2 ) .	14	3.5. THE MARR FAMILY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	yihU	regulator	21148209	4	ver/dev	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of the yihU , showing that yshA operon belongs to the CRP regulon in Salmonella .	31	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of the yihU -- yshA transcriptional unit , showing that the yihU -- yshA operon belongs to the CRP regulon in Salmonella .	3	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yihU	regulator	21148209	4	ver/dev	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of the yihU , showing that the yihU belongs to the CRP regulon in Salmonella .	31	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of the yihU -- yshA transcriptional unit , showing that the yihU -- yshA operon belongs to the CRP regulon in Salmonella .	3	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yihU	regulator	21148209	5	ver/dev	Construction of S. Typhi mutant strains In order to evaluate the functional role of CRP in the regulation of the yihU -- a crp mutant in S. Typhi was obtained by substitution of the crp gene with the Km-resistance cassette .	47	Construction of S. Typhi mutant strains In order to evaluate the functional role of CRP in the regulation of the yihU -- yshA operon , a crp mutant in S. Typhi was obtained by substitution of the crp gene with the Km-resistance cassette ( Datsenko & Wanner , 2000 ) .	5	METHODS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yihU	regulator	21148209	5	ver/dev	Construction of S. Typhi mutant strains In order to evaluate the functional role of CRP in the regulation of the yihU -- yshA operon was obtained by substitution of the crp gene with the Km-resistance cassette .	47	Construction of S. Typhi mutant strains In order to evaluate the functional role of CRP in the regulation of the yihU -- yshA operon , a crp mutant in S. Typhi was obtained by substitution of the crp gene with the Km-resistance cassette ( Datsenko & Wanner , 2000 ) .	5	METHODS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yihU	regulator	21148209	7	ver/dev	the results suggested that the yihU is regulated by the global regulatory protein CRP	161	In order to identify global regulatory proteins involved in the genetic expression of the yihU -- yshA operon , bioinformatics analyses of the 59 region of yihU were performed , and the results suggested that the yihU -- yshA transcriptional unit is regulated by the global regulatory protein CRP .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	yihU	regulator	21148209	9	ver/dev	This expression profile indicated that CRP is a positive regulator of the yihU .	167	This expression profile indicated that CRP is a positive regulator of the yihU -- yshA operon ( Fig. 3 ) .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	yihU	regulator	21148209	10	ver/dev	In order to determine whether the CRP protein directly regulates the genetic expression of yihU , EMSAs were performed with the entire yihU regulatory region .	175	In order to determine whether the CRP protein directly regulates the genetic expression of yihU -- yshA , EMSAs were performed with purified CRP and with the entire yihU regulatory region .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	yihU	regulator	21148209	10	ver/dev	In order to determine whether the CRP protein directly regulates the genetic expression of yihU , EMSAs were performed with purified CRP .	175	In order to determine whether the CRP protein directly regulates the genetic expression of yihU -- yshA , EMSAs were performed with purified CRP and with the entire yihU regulatory region .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	yihU	regulator	21148209	11	ver/dev	The CRP protein was capable of binding to the 59 region of yihU in the presence of 100 mM cAMP	176	The CRP protein was capable of binding to the 59 region of yihU in the presence of 100 mM cAMP , and a significant electrophoretic mobility shift occurred at 400 nM CRP ( Fig. 4 ) .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yihU	regulator	21148209	12	ver/dev	Moreover , no binding of CRP to the 59 region of yihU was observed in the absence of cAMP .	178	Moreover , no binding of CRP to the 59 region of yihU was observed in the absence of cAMP ( Fig. 7a , b ) .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CRP	gene	yihU	regulator	21148209	16	ver/dev	CRP binds to the yihU regulatory region	198	CRP binds to the yihU regulatory region	9	TWO CRP BOXES MEDIATE YIHU TRANSCRIPTIONAL ACTIVATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	yihU	regulator	21148209	21	ver/dev	These data are in accordance with the transcriptional-fusion data , which reveal CRP boxes in the regulation of yihU .	210	These data are in accordance with the transcriptional fusion data presented above , which reveal the role of both CRP boxes in the regulation of yihU ( Fig. 6b ) .	9	TWO CRP BOXES MEDIATE YIHU TRANSCRIPTIONAL ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	yihU	regulator	21148209	26	ver/dev	CRP binds to different regions of the yihU promoter .	256	CRP binds to different regions of the yihU promoter .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	yihU	regulator	21148209	29	ver/dev	CRP directly regulates by binding to the promoter region of yihU in the presence of cAMP .	263	CRP directly regulates by binding to the promoter region of yihU in the presence of cAMP ( Fig. 4 ) .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	yihU	regulator	21148209	29	ver/dev	CRP directly regulates by binding to the promoter region of yihU in the presence of cAMP .	263	CRP directly regulates by binding to the promoter region of yihU in the presence of cAMP ( Fig. 4 ) .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	cfa	repressor	30682134	24	ver/dev	CsrA also repressed translation of another acid-inducible gene in mLPM , cfa	242	CsrA also repressed translation of another acid-inducible gene in mLPM , cfa	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	Cell fusing agent virus	0	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	csrB	regulator	10672185	3	ver/dev	If regulation by csr was mediated exclusively by modulating the level of HilA , null mutations in csrB would be without effect in these two settings because , in the ® rst case , HilA is absent and , in the second case , it is maintained at a constant level .	140	If regulation by barA and csr was mediated exclusively by modulating the level of HilA , null mutations in barA and csrB would be without effect in these two settings because , in the ® rst case , HilA is absent and , in the second case , it is maintained at a constant level .	8	INTEGRATION OF MULTIPLE INVASION REGULATORS	nan	1	L1	SPEC	Other	NEG	Other	Level 1
HilA	gene	csrB	regulator	10672185	6	ver/dev	Together , these results suggest that the principal effects of chromosomal csrB are mediated by control of HilA levels	152	Together , these results suggest that the principal effects of chromosomal csrB are mediated by control of HilA levels , but they raise the possibility that csr , depending on the expression level of its components , could also exert a regulatory effect that is independent of HilA Another issue raised by our results is the relationship between BarA , a member of the two-component sensor kinase family , and SirA , a member of the phosphorylated response regulator family .	8	INTEGRATION OF MULTIPLE INVASION REGULATORS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NsrR	gene	STM1808	activator	24021902	1	att	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	78	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tolB	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	tolB	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
NtrC	gene	ompF	regulator	32265871	4	ver/dev	Importantly , it was found that expression of ompF is controlled by NtrC in E. coli .	347	Importantly , it was found that expression of ompF is controlled by NtrC in E. coli ( Zimmer et al. , 2000 ) .	24	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtB	activator	28181542	1	att	Indeed , when grown in media containing 500 μM Mg2 + for 1 h to initiate transcription from the PhoP-dependent promoter , the efp mutant increased mRNA levels of both the mgtC and mgtB genes by ~ 100 fold ( Fig .	61	Indeed , when grown in media containing 500 μM Mg2 + for 1 h to initiate transcription from the PhoP-dependent promoter , the efp mutant increased mRNA levels of both the mgtC and mgtB genes by ~ 100 fold ( Fig .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	sseJ	activator	21059643	2	ver/dev	In this study , we demonstrate that SsrB directly stimulates transcription of sseJ by binding upstream of their respective promoters .	66	In this study , we demonstrate that SsrB directly stimulates transcription of sifA , sifB , and sseJ by binding upstream of their respective promoters .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	prgH	regulator	12535071	88	ver/dev	HilC do not seem to regulate expression of prgH .	251	HilD and HilC do not seem to regulate expression of hilD or prgH ( Olekhnovich and Kadner , 2002 ) ( Figs 1 and 2B ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Other	NEG	New	Level 1
PhoP	gene	iacP	activator	11918812	0	att	As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	116	As a first application of the two-colour flow cytometric technique , the in vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	6	IN VITRO CHARACTERIZATION OF TRANSCRIPTIONAL FUSIONS TO VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoR	gene	phoR	regulator	31346161	2	ver/dev	To get a further insight into the MgtC-mediated control of PhoR histidine kinase , we created a phoR chromosomal mutant .	267	To get a further insight into the MgtC-mediated control of PhoR histidine kinase , we created a phoR chromosomal mutant where Leu421 was substituted by either the Ala or Gly ( phoRL421A to phoRL421G ) ( Fig. 4a ) , lacking the ability to interact with MgtC ( Fig. 2c -- f , and Supplementary Fig. 4 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mig-14	regulator	12675799	9	ver/dev	Previous work from our laboratory demonstrated that PhoP also regulates mig-14 .	310	Previous work from our laboratory demonstrated that PhoP also regulates mig-14 , a gene that is immediately adjacent to Salmonella virK in a Salmonella-specific region of the chromosome that appears to have been acquired horizontally ( Baumler and Heffron , 1998 ; Valdivia et al. , 2000 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mig-14	regulator	15225317	28	att	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	338	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	mig-14	regulator	15703297	12	att	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mig-14	regulator	15703297	5	att	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	105	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mig-14	regulator	17158330	15	att	mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .	158	mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .	10	REFERENCES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mig-14	regulator	18221392	3	ver/dev	The mig-14 genes appear to be regulated by both PhoP , by a mechanism .	67	The mig-14 and pagC genes appear to be regulated by both SlyA and PhoP , by a mechanism that is not yet understood ( Navarre et al. , 2005 ) .	9	SALMONELLA VIRULENCE GENES ARE SPECIFICALLY EXPRESSED IN VIVO DURING INFECTION OF C. ELEGANS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mig-14	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mig-14	regulator	30685290	0	ver/dev	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal-medium , when treated with antimicrobial peptides , indicating it is controlled by the global regulator PhoP .	296	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal medium containing low magnesium , within macrophages , or when treated with antimicrobial peptides , indicating it is controlled by the global regulator PhoP ( Brodsky et al. , 2002 , 2005 ) .	20	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mig-14	regulator	30685290	0	ver/dev	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal-medium , within macrophages , indicating it is controlled by the global regulator PhoP .	296	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal medium containing low magnesium , within macrophages , or when treated with antimicrobial peptides , indicating it is controlled by the global regulator PhoP ( Brodsky et al. , 2002 , 2005 ) .	20	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NsrR	gene	yoaG	regulator	32231649	3	att	Transcription of the NsrR-regulated hmpA and yoaG genes in Salmonella on fruit was also higher when ROS was not attenuated , suggesting that higher levels of ROS may be related to NO levels .	400	Transcription of the NsrR-regulated hmpA and yoaG genes in Salmonella on fruit was also higher when ROS was not attenuated , suggesting that higher levels of ROS may be related to NO levels .	18	MODULATING TOMATO SURFACE NO LEVELS SIGNIFICANTLY AFFECTED SEN COLONIZATION	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	bapA	activator	16313619	6	att	The results showed that the bapA mRNA level was significantly downregulated in the mlrA mutant strain and that bapA activation through MlrA was exclusively CsgD-dependent , because bapA transcription levels in csgD mutant and csgD mutant complemented with MlrA were comparable ( Fig. 7 ) .	246	The results showed that the bapA mRNA level was significantly downregulated in the mlrA mutant strain and that bapA activation through MlrA was exclusively CsgD-dependent , because bapA transcription levels in csgD mutant and csgD mutant complemented with MlrA were comparable ( Fig. 7 ) .	10	TRANSCRIPTIONAL REGULATION OF BAPA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	bapA	activator	16313619	6	att	The results showed that the bapA mRNA level was significantly downregulated in the mlrA mutant strain and that bapA activation through MlrA was exclusively CsgD-dependent , because bapA transcription levels in csgD mutant and csgD mutant complemented with MlrA were comparable ( Fig. 7 ) .	246	The results showed that the bapA mRNA level was significantly downregulated in the mlrA mutant strain and that bapA activation through MlrA was exclusively CsgD-dependent , because bapA transcription levels in csgD mutant and csgD mutant complemented with MlrA were comparable ( Fig. 7 ) .	10	TRANSCRIPTIONAL REGULATION OF BAPA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	bapA	activator	16313619	11	ver/dev	Alternatively , CsgD could stimulate bapA transcription indirectly via the activation of an intermediate regulatory gene .	425	Alternatively , CsgD could stimulate bapA transcription indirectly via the activation of an intermediate regulatory gene .	14	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CsgD	gene	bapA	activator	16313619	11	ver/dev	Alternatively , CsgD could stimulate bapA transcription indirectly via the activation of an intermediate regulatory gene .	425	Alternatively , CsgD could stimulate bapA transcription indirectly via the activation of an intermediate regulatory gene .	14	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
LexA	gene	uvrD	regulator	30201777	18	att	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	194	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Escherichia coli	0.5	L3	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas3 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas2 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas1 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas6e mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
HilD	gene	ssrA	regulator	21984608	1	ver/dev	HilD binds directly to the regulatory regions of the coding regions of ssrA .	141	HilD binds directly to the regulatory regions of the ssrAB operon ( the coding regions of ssrA and ssrB ) and counteracts the repression exerted by the negative regulator , H-NS , or ompR ( a factor required for the activation of SPI-2 genes ) .	6	SALMONELLA RELIES ON T3SS2 TO SURVIVE AND REPLICATE INTRACELLULARLY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	araJ	activator	24272778	2	ver/dev	E. coli AraC activates transcription of araJ transcripts in the presence of its inducer , L-arabinose .	12	E. coli AraC activates transcription of the araBAD , araFGH , araE , and araJ transcripts in the presence of its inducer , L-arabinose ( 5 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
EmrR	TU	emrAB	repressor	19230852	1	ver/dev	EmrR is reported to be a repressor for the emrAB efflux genes .	181	EmrR is reported to be a repressor for the emrAB efflux genes [ 56 ] .	7	4. REGULATORY NETWORK OF DRUG EFFLUX PUMPS IN E. COLI	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	ompS1	regulator	17908208	8	ver/dev	We report here that StpA are the main negative regulators of ompS1 expression in Salmonella .	48	We report here that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	3	B	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	ompS1	regulator	17908208	8	ver/dev	We report here that StpA are the main positive regulators of ompS1 expression in Salmonella .	48	We report here that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	3	B	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	ompS1	regulator	19406898	3	ver/dev	a static curvature plays an important role in the binding of StpA , the silencer proteins of ompS1	37	Here we present a topological analysis of the ompS1 59 upstream regulatory region and the identification of a static curvature that plays an important role in the binding of H-NS and StpA , the silencer proteins of ompS1 .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	regulator	19406898	20	ver/dev	Effect of DNA curvature on the binding of StpA to ompS1 .	184	Effect of DNA curvature on the binding of H-NS , StpA and LeuO to ompS1 .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	regulator	19447191	4	ver/dev	Moreover it has been reported that StpA are the main negative regulators of ompS1 expression in Salmonella .	96	Moreover it has been reported that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	6	4.2. LEUO	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	ompS1	regulator	19447191	4	ver/dev	Moreover it has been reported that StpA are the main positive regulators of ompS1 expression in Salmonella .	96	Moreover it has been reported that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	6	4.2. LEUO	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sifA	activator	21059643	2	ver/dev	In this study , we demonstrate that SsrB directly stimulates transcription of sifA by binding upstream of their respective promoters .	66	In this study , we demonstrate that SsrB directly stimulates transcription of sifA , sifB , and sseJ by binding upstream of their respective promoters .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sifA	activator	21059643	12	ver/dev	SsrB was able to activate transcription of sifA in 1.7-fold or absence -LRB- 3-fold -RRB- of CTD .	223	SsrB was able to activate transcription of sifA in the C presence ( 1.7-fold ) or absence ( 3-fold ) of CTD .	6	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SsrB	gene	sifA	activator	21059643	12	ver/dev	SsrB was able to activate transcription of sifA in the C presence or absence -LRB- 3-fold -RRB- of CTD .	223	SsrB was able to activate transcription of sifA in the C presence ( 1.7-fold ) or absence ( 3-fold ) of CTD .	6	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SsrB	gene	sifA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : sifA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sifA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : sifA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sifA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : sifA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sifA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : sifA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sifA	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : sifA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sifA	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : sifA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LsrR	gene	luxS	repressor	11722742	1	ver/dev	Because inactivation of the lsrR gene results in high-level expression of the lsr operon in a luxS null background , these results strongly suggest that the wild-type function of LsrR is to repress the expression of the lsr operon in the absence of AI-2 .	214	Because inactivation of the lsrR gene results in high-level expression of the lsr operon in a luxS null background , these results strongly suggest that the wild-type function of LsrR is to repress the expression of the lsr operon in the absence of AI-2 .	7	AI-2 REGULATES THE TRANSCRIPTION OF THE LSR OPERON	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	hilC	repressor	24354910	12	ver/dev	One such isolate was re-constructed by P22 HT transduction to confirm that the Tn10dCm insertion suppressed hilC : : lac downregulation by LeuO .	75	One such isolate was purified and re-constructed by P22 HT transduction to confirm that the Tn10dCm insertion suppressed hilC : : lac downregulation by LeuO .	9	RESULTS	Salmonella virus P22	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	hilC	repressor	24354910	12	ver/dev	One such isolate was purified by P22 HT transduction to confirm that the Tn10dCm insertion suppressed hilC : : lac downregulation by LeuO .	75	One such isolate was purified and re-constructed by P22 HT transduction to confirm that the Tn10dCm insertion suppressed hilC : : lac downregulation by LeuO .	9	RESULTS	Salmonella virus P22	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	hilC	repressor	24354910	13	ver/dev	Use of a HilE − null mutant constructed ad ( strain SV55 provided independent evidence that lack of HilE suppressed hilC : : lac downregulation by LeuO .	78	Use of a HilE − null mutant constructed ad hoc ( strain SV5586 ) provided independent evidence that lack of HilE suppressed hilC : : lac downregulation by LeuO .	9	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
LeuO	gene	hilC	repressor	24354910	13	ver/dev	Use of a HilE − null mutant constructed ad d h provided independent evidence that lack of HilE suppressed hilC : : lac downregulation by LeuO .	78	Use of a HilE − null mutant constructed ad hoc ( strain SV5586 ) provided independent evidence that lack of HilE suppressed hilC : : lac downregulation by LeuO .	9	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
SsrB	gene	sifB	activator	21059643	2	ver/dev	In this study , we demonstrate that SsrB directly stimulates transcription of sifB by binding upstream of their respective promoters .	66	In this study , we demonstrate that SsrB directly stimulates transcription of sifA , sifB , and sseJ by binding upstream of their respective promoters .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sifB	activator	33045730	68	att	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type or defective SsrB binding site in the ugtL-sifB intergenic region ( ugtL-sifBmu ; Figure 3B ) , and , as controls , mutants lacking the ssrB or sifB genes .	288	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type or defective SsrB binding site in the ugtL-sifB intergenic region ( ugtL-sifBmu ; Figure 3B ) , and , as controls , mutants lacking the ssrB or sifB genes .	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	sifB	activator	33045730	68	ver/dev	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a defective SsrB binding site in the ugtL-sifB intergenic region , and , as controls , mutants .	288	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type or defective SsrB binding site in the ugtL-sifB intergenic region ( ugtL-sifBmu ; Figure 3B ) , and , as controls , mutants lacking the ssrB or sifB genes .	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	sifB	activator	33045730	68	ver/dev	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type SsrB binding site in the ugtL-sifB intergenic region , and , as controls , mutants .	288	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type or defective SsrB binding site in the ugtL-sifB intergenic region ( ugtL-sifBmu ; Figure 3B ) , and , as controls , mutants lacking the ssrB or sifB genes .	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LysR	gene	lysA	activator	28373272	2	ver/dev	Expression of lysA is activated by LysR in the presence of diaminopimelate .	315	Expression of lysA is activated by LysR in the presence of diaminopimelate and is repressed in the presence of lysine ( 48 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hupB	repressor	21212121	0	ver/dev	In contrast , inactivation of just the hupB gene correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures .	19	In contrast , inactivation of just the hupB gene resulted in increased fitness and correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hupB	repressor	21212121	12	ver/dev	Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .	348	Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .	11	HU AND THE RPOS REGULON	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hupB	repressor	21212121	12	ver/dev	Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .	348	Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .	11	HU AND THE RPOS REGULON	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	fimZ	repressor	31139165	10	ver/dev	Lrp directly affects fimZ expression , probably by displacement of N-HS protein , a global repressor of gram-negative bacteria .	124	Lrp directly affects fimZ expression , probably by displacement of histone-like nucleoidstructuring ( N-HS ) protein , a global repressor of gram-negative bacteria ( reviewed in Dorman , 2004 ) , which binds to fimZ promoter via AT-rich sequences ( Navarre et al. , 2006 ) .	5	GLOBAL REGULATION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
Lrp	gene	fimZ	repressor	31139165	10	ver/dev	Lrp directly affects fimZ expression , probably by displacement of histone-like nucleoidstructuring protein , a global repressor of gram-negative bacteria .	124	Lrp directly affects fimZ expression , probably by displacement of histone-like nucleoidstructuring ( N-HS ) protein , a global repressor of gram-negative bacteria ( reviewed in Dorman , 2004 ) , which binds to fimZ promoter via AT-rich sequences ( Navarre et al. , 2006 ) .	5	GLOBAL REGULATION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
Sigma28	gene	lacZ	activator	9765212	12	att	TH3920 is deleted for the flgM locus , and contains a transcriptional-fusion of lacZ to the fliC gene , which serves as a reporter for s28-dependent transcription .	328	TH3920 is deleted for the flgM locus , and contains a transcriptional fusion of lacZ to the fliC gene , which serves as a reporter for s28-dependent transcription .	9	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	lacZ	activator	9765212	13	att	b-Ga-lactosidase assays demonstrating inhibition of s28-dependent lacZ expression by the His -- FlgM proteins ( both wild type and mutant ) in-vivo .	361	b-Ga-lactosidase assays demonstrating inhibition of s28-dependent lacZ expression by the His -- FlgM proteins ( both wild type and mutant ) in vivo .	12	PURIFICATION OF FLGM AND DERIVATIVES	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Sigma28	gene	lacZ	activator	9765212	14	att	The ability of the His -- FlgM proteins to inhibit s28-dependent expression of lacZ was measured in strains grown to mid-log phase in the presence of 1.3 µM arabinose .	363	The ability of the His -- FlgM proteins to inhibit s28-dependent expression of lacZ was measured in strains grown to mid-log phase in the presence of 1.3 µM arabinose .	12	PURIFICATION OF FLGM AND DERIVATIVES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SsrB	gene	srfM	regulator	10844662	3	att	Five additional distinct SsrB-regulated genes outside SPI-2 were identified : srfI , srfD , srIG , srfL and srfM .	124	Five additional distinct SsrB-regulated genes outside SPI-2 were identified : srfI , srfD , srIG , srfL and srfM .	10	MOLECULAR CHARACTERIZATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	aceB	regulator	12791144	9	ver/dev	Conversely , two glyoxyate shunt genes under the positive control of CsrA in E. coli , aceB , were induced twofold in the S. typhimu-rium csrA mutant .	221	Conversely , two glyoxyate shunt genes under the positive control of CsrA in E. coli , aceA and aceB , were induced twofold in the S. typhimu-rium csrA mutant .	9	REGULATION OF CARBON METABOLISM BY CSRA	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	rpoS	activator	9284144	9	att	SlyA-dependent protein expression was detected both during stationary-phase growth and during infection of macrophages but was not dependent on rpoS .	176	SlyA-dependent protein expression was detected both during stationary-phase growth and during infection of macrophages but was not dependent on rpoS .	4	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CRP	TU	flhDC	activator	25161191	0	ver/dev	The cAMP-CRP complex positively regulates the transcription of the flhDC operon .	26	The cAMP-CRP complex positively regulates the transcription of the flhDC operon , which contains the genes encoding the master flagellar regulator , FlhD4C2 ( 5 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	TU	flhDC	activator	30373755	4	ver/dev	For example , the response regulator PhoP , is a repressor , whereas the adenylate cyclase receptor protein CRP , is an activator of flhDC transcription .	44	For example , the response regulator PhoP , which is activated under low Mg2 and/or low pH conditions , is a repressor ( 20 , 29 ) , whereas the adenylate cyclase receptor protein CRP , which is activated by binding to intracellular cyclic 3 = ,5 = - AMP ( cAMP ) , is an activator of flhDC transcription ( 18 ) .	3	KEYWORDS SMALL PROTEINS, INTRINSICALLY DISORDERED PROTEINS, FLAGELLA, MOTILITY, SALMONELLA, PHOP	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	activator	31262841	13	ver/dev	CRP also directly activates flhDC transcription .	187	cAMP receptor protein ( CRP ) also directly activates flhDC transcription ( 74 -- 76 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	TU	flhDC	activator	31262841	13	ver/dev	cAMP-receptor-protein also directly activates flhDC transcription .	187	cAMP receptor protein ( CRP ) also directly activates flhDC transcription ( 74 -- 76 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	yoaE	activator	31915212	8	ver/dev	In Shigella , yoaE was shown to be directly upregulated by PhoP in Luria-Bertani -LRB- LB -RRB- medium , whereas no significant difference was found between yoaE strains in a gentamicin protection assay of HeLa cells .	48	In Shigella , yoaE was shown to be directly upregulated by PhoP in Luria-Bertani ( LB ) medium , whereas no significant difference was found between wild-type and yoaE strains in a gentamicin protection assay of HeLa cells ( 23 ) .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	yoaE	activator	31915212	8	ver/dev	In Shigella , yoaE was shown to be directly upregulated by PhoP in Luria-Bertani -LRB- LB -RRB- medium , whereas no significant difference was found between wild-type strains in a gentamicin protection assay of HeLa cells .	48	In Shigella , yoaE was shown to be directly upregulated by PhoP in Luria-Bertani ( LB ) medium , whereas no significant difference was found between wild-type and yoaE strains in a gentamicin protection assay of HeLa cells ( 23 ) .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CsgD	gene	STM3611	repressor	19376870	34	ver/dev	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM3611 , required for the downregulation of CsgD expression .	380	STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 and STM3611 , required for the downregulation of CsgD expression ( 37 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3611	repressor	22164276	9	ver/dev	In the STM3611 mutant background , however , relieve of repression of TTSS-1 secretion by CsgD is not sufficient to restore invasion .	257	In the STM3611 mutant background , however , relieve of repression of TTSS-1 secretion by CsgD is not sufficient to restore invasion .	9	EFFECT OF DOUBLE MUTANTS ON THE INVASION PHENOTYPE	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	STM3611	repressor	22164276	12	ver/dev	In the STM3611 mutant , however , deletion of CsgD relieves repression of SipA secretion .	376	In the STM3611 mutant , however , deletion of CsgD relieves repression of SipA secretion but does not restore invasion .	13	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3611	repressor	24127899	3	ver/dev	YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 .	47	YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 ( YhjH ) , which is part of the flagellar regulon ( Simm et al. , 2009 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	STM3611	repressor	25153529	3	ver/dev	GGDEF domain proteins STM3611 inhibit expression of CsgD .	130	The GGDEF/EAL domain protein STM1703 ( yciR ) and GGDEF domain proteins STM3611 ( yhjH ) and STM4264 ( yjcC ) each inhibit expression of CsgD and hence rdar morphotype development [ 57 ] .	8	GGDEF/EAL DOMAIN PROTEINS AND RDAR MORPHOTYPE DEVELOPMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM3611	repressor	26655751	2	ver/dev	STM3611 inhibit CsgD function .	43	PDEs ( STM1703 , STM3611 , STM4264 , and STM1827 ) inhibit CsgD function ( 13 , 14 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	lacZ	activator	12218035	0	att	Briefly , pNL3 is a pBR322-derived reporter plasmid in which the PhoP-activated phoN promoter region of S. enterica serovar Typhimurium is fused to the lacZ structural gene .	46	Briefly , pNL3 is a pBR322-derived reporter plasmid in which the PhoP-activated phoN promoter region of S. enterica serovar Typhimurium is fused to the lacZ structural gene .	3	MATERIALS AND METHODS	unidentified plasmid;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	lacZ	activator	23782700	0	att	Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. Typhimurium strain that harbors a reporter transcriptional lacZ fusion to virK , a previously characterized PhoP-activated gene ( 12 , 34 ) .	161	Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. Typhimurium strain that harbors a reporter transcriptional lacZ fusion to virK , a previously characterized PhoP-activated gene ( 12 , 34 ) .	3	EXPERIMENTAL PROCEDURES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	lacZ	activator	23782700	1	att	We tested the activity of seven different PhoP-activated genes with transcriptional-fusions to lacZ when bacteria were grown in LB ( PhoP/PhoQ-activating condition ) or in LB supplemented with 5 mM MgCl2 ( PhoP / PhoQ-repressing condition ) or a 1 or 4 mg ml 1 concentration	164	We tested the activity of seven different PhoP-activated genes with transcriptional fusions to lacZ when bacteria were grown in LB ( PhoP/PhoQ-activating condition ) or in LB supplemented with 5 mM MgCl2 ( PhoP / PhoQ-repressing condition ) or a 1 or 4 mg ml 1 concentration	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	lacZ	activator	24185747	3	att	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB-medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	87	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	12	STAINING SOLUTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Chryseobacterium gallinarum	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	yrbL	activator	15703297	10	att	We hypothesized that the PhoP-activated yrbL gene of Escherichia coli might participate in an analogous loop with the PmrA protein because both the Salmonella pmrD and Escherichia coli yrbL promoters can be found in the same promoter profile and harbor similarly arranged PhoP and PmrA boxes ( Fig. 1 D and E ) .	116	We hypothesized that the PhoP-activated yrbL gene of Escherichia coli might participate in an analogous loop with the PmrA protein because both the Salmonella pmrD and Escherichia coli yrbL promoters can be found in the same promoter profile and harbor similarly arranged PhoP and PmrA boxes ( Fig. 1 D and E ) .	4	RESULTS	Escherichia coli;Salmonella;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	yrbL	activator	15703297	11	att	In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fe3 ( Fig. 1F ) , which is the specific signal that activates the PmrA protein ( 11 ) .	117	In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fe3 ( Fig. 1F ) , which is the specific signal that activates the PmrA protein ( 11 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	yrbL	activator	15703297	8	att	A possible multicomponent loop involving the PhoP-activated yrbL gene .	114	A possible multicomponent loop involving the PhoP-activated yrbL gene .	4	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	yrbL	activator	23504014	16	att	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	277	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	entE	regulator	18554972	0	att	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	215	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	15	3.1. TRANSPOSON MUTAGENESIS IDENTIFIES IRON RESPONSE GENES INVOLVED IN NOREPINEPHRINE-ENHANCED GROWTH OF SALMONELLA TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	entE	regulator	24858080	11	att	To confirm this induction as well as the repression by Fe ( II ) -- an expected behaviour for a Fur-regulated locus ( Tsolis et al. , 1995 ) -- we employed a strain carrying an entE : : MudJ transcriptional-fusion ( Table S1 ) .	376	To confirm this induction as well as the repression by Fe ( II ) -- an expected behaviour for a Fur-regulated locus ( Tsolis et al. , 1995 ) -- we employed a strain carrying an entE : : MudJ transcriptional fusion ( Table S1 ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	sipA	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of orgA remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipA	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgK remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipA	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgH remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipA	activator	21168230	5	ver/dev	In addition , HilD directly activate sipA in non-HilA dependent manner .	344	In addition , HilD and HilC directly activate invF , sipA and sipC in non-HilA dependent manner ( Akbar et al. , 2003 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilC	regulator	15966862	1	ver/dev	H-NS binds to the hilC promoter in a temperature-dependent manner	174	H-NS binds to the hilC promoter and structural gene in a temperature-dependent manner	12	H-NS BINDS TO THE HILC PROMOTER AND STRUCTURAL GENE IN A TEMPERATURE-DEPENDENT MANNER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilC	regulator	15966862	2	ver/dev	To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 37 ◦ .	175	To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 25 and 37 ◦ C .	12	H-NS BINDS TO THE HILC PROMOTER AND STRUCTURAL GENE IN A TEMPERATURE-DEPENDENT MANNER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilC	regulator	15966862	2	ver/dev	To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 25 .	175	To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 25 and 37 ◦ C .	12	H-NS BINDS TO THE HILC PROMOTER AND STRUCTURAL GENE IN A TEMPERATURE-DEPENDENT MANNER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilC	regulator	15966862	7	ver/dev	Another interesting observation from these experiments is that H-NS binds to the hilC structural gene in addition to the promoter .	256	Another interesting observation from these experiments is that H-NS binds to the hilC structural gene in addition to the promoter .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hilC	regulator	21573071	12	ver/dev	Specifically , Fur is able to indirectly through H-NS ( in hilC ) , all the main regulators of SPI1 .	344	Specifically , Fur is able to control , either directly ( in the case of HilD ) or indirectly through H-NS ( in hilA , hilD , hilC , and rtsA ) , all the main regulators of SPI1 .	17	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	hilC	regulator	21573071	13	ver/dev	H-NS control of the hilC promoters is also shown .	358	H-NS control of the hilD , hilC , rtsA and hilA promoters is also shown [ 21,22,31 ] .	19	ACKNOWLEDGMENTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseI	activator	19126546	5	ver/dev	In SsrB , a negatively charged glutamic-acid res - These results demonstrate that Met186 are both idue replaces Lys188 of NarL , whereas in RcsB , it is replaced by a important for sseI promoter activation by SsrB , whereas Thr183 serine .	228	In SsrB , a negatively charged glutamic acid res - These results demonstrate that Lys179 and Met186 are both idue replaces Lys188 of NarL , whereas in RcsB , it is replaced by a important for sseI promoter activation by SsrB , whereas Thr183 serine .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseI	activator	19126546	5	ver/dev	In SsrB , a negatively charged glutamic-acid res - These results demonstrate that Lys179 are both idue replaces Lys188 of NarL , whereas in RcsB , it is replaced by a important for sseI promoter activation by SsrB , whereas Thr183 serine .	228	In SsrB , a negatively charged glutamic acid res - These results demonstrate that Lys179 and Met186 are both idue replaces Lys188 of NarL , whereas in RcsB , it is replaced by a important for sseI promoter activation by SsrB , whereas Thr183 serine .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseI	activator	19126546	8	ver/dev	This result also suggests Asn203 occupy the corresponding positions of that dimerization is required for SsrB activation of the sseI pro-the two valines of NarL .	248	This result also suggests ture , Ile199 and Asn203 occupy the corresponding positions of that dimerization is required for SsrB activation of the sseI pro-the two valines of NarL .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	sseI	activator	19126546	8	ver/dev	This result also suggests Ile199 occupy the corresponding positions of that dimerization is required for SsrB activation of the sseI pro-the two valines of NarL .	248	This result also suggests ture , Ile199 and Asn203 occupy the corresponding positions of that dimerization is required for SsrB activation of the sseI pro-the two valines of NarL .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	sseI	activator	19126546	8	ver/dev	This result also suggests ture occupy the corresponding positions of that dimerization is required for SsrB activation of the sseI pro-the two valines of NarL .	248	This result also suggests ture , Ile199 and Asn203 occupy the corresponding positions of that dimerization is required for SsrB activation of the sseI pro-the two valines of NarL .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	sseI	activator	19126546	10	ver/dev	SsrB expression resulted in activation of the sseI promoter , whereas expression of SsrB D56A did not activate sseI .	268	SsrB expression resulted in activation of the sseI promoter , whereas expression of SsrB D56A did not activate sseI ( Fig. 9 , columns 1 -- 3 ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	TU	ssrAB	repressor	25135218	12	ver/dev	This suggests that HilD induces the expression of ssrAB also by counteracting H-NS-me-diated repression of its promoter .	42	This suggests that HilD induces the expression of ssrAB also by counteracting H-NS-me-diated repression of its promoter .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	ssrAB	repressor	25135218	13	ver/dev	However , how HilD counteracts the H-NS-mediated repression of ssrAB , or even of other target genes , had not yet been determined .	43	However , how HilD counteracts the H-NS-mediated repression of ssrAB , or even of other target genes , had not yet been determined .	2	MAIN	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilD	TU	ssrAB	repressor	25135218	85	ver/dev	Therefore , SlyA might replace HilD to counteract H-NS-mediated repression of ssrAB when Salmonella is grown in minimal media .	237	Therefore , SlyA might replace HilD to counteract H-NS-mediated repression of ssrAB when Salmonella is grown in minimal media .	5	DISCUSSION	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	ssrAB	repressor	26300871	39	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	607	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	19	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	28329249	20	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	284	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	19	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	28426789	18	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	607	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	26	12	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	28426789	20	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	641	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	26	12	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	29447698	1	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	484	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	20	APPL. ENVIRON. MICROBIOL. 72, 946–949.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	30682134	55	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	754	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	33	KNUFF K, FINLAY BB. WHAT THE SIF IS HAPPENING-THE ROLE OF INTRACELLULAR SALMONELLA-INDUCED FILA- MENTS. FRONT CELL INFECT MICROBIOL. 2017; 7: 335. HTTPS://DOI.ORG/10.3389/FCIMB.2017.00335 PMID: 28791257	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	30718301	65	ver/dev	Therefore , the expression of ssrAB would involve two steps , as follows : the relief of H-NS-mediated repression by HilD and the recruitment of the RNA polymerase by OmpR .	185	Therefore , the expression of ssrAB mediated by SyA , HilD , and OmpR would involve two steps , as follows : the relief of H-NS-mediated repression by SlyA and HilD or only SlyA and the recruitment of the RNA polymerase by OmpR ( Fig. 8 ) .	4	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	ssrAB	repressor	33119619	30	ver/dev	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	441	HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	38	DORMAN CJ. 2013. GENOME ARCHITECTURE AND GLOBAL GENE REGULATION IN BACTERIA: MAKING PROGRESS TOWARDS A UNIFIED MODEL? NAT REV MICROBIOL. 11(5): 349–355. HTTPS://DOI.ORG/10.1038/NRMICRO3007 PMID: 23549066	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	33201432	6	ver/dev	HilD induces expression of Salmo-nella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	452	HilD induces expression of Salmo-nella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	29	REFERENCES	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	repressor	33853321	21	ver/dev	ustamante , V. H. HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	625	( 59 ) Martinez , L. C. , Banda , M. M. , Fernandez-Mora , M. , Santana , F. J. , and Bustamante , V. H. ( 2014 ) HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .	10	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PgtA	gene	pgtP	activator	2842312	3	ver/dev	the fact that induction of to inducer pgtP expression responds exogenous suggests that a mechanism involving protein-protein interactions between PgtA proteins occurs within the membrane .	205	The membrane location of these three proteins ( 9 , 10 ) and the fact that induction of to inducer pgtP expression responds exogenous suggests that a mechanism involving protein-protein interactions between the PgtC , PgtB , and PgtA proteins occurs within the membrane .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagP	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
FliZ	gene	hilA	regulator	11162188	1	ver/dev	The fliZ mutation did not have a significant effect on the sirA expression , indicating that FliZ control of the hilA expression is not mediated by transcriptional activation of the sirA gene .	110	The fliZ mutation did not have a significant effect on the sirA expression , indicating that FliZ control of the hilA expression is not mediated by transcriptional activation of the sirA gene .	6	TRANSCRIPTION OF THE VIRULENCE-ASSOCIATED GENES IN THE FLIZ MUTANT	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
FliZ	gene	hilA	regulator	11162188	3	ver/dev	These results suggest that FliZ may directly regulate the hilA transcription .	113	These results suggest that FliZ may directly regulate the hilA transcription .	6	TRANSCRIPTION OF THE VIRULENCE-ASSOCIATED GENES IN THE FLIZ MUTANT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FliZ	gene	hilA	regulator	29150501	0	ver/dev	In addition to being a positive regulator of FlhD4C2 activity , FliZ posttranslationally activates the regulatory protein HilD , which , in turn , positively regulates the expression of hilA .	226	In addition to being a positive regulator of FlhD4C2 activity ( 50 ) , FliZ posttranslationally activates the regulatory protein HilD , which , in turn , positively regulates the expression of hilA , the gene for a key regulator of the SPI-1 system ( 45 , 51 , 52 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	hilA	regulator	30941426	20	ver/dev	the promoter activity of hilA 10-fold _ supporting the positive regulation of SPI-1 genes by FliZ	282	Deleting fliZ in the WT reduced the promoter activity of hilA 10-fold ( Figure 7C ) , supporting the positive regulation of SPI-1 genes by FliZ .	25	NON-OPTIMAL TRANSLATIONAL FIDELITY PROMOTES DEGRADATION OF HILD BY LON	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	TU	acrAB	activator	15073288	9	ver/dev	RpoS , were also examined for their potential role in bile-mediated activation of acrAB	276	PhoP -- PhoQ , an important virulence regulator implicated in bile resistance , and RpoS , a global stationary-phase regulator , were also examined for their potential role in bile-mediated activation of acrAB .	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	nan	1	L1	OTHER	Investigation	OTHER	Other	Level 1
RpoS	TU	acrAB	activator	15073288	10	ver/dev	Analysis of trans-criptional data demonstrated that there is no observed role for PhoP -- RpoS in bile activation of acrAB ( data not shown ) .	277	Analysis of trans-criptional data demonstrated that there is no observed role for PhoP -- PhoQ or RpoS in bile activation of acrAB ( data not shown ) .	11	BILE PROMOTES INCREASED RESISTANCE TO BILE AND ANTIBIOTICS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	TU	acrAB	activator	18577510	10	ver/dev	Prouty et al. further reported that acrAB activation by bile is independent of RpoS .	153	Prouty et al. ( 47 ) further reported that acrAB activation by bile is independent of MarA , Rob , PhoP/PhoQ , and RpoS .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM2123	regulator	16629664	34	ver/dev	STM2123 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	389	STM2123 and STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM2123	regulator	16629664	38	ver/dev	STM2123 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	435	STM2123 and STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	gogB	activator	15843015	2	ver/dev	One of the interesting features of autonomous gogB expression was its co-regulation with other SPI-2 virulence genes by SsrB , the transcriptional activator of the SsrA/SsrB two-component regulatory system .	240	One of the interesting features of autonomous gogB expression was its co-regulation with other SPI-2 virulence genes by SsrB , the transcriptional activator of the SsrA/SsrB two-component regulatory system .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimY	gene	fimW	activator	31139165	5	ver/dev	On the other hand , FimY is able to induce expression of fimW .	108	On the other hand , FimY is able to induce expression of fimW , which results in repression of PfimY .	4	DIRECT REGULATION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	STM1269	activator	15681155	28	att	Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .	334	Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .	14	4. DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	STM1269	activator	15681155	9	att	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	206	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	11	3. RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilE	gene	sirA	regulator	19537165	9	ver/dev	However , the sirA knock-out does not lead to a complete loss in HilD levels since HilD is regulated by HilE , EnvZ/OmpRr , etc. .	270	However , the sirA knock-out does not lead to a complete loss in HilD levels since HilD is regulated by other factors such as HilE , EnvZ/OmpRr , etc. [ Baxter et al. , 2003 ] .	18	PARAMETER ESTIMATION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgrB	regulator	23504014	10	att	Interestingly , mgrB is a PhoP-regulated gene that has been found to mediate feedback in this system , since deletion of this gene results in a potent increase in PhoP-regulated transcription in E. coli .	250	Interestingly , mgrB is a PhoP-regulated gene that has been found to mediate feedback in this system , since deletion of this gene results in a potent increase in PhoP-regulated transcription in E. coli .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgrB	regulator	23504014	11	att	In addition , overexpression of mgrB decreases PhoP-regulated transcription in E. coli , S. enterica , and Yersinia pestis ( 47 ) .	251	In addition , overexpression of mgrB decreases PhoP-regulated transcription in E. coli , S. enterica , and Yersinia pestis ( 47 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	Escherichia coli;Salmonella;Salmonella;Yersinia pestis	0.5	L3	OTHER	Other	OTHER	New	Level 2
DksA	gene	feoB	activator	27065993	1	att	To validate • NO - and DksA-dependent regulatory control in aspects of iron homeostasis , we used quantitative real-time PCR ( qPCR ) to measure the mRNA levels of feoB , sitA , and sufA in wild-type and 1dksA Salmonella treated ± dNO ( Figure 3 ) .	173	To validate • NO - and DksA-dependent regulatory control in aspects of iron homeostasis , we used quantitative real-time PCR ( qPCR ) to measure the mRNA levels of feoB , sitA , and sufA in wild-type and 1dksA Salmonella treated ± dNO ( Figure 3 ) .	12	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
LysR	gene	STM3120	regulator	19583791	6	ver/dev	STM3120 encodes a possible citrate lyase and STM3121 , is a putative transcriptional regulators of the LysR family .	276	STM3120 encodes a possible citrate lyase and STM3121 , termed stmR ( Morrow et al. , 1999 ) , is a putative transcriptional regulators of the LysR family .	18	CI ASSAYS. DELETIONS ON THE CHROMOSOME OF S. TYPHIMURIUM ARE INDICATED AS OPEN BOXES. SIGNIFICANTLY DIFFERENT FROM THE CI OF S. TYPHIMURIUM ATCC 14028 (WILD TYPE) VS. ISOGENIC SPONTANEOUS NAL STRAIN SH100 (P R O 0.05).1PLASMID, THE CI VALUES FROM THE WILD-TYPE STRAIN VS. A SINGLE-GENE DELETION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
DksA	gene	ssrA	activator	29930310	8	ver/dev	We examined whether DksA participate in the transcriptional activation of the ssrA genes .	80	We examined whether DksA and ( p ) ppGpp participate in the transcriptional activation of the ssrA and ssrB genes that encode the master two-component regulatory system that activates SPI2 expression .	3	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	New	Level 1
SsrB	gene	slyA	regulator	19229334	11	ver/dev	Thus , one explanation for the transcription we observe following overexpression of slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins .	519	Thus , one explanation for the transcription we observe following overexpression of ssrB or slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins including both H-NS and YdgD/Hha in this A+T rich SPI-2 region [ 70 ] .	15	WHAT ARE THE SIGNALS BEING SENSED DURING SYSTEMIC INFECTION AND HOW ARE THEY INTEGRATED TO EXPRESS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	flhDC	activator	31501286	26	ver/dev	When flhDC expression levels were increased by induction with the high ATc concentration , we still found that all MarA homologs significantly reduced fliC expression , with Rob .	209	When flhDC expression levels were increased by induction with the high ATc concentration , we still found that all MarA homologs significantly reduced fliC expression ( all P 9.85 10 5 , Tukey 's HSD test ) , with MarA and Rob having equivalent effects .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
MarA	TU	flhDC	activator	31501286	26	ver/dev	When flhDC expression levels were increased by induction with the high ATc concentration , we still found that all MarA homologs significantly reduced fliC expression , with MarA .	209	When flhDC expression levels were increased by induction with the high ATc concentration , we still found that all MarA homologs significantly reduced fliC expression ( all P 9.85 10 5 , Tukey 's HSD test ) , with MarA and Rob having equivalent effects .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
MarA	TU	flhDC	activator	31501286	29	ver/dev	These data demonstrate that all four MarA homologs are capable of activating -LRB- or repressing -RRB- a posttranscriptional regulatory pathway for flhDC .	212	These data demonstrate that all four MarA homologs are capable of activating ( or repressing ) a posttranscriptional regulatory pathway for flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SlyA	gene	mig-14	activator	18270203	71	att	This form of regulation is in striking parallel to that controlling expression of the ugtL gene ( 23 ) , and it may apply to other PhoP - and SlyA-dependent genes , such as mig-14 and virK ( which also seem to have been horizontally acquired ) , because the PhoP protein has been shown to bind to their respective promoters in-vitro and in-vivo ( 26 ) .3	296	This form of regulation is in striking parallel to that controlling expression of the ugtL gene ( 23 ) , and it may apply to other PhoP - and SlyA-dependent genes , such as mig-14 and virK ( which also seem to have been horizontally acquired ) , because the PhoP protein has been shown to bind to their respective promoters in vitro and in vivo ( 26 ) .3	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
IscR	gene	hilD	regulator	27704705	4	ver/dev	2.3 IscR binds on the promoter of hilD	104	2.3 | IscR binds on the promoter of hilD	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IscR	gene	hilD	regulator	27704705	6	ver/dev	The two putative IscR binding sites upstream of hilD resemble type 2 motifs that can be bound by both d apo‐IscR -LRB- Giel , Rodionov , Liu , Blattner , & Kil	108	The two putative IscR binding sites upstream of hilD resemble type 2 motifs that can be bound by both holo‐IscR and apo‐IscR ( Giel , Rodionov , Liu , Blattner , & Kiley ,	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
IscR	gene	hilD	regulator	27704705	6	ver/dev	The two putative IscR binding sites upstream of hilD resemble type 2 motifs that can be bound by both holo‐Is	108	The two putative IscR binding sites upstream of hilD resemble type 2 motifs that can be bound by both holo‐IscR and apo‐IscR ( Giel , Rodionov , Liu , Blattner , & Kiley ,	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L2	SPEC	Other	OTHER	New	Level 1
IscR	gene	hilD	regulator	27704705	12	ver/dev	FIGURE 3 IscR binds to the hilD promoter in-vitro .	149	FIGURE 3 IscR binds to the hilD promoter in vitro .	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slyB	regulator	19783623	0	ver/dev	multiple genomes found that the only targets directly regulated by PhoP in all species were its negative regulator slyB	292	This finding is somewhat reminiscent of a recent study of the PhoP regulon across multiple genomes , which found that the only targets directly regulated by PhoP in all species were the phoPQ operon itself and its negative regulator slyB ( 36 ) .	5	AVG 20.1 3.4 6.6 3.6 5.7 13.1 3.1 2.9	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyB	regulator	23504014	20	ver/dev	As seen in Fig. 5 , phosphorylated PhoP was able to bind to the promoter of slyB with similar kinetics , whereas no binding was detected to the promoter of phoN .	299	As seen in Fig. 5 , phosphorylated PhoP was able to bind to the promoter of steA and slyB with similar kinetics , whereas no binding was detected to the promoter of phoN .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	slyB	regulator	25182488	15	ver/dev	As seen in Fig. 7B , PhoP was able to bind to the promoters of slyB .	258	As seen in Fig. 7B , PhoP was able to bind to the promoters of slrP and slyB but not to the phoN promoter .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	slyB	regulator	25972862	2	ver/dev	As seen in Figure 6A , PhoP was able to bind to the slyB promoters	381	As seen in Figure 6A , PhoP was able to bind to the slyB and sseK1 promoters and no binding was observed to the phoN promoter .	21	SYNTHESIS AND TRANSLOCATION INTO MAMMALIAN CELLS OF SSEK1 UNDER SPI1 AND	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	slyB	regulator	29324231	11	att	We also compared the expression of other PhoP-regulated genes in the wild-type and Δhns / ΔphoPQ strains , including genes whose expression in S. Typhimurium is dependent ( pagC ) or independent ( slyB and mgtA ) of H-NS ( Perez et al. , 2008 ) .	161	We also compared the expression of other PhoP-regulated genes in the wild-type and Δhns / ΔphoPQ strains , including genes whose expression in S. Typhimurium is dependent ( pagC ) or independent ( slyB and mgtA ) of H-NS ( Perez et al. , 2008 ) .	5	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	flgA	activator	11244064	13	att	SirA-dependent regulation of sopB and flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar containing kanamycin and X-Gal at 37 °C .	286	SirA-dependent regulation of sopB and flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar containing kanamycin and X-Gal at 37 °C .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	himD	activator	21388802	6	ver/dev	SlyA activates himD expression .	201	SlyA activates himD , phoP and ssrB expression .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssrB	regulator	10844662	4	att	The next column demonstrates the specificity of the regulation to the intracellular environment by comparing the expression ratio of the three most highly SsrB-regulated fusions in a wild-type versus ssrB : : cm background in DMEM .	181	The next column demonstrates the specificity of the regulation to the intracellular environment by comparing the expression ratio of the three most highly SsrB-regulated fusions in a wild-type versus ssrB : : cm background in DMEM .	12	OMPR AND PHOP REGULATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	ssrB	regulator	15491370	2	ver/dev	Results from DNase-I-protection assays provide direct evidence that SsrB binds at ssrB , although the binding sites lie within the .	17	Results from DNase I protection assays provide direct evidence that SsrB binds at ssrA and ssrB , although the binding sites lie within the transcribed regions .	3	SUMMARY	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
SsrB	gene	ssrB	regulator	19229334	1	ver/dev	Expression of an episomal copy of ssrB resulted in expression of SPI-2 genes in each mutant background , suggesting that SsrB is epistatic to other regulators for SPI-2 transcription .	402	Expression of an episomal copy of ssrB resulted in expression of SPI-2 genes in each mutant background , suggesting that SsrB is epistatic to other regulators for SPI-2 transcription .	12	SSRB CAN COMPLEMENT OTHER REGULATORS OF SPI-2 TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssrB	regulator	19229334	11	ver/dev	Thus , one explanation for the transcription we observe following overexpression of ssrB may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins .	519	Thus , one explanation for the transcription we observe following overexpression of ssrB or slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins including both H-NS and YdgD/Hha in this A+T rich SPI-2 region [ 70 ] .	15	WHAT ARE THE SIGNALS BEING SENSED DURING SYSTEMIC INFECTION AND HOW ARE THEY INTEGRATED TO EXPRESS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssrB	regulator	24643535	0	ver/dev	In addition , the SsrB regulator also directly binds and autoregulates the ssrB promoters to activate their expression .	20	In addition , the SsrB regulator also directly binds and autoregulates the ssrA and ssrB promoters to activate their expression ( 7 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssrB	regulator	24643535	9	ver/dev	Taken together , these lines of evidence suggest that the Fur repressor could interfere with binding of the SsrB activator to the ssrB promoter , leading to repression of ssrB transcription .	213	Taken together , these lines of evidence suggest that the Fur repressor could interfere with binding of the SsrB activator to the ssrB promoter , leading to repression of ssrB transcription .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	ssrB	regulator	26880544	53	att	Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .	369	Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .	16	THE IMPORTANCE OF ANTI-SILENCING IN GENE REGULATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssrB	regulator	30524381	18	ver/dev	Apart from ssrB , none of the other SPI-2 genes have been shown to be direct targets of OmpR regulation , although many of them are directly regulated by SsrB .	246	Apart from ssrA and ssrB , none of the other SPI-2 genes have been shown to be direct targets of OmpR regulation ( Lee et al. , 2000 ; Feng et al. , 2003 , 2004 ) , although many of them are directly regulated by SsrB ( Feng et al. , 2004 ; Walthers et al. , 2007 , 2011 ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	fur	activator	11932449	3	att	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , as well as the basal expression of the cAMP-regulated S. typhimurium pepE gene ( Conlin et al. , 1994 ) , encoding an - aspartyl α dipeptidase , was analysed .	231	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , as well as the basal expression of the cAMP-regulated S. typhimurium pepE gene ( Conlin et al. , 1994 ) , encoding an - aspartyl α dipeptidase , was analysed .	6	EXPRESSION OF CAMP-REGULATED GENES IN S. TYPHIMURIUM FUR CELLS	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	fur	activator	11932449	1	ver/dev	In agreement with this possibility , it has been recently demonstrated that the fur gene of Pasteurella multocida , is positively regulated by the cAMP-CRP complex .	40	In agreement with this possibility , it has been recently demonstrated that the fur gene of Pasteurella multocida , which belongs to the γ-Proteobacteria , as does E. coli , is positively regulated by the cAMP-CRP complex ( Bosch et al. , 2001 ) .	3	INTRODUCTION	Pasteurella multocida	0	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	fur	activator	11932449	3	ver/dev	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the basal expression of the cAMP-regulated S. typhimurium pepE gene , was analysed .	231	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , as well as the basal expression of the cAMP-regulated S. typhimurium pepE gene ( Conlin et al. , 1994 ) , encoding an - aspartyl α dipeptidase , was analysed .	6	EXPRESSION OF CAMP-REGULATED GENES IN S. TYPHIMURIUM FUR CELLS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	fur	activator	11932449	3	ver/dev	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , was analysed .	231	To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , as well as the basal expression of the cAMP-regulated S. typhimurium pepE gene ( Conlin et al. , 1994 ) , encoding an - aspartyl α dipeptidase , was analysed .	6	EXPRESSION OF CAMP-REGULATED GENES IN S. TYPHIMURIUM FUR CELLS	Escherichia coli	0	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	ompR	activator	21388802	0	ver/dev	SPI2 Description Crp activates ompR expression .	141	SPI2 Description Crp activates spvR and ompR expression .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
NsrR	gene	hmp	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
NsrR	gene	hmp	regulator	20829289	1	ver/dev	NsrR regulates expression of not only hmp .	119	NsrR regulates expression of not only hmp but also several other genes in a small regulon .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L3	OTHER	Other	NEG	New	Level 1
FlhDC	gene	fliC	repressor	30373755	7	ver/dev	Consistent with Fig. 5A , the PflhDC-lux activity was 2-fold lower in the mutant than in Fig. 5B , suggesting that the downregulation of fliC was due at least in part to the decreased expression of the master regulator FlhDC .	165	Consistent with the RNA-seq result ( Fig. 5A ) , the PflhDC-lux activity was 2-fold lower in the ΔSTM14_1829 mutant than in the wild type ( Fig. 5B ) , suggesting that the downregulation of fliC and other flagellum-related genes in the ΔSTM14_1829 mutant was due at least in part to the decreased expression of the master regulator FlhDC .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	fliC	repressor	30373755	7	ver/dev	Consistent with Fig. 5A , the PflhDC-lux activity was 2-fold lower in the mutant than in the wild type , suggesting that the downregulation of fliC was due at least in part to the decreased expression of the master regulator FlhDC .	165	Consistent with the RNA-seq result ( Fig. 5A ) , the PflhDC-lux activity was 2-fold lower in the ΔSTM14_1829 mutant than in the wild type ( Fig. 5B ) , suggesting that the downregulation of fliC and other flagellum-related genes in the ΔSTM14_1829 mutant was due at least in part to the decreased expression of the master regulator FlhDC .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	fliC	repressor	30373755	7	ver/dev	Consistent with the RNA-seq result , the PflhDC-lux activity was 2-fold lower in the mutant than in Fig. 5B , suggesting that the downregulation of fliC was due at least in part to the decreased expression of the master regulator FlhDC .	165	Consistent with the RNA-seq result ( Fig. 5A ) , the PflhDC-lux activity was 2-fold lower in the ΔSTM14_1829 mutant than in the wild type ( Fig. 5B ) , suggesting that the downregulation of fliC and other flagellum-related genes in the ΔSTM14_1829 mutant was due at least in part to the decreased expression of the master regulator FlhDC .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	fliC	repressor	30373755	7	ver/dev	Consistent with the RNA-seq result , the PflhDC-lux activity was 2-fold lower in the mutant than in the wild type , suggesting that the downregulation of fliC was due at least in part to the decreased expression of the master regulator FlhDC .	165	Consistent with the RNA-seq result ( Fig. 5A ) , the PflhDC-lux activity was 2-fold lower in the ΔSTM14_1829 mutant than in the wild type ( Fig. 5B ) , suggesting that the downregulation of fliC and other flagellum-related genes in the ΔSTM14_1829 mutant was due at least in part to the decreased expression of the master regulator FlhDC .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhD	gene	STM1697	repressor	24127899	14	ver/dev	These findings suggest that STM1697 inhibits motility by interacting at the post-transcriptional level with the FlhD C functionality as demonstrated previously for STM1344 .	141	These findings suggest that STM1697 inhibits motility by interacting at the post-transcriptional level with the FlhD C 4 2 expression or functionality as demonstrated previously for STM1344 ( Wada et al. , 2011 ; Li et al. , 2012 ; Takaya et al. , 2012b ) .	8	INTERACTION OF STM1697 WITH FLAGELLA REGULON COMPONENTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhD	gene	STM1697	repressor	24127899	14	ver/dev	These findings suggest that STM1697 inhibits motility by interacting at the post-transcriptional level with the FlhD C 4 2 expression .	141	These findings suggest that STM1697 inhibits motility by interacting at the post-transcriptional level with the FlhD C 4 2 expression or functionality as demonstrated previously for STM1344 ( Wada et al. , 2011 ; Li et al. , 2012 ; Takaya et al. , 2012b ) .	8	INTERACTION OF STM1697 WITH FLAGELLA REGULON COMPONENTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FlhD	gene	STM1697	repressor	28973452	66	ver/dev	The expression of the FlhD-free mutants of STM1697 showed similar motility phenotypes as the stm1697 strain suggesting that the motility inhibition of STM1697 is directly mediated by interaction with FlhD .	284	The expression of the FlhD-free mutants of STM1697 showed similar motility phenotypes as the stm1697 strain suggesting that the motility inhibition of STM1697 is directly mediated by interaction with FlhD ( Figure 7D ) .	27	THE STM1697 SUPPRESSION OF CELL MOTILITY IS MEDIATED BY ITS INTERACTION WITH FLHD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	15661008	25	ver/dev	RtsA can directly induce the hilA expression independent of HilD .	324	RtsA belongs to the AraC/XylS family of regulators , and can directly bind the hilA promoter and induce the hilA expression independent of HilC and HilD .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilA	activator	15661008	25	ver/dev	RtsA can directly induce the hilA expression independent of HilC .	324	RtsA belongs to the AraC/XylS family of regulators , and can directly bind the hilA promoter and induce the hilA expression independent of HilC and HilD .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilA	activator	15661008	26	ver/dev	In the present study , the expression from lac fusion was retained after disruption in Fig. 2A in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	15661008	26	ver/dev	In the present study , the expression from the hilA was retained after disruption in Fig. 2A in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	15765064	15	ver/dev	RtsA increases invasion gene expression by increasing transcription of hilA .	101	RtsA increases invasion gene expression by increasing transcription of hilA , which is independent of HilC and HilD .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	15765064	16	ver/dev	These data suggest that RtsA may activate hilA expression in response to a set of signals .	103	These data suggest that HilC and RtsA may activate hilA expression in response to a set of signals that are not present in laboratory conditions .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RtsA	gene	hilA	activator	16045614	0	ver/dev	Like HilD , RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression .	11	Like HilC and HilD , RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	16045614	0	ver/dev	Like HilC , RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression .	11	Like HilC and HilD , RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	16045614	22	ver/dev	We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .	86	We have shown that RtsA ( Ellermeier and Slauch , 2003 ) , like HilC and HilD ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ) , induces expression of hilA by binding to the HilA promoter region .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	16045614	22	ver/dev	We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .	86	We have shown that RtsA ( Ellermeier and Slauch , 2003 ) , like HilC and HilD ( Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ) , induces expression of hilA by binding to the HilA promoter region .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	16045614	24	ver/dev	We wanted to determine if RtsA could induce expression of hilA in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
RtsA	gene	hilA	activator	16045614	26	ver/dev	The data in Fig. 2 demonstrate that RtsA are able to induce expression of hilA in the absence of the other regulators .	127	The data in Fig. 2 demonstrate that RtsA , HilC and HilD are able to induce expression of hilA in the absence of the other regulators .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	16045614	27	ver/dev	Production of HilC induced expression of hilA ~ 120-fold , while RtsA induced expression of hilA 30 - to 40-fold , similar to previously reported values .	128	Production of HilC induced expression of hilA ~ 120-fold , while RtsA and HilD induced expression of hilA 30 - to 40-fold , similar to previously reported values ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Schechter et al. , 1999 ; Schechter and Lee , 2001 ; Ellermeier and Slauch , 2003 ) .	5	RESULTS	Terfezia pini	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilA	activator	16045614	69	ver/dev	We show that RtsA can each independently activate expression of the hilA genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilA	activator	16045614	70	ver/dev	However , RtsA normally act in concert to activate hilA .	466	However , HilD , HilC and RtsA normally act in concert to activate hilA .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	16443238	2	ver/dev	RtsA can activate expression of hilA .	39	Three homologous proteins , 8,13,14 HilC , HilD , and RtsA , which belong to the AraC/XylS family of transcription factors can activate expression of hilA and some of its target genes .	5	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilA	activator	17208038	10	ver/dev	The mechanism by which RtsA activate expression of hilA	85	The mechanism by which HilC , HilD and RtsA activate expression of hilA ( and possibly of each other ) apparently involves counteracting silencing by the nucleoid protein Hns [ 30,31 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	17675384	3	ver/dev	That means that at least hilA are induced by RtsA proteins .	43	That means that at least hilA and rtsA are induced by HilD , HilC , and RtsA proteins .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	17675384	15	ver/dev	Under high-osmolarity conditions , RtsA activate SPI1 genes indirectly through hilA .	288	Under high-osmolarity conditions , HilD , HilC , and RtsA activate SPI1 genes directly and indirectly through hilA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	17675384	15	ver/dev	Under high-osmolarity conditions , RtsA activate SPI1 genes directly through hilA .	288	Under high-osmolarity conditions , HilD , HilC , and RtsA activate SPI1 genes directly and indirectly through hilA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	17993530	13	ver/dev	RtsA are each capable of activating hilA transcription .	86	HilD , HilC , and RtsA are each capable of activating hilA transcription .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	19537165	3	ver/dev	Earlier work on mathematical modeling of regulation of expression of hilA by RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .	44	Earlier work on mathematical modeling of regulation of expression of hilA by HilC , HilD and RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop [ Maithreye and Mande , 2007 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	23676436	1	ver/dev	RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Schechter et al. ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	23676436	1	ver/dev	RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; 2001 ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	23676436	1	ver/dev	RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lee ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	23676436	1	ver/dev	RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	25375226	29	ver/dev	hilA expression is induced by three transcriptional activators , RtsA .	402	hilA expression is induced by three transcriptional activators , HilC , HilD and RtsA [ 70 ] .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	26039089	8	ver/dev	RtsA is a major regulator of both hilA of a feed-forward loop for activation of SPI1 expression .	181	RtsA is a major regulator of both hilA and hilD expression and forms part of a feed-forward loop for activation of SPI1 expression [ 53 ] .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	26386070	1	ver/dev	Inducible expression RtsA protein was sufficient to activate hilA following growth at 42 °C .	84	Inducible expression of either HilC or RtsA protein , but not of Fur , FliZ , or HilD , was sufficient to activate hilA following growth at 42 °C .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	27601571	4	ver/dev	Indeed , this is the case for activation of hilA by HilD/HilC / RtsA .	72	Indeed , this is the case for activation of hilD , hilC , rtsA , and hilA by HilD/HilC / RtsA ( 29 , 30 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	28335027	10	ver/dev	H-NS repression of hilA counteracts transcriptional activation by RtsA	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	29378886	1	ver/dev	Transcriptional activation of hilA is dependent upon three AraC-like proteins , RtsA , .	45	Transcriptional activation of hilA is dependent upon three AraC-like proteins , HilD , HilC , and RtsA , which bind to the same sites upstream of activated promoters ( 11 , 12 ) .	3	KEYWORDS SALMONELLA, SPI1, HILD, HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	31182495	4	ver/dev	The hilA gene is transcriptionally activated by three AraC-like regulatory proteins , RtsA , .	33	The hilA gene is transcriptionally activated by three AraC-like regulatory proteins , HilD , HilC , and RtsA , each of which can activate expression of the hilD , hilC , rtsA , and hilA genes , creating a complex feed-forward regulatory loop ( Fig. 1 ) ( 8 , 12 , 18 ) .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	31182495	53	ver/dev	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though RtsA are still required for full stimulation of the polymerase .	227	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD , HilC , and RtsA are still required for full stimulation of the polymerase .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of rtsA .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	activator	31182495	56	ver/dev	FIG 8 RtsA activate hilA expression independently of H-NS .	246	FIG 8 HilD , HilC , and RtsA activate hilA expression independently of H-NS .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	0	ver/dev	Expression of hilA is activated by RtsA , .	9	Expression of hilA is activated by HilD , HilC , and RtsA , which act in a complex feed-forward regulatory loop .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	31262841	2	ver/dev	RtsA , activate transcription of hilA by binding the promoter .	39	Three AraC-like proteins , HilD , HilC , and RtsA , activate transcription of hilA by binding the promoter ( 15 ) .	3	KEYWORDS PHOPQ, SPI1, SALMONELLA, SRNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	6	ver/dev	RtsA , however , contributes to the transcription of hilA .	118	RtsA , however , contributes to the transcription of hilA .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of = lacZ in an rtsA null background , PinT caused only a 2-fold repression of Fig. 4A , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of = lacZ in an rtsA null background , PinT caused only a 2-fold repression of Fig. 4A , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of PinT on hilA = , PinT caused only a 2-fold repression of Fig. 4A , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of PinT on hilA = , PinT caused only a 2-fold repression of Fig. 4A , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of PinT on hilA = , PinT caused only a 2-fold repression of hilA expression , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	31262841	7	ver/dev	When we tested the overexpression of PinT on hilA = , PinT caused only a 2-fold repression of hilA expression , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	32041797	5	ver/dev	RtsA activate transcription of hilA , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	activator	32571967	0	ver/dev	Transcription of hilA , is activated by three AraC-like regulators , RtsA , .	8	Transcription of hilA , encoding the transcriptional activator of the SPI1 structural genes , is activated by three AraC-like regulators , HilD , HilC , and RtsA , that act in a complex feed-forward loop .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	32571967	2	ver/dev	The hilA gene is directly activated by three AraC-like regulators , RtsA , .	36	The hilA gene is directly activated by three AraC-like regulators , HilD , HilC , and RtsA , which act in a feed-forward loop to activate expression of themselves , each other , and hilA ( Fig. 1 ) ( 2 ) .	3	KEYWORDS BAM, RCSCDB, SPI1, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilA	activator	33593291	10	ver/dev	RtsA can independently activate hilA expression	100	HilD also activates two additional transcription factors , HilC and RtsA , that can independently activate hilA expression .	6	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RpoS	gene	hlyE	regulator	24885225	7	ver/dev	Conclusions : All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating global regulators .	18	Conclusions : All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating multiple environmental signals and global regulators .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	7	ver/dev	Conclusions : All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating multiple environmental signals .	18	Conclusions : All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating multiple environmental signals and global regulators .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	16	ver/dev	All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network .	56	All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating multiple environmental signals .	3	BACKGROUND	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	64	ver/dev	RpoS integrates global regulators , to control S. Typhi hlyE expression .	248	RpoS integrates multiple environmental signals and global regulators , including CRP , Fis , and PhoP signaling pathways , to control S. Typhi hlyE expression .	7	CONCLUSIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	64	ver/dev	RpoS integrates multiple environmental signals , to control S. Typhi hlyE expression .	248	RpoS integrates multiple environmental signals and global regulators , including CRP , Fis , and PhoP signaling pathways , to control S. Typhi hlyE expression .	7	CONCLUSIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	64	ver/dev	RpoS integrates PhoP signaling pathways , to control S. Typhi hlyE expression .	248	RpoS integrates multiple environmental signals and global regulators , including CRP , Fis , and PhoP signaling pathways , to control S. Typhi hlyE expression .	7	CONCLUSIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	64	ver/dev	RpoS integrates Fis , to control S. Typhi hlyE expression .	248	RpoS integrates multiple environmental signals and global regulators , including CRP , Fis , and PhoP signaling pathways , to control S. Typhi hlyE expression .	7	CONCLUSIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	24885225	64	ver/dev	RpoS integrates CRP , to control S. Typhi hlyE expression .	248	RpoS integrates multiple environmental signals and global regulators , including CRP , Fis , and PhoP signaling pathways , to control S. Typhi hlyE expression .	7	CONCLUSIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	25913156	0	ver/dev	RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression .	515	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	32	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	27260307	1	ver/dev	RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression .	575	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	11	ESCHERICHIA COLI. INFECT IMMUN 72, 2879–2888.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	27567490	0	ver/dev	RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression .	514	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	37	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	30778340	5	ver/dev	RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression .	568	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	20	SUPPLEMENTARY MATERIAL	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	33348574	2	ver/dev	-LSB- CrossRef -RSB- Jofré , M.R. ; Rodríguez , L.M. ; Villagra , N.A. ; Hidalgo , A.A. ; Mora , G.C. ; Fuentes , J.A. RpoS integrates d PhoP signaling pathwa to control Salmonella Typhi hlyE expression .	529	[ CrossRef ] Jofré , M.R. ; Rodríguez , L.M. ; Villagra , N.A. ; Hidalgo , A.A. ; Mora , G.C. ; Fuentes , J.A. RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	14	5. 6. 7.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hlyE	regulator	33348574	2	ver/dev	-LSB- CrossRef -RSB- Jofré , M.R. ; Rodríguez , L.M. ; Villagra , N.A. ; Hidalgo , A.A. ; Mora , G.C. ; Fuentes , J.A. RpoS integrates s C to control Salmonella Typhi hlyE expression .	529	[ CrossRef ] Jofré , M.R. ; Rodríguez , L.M. ; Villagra , N.A. ; Hidalgo , A.A. ; Mora , G.C. ; Fuentes , J.A. RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	14	5. 6. 7.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsC	activator	32392214	0	att	Surprisingly , full expression of RcsB-activated genes has been observed in mutants lacking either the rcsC or rcsD gene [ 15 , 16 ] , raising the possibility of RcsB being activated by signaling	63	Surprisingly , full expression of RcsB-activated genes has been observed in mutants lacking either the rcsC or rcsD gene [ 15 , 16 ] , raising the possibility of RcsB being activated by signaling	6	INTRODUCTION	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	1	att	We hypothesized that RcsB is activated by a non-cognate sensor because RcsB-dependent genes are fully expressed in the absence of either the rcsC or rcsD gene [ 15 , 16 ] , and also because the possibility of RcsC phosphorylating RcsB in the absence of RcsD , or of RcsD phosphorylating RcsB in the absence of RcsC [ 16 ] , seemed unlikely [ 10 ] .	77	We hypothesized that RcsB is activated by a non-cognate sensor because RcsB-dependent genes are fully expressed in the absence of either the rcsC or rcsD gene [ 15 , 16 ] , and also because the possibility of RcsC phosphorylating RcsB in the absence of RcsD , or of RcsD phosphorylating RcsB in the absence of RcsC [ 16 ] , seemed unlikely [ 10 ] .	9	A CONDITION THAT ACTIVATES THE REGULATOR RCSB INDEPENDENTLY OF THE RCSC, RCSD, AND RCSF PROTEINS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsC	activator	32392214	8	att	To identify the gene ( s ) responsible for the RcsB-dependent RcsC - and RcsD-independent activation of the rprA promoter , we screened ~ 9,000 transposon Tn10dTc-generated mutants of the rcsC rcsD strain carrying the rprA-gfp fusion for decreased fluorescence on LB agar plates .	110	To identify the gene ( s ) responsible for the RcsB-dependent RcsC - and RcsD-independent activation of the rprA promoter , we screened ~ 9,000 transposon Tn10dTc-generated mutants of the rcsC rcsD strain carrying the rprA-gfp fusion for decreased fluorescence on LB agar plates .	10	RCSB ACTIVATION BY THE PHOSPHORELAY SENSOR BARA	Transposon Tn10	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	rcsC	activator	32392214	1	ver/dev	We hypothesized that RcsB is activated by a non-cognate sensor because RcsB-dependent genes are fully expressed in the absence of either the rcsC .	77	We hypothesized that RcsB is activated by a non-cognate sensor because RcsB-dependent genes are fully expressed in the absence of either the rcsC or rcsD gene [ 15 , 16 ] , and also because the possibility of RcsC phosphorylating RcsB in the absence of RcsD , or of RcsD phosphorylating RcsB in the absence of RcsC [ 16 ] , seemed unlikely [ 10 ] .	9	A CONDITION THAT ACTIVATES THE REGULATOR RCSB INDEPENDENTLY OF THE RCSC, RCSD, AND RCSF PROTEINS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsC	activator	32392214	20	ver/dev	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under Fig 3B , left panel , one may expect CsrC to activate RcsB under low-osmolarity conditions by reducing RcsC expression .	196	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under the same experimental conditions ( Fig 3B , left panel ) , one may expect CsrB and CsrC to activate RcsB under low osmolarity conditions by reducing RcsC expression .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	rcsC	activator	32392214	20	ver/dev	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under Fig 3B , left panel , one may expect CsrB to activate RcsB under low-osmolarity conditions by reducing RcsC expression .	196	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under the same experimental conditions ( Fig 3B , left panel ) , one may expect CsrB and CsrC to activate RcsB under low osmolarity conditions by reducing RcsC expression .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	rcsC	activator	32392214	20	ver/dev	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under the same experimental conditions , one may expect CsrC to activate RcsB under low-osmolarity conditions by reducing RcsC expression .	196	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under the same experimental conditions ( Fig 3B , left panel ) , one may expect CsrB and CsrC to activate RcsB under low osmolarity conditions by reducing RcsC expression .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	rcsC	activator	32392214	20	ver/dev	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under the same experimental conditions , one may expect CsrB to activate RcsB under low-osmolarity conditions by reducing RcsC expression .	196	As a rcsC single mutant exhibited increased RcsB activity compared to wild-type Salmonella under the same experimental conditions ( Fig 3B , left panel ) , one may expect CsrB and CsrC to activate RcsB under low osmolarity conditions by reducing RcsC expression .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both RcsD proteins	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	The rcsB , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both RcsD proteins	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	The rcsB , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of 8B , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both RcsD proteins	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of 8B , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of Fig 8A , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both RcsD proteins	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of Fig 8A , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	The rcsB , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of 8B , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both RcsD proteins	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	The rcsB , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of 8B , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	The rcsB , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of Fig 8A , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both RcsD proteins	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
RcsB	gene	rcsC	activator	32392214	29	ver/dev	The rcsB , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of Fig 8A , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC	309	The rcsB , rcsC , and rcsD single mutants , and the rcsC rcsD double mutants showed no significant increase in fluorescence upon addition of either agent ( Fig 8A and 8B ) , in agreement with the notion that RcsB activation by polymyxin B and mecillinam is dependent on both the RcsC and RcsD proteins [ 22 , 39 ]	16	AGENTS THAT DAMAGE THE OUTER MEMBRANE OR CELL WALL ACTIVATE RCSB IN A BARA-INDEPENDENT MANNER	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
Fur	gene	hilC	activator	17993530	17	att	As expected from the results described above , deletion of hilC or rtsA decreased but did not abrogate Fur-dependent induction of hilA .	197	As expected from the results described above , deletion of hilC or rtsA decreased but did not abrogate Fur-dependent induction of hilA .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
CsrA	gene	glpF	activator	30682134	51	ver/dev	glpF , was activated by CsrA in mLPM	430	Indeed , glpF , encoding the glycerol uptake facilitator protein , was activated by CsrA in mLPM , and there are CsrA binding sites identified by CLIP-seq on both glpF and glpK , encoding the glycerol kinase ( S2 Table ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	lacZ	activator	11673423	2	att	As explained above , all lac expression values were obtained in , and are reported for , pairs of isogenic rpoS and rpoS deriv-atives , whose difference has been taken to represent the in-vivo activity of the RpoS-dependent proU P1 promoter under the particular test conditions ; by these criteria , the plasmid vectors pMU575 and pMU2385 carrying the promoterless lacZ reporter gene displayed insignificant RpoS-dependent lac expression under any of the conditions tested in this study ( data not shown ) .	97	As explained above , all lac expression values were obtained in , and are reported for , pairs of isogenic rpoS and rpoS deriv-atives , whose difference has been taken to represent the in vivo activity of the RpoS-dependent proU P1 promoter under the particular test conditions ; by these criteria , the plasmid vectors pMU575 and pMU2385 carrying the promoterless lacZ reporter gene displayed insignificant RpoS-dependent lac expression under any of the conditions tested in this study ( data not shown ) .	6	RESULTS	unidentified plasmid;unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	lacZ	activator	11673423	2	att	As explained above , all lac expression values were obtained in , and are reported for , pairs of isogenic rpoS and rpoS deriv-atives , whose difference has been taken to represent the in-vivo activity of the RpoS-dependent proU P1 promoter under the particular test conditions ; by these criteria , the plasmid vectors pMU575 and pMU2385 carrying the promoterless lacZ reporter gene displayed insignificant RpoS-dependent lac expression under any of the conditions tested in this study ( data not shown ) .	97	As explained above , all lac expression values were obtained in , and are reported for , pairs of isogenic rpoS and rpoS deriv-atives , whose difference has been taken to represent the in vivo activity of the RpoS-dependent proU P1 promoter under the particular test conditions ; by these criteria , the plasmid vectors pMU575 and pMU2385 carrying the promoterless lacZ reporter gene displayed insignificant RpoS-dependent lac expression under any of the conditions tested in this study ( data not shown ) .	6	RESULTS	unidentified plasmid;unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	lacZ	activator	26039089	12	att	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary-phase ( Fig 5 ) .	214	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary phase ( Fig 5 ) .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	lacZ	activator	26039089	12	ver/dev	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced : lacZ activity compared to the parent strain during stationary-phase .	214	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary phase ( Fig 5 ) .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
YdcI	gene	acnB	repressor	30038032	8	ver/dev	The transcription of acnB , icdA , sdhC was most repressed by YdcI .	318	The transcription of acnB , icdA , sdhC , and fumA genes was most repressed by YdcI ( about 50 -- 100 fold higher in the ydcI strain ) .	7	REPRESSION OF THE ETHANOLAMINE UTILIZATION OPERON BY ARCA—	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ydhI	repressor	29857034	15	ver/dev	For genes , we found two genes , ydhI are negatively regulated by SlyA .	312	For genes involved in multidrug resistance , we found two genes , ydhJ and ydhI ( STM14_1740 ; STM14_1741 ) , which are transcribe divergent to slyA and are negatively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxR	activator	23637460	8	ver/dev	the soxR mutant is consistent with SoxR activation of PacnA	240	However , acnA expression was enhanced ( 1.7-fold ) in the parent , but not in the soxR mutant , which is consistent with SoxR activation of PacnA ( Fig. 3a ) .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	cobB	regulator	26943369	5	att	The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .	84	The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SsrB	TU	ssrAB	repressor	27564394	8	ver/dev	Mechanistically , HilD indirectly regulates SsrB-regulated genes by antagonizing the H-NS-mediated repression of ssrAB at stationary-phase under SPI-1 .	291	Mechanistically , HilD indirectly regulates SsrB-regulated genes by antagonizing the H-NS-mediated repression of ssrAB at stationary phase under SPI-1 inducing conditions [ 30 ] ( see also Fig 2 ) .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	sspH2	activator	29034217	0	att	Transcription of the sspH2 gene is induced in an SsrB-dependent manner during survival within RAW264 .7 macrophages , and sspH2 mutants do not induce lethal infection of calves ( Miao et al. , 1999 ; Tomljenovic-Berube et al. , 2013 ) .	178	Transcription of the sspH2 gene is induced in an SsrB-dependent manner during survival within RAW264 .7 macrophages , and sspH2 mutants do not induce lethal infection of calves ( Miao et al. , 1999 ; Tomljenovic-Berube et al. , 2013 ) .	4	LUMINAL COLONIZATION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SsrB	gene	sspH2	activator	29034217	0	att	Transcription of the sspH2 gene is induced in an SsrB-dependent manner during survival within RAW264 .7 macrophages , and sspH2 mutants do not induce lethal infection of calves ( Miao et al. , 1999 ; Tomljenovic-Berube et al. , 2013 ) .	178	Transcription of the sspH2 gene is induced in an SsrB-dependent manner during survival within RAW264 .7 macrophages , and sspH2 mutants do not induce lethal infection of calves ( Miao et al. , 1999 ; Tomljenovic-Berube et al. , 2013 ) .	4	LUMINAL COLONIZATION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FlhDC	gene	flgM	regulator	17725646	2	ver/dev	FlhDC acts as a positive regulator for class flgM .	185	FlhDC acts as a positive regulator for class II promoter-transcribed genes , such as fliA and flgM .	7	THE TVIA-DEPENDENT DECREASE IN IL-8 EXPRESSION IS INDEPENDENT OF THE INVASION-ASSOCIATED TYPE III SECRETION SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	marA	regulator	15155237	5	att	This result demonstrates that in E. coli RamA can mediate an MDR phenotype independently of a functionally intact marA , likely by direct activation of MarA-controlled genes .	78	This result demonstrates that in E. coli RamA can mediate an MDR phenotype independently of a functionally intact marA , likely by direct activation of MarA-controlled genes .	3	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	marA	regulator	20237076	3	auto	The expression of MarA is further activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes involved in adaptation to stress conditions , such as oxidative-stress , heavy metals or antimicrobials .10	29	The expression of MarA is further activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes involved in adaptation to stress conditions , such as oxidative stress , heavy metals or antimicrobials .10	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	6	att	At 30 °C , both plasmids pHYD394 and pHYD395 conferred nil lac expression in wild-type or rho strains ; RpoS-dependent expression was induced around 50-fold in the hns mutant , and there was a further marginal elevation in the hns rho double mutant ( Table 2 ) .	155	At 30 °C , both plasmids pHYD394 and pHYD395 conferred nil lac expression in wild-type or rho strains ; RpoS-dependent expression was induced around 50-fold in the hns mutant , and there was a further marginal elevation in the hns rho double mutant ( Table 2 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	8	att	RpoS-dependent expression of osmY-lac in LBON medium was unaffected by rho but was increased around 6-fold by hns ( comparable to that reported earlier [ 5 ] ) and around 25-fold by growth at 10 °C ( Table 3 ) .	160	RpoS-dependent expression of osmY-lac in LBON medium was unaffected by rho but was increased around 6-fold by hns ( comparable to that reported earlier [ 5 ] ) and around 25-fold by growth at 10 °C ( Table 3 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	9	att	RpoS-dependent expression of csiD-lac was not affected by any of the conditions , that is , by rho or hns mutations or growth at low-temperature ( Table 3 ) .	164	RpoS-dependent expression of csiD-lac was not affected by any of the conditions , that is , by rho or hns mutations or growth at low temperature ( Table 3 ) .	6	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RpoS	gene	hns	activator	11673423	6	ver/dev	RpoS-dependent expression was induced around 50-fold in the hns mutan	155	At 30 °C , both plasmids pHYD394 and pHYD395 conferred nil lac expression in wild-type or rho strains ; RpoS-dependent expression was induced around 50-fold in the hns mutant , and there was a further marginal elevation in the hns rho double mutant ( Table 2 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	6	ver/dev	RpoS-dependent expression was induced around 50-fold in the hns mutan	155	At 30 °C , both plasmids pHYD394 and pHYD395 conferred nil lac expression in wild-type or rho strains ; RpoS-dependent expression was induced around 50-fold in the hns mutant , and there was a further marginal elevation in the hns rho double mutant ( Table 2 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	6	ver/dev	RpoS-dependent expression was induced around 50-fold in the hns mutan	155	At 30 °C , both plasmids pHYD394 and pHYD395 conferred nil lac expression in wild-type or rho strains ; RpoS-dependent expression was induced around 50-fold in the hns mutant , and there was a further marginal elevation in the hns rho double mutant ( Table 2 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	6	ver/dev	RpoS-dependent expression was induced around 50-fold in the hns mutan	155	At 30 °C , both plasmids pHYD394 and pHYD395 conferred nil lac expression in wild-type or rho strains ; RpoS-dependent expression was induced around 50-fold in the hns mutant , and there was a further marginal elevation in the hns rho double mutant ( Table 2 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	hns	activator	11673423	8	ver/dev	RpoS-dependent expression of osmY-lac in LBON medium was increased around 6-fold by hns and around 25-fold by growth at 10 ° .	160	RpoS-dependent expression of osmY-lac in LBON medium was unaffected by rho but was increased around 6-fold by hns ( comparable to that reported earlier [ 5 ] ) and around 25-fold by growth at 10 °C ( Table 3 ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysC	activator	25637663	4	att	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	39	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	6	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	phoP	repressor	32209674	4	ver/dev	For unknown reasons , H-NS basal amounts were slightly lower in the phoP mutants than in the wild-type strain in some of the biological replicates .	55	For unknown reasons , H-NS basal amounts were slightly lower in the phoP and lon mutants than in the wild-type strain in some of the biological replicates ( Fig. 1A , − 0.5 h ; see Mendeley : doi : 10.17632 / m4vt7hwrgc .1 ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	phoP	repressor	32209674	7	ver/dev	In agreement with the results of the biochemical experiments , H-NS amounts were lower in wild-type Salmonella than in the phoP mutant at 6 h post internalization by Fig. 1A .	128	In agreement with the results of the biochemical experiments presented above , H-NS amounts were lower in wild-type Salmonella than in the phoP mutant at 6 h post internalization by macrophages ( Fig. 1A ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	phoP	repressor	32209674	7	ver/dev	In agreement with the results of the biochemical experiments , H-NS amounts were lower in wild-type Salmonella than in the phoP mutant at 6 h post internalization by macrophages .	128	In agreement with the results of the biochemical experiments presented above , H-NS amounts were lower in wild-type Salmonella than in the phoP mutant at 6 h post internalization by macrophages ( Fig. 1A ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmY	regulator	21311887	1	ver/dev	Among the 38 genes , osmY were previously reported to be regulated by RpoS .	120	Among the 38 genes , four ( osmC , osmY , osmB , and otsBA ) were previously reported to be regulated by RpoS [ 4 , 7 , 10 , 12 , 16 , 37 ] .	9	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	osmY	regulator	23376784	0	att	The RpoS-regulated osmY gene encodes a periplasmic protein of unknown function that has been found to be induced by both osmotic and growth phase signals ( Yim and Villarejo , 1992 ) .	261	The RpoS-regulated osmY gene encodes a periplasmic protein of unknown function that has been found to be induced by both osmotic and growth phase signals ( Yim and Villarejo , 1992 ) .	13	3. RESULTS AND DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	osmY	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , osmY are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	basS	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM4264	repressor	17322315	25	ver/dev	On the other hand , STM4264 expression could not downregulate CsgD in the STM1703 mutant .	260	On the other hand , STM4264 expression could not downregulate CsgD in the STM1703 ( 1703 ) mutant .	4	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CsgD	gene	STM4264	repressor	22164276	8	ver/dev	Collectively , these findings suggest that CsgD -LRB- at least partially -RRB- inhibits invasion in the STM4264 mutant through repression of secretion of other TTSS-1 effector proteins .	256	Collectively , these findings suggest that CsgD ( at least partially ) inhibits invasion in the STM4264 mutant through repression of secretion of SipA and other TTSS-1 effector proteins ( our unpublished data ; [ 15 ] ) .	9	EFFECT OF DOUBLE MUTANTS ON THE INVASION PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	STM4264	repressor	22164276	8	ver/dev	Collectively , these findings suggest that CsgD -LRB- at least partially -RRB- inhibits invasion in the STM4264 mutant through repression of secretion of other TTSS-1 effector proteins .	256	Collectively , these findings suggest that CsgD ( at least partially ) inhibits invasion in the STM4264 mutant through repression of secretion of SipA and other TTSS-1 effector proteins ( our unpublished data ; [ 15 ] ) .	9	EFFECT OF DOUBLE MUTANTS ON THE INVASION PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	STM4264	repressor	22164276	8	ver/dev	Collectively , these findings suggest that CsgD -LRB- at least partially -RRB- inhibits invasion in the STM4264 mutant through repression of secretion of SipA TTSS-1 effector proteins .	256	Collectively , these findings suggest that CsgD ( at least partially ) inhibits invasion in the STM4264 mutant through repression of secretion of SipA and other TTSS-1 effector proteins ( our unpublished data ; [ 15 ] ) .	9	EFFECT OF DOUBLE MUTANTS ON THE INVASION PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	STM4264	repressor	22164276	8	ver/dev	Collectively , these findings suggest that CsgD -LRB- at least partially -RRB- inhibits invasion in the STM4264 mutant through repression of secretion of SipA TTSS-1 effector proteins .	256	Collectively , these findings suggest that CsgD ( at least partially ) inhibits invasion in the STM4264 mutant through repression of secretion of SipA and other TTSS-1 effector proteins ( our unpublished data ; [ 15 ] ) .	9	EFFECT OF DOUBLE MUTANTS ON THE INVASION PHENOTYPE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	STM4264	repressor	22164276	11	ver/dev	In the STM4264 mutant , inhibition of expression of the biofilm regulator CsgD contribute to down-regulation of Fig. 11A .	357	In the STM4264 mutant , inhibition of the secretion of the TTSS-1 effector protein SipA and expression of the biofilm regulator CsgD and the cellulose synthase BcsA contribute to down-regulation of invasion ( Fig. 11A ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	STM4264	repressor	22164276	11	ver/dev	In the STM4264 mutant , inhibition of expression of the biofilm regulator CsgD contribute to down-regulation of invasion .	357	In the STM4264 mutant , inhibition of the secretion of the TTSS-1 effector protein SipA and expression of the biofilm regulator CsgD and the cellulose synthase BcsA contribute to down-regulation of invasion ( Fig. 11A ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	STM4264	repressor	26655751	2	ver/dev	STM4264 inhibit CsgD function .	43	PDEs ( STM1703 , STM3611 , STM4264 , and STM1827 ) inhibit CsgD function ( 13 , 14 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	cydA	activator	30682134	44	ver/dev	Additional qRT-PCR experiments confirmed that CsrA activated cydA expression in Fig 7B .	319	Additional qRT-PCR experiments confirmed that CsrA activated cydA expression in LB ( Fig 7B ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	cydA	activator	30682134	44	ver/dev	Additional qRT-PCR experiments confirmed that CsrA activated cydA expression in LB .	319	Additional qRT-PCR experiments confirmed that CsrA activated cydA expression in LB ( Fig 7B ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	fepE	regulator	33638994	19	ver/dev	These assays confirmed binding of phosphorylated RcsB to fepE promoters .	398	These assays confirmed binding of phosphorylated RcsB to fepE , osmB and ytfK promoters and to flgA and nlpD Intra-CDS sequences ( Figure 7A and C ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Rho	gene	ribB	activator	22431636	13	att	We posited that the FMN-sensing riboswitch located in the E. coli ribB leader might also function by controlling Rho-dependent termination because this leader encodes a known sRNA but lacks an obvious intrinsic terminator ( Fig. 3A ) ( 9 , 10 ) .	133	We posited that the FMN-sensing riboswitch located in the E. coli ribB leader might also function by controlling Rho-dependent termination because this leader encodes a known sRNA but lacks an obvious intrinsic terminator ( Fig. 3A ) ( 9 , 10 ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	Escherichia coli	0	L2	SPEC	Fact	NEG	Other	Level 1
Rho	gene	ribB	activator	22431636	14	att	FMN stimulates Rho-dependent termination directly , because addition of FMN to in-vitro-transcription reactions enhanced Rho 's ability to terminate transcription in the wild-type ribB leader but had no effect in the absence of Rho ( Fig. 3C and Fig .	139	FMN stimulates Rho-dependent termination directly , because addition of FMN to in vitro transcription reactions enhanced Rho 's ability to terminate transcription in the wild-type ribB leader but had no effect in the absence of Rho ( Fig. 3C and Fig .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	OTHER	Other	NEG	Other	Level 1
Rho	gene	ribB	activator	22431636	15	att	Taken together , these data establish that the ribB leader contains a Rho-dependent terminator that inhibits transcription elongation into the ribB coding region in the presence of FMN .	141	Taken together , these data establish that the ribB leader contains a Rho-dependent terminator that inhibits transcription elongation into the ribB coding region in the presence of FMN .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	ribB	activator	22431636	15	att	Taken together , these data establish that the ribB leader contains a Rho-dependent terminator that inhibits transcription elongation into the ribB coding region in the presence of FMN .	141	Taken together , these data establish that the ribB leader contains a Rho-dependent terminator that inhibits transcription elongation into the ribB coding region in the presence of FMN .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	ribB	activator	22431636	16	att	To investigate whether alternate folding of the ribB riboswitch in response to the availability of FMN controls the ability of Rho to terminate transcription , we examined the effect of mutations that favor different riboswitch conformers on Rho-dependent termination in-vivo and in-vitro .	143	To investigate whether alternate folding of the ribB riboswitch in response to the availability of FMN controls the ability of Rho to terminate transcription , we examined the effect of mutations that favor different riboswitch conformers on Rho-dependent termination in vivo and in vitro .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	SPEC	Investigation	OTHER	New	Level 1
Rho	gene	ribB	activator	22431636	17	att	These data indicate that FMN inhibits transcription elongation into the ribB coding region by promoting an RNA conformation that enhances Rho-dependent transcription termination .	146	These data indicate that FMN inhibits transcription elongation into the ribB coding region by promoting an RNA conformation that enhances Rho-dependent transcription termination .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Rho	gene	ribB	activator	22431636	18	att	Apart from regulating translation , the ribB riboswitch directly controls transcription termination within the leader region because FMN clearly stimulated Rho-dependent termination ( Fig. 3 B and C ) in the absence of the translation machinery ( Fig. 3C ) .	151	Apart from regulating translation , the ribB riboswitch directly controls transcription termination within the leader region because FMN clearly stimulated Rho-dependent termination ( Fig. 3 B and C ) in the absence of the translation machinery ( Fig. 3C ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	ribB	activator	22431636	19	att	Moreover , in the presence of FMN , Rho-dependent termination takes place upstream of the ribB start codon ( Fig .	152	Moreover , in the presence of FMN , Rho-dependent termination takes place upstream of the ribB start codon ( Fig .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	ribB	activator	22431636	20	att	The E. coli ribB leader contains a riboswitch that promotes Rho-dependent termination in the presence of FMN .	162	The E. coli ribB leader contains a riboswitch that promotes Rho-dependent termination in the presence of FMN .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	ribB	activator	22431636	21	att	Zones of Rho-de-pendent termination are shown by red lines ( solid red lines represent zones of Rho-dependent termination observed for the wild-type ribB leader only in the presence of FMN ; dashed red lines represent zones of termination observed without and with FMN ) .	170	Zones of Rho-de-pendent termination are shown by red lines ( solid red lines represent zones of Rho-dependent termination observed for the wild-type ribB leader only in the presence of FMN ; dashed red lines represent zones of termination observed without and with FMN ) .	4	THE AUTHORS DECLARE NO CONFLICT OF INTEREST. THIS ARTICLE IS A PNAS DIRECT SUBMISSION.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	hilA	activator	27601571	5	ver/dev	IHF , also positively regulates hilA by displacing H-NS .	73	Another NAP , IHF , also positively regulates hilA by displacing H-NS ( 31 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EmrR	TU	emrAB	regulator	30992361	30	ver/dev	Our RNA-Seq results showed that transcription of the emrB genes in the ΔemrR mutant 5.94-fold higher than those in the wild-type strai , thus reconfirming that EmrR was a negative regulator of the emrAB operon .	239	Our RNA-Seq results showed that transcription of the emrA and emrB genes in the ΔemrR mutant were 5.75 - and 5.94-fold higher than those in the wild-type strain ( see Table S3 in the supplemental material ) , thus reconfirming that EmrR was a negative regulator of the emrAB operon ( 9 ) .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
EmrR	TU	emrAB	regulator	30992361	30	ver/dev	Our RNA-Seq results showed that transcription of the emrB genes in the ΔemrR mutant were 5.7 , thus reconfirming that EmrR was a negative regulator of the emrAB operon .	239	Our RNA-Seq results showed that transcription of the emrA and emrB genes in the ΔemrR mutant were 5.75 - and 5.94-fold higher than those in the wild-type strain ( see Table S3 in the supplemental material ) , thus reconfirming that EmrR was a negative regulator of the emrAB operon ( 9 ) .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
EmrR	TU	emrAB	regulator	30992361	30	ver/dev	Our RNA-Seq results showed that transcription of the emrA genes in the ΔemrR mutant 5.94-fold higher than those in the wild-type strai , thus reconfirming that EmrR was a negative regulator of the emrAB operon .	239	Our RNA-Seq results showed that transcription of the emrA and emrB genes in the ΔemrR mutant were 5.75 - and 5.94-fold higher than those in the wild-type strain ( see Table S3 in the supplemental material ) , thus reconfirming that EmrR was a negative regulator of the emrAB operon ( 9 ) .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
EmrR	TU	emrAB	regulator	30992361	30	ver/dev	Our RNA-Seq results showed that transcription of the emrA genes in the ΔemrR mutant were 5.7 , thus reconfirming that EmrR was a negative regulator of the emrAB operon .	239	Our RNA-Seq results showed that transcription of the emrA and emrB genes in the ΔemrR mutant were 5.75 - and 5.94-fold higher than those in the wild-type strain ( see Table S3 in the supplemental material ) , thus reconfirming that EmrR was a negative regulator of the emrAB operon ( 9 ) .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	TU	phoPQ	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ at the CpxR box-like sequences .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	TU	phoPQ	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ at the CpxR box-like sequences .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	TU	phoPQ	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ promoters .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	TU	phoPQ	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ promoters .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	TU	phoPQ	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ at the CpxR box-like sequences .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	TU	phoPQ	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ at the CpxR box-like sequences .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	TU	phoPQ	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of CRRGs , binding directly to the phoPQ .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	TU	phoPQ	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of colistin resistance-related genes , binding directly to the phoPQ .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	ompC	repressor	23938383	5	ver/dev	Lrp negatively regulates the porin gene ompC expression in E. coli	167	For example , Lrp negatively regulates the porin gene ompC expression in E. coli ( Ferrario et al. 1995 ) , and OmpC are required for optimal growth at an acidic pH ( Ferrario et al. 1995 ; Sato et al. 2000 ) .	16	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilA	activator	16023758	10	ver/dev	Organic acid acidification shoul lead primarily to OmpR activation of hilA while inorganic acid stress should lead to ssrAB activation inside the eucaryotic cell in the nutrient-deprived environment .	188	Organic acid acidification shoul lead primarily to OmpR activation of hilA while inorganic acid stress should lead to ssrAB activation inside the eucaryotic cell in the nutrient-deprived environment .	11	2.4. OMPR/ENVZ AND THE ACID STRESS RESPONSE	nan	1	L2	OTHER	Other	OTHER	New	Level 1
OmpR	gene	hilA	activator	16443238	1	ver/dev	Expression of hilA is increased by the pleiotropic activator proteins OmpR for Inversion Stimulation , Fis .	38	Expression of hilA is increased by the pleiotropic activator proteins OmpR , PhoPQ , and the Factor for Inversion Stimulation , Fis .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	lacZ	regulator	29866803	6	att	( C ) - Galactosidase activity determined for wild-type cells carrying scsA : : lacZ ( scsA-lacZ ) or cpxP : : lacZ ( cpxP-lacZ ) ( included as a CpxR-regulated positive control ) transcriptional-fusions and transformed either with the empty vector pUHE21-2lacIq ( vector ) or with pNlpE and then grown in LB-medium with the addition of 100 M IPTG .	118	( C ) - Galactosidase activity determined for wild-type cells carrying scsA : : lacZ ( scsA-lacZ ) or cpxP : : lacZ ( cpxP-lacZ ) ( included as a CpxR-regulated positive control ) transcriptional fusions and transformed either with the empty vector pUHE21-2lacIq ( vector ) or with pNlpE and then grown in LB medium with the addition of 100 M IPTG .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
HilD	gene	leuO	activator	24354910	17	ver/dev	Western blot analysis revealed that activation of leuO transcription decreased the HilD level	84	Western blot analysis revealed that activation of leuO transcription decreased the HilD level , and the decrease was suppressed in a ΔleuO background ( Fig. 3 ) .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	leuO	activator	24354910	50	ver/dev	activation of leuO transcription decreases the level of HilD protein	200	The existence of a LeuO-HilE-HilD ` pathway ' of SPI-1 repression in S. enterica serovar Typhimurium is supported by several lines of evidence : ( i ) lack of HilE relieves LeuO-mediated repression of SPI-1 ( Fig. 2 ) ; ( ii ) activation of leuO transcription decreases the level of HilD protein ( Fig. 3 ) ; ( iii ) the HilD protein decrease caused by LeuO is suppressed by a hilE mutation ( Fig. 3 ) ; and ( iv ) LeuO activates transcription of hilE ( Fig. 5 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cra	gene	adhE	regulator	19389776	2	ver/dev	Regulation of expression of the ethanol dehydrogenase gene ( adhE ) in Escherichia coli by catabolite repressor activator protein Cra .	602	Regulation of expression of the ethanol dehydrogenase gene ( adhE ) in Escherichia coli by catabolite repressor activator protein Cra .	53	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	flhC	regulator	12115054	3	ver/dev	that either SdiA regulates flhC	235	This could mean that either SdiA regulates flhC or luxS , or that there are multiple , quorum-sensing-independent systems capable of monitoring the changing environment of a growing population .	17	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
FliA	gene	STM1697	regulator	25437188	48	ver/dev	STM3611 , as a class III flagellar gene , is indirectly regulated by STM1697 via FliA .	556	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC , STM1344 and STM1697 via FliA ( Figure 2 ) .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	bapA	regulator	18790861	7	att	In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary-phase ( 4 ) .	33	In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary phase ( 4 ) .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	acnA	regulator	19917752	0	ver/dev	SoxS _ regulated , including acnA	266	Among the genes that were upregulated in 104-cip , a number were SoxS regulated , including acnA , fpr , ribA , sodA , lpxC , and soxS itself .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cbl	gene	sbp	activator	18957594	7	ver/dev	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources .	329	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ( Kredich , 1996 ; Stec et al. , 2006 ; Van Der Ploeg et al. , 1997 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
CspE	gene	cspE	activator	32159509	1	att	To confirm the importance of CspE-dependent biofilm formation , a cspE complementation approach was utilized ( pcspE -- cspE was expressed in the pRS424 plasmid under the control of its native promoter ) .	148	To confirm the importance of CspE-dependent biofilm formation , a cspE complementation approach was utilized ( pcspE -- cspE was expressed in the pRS424 plasmid under the control of its native promoter ) .	13	RESULTS	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	slrP	regulator	31484980	58	ver/dev	The previously defined regulation of slrP by SlyA and/or PhoP is not depicted in the model	297	The previously defined regulation of ugtL and slrP by SlyA and/or PhoP is not depicted in the model but it is described in text .	4	METHODS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	flhD	repressor	30355489	12	ver/dev	Expression of PflhDCSBG does not show SsrB-dependent repression of TM flhD .	133	( B ) Expression of PflhDCSBG does not show SsrB-dependent repression of STM flhD , measured by RT-qPCR .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
InvF	gene	lacZ	regulator	24018968	6	att	The Hfq-dependent stationary-phase expression of SPI1 genes was also clearly observed in an InvF-regulated gene , sipC : a sipC : : lacZ chromosomal fusion expressed 3,761 ± 292 and 1,120 ± 12 Miller units of β-galactosidase at 4 and 12 h p.i. , respectively , in wild-type cells , whereas the sipC : : lacZ fusion in ∆ hfq cells expressed 1,486 ± 192 and 830 ± 67 Miller units of β-galactosidase at the same time points ( data	177	The Hfq-dependent stationary-phase expression of SPI1 genes was also clearly observed in an InvF-regulated gene , sipC : a sipC : : lacZ chromosomal fusion expressed 3,761 ± 292 and 1,120 ± 12 Miller units of β-galactosidase at 4 and 12 h p.i. , respectively , in wild-type cells , whereas the sipC : : lacZ fusion in ∆ hfq cells expressed 1,486 ± 192 and 830 ± 67 Miller units of β-galactosidase at the same time points ( data	14	STATIONARY PHASE UNDER SHAKING CULTURE CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	STM1554	regulator	25080967	4	ver/dev	Besides the putative ` rck operon ' , SdiA regulates the transcription of STM1554 .	62	Besides the putative ` rck operon ' , SdiA regulates the transcription of srgE ( STM1554 ) , an apparently horizontally acquired gene encoding a type III secreted effector whose function remains unknown ( Habyarimana et al. , 2014 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Other	OTHER	New	Level 1
FNR	gene	sodCII	repressor	18362154	1	ver/dev	Finding this relief to be incomplete suggests that additional factors besides FNR are involved in the repression of sodCII when oxygen is limiting .	255	Finding this relief to be incomplete suggests that additional factors besides FNR are involved in the repression of sodCII when oxygen is limiting .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilE	activator	22291968	2	ver/dev	Transcription of hilE is activated by the fimbrial regulator FimYZ , thus transmitting inputs to SPI-1 through HilD .	46	Transcription of hilE is activated by the fimbrial regulator FimYZ [ 27 ] , and is repressed by the PTS-dependent regulator Mlc [ 28 ] , thus transmitting inputs to SPI-1 through HilD .	4	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the occurrence of autogenous activation of hilD transcription .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in the occurrence of autogenous activation of hilD transcription .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in accordance with two well known facts .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in accordance with two well known facts .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	activator	29378886	32	ver/dev	However , our data show that PhoPQ can repress the system independently of HilD ; thus , this transcriptional induction of hilE is apparently superfluous .	266	However , our data show that PhoPQ can repress the system independently of HilD and HilE ( reference 6 and unpublished data ) ; thus , this transcriptional induction of hilE is apparently superfluous .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SoxS	gene	acrB	repressor	32468234	10	ver/dev	The study also reports suppression of acrB expression along with downregulation of SoxS regulators .	146	The study also reports suppression of acrB expression along with downregulation of SoxS and MarA regulators ( Huang et al. 2016 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	rhoL	activator	30201777	26	att	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	259	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	rhoL	activator	30201777	26	att	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	259	The transcripts that hybridized to the probe for rhoL ( Fig. 7A ) included the following : an 1,500-nucleotide ( nt ) transcript that is the appropriate length for the full rho mRNA , based on the S. Typhimurium transcriptome data from Kröger et al. ( 9 ) ; an 700-nt transcript , which may result from Rho-dependent intragenic termination ( 67 ) ; and an 260-nt transcript that corresponds to the leader region , carrying rhoL , which is involved in the Rho-dependent attenuation of rho transcription in E. coli ( 67 ) ( Fig. 7A ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RhaS	TU	rhaBAD	activator	24391637	0	ver/dev	RhaS activates the rhaBAD genes via binding to another inverted repeat of two sites .	39	RhaS activates the rhaBAD and rhaT genes via binding to another inverted repeat of two sites whose sequence differs from the RhaR consensus binding site .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FabR	gene	yqfA	regulator	27004424	14	ver/dev	In S. Typhimurium , this represents the first evidence for direct in-vivo binding of FabR to the yqfA promoters .	196	In S. Typhimurium , this represents the first evidence for direct in vivo binding of FabR to the fabB , fabA and yqfA promoters .	11	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FabR	gene	yqfA	regulator	27004424	17	ver/dev	Moreover , combination of the ChIP-chip results provides the first experimental evidence that FabR directly binds to the yqfA promoter .	280	Moreover , combination of the transcriptomic and the ChIP-chip results provides the first experimental evidence that FabR directly binds to the yqfA promoter and regulates its expression .	12	TRANSCRIPTIONAL PROFILING OF A FABR MUTANT	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FabR	gene	yqfA	regulator	27004424	17	ver/dev	Moreover , combination of the transcriptomic results provides the first experimental evidence that FabR directly binds to the yqfA promoter .	280	Moreover , combination of the transcriptomic and the ChIP-chip results provides the first experimental evidence that FabR directly binds to the yqfA promoter and regulates its expression .	12	TRANSCRIPTIONAL PROFILING OF A FABR MUTANT	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FabR	gene	yqfA	regulator	27004424	25	ver/dev	This combinatorial approach provides the first experimental evidence that FabR regulates the expression of yqfA , whereas for E. coli only evidence for binding has been given .	425	This combinatorial approach provides the first experimental evidence that FabR directly binds to and regulates the expression of yqfA , whereas for E. coli only evidence for binding has been given [ 29 ] .	13	DISCUSSION	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
RstA	gene	feoA	activator	18790861	2	att	This FeoB induction resulted in increased ferrous iron uptake , which associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein .	12	This FeoB induction resulted in increased ferrous iron uptake , which associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoA	activator	18790861	39	att	This result was dependent on RstA-activated feoAB transcription because Fe ( II ) uptake in the feoA promoter mutant strain reached wild-type levels upon RstA expression ( Fig. 3A ) .	218	This result was dependent on RstA-activated feoAB transcription because Fe ( II ) uptake in the feoA promoter mutant strain reached wild-type levels upon RstA expression ( Fig. 3A ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoA	activator	18790861	40	att	We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .	219	We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	feoA	activator	18790861	49	att	Indeed , lack of RstA-dependent transcriptional activation of the feoA promoter partially restored growth of the strain expressing the RstA protein ( Fig. 5A ) .	248	Indeed , lack of RstA-dependent transcriptional activation of the feoA promoter partially restored growth of the strain expressing the RstA protein ( Fig. 5A ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
RstA	gene	feoA	activator	18790861	55	att	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoA	activator	18790861	59	att	This phenotypic defect became more prominent when cells expressing the RstA protein were grown with the iron-reducing agent , whereas lack of the RstA-dependent activation of the feoA promoter or the Fe ( II ) chelator significantly eliminated the RstA-mediated growth inhibition ( Fig. 5 ) .	296	This phenotypic defect became more prominent when cells expressing the RstA protein were grown with the iron-reducing agent , whereas lack of the RstA-dependent activation of the feoA promoter or the Fe ( II ) chelator significantly eliminated the RstA-mediated growth inhibition ( Fig. 5 ) .	5	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RstA	gene	feoA	activator	18790861	1	ver/dev	The RstA protein maintained wild-type levels of the Fur protein but exceptionally activated transcription of the feoAB operon directly to the feoA promoter .	11	The RstA protein maintained wild-type levels of the Fur protein but exceptionally activated transcription of the feoAB operon encoding the ferrous iron transporter FeoB by binding directly to the feoA promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	feoA	activator	18790861	2	ver/dev	increased ferrous iron uptake associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein	12	This FeoB induction resulted in increased ferrous iron uptake , which associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoA	activator	18790861	32	ver/dev	The labeled wild-type feoA promoter was incubated with increasing concentrations of the RstA protein .	207	The labeled wild-type feoA promoter was incubated with increasing concentrations of the RstA protein ( left panel , lanes 1 to 4 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	feoA	activator	18790861	37	ver/dev	In sum , our experiments dem-onstrated that the RstA protein activates transcription of the feoAB operon via its direct binding to the feoA promoter .	214	In sum , our experiments dem-onstrated that the RstA protein activates transcription of the feoAB operon via its direct binding to the feoA promoter .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	feoA	activator	18790861	49	ver/dev	Indeed , lack of RstA-dependent transcriptional activation of the feoA promoter partially restored growth of the strain .	248	Indeed , lack of RstA-dependent transcriptional activation of the feoA promoter partially restored growth of the strain expressing the RstA protein ( Fig. 5A ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
RstA	gene	feoA	activator	18790861	55	ver/dev	the RstA-dependent activation of feoAB transcription increased Fe uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	feoA	activator	18790861	59	ver/dev	This phenotypic defect became more prominent when cells were grown with the iron-reducing agent , whereas lack of the RstA-dependent activation of the feoA promoter significantly eliminated the RstA-mediated growth inhibition .	296	This phenotypic defect became more prominent when cells expressing the RstA protein were grown with the iron-reducing agent , whereas lack of the RstA-dependent activation of the feoA promoter or the Fe ( II ) chelator significantly eliminated the RstA-mediated growth inhibition ( Fig. 5 ) .	5	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	sinR	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the sinR genes , independently of InvF .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sinR	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the sinR genes , independently of HilA .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sinR	activator	27886269	7	ver/dev	HilD induces the expression of sinR , in the absence of other Salmonella-specific regulators .	82	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not that of SL1896 , in the absence of other Salmonella-specific regulators .	3	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	sinR	activator	27886269	21	ver/dev	Thus , HilD positively regulates the expression of the sinR genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sinR	activator	27886269	22	ver/dev	HilD positively regulates sinR in S. Typhimurium .	132	HilD positively regulates gtgE , phoH , sinR , lpxR , SL1896 and SL4247 in S. Typhimurium .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sinR	activator	27886269	23	ver/dev	HilD induces the expression of sinR , in E. coli MC4100 .	151	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not SL1896 , in E. coli MC4100 .	4	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	envR	activator	22804842	26	ver/dev	The results of this analysis suggest that LeuO activates transcription of envR , perhaps by antagonizing H-NS .	411	The results of this analysis suggest that LeuO activates transcription of envR , perhaps by antagonizing H-NS , but appears to function as a repressor at the other target genes .	8	GENOME-WIDE PREDICTION AND VALIDATION OF LEUO BINDING SITES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	yhjH	regulator	28553268	8	att	The FlhDC-regulated ycgR and yhjH genes ( Ko and Park , 2000 ) were also strongly repressed ( 0.08 - and 0.18-fold at 45 min respectively ; Table 8 ) .	585	The FlhDC-regulated ycgR and yhjH genes ( Ko and Park , 2000 ) were also strongly repressed ( 0.08 - and 0.18-fold at 45 min respectively ; Table 8 ) .	22	CELL DAMAGE/STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	asmA	regulator	19346309	1	att	A tentative hypothesis is that asmA mutations might activate a MarA-regulated efflux pump hitherto unknown to transport bile-salts .	327	A tentative hypothesis is that asmA mutations might activate a MarA-regulated efflux pump hitherto unknown to transport bile salts .	5	DISCUSSION	unidentified	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	11162188	2	ver/dev	As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .	112	As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .	6	TRANSCRIPTION OF THE VIRULENCE-ASSOCIATED GENES IN THE FLIZ MUTANT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	7	att	Therefore , PhoPQ repression of hilA was demonstrated using an allele of phoQ , phoQ24 , which has been shown to have a reduced sensitivity to Ca2 and activates PhoP-regulated genes in an essentially constitutive manner ( 44 , 51 ) .	61	Therefore , PhoPQ repression of hilA was demonstrated using an allele of phoQ , phoQ24 , which has been shown to have a reduced sensitivity to Ca2 and activates PhoP-regulated genes in an essentially constitutive manner ( 44 , 51 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	regulator	31182495	3	ver/dev	electrophoretic-mobility-shift assays suggest that PhoP specifically binds the hilA promoter to block binding of RtsA as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	3	ver/dev	electrophoretic-mobility-shift assays suggest that PhoP specifically binds the hilA promoter to block binding of HilC as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	3	ver/dev	electrophoretic-mobility-shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	3	ver/dev	Genetic analyses suggest that PhoP specifically binds the hilA promoter to block binding of RtsA as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	3	ver/dev	Genetic analyses suggest that PhoP specifically binds the hilA promoter to block binding of HilC as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	3	ver/dev	Genetic analyses suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD as a mechanism of repression .	14	Genetic analyses and electrophoretic mobility shift assays suggest that PhoP specifically binds the hilA promoter to block binding of activators HilD , HilC , and RtsA as a mechanism of repression .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	regulator	31182495	34	ver/dev	Phosphorylated PhoP binds the hilA promoter directly in-vitro .	163	Phosphorylated PhoP binds the hilA promoter directly in vitro .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	regulator	31182495	35	ver/dev	We hypothesized that PhoP represses transcription through direct binding to the hilA promoter .	164	We hypothesized that PhoP represses transcription through direct binding to the hilA promoter , which we tested through an electrophoretic mobility shift assay .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	regulator	31182495	39	ver/dev	Together , these data suggest that PhoP binds the hilA promoter directly	186	Together , these data suggest that PhoP binds the hilA promoter directly and possibly through multiple binding sites , but the specific binding sites remain unclear .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	regulator	31182495	40	ver/dev	the 72 to 1 hilA-lacZ fusion was not regulated by PhoP	194	Gel shift assays demonstrated that the 203 to 1 fragment of hilA shifted similarly to that of the positive control , and the 72 to 1 hilA-lacZ fusion was not regulated by PhoP .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	hilA	regulator	31182495	45	ver/dev	a model in which PhoP binds the hilA promoter	211	These data support a model in which PhoP binds the hilA promoter and primarily blocks binding of activator proteins , leading to repression of SPI1 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	regulator	31182495	45	ver/dev	a model in which PhoP binds the hilA promoter	211	These data support a model in which PhoP binds the hilA promoter and primarily blocks binding of activator proteins , leading to repression of SPI1 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	regulator	31182495	47	ver/dev	The data suggest that PhoP could repress hilA transcription by blocking binding of HilD/HilC/RtsA .	213	The data described above suggest that PhoP could repress hilA transcription by blocking binding of HilD/HilC/RtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	regulator	31182495	55	ver/dev	This is difficult to test PhoP regulation of hilA .	242	This is difficult to test in vivo specifically due to the complexity of the PhoPQ regulon and PhoP regulation of hilA .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	regulator	31182495	67	ver/dev	PhoP binds directly to the hilA promoter , as evidenced by electrophoretic-mobility-shift assays .	276	PhoP binds directly to the hilA promoter , as evidenced by electrophoretic mobility shift assays .	4	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	regulator	34202800	14	ver/dev	PhoP specifically binds the hilA promoter to block the binding of RtsA activators as a repression mechanism	329	PhoP specifically binds the hilA promoter to block the binding of HilD , HilC , and RtsA activators as a repression mechanism [ 126 ]	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	regulator	34202800	14	ver/dev	PhoP specifically binds the hilA promoter to block the binding of HilC as a repression mechanism	329	PhoP specifically binds the hilA promoter to block the binding of HilD , HilC , and RtsA activators as a repression mechanism [ 126 ]	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	regulator	34202800	14	ver/dev	PhoP specifically binds the hilA promoter to block the binding of HilD as a repression mechanism	329	PhoP specifically binds the hilA promoter to block the binding of HilD , HilC , and RtsA activators as a repression mechanism [ 126 ]	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	regulator	34424033	42	ver/dev	This is consistent with our previous data suggesting that PhoP is a negative regulator of the hilA promoter , blocking activation .	533	This is consistent with our previous data suggesting that PhoP is a negative regulator of the hilA promoter that binds to a site overlapping the HilD/HilC/RtsA binding site , blocking activation ( 36 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YdcR	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR may come into play .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Crl	gene	adrA	activator	16707690	1	ver/dev	potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the adrA promoters .	11	In vitro transcription assays and potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD and adrA promoters .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	adrA	activator	16707690	1	ver/dev	In vitro transcription assays with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the adrA promoters .	11	In vitro transcription assays and potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD and adrA promoters .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	adrA	activator	16707690	6	ver/dev	In vitro transcription experiments with purified Crl protein of Salmonella showed that Crl stimulates S-dependent transcription at the adrA promoters .	52	In vitro transcription experiments with purified Crl protein of Salmonella showed that Crl stimulates S-dependent transcription at the adrA and csgD promoters .	2	MAIN	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	adrA	activator	16707690	14	ver/dev	Crl protein activates in-vitro-transcription by E S from the adrA promoters .	314	Crl protein activates in vitro transcription by E S from the csgD and adrA promoters .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	adrA	activator	16707690	21	ver/dev	Together , these results showed that Crl enhanced both the rate of formation of open complexes by E S from the adrA promoters .	369	Together , these results showed that Crl enhanced both the quantity of open complexes and the rate of formation of open complexes by E S from the csgD and adrA promoters .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	adrA	activator	16707690	21	ver/dev	Together , these results showed that Crl enhanced both the quantity of open complexes by E S from the adrA promoters .	369	Together , these results showed that Crl enhanced both the quantity of open complexes and the rate of formation of open complexes by E S from the csgD and adrA promoters .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Crl	gene	adrA	activator	17293430	2	ver/dev	In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA genes ; these genes are involved in the biosynthesis of cellulose .	38	In vitro transcription experiments with the purified Salmonella Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA and csgD genes ; these genes are involved in the biosynthesis of curli and cellulose ( 32 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	adrA	activator	17293430	2	ver/dev	In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA genes ; these genes are involved in the biosynthesis of curli .	38	In vitro transcription experiments with the purified Salmonella Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA and csgD genes ; these genes are involved in the biosynthesis of curli and cellulose ( 32 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	bcsZ	activator	27756305	7	ver/dev	These findings indicate that enhanced CsgD dependent cellulose production contributes to the uptake of the bcsZ mutant into macrophages .	551	These findings indicate that enhanced CsgD dependent cellulose production contributes to diminished intracellular proliferation , but not to the uptake of the bcsZ mutant into macrophages ( Fig. 6b , c ) .	25	ROLE OF BCSZ IN HOST‑PATHOGEN INTERACTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR-P	gene	ssrA	repressor	12753201	48	ver/dev	An increase in OmpR-P levels would enable OmpR-P to bind to lower affinity sites , repressing ssrA .	248	An increase in OmpR-P levels would enable OmpR-P to bind to lower affinity sites , repressing ssrA and ssrB .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L1	SPEC	Other	OTHER	New	Level 1
FliA	gene	rck	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	soxS	repressor	30682134	38	ver/dev	In LB , CsrA also repressed expression of soxS , regulators .	279	In LB , CsrA also repressed expression of slyA , rpoS , and soxS , regulators that contribute to resistance to oxidative stress in Salmonella [ 71,109,110 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	soxS	repressor	30682134	40	ver/dev	In contrast , the stress resistant phenotype may be apparent in LB because CsrA represses the expression of soxS	287	In contrast , the stress resistant phenotype may be apparent in LB because CsrA represses the expression of multiple regulators ( slyA , soxS , and rpoS ) that induce expression of	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	mdtA	regulator	22173828	1	ver/dev	the mdtA expression is directly regulated by binding of BaeR at the promoter region	10	Moreover , the mdtA expression is directly regulated by binding of BaeR at the promoter region , and this interaction is enhanced when the protein is phosphorylated .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	mdtA	regulator	22173828	1	ver/dev	the mdtA expression is directly regulated by binding of BaeR at the promoter region	10	Moreover , the mdtA expression is directly regulated by binding of BaeR at the promoter region , and this interaction is enhanced when the protein is phosphorylated .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	mdtA	regulator	22173828	6	ver/dev	Moreover , we show that both members of this system conWrmed that His 250 from BaeS are required , even though BaeR binds speciWcally to the mdtA promoter with more aYnity .	31	Moreover , we show that both members of this system are required for mdtA activation under ciproXoxacin treatment and conWrmed that His 250 from BaeS and Asp 61 from BaeR are required , even though BaeR binds speciWcally to the mdtA promoter with more aYnity when the protein is phosphorylated .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	mdtA	regulator	34202800	19	ver/dev	Guerrero et al. showed that in Salmonella , mdtA expression is regulated directly by BaeR binding in the promoter region	380	Guerrero et al. [ 133 ] showed that in Salmonella , mdtA expression is regulated directly by BaeR binding in the promoter region , and this interaction is strengthened by protein phosphorylation .	10	3.3.3. THE BAESR SYSTEM	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysM	regulator	30538683	4	ver/dev	CysB has not yet been shown to directly regulate cysM .	346	CysB has not yet been shown to directly regulate cysM and may be the reason differences were not seen .	21	OVEREXPRESSION OF OATA LEADS TO INCREASED TRANSCRIPTION OF CYS GENES	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
Fis	gene	dps	regulator	32900812	8	ver/dev	On the other hand , placing fis under the control of the dps regulatory sequences at the dps locus , while driving dps gene expression with the dusB-fis regulatory sequences at the dusB-fis locus , had profound effects on the physiology of the bacterium at Fis binding patterns around the chromosome to infect human cells .	78	On the other hand , placing fis under the control of the dps regulatory sequences at the dps locus , while driving dps gene expression with the dusB-fis regulatory sequences at the dusB-fis locus , had profound effects on the physiology of the bacterium at the levels of global gene expression , Fis binding patterns around the chromosome , and the ability of the bacterium to infect human cells .	2	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493;Homo sapiens	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	dps	regulator	32900812	9	ver/dev	This may reflect the influence of the new chromosomal neighborhood following the relocation of those Fis binding sites together with dusB-fis to the dps locus in GX .	137	This may reflect the influence of the new chromosomal neighborhood following the relocation of those Fis binding sites together with dusB-fis to a novel chromosomal site ( the dps locus ) in GX .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilC	activator	15130116	8	ver/dev	In Salmonella , SirA also directly activates the horizontally acquired regulatory genes hilC .	221	In Salmonella , SirA also directly activates the horizontally acquired regulatory genes hilA and hilC , the products of which control the majority of genes within Salmonella pathogenicity island 1 ( SPI1 ) ( Johnston et al. , 1996 ; Ahmer et al. , 1999 ; Altier et al. , 2000 ; Teplitski et al. , 2003 ) .	5	THE SALMONELLA SDIA SYSTEM	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	activator	16045614	48	ver/dev	In contrast , the presence of a hilD mutation completely blocked SirA induction of hilC .	292	In contrast , the presence of a hilD mutation completely blocked SirA induction of rtsA and hilC ( Fig. 5A ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	activator	16045614	55	ver/dev	Our data suggest that SirA induces expression of hilC via HilD .	391	Our data suggest that SirA induces expression of hilC and rtsA via HilD .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SirA	gene	hilC	activator	16045614	78	ver/dev	In support of our model , we demonstrate that SirA induction of hilC requires the presence of HilD .	549	In support of our model , we demonstrate that SirA induction of hilC , rtsA , hilA and invF requires the presence of HilD .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilC	activator	16949866	0	ver/dev	SirA does this by directly activating hilC regulatory genes .	11	SirA does this by directly activating the hilA and hilC regulatory genes encoded within SPI1 .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilC	activator	16949866	30	ver/dev	SirA controls these genes by directly activating hilC regulatory genes .	455	SirA controls these genes by directly binding and activating the hilA and hilC regulatory genes that are encoded within the horizontal acquisition , SPI1 ( Teplitski et al. , 2003 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	activator	17208038	21	ver/dev	On the basis of these data , the authors concluded that SirA activates the system by direct action on hilC .	122	On the basis of these data , the authors concluded that SirA activates the system by direct action on hilC and hilA [ 44 ] .	8	BARA/SIRA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilC	activator	19537165	5	ver/dev	SirA has been shown to activate the promoters of hilC .	58	SirA has been shown to activate the promoters of hilA and hilC [ Teplitski et al. , 2003 ] .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilC	activator	24500522	1	ver/dev	SirA , positively regulates hilC .	170	The global response regulator , SirA , positively regulates the expression of hilA , hilC , and hilD encoded within SPI-1 and SPI-2 ( Teplitski et al. 2006 ; Martínez et al. 2011 ) .	19	VIABILITY AND MOTILITY OF S. TYPHIMURIUM EXPOSED TO THE SIMULATED INTESTINAL CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilC	activator	27565525	2	ver/dev	SirA , positively regulates the transcription of hilC .	365	SirA , when activated , positively regulates the transcription of hilA and hilC , that serves as an initial effector of bacterial invasion pathway ( Johnston et al. , 1996 ; Teplitski et al. , 2006 ) ; therefore the induction of sirA in Salmonella leads to bacterial association and biofilm formation ( Salazar et al. , 2013 ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	iroA	regulator	28859315	0	att	Identification of Fur-regulated genes in this serovar was determined using the Fur titration assay and led to the identification of the iroBC genes from the iroA locus ( Bäumler et al. 1996 ) .	53	Identification of Fur-regulated genes in this serovar was determined using the Fur titration assay and led to the identification of the iroBC genes from the iroA locus ( Bäumler et al. 1996 ) .	6	ADVANCE ACCESS PUBLICATION DATE: 13 JULY 2017 RESEARCH LETTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RstA	gene	rcsB	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RstA	gene	rcsB	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
SlyA	gene	spoT	activator	19091955	30	att	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	187	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	spoT	activator	19091955	30	att	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	187	SlyA-dependent but PhoP-independent transcription of the Salmo-nella pathogenicity island II gene , ssrA , ( 3 ) is repressed significantly in a relA spoT mutant ( 32 ) , further suggesting that ppGpp stimulates SlyA-dependent gene regulation .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
NarL	gene	rcsA	regulator	29186528	15	ver/dev	In this , the DBD acquires an organization competent to bind promoters in a tail-to-tail arrangement , as we have confirmed in-vitro by checking the binding of different mutants to the rcsA promoters , similar to NarL with its nirB promoter .	410	In this phosphorylated asymmetric conformation , the DBD acquires an organization competent to bind promoters in a tail-to-tail arrangement , as we have confirmed in vitro by checking the binding of different mutants to P1flhDC and the rcsA promoters , similar to the organization observed in the complex structure of DBD -- NarL with its nirB promoter ( 38 ) .	20	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarR	gene	marA	repressor	19120970	1	ver/dev	marA transcription is repressed by MarR .	26	marA transcription is repressed by MarR and is de-repressed by compounds such as salicylate , benzoate , dinitrophenol and plumbagin , probably through their binding to MarR ( 12 ) .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	gene	marA	repressor	19120970	1	ver/dev	marA transcription is de-repressed by compounds , probably through their binding to MarR .	26	marA transcription is repressed by MarR and is de-repressed by compounds such as salicylate , benzoate , dinitrophenol and plumbagin , probably through their binding to MarR ( 12 ) .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
MarR	gene	marA	repressor	19120970	1	ver/dev	marA transcription is de-repressed by plumbagin , probably through their binding to MarR .	26	marA transcription is repressed by MarR and is de-repressed by compounds such as salicylate , benzoate , dinitrophenol and plumbagin , probably through their binding to MarR ( 12 ) .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
MarR	gene	marA	repressor	19120970	1	ver/dev	marA transcription is de-repressed by dinitrophenol , probably through their binding to MarR .	26	marA transcription is repressed by MarR and is de-repressed by compounds such as salicylate , benzoate , dinitrophenol and plumbagin , probably through their binding to MarR ( 12 ) .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
MarR	gene	marA	repressor	19120970	1	ver/dev	marA transcription is de-repressed by benzoate , probably through their binding to MarR .	26	marA transcription is repressed by MarR and is de-repressed by compounds such as salicylate , benzoate , dinitrophenol and plumbagin , probably through their binding to MarR ( 12 ) .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
MarR	gene	marA	repressor	19120970	1	ver/dev	marA transcription is de-repressed by salicylate , probably through their binding to MarR .	26	marA transcription is repressed by MarR and is de-repressed by compounds such as salicylate , benzoate , dinitrophenol and plumbagin , probably through their binding to MarR ( 12 ) .	4	ABSTRACT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
MarR	gene	marA	repressor	33024855	8	ver/dev	Salicylate binding to MarR lifts repression of marA .	317	Salicylate binding to MarR lifts repression of marA , a transcription factor that controls multidrug efflux and porin synthesis ( Cohen et al. , 1993 ) .	11	3.2. STRESS RESPONSE AND PLANT HOST ADAPTATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	rpoS	regulator	19835951	23	ver/dev	Lee , H.J. , Park , S.J. , Choi , S.H. , Lee , K.H. Vibrio vulnificus rpoS expression is repressed by direct binding of cAMP-CRP complex to its two promoter regions .	323	[ 33 ] Lee , H.J. , Park , S.J. , Choi , S.H. , Lee , K.H. ( 2008 ) Vibrio vulnificus rpoS expression is repressed by direct binding of cAMP-CRP complex to its two promoter regions .	28	REFERENCES	Vibrio vulnificus	0	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	rpoS	regulator	20075614	1	ver/dev	The binding of cAMP-CRP complex to rpoS promoter were proved through exogenous cAMP addition , respectively .	8	The binding of cAMP-CRP complex to rpoS promoter and further stimulation of its transcription were proved through electrophoretic mobility shift assay , lacZ fusion , and exogenous cAMP addition , respectively .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	rpoS	regulator	20075614	1	ver/dev	The binding of cAMP-CRP complex to rpoS promoter were proved through lacZ fusion , respectively .	8	The binding of cAMP-CRP complex to rpoS promoter and further stimulation of its transcription were proved through electrophoretic mobility shift assay , lacZ fusion , and exogenous cAMP addition , respectively .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	rpoS	regulator	20075614	1	ver/dev	The binding of cAMP-CRP complex to rpoS promoter were proved through electrophoretic-mobility-shift assay , respectively .	8	The binding of cAMP-CRP complex to rpoS promoter and further stimulation of its transcription were proved through electrophoretic mobility shift assay , lacZ fusion , and exogenous cAMP addition , respectively .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	rpoS	regulator	20075614	16	ver/dev	The whole rpoS promoter bound to CRP in data not shown .	193	The whole rpoS promoter bound to CRP in EMSA ( data not shown ) .	11	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	New	Level 1
CRP	gene	rpoS	regulator	20075614	16	ver/dev	The whole rpoS promoter bound to CRP in EMSA .	193	The whole rpoS promoter bound to CRP in EMSA ( data not shown ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	rpoS	regulator	20075614	22	ver/dev	cAMP-CRP specifically bound to two sites of the rpoS promoter in-vitro .	231	cAMP-CRP specifically bound to two sites of the rpoS promoter in vitro .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	rpoS	regulator	20075614	24	ver/dev	The cAMP-CRP complex is thought to be involved in the control of rpoS transcription	242	The cAMP-CRP complex is thought to be involved in the control of rpoS transcription , and its regulatory role has been investigated under various genetic backgrounds and growth conditions .	12	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	rpoS	regulator	20075614	29	ver/dev	It suggests that , except for cAMP-CRP , additional factors may also be involved in the regulation of rpoS transcription .	256	It suggests that , except for cAMP-CRP , additional factors may also be involved in the regulation of rpoS transcription and need to be identified in further research .	12	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CRP	gene	rpoS	regulator	24885225	45	ver/dev	On the other hand , it has been reported that rpoS expression is repressed by direct binding of CRP-cAMP to its promoter region in Vibrio vulnificus .	192	On the other hand , it has been reported that rpoS expression is repressed by direct binding of CRP-cAMP to its promoter region in Vibrio vulnificus [ 24 ] .	6	DISCUSSION	Vibrio vulnificus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	rpoS	regulator	24885225	47	ver/dev	Sun demonstrated direct binding of CRP to the rpoS promoter region in S. Typhimurium , where it is able to bind to two sites in this sequence .	195	Cheng and Sun demonstrated direct binding of CRP to the rpoS promoter region in S. Typhimurium , where it is able to bind to two sites in this sequence .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CRP	gene	rpoS	regulator	24885225	47	ver/dev	Cheng demonstrated direct binding of CRP to the rpoS promoter region in S. Typhimurium , where it is able to bind to two sites in this sequence .	195	Cheng and Sun demonstrated direct binding of CRP to the rpoS promoter region in S. Typhimurium , where it is able to bind to two sites in this sequence .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CRP	gene	rpoS	regulator	24885225	48	ver/dev	Both sites are conserved in S. Typhi rpoS promoter , suggesting a dir-ect binding by CRP .	196	Both sites are conserved in S. Typhi rpoS promoter , suggesting a dir-ect binding by CRP .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	rpoS	regulator	24885225	50	ver/dev	This versatility can be explained , at least in part , by the fact that CRP is regulating rpoS .	201	This versatility can be explained , at least in part , by the fact that CRP is regulating rpoS .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
LuxS	gene	cas	regulator	31936769	0	att	Comparison of the expression level of some key genes acquired from RNA-Seq and RT-including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1-T3SS genes qPCR , including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1 - ( Salmonella pathogenicity island 1 genes related to the type three secretion system ) ( C ) .	405	Comparison of the expression level of some key genes acquired from RNA-Seq and RT-including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1-T3SS genes qPCR , including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1 - ( Salmonella pathogenicity island 1 genes related to the type three secretion system ) ( C ) .	21	33.4 . - L .4.22..TTHHEEPPAATTTTEERRNNSSOOFFDDEEGGSSAARREESSIIMMIILLAARRLLYYRREEVVEEAALLEEDDBBYYRRTT-QQPPCCRRAANNAALYYSSISIS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
LuxS	gene	cas	regulator	31936769	0	att	Comparison of the expression level of some key genes acquired from RNA-Seq and RT-including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1-T3SS genes qPCR , including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1 - ( Salmonella pathogenicity island 1 genes related to the type three secretion system ) ( C ) .	405	Comparison of the expression level of some key genes acquired from RNA-Seq and RT-including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1-T3SS genes qPCR , including cas operon genes ( A ) , lsr ( LuxS-regulated ) operon genes ( B ) , and some of the SPI-1 - ( Salmonella pathogenicity island 1 genes related to the type three secretion system ) ( C ) .	21	33.4 . - L .4.22..TTHHEEPPAATTTTEERRNNSSOOFFDDEEGGSSAARREESSIIMMIILLAARRLLYYRREEVVEEAALLEEDDBBYYRRTT-QQPPCCRRAANNAALYYSSISIS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	repressor	15126450	29	ver/dev	Our present model for ompS2 expression implies that LeuO relieves repression by disrupting either a structure in the region from 413 to 97 .	296	Our present model for ompS2 expression implies that LeuO relieves repression by disrupting either a structure in the region from 413 to 97 or by antagonizing the effect of an unknown repressor that binds to such region or both .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS2	repressor	15126450	29	ver/dev	Our present model for ompS2 expression implies that LeuO relieves repression by antagonizing the effect of an unknown repressor .	296	Our present model for ompS2 expression implies that LeuO relieves repression by disrupting either a structure in the region from 413 to 97 or by antagonizing the effect of an unknown repressor that binds to such region or both .	5	DISCUSSION	unidentified	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS2	repressor	17908208	59	ver/dev	The repression of ompS2 could be due to the competition of LeuO for the binding site of the OmpR transcriptional activator as ompS2 expression is dependent of OmpR .	243	The repression of ompS2 observed at the higher levels of induction of the leuO gene could be due to the competition of LeuO for the binding site of the OmpR transcriptional activator as ompS2 expression is dependent of LeuO and OmpR ( Fernández-Mora et al. , 2004 ) .	13	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	ompS2	repressor	17908208	59	ver/dev	The repression of ompS2 could be due to the competition of LeuO for the binding site of the OmpR transcriptional activator as ompS2 expression is dependent of LeuO .	243	The repression of ompS2 observed at the higher levels of induction of the leuO gene could be due to the competition of LeuO for the binding site of the OmpR transcriptional activator as ompS2 expression is dependent of LeuO and OmpR ( Fernández-Mora et al. , 2004 ) .	13	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	ompS2	repressor	25566242	10	ver/dev	The ompS2 gene is expressed at lower concentrations of LeuO , whereas ompS1 is expressed at higher concentrations .	80	The ompS2 gene is expressed at lower concentrations of LeuO , whereas ompS1 is expressed at higher concentrations where ompS2 expression is repressed .	5	THE LEUO REGULATOR IN OTHER GRAM-NEGATIVE BACTERIA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
GlrR	gene	glrR	activator	20965974	2	ver/dev	In order to monitor activation by the cognate GlrR protein , Y. pseudotuberculosis glrR was expressed from plasmid pYG6 , while the endogenous glrR gene was deleted .	320	In order to monitor activation by the cognate GlrR protein , Y. pseudotuberculosis glrR was expressed from plasmid pYG6 , while the endogenous glrR gene was deleted .	14	EXPRESSION OF GLMY AND GLMZ IN Y. PSEUDOTUBERCULOSIS	Varanus togianus;unidentified plasmid	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PocR	gene	hilA	activator	16585772	6	ver/dev	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of the cofactor of PocR .	146	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of PDL , the cofactor of PocR .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PocR	gene	hilA	activator	16585772	6	ver/dev	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of PDL .	146	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of PDL , the cofactor of PocR .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SoxS	gene	micF	regulator	19120970	0	ver/dev	In E. coli , the transcription of micF is controlled by SoxS .	23	In E. coli , the transcription of acrAB and micF is controlled by the homologous proteins MarA , SoxS and Rob ( 9 , 10 ) , but may be affected by other proteins such as AcrR ( 11 ) .	4	ABSTRACT	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpmB	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	adrA	repressor	16629664	12	ver/dev	However , adrA transcription was also diminished when AdrA was overexpressed , suggesting that elevated CsgD expression far above wild-type levels inhibited the transcription of adrA .	187	However , adrA transcription was also diminished when AdrA was overexpressed , suggesting that elevated CsgD expression far above wild-type levels inhibited the transcription of adrA .	9	CSGD EXPRESSION IS REGULATED BY C-DI-GMP ON A TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL LEVEL	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	crp	repressor	33563986	9	ver/dev	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence-factors .	346	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , as well as SPI-2 genes when STM is inside macrophages65 , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence factors .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	sseL	activator	21625519	13	ver/dev	Subsequently , we were interested in assessing the relative contribution of SsrB to the integrated regulation of sseL .	69	Subsequently , we were interested in assessing the relative contribution of PhoP and SsrB to the integrated regulation of sseL .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseL	activator	21625519	35	ver/dev	To further characterize the relative contribution of SsrB to the transcriptional output of sseL we sought to analyze sseL : : lacZ expression in two SsrB-free heterologous hosts , E. coli and	132	To further characterize the relative contribution of PhoP and SsrB to the transcriptional output of sseL we sought to analyze sseL : : lacZ expression in two SsrB-free heterologous hosts , E. coli and	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	sseL	activator	21625519	66	ver/dev	Similarly , introducing SsrB into S. bongori resulted in a much higher induction of sseL expression than in S. Typhimurium background , implying the possibility that a particular sseL-negative regulator , not present in S. bongori , may play a role in S. Typhimurium .	227	Similarly , introducing SsrB or PhoP into S. bongori resulted in a much higher induction of sseL expression than in S. Typhimurium background ( Fig. 5 ) , implying the possibility that a particular sseL-negative regulator , not present in S. bongori , may play a role in S. Typhimurium .	7	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
SsrB	gene	phoP	activator	24144726	1	ver/dev	In agreement with the published transcriptomic data , SsrB was upregulated in the overgrowing phoP mutant at Fig. 1B .	121	In agreement with the published transcriptomic data ( 29 ) , SsrB was upregulated in nongrowing dormant intracellular wild-type bacteria and the overgrowing phoP mutant at 24 h postinfection ( Fig. 1B ) .	5	RESULTS DISSIMILAR CONTRIBUTION OF PHOP-PHOQ AND ENVZ-OMPR TO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	phoP	activator	24144726	1	ver/dev	In agreement with the published transcriptomic data , SsrB was upregulated in the overgrowing phoP mutant at 24 h postinfection .	121	In agreement with the published transcriptomic data ( 29 ) , SsrB was upregulated in nongrowing dormant intracellular wild-type bacteria and the overgrowing phoP mutant at 24 h postinfection ( Fig. 1B ) .	5	RESULTS DISSIMILAR CONTRIBUTION OF PHOP-PHOQ AND ENVZ-OMPR TO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	phoP	activator	33045730	7	ver/dev	S. Typhimurium acquired the ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in purple , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of phoP genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	phoP	activator	33045730	7	ver/dev	S. Typhimurium acquired the ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of phoP genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	phoP	activator	33045730	7	ver/dev	S. Typhimurium acquired the spiR genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in purple , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of phoP genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	phoP	activator	33045730	7	ver/dev	S. Typhimurium acquired the spiR genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of phoP genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	phoP	activator	33045730	9	ver/dev	The SsrB protein is a direct transcriptional activator of the phoP gene .	67	The SsrB protein is a direct transcriptional activator of the phoP gene .	8	QUANTITATIVE RT-PCR (QRT-PCR)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	phoP	activator	33045730	57	ver/dev	As detailed below , we have now established that SsrB is a direct transcriptional activator of the phoP gene .	256	As detailed below , we have now established that SsrB is a direct transcriptional activator of the phoP gene .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	phoP	activator	33045730	90	ver/dev	In addition , SsrB furthers PhoP amounts by increasing phoP transcription .	398	In addition , SsrB furthers PhoP amounts by increasing phoP transcription ( Figure 4 ) .	35	CONTROL OF THE VIRULENCE REGULATOR PHOP BY THE SSRB PROTEIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	phoP	activator	33045730	108	ver/dev	SsrB also increases phoP transcription by directly binding to the purB .	451	SsrB also increases phoP transcription by directly binding to the purB coding region upstream of the phoP promoter region .	37	DIFFERENT HORIZONTALLY ACQUIRED GENES ENABLE ESCHERICHIA COLI TO ACTIVATE PHOP/PHOQ IN MILDLY ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	acrB	activator	21982147	0	ver/dev	the two-step regulon activates PmrD , which in turn activates the global regulator of efflux pumps , the MarA operon , eventually leads to the activation of acrB	42	Failure of antibiotic therapy is also assured by the two-step regulon that activates PmrD , which in turn activates the global regulator of efflux pumps , the MarA operon , that eventually leads to the activation of acrB , the gene coding for the transporter component of the main efflux pump ( AcrAB ) of the organism [ 5 ] .	2	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	acrB	activator	34202800	6	ver/dev	MarA , , are involved in activating acrB expression .	254	Three homologous transcriptional activators , RamA , SoxS , and MarA , controlled by RamR , SoxR , and MarR , are involved in activating acrB and tolC expression [ 68 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	nlpD	regulator	33638994	19	ver/dev	These assays confirmed binding of phosphorylated RcsB to nlpD Intra-CDS sequences .	398	These assays confirmed binding of phosphorylated RcsB to fepE , osmB and ytfK promoters and to flgA and nlpD Intra-CDS sequences ( Figure 7A and C ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	sirA	repressor	17074910	20	ver/dev	Given that both sirA are required , we hypothesize that fim gene expression requires the csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Sigma32	gene	rpoE	activator	15895724	0	ver/dev	For example , the activation of transcription of rpoE , leads to the activation of transcription at degP , s32 genes .	424	For example , the activation of transcription of rpoE , which encodes sE , leads to the activation of transcription at promoters for fkpA , degP , rpoH ( s32 genes ) , and rpoE itself ( 25 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	gltA	repressor	30524381	19	att	Interestingly , gltA was the only OmpR-repressed target that was sensitive to acid , sucrose and salt stress in S. Typhimurium ( Figure 8D ) and in E. coli during acid and sucrose stress ( Figure 5D ) .	248	Interestingly , gltA was the only OmpR-repressed target that was sensitive to acid , sucrose and salt stress in S. Typhimurium ( Figure 8D ) and in E. coli during acid and sucrose stress ( Figure 5D ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	gltA	repressor	30524381	9	ver/dev	Thus , OmpR repression of gltA contributes to optimum growth when E. coli are acidified .	175	Thus , OmpR repression of gltA contributes to optimum growth when S. Typhimurium and E. coli are acidified .	16	IDENTIFICATION OF THE OMPR ACID STRESS REGULON	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	gltA	repressor	30524381	9	ver/dev	Thus , OmpR repression of gltA contributes to optimum growth when S. Typhimurium are acidified .	175	Thus , OmpR repression of gltA contributes to optimum growth when S. Typhimurium and E. coli are acidified .	16	IDENTIFICATION OF THE OMPR ACID STRESS REGULON	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	gltA	repressor	30524381	13	ver/dev	Thus , OmpR repression of gltA appears to play a major role in supressing growth defects upon E. coli in response to both acid and osmotic-stress .	216	Thus , OmpR repression of gltA appears to play a major role in supressing growth defects upon intracellular acidification in wild-type S. Typhimurium and E. coli in response to both acid and osmotic stress .	17	COMMON OMPR TARGETS IN ACID AND OSMOTIC STRESS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	gltA	repressor	30524381	13	ver/dev	Thus , OmpR repression of gltA appears to play a major role in supressing growth defects upon intracellular acidification in wild-type S. Typhimurium to both acid and osmotic-stress .	216	Thus , OmpR repression of gltA appears to play a major role in supressing growth defects upon intracellular acidification in wild-type S. Typhimurium and E. coli in response to both acid and osmotic stress .	17	COMMON OMPR TARGETS IN ACID AND OSMOTIC STRESS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	gltA	repressor	30524381	16	ver/dev	Thus , OmpR represses gltA during acidification via a direct interaction at its promoter to enable optimum growth in both E. coli .	232	Thus , OmpR represses gltA during acidification via a direct interaction at its promoter to enable optimum growth in both S. Typhimurium and E. coli .	17	COMMON OMPR TARGETS IN ACID AND OSMOTIC STRESS	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	gltA	repressor	30524381	16	ver/dev	Thus , OmpR represses gltA during acidification via a direct interaction at its promoter to enable optimum growth in both S. Typhimurium .	232	Thus , OmpR represses gltA during acidification via a direct interaction at its promoter to enable optimum growth in both S. Typhimurium and E. coli .	17	COMMON OMPR TARGETS IN ACID AND OSMOTIC STRESS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	gltA	repressor	30524381	20	ver/dev	Our findings suggest that in E. coli , OmpR repression of gltA plays a major role in maintaining optimum cell growth during stress .	249	Our findings suggest that in both S. Typhimurium , S. Typhi ( Perkins et al. , 2013 ) and E. coli , OmpR repression of gltA plays a major role in maintaining optimum cell growth during stress .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Escherichia coli	0	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	gltA	repressor	30524381	20	ver/dev	Our findings suggest that in S. Typhi , OmpR repression of gltA plays a major role in maintaining optimum cell growth during stress .	249	Our findings suggest that in both S. Typhimurium , S. Typhi ( Perkins et al. , 2013 ) and E. coli , OmpR repression of gltA plays a major role in maintaining optimum cell growth during stress .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	gltA	repressor	30524381	20	ver/dev	Our findings suggest that in both S. Typhimurium , OmpR repression of gltA plays a major role in maintaining optimum cell growth during stress .	249	Our findings suggest that in both S. Typhimurium , S. Typhi ( Perkins et al. , 2013 ) and E. coli , OmpR repression of gltA plays a major role in maintaining optimum cell growth during stress .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
LeuO	gene	ompS2	activator	15126450	4	ver/dev	Thus , the LeuO regulators positively regulate ompS2 .	15	Thus , the OmpR and LeuO regulators positively regulate ompS2 .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	ompS2	activator	15126450	12	ver/dev	LeuO positively regulates ompS2 .	216	LeuO positively regulates ompS2 .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	15126450	24	ver/dev	Moreover , the LeuO activator of the LysR family was identified as a regulator for ompS2 .	273	Moreover , the LeuO activator of the LysR family was identified ( 21 ) as a regulator for ompS2 .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	16428792	1	ver/dev	ompS2 is positively regulated by the LeuO regulator	13	In addition , ompS1 is negatively regulated by the HN-S nucleoid protein , and ompS2 is positively regulated by the LeuO regulator ( 10 , 11 , 26 , 27 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	16428792	2	ver/dev	The ompS2 mutant was further characterized by the lack of induction of the OmpS2 porin in the presence of the cloned LeuO positive regulator .	35	The ompS2 mutant was further characterized by the lack of induction of the OmpS2 porin in the presence of the cloned LeuO positive regulator ( Fig. 1 , lane 2 ) .	5	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	16428792	7	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	196	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	17908208	7	ver/dev	Interestingly , we had shown previously that LeuO positively regulates ompS2 .	47	Interestingly , we had shown previously that LeuO positively regulates ompS2 ( Fernández-Mora et al. , 2004 ) .	3	B	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	17908208	65	ver/dev	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter , the induction of ompS1 can occur independent of OmpR .	257	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter ( Fernández-Mora et al. , 2004 ) , the induction of ompS1 can occur independent of OmpR .	13	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS2	activator	17908208	81	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	451	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	24	ACKNOWLEDGEMENTS	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	18156266	36	att	The results showed that two LeuO protected sites were found in the LeuO-dependent genes reported in this work , and a DNase I hypersensitivity region was observed when increasing amounts of LeuO were used , suggesting that there was a DNA conformational change upon binding of LeuO ( Fig. 3 ) , which is consistent with our previous observations for the ompS2 and ompS1 genes ( 5 , 12 ) .	336	The results showed that two LeuO protected sites were found in the LeuO-dependent genes reported in this work , and a DNase I hypersensitivity region was observed when increasing amounts of LeuO were used , suggesting that there was a DNA conformational change upon binding of LeuO ( Fig. 3 ) , which is consistent with our previous observations for the ompS2 and ompS1 genes ( 5 , 12 ) .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS2	activator	18156266	7	ver/dev	For ompS2 , we found that in the absence of IPTG considerable transcriptional activity was detected only at 12 h , showing that , as observed for STY3070 , the basal expression from the recombinant LeuO plasmid was enough for induction of the putative operon .	179	For ompS2 , we found that in the absence of IPTG considerable transcriptional activity was detected only at 12 h , showing that , as observed for STY3070 , the basal expression from the recombinant LeuO plasmid was enough for induction of the quiescent porin and the putative operon .	4	RESULTS	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	ompS2	activator	18156266	7	ver/dev	For ompS2 , we found that in the absence of IPTG considerable transcriptional activity was detected only at 12 h , showing that , as observed for STY3070 , the basal expression from the recombinant LeuO plasmid was enough for induction of the quiescent porin .	179	For ompS2 , we found that in the absence of IPTG considerable transcriptional activity was detected only at 12 h , showing that , as observed for STY3070 , the basal expression from the recombinant LeuO plasmid was enough for induction of the quiescent porin and the putative operon .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	18156266	34	ver/dev	if the amount of LeuO increased , ompS2 expression diminished , supporting the observation that an ompS2 gene fusion is expressed at higher levels at an OD of 0.6 upon induction of LeuO with 20 M IPTG from pFMTrcleuO-50	332	In the case of ompS2 , LeuO also acted positively when it was present at low levels , but if the amount of LeuO increased , ompS2 expression diminished ( Fig. 2d ) , supporting the observation that an ompS2 gene fusion is expressed at higher levels at an OD of 0.6 upon induction of LeuO with 20 M IPTG from pFMTrcleuO-50 ( 5 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	18156266	50	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	449	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	17	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	19447191	3	ver/dev	ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action	94	Curiously , ompS1 is negatively regulated by the HN-S nucleoid protein , and ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action .	6	4.2. LEUO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	19447191	19	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	197	Fernandez-Mora M , Puente JL , Calva E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	21398529	11	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	456	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	22149171	67	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	562	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	35	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	22343301	39	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	408	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	29	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	22804842	9	ver/dev	LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 , consistent with LeuO .	147	LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 ( De la Cruz et al. , 2007 ) , consistent with LeuO having a higher affinity for the regulatory region of ompS2 .	6	EXTENSION OF THE LEUO REGULON	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
LeuO	gene	ompS2	activator	22804842	32	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	647	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	26	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	24354910	59	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	414	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	36	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	24659766	1	ver/dev	In Salmonella enterica serovar Typhi , LeuO activates the expression of ompS2 .	11	In Salmonella enterica serovar Typhi , LeuO activates the expression of ompS1 and ompS2 ( 12 , 13 ) .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	24659766	23	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	412	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	20	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	24720747	23	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	495	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	31	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	28337196	0	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	277	Fernandez-Mora M , Puente JL , Calva E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	8	FUNDING	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS2	activator	33854491	1	ver/dev	Even more , the expression of a transcriptional-fusion of the 5 ' intergenic region of ompS2 , upon induction of the LeuO regulator at various points in the growth curve , was essentially abolished in the ∆ CRISPR-cas as compared with the wild-type strain .	171	Even more , the expression of a transcriptional fusion of the 5 ' intergenic region of ompS2 ( pKK9/ompS2 -482 + 77 , Supplementary Table S1 ) , upon induction of the LeuO regulator at various points in the growth curve , was essentially abolished in the ∆ CRISPR-cas as compared with the wild-type strain ( Figure 3B ) .	18	CRISPR-CAS IS FUNDAMENTAL FOR THE SYNTHESIS OF MAJOR AND QUIESCENT OUTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS2	activator	33854491	18	ver/dev	LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	377	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	25	THIS WORK WAS SUPPORTED BY GRANTS FROM THE DIRECCIÓN GENERAL AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB.2021.657404/ DE ASUNTOS DEL PERSONAL ACADÉMICO, DGAPA/UNAM (IN203618 FULL#SUPPLEMENTARY-MATERIAL	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	wraB	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilA	gene	phoH	regulator	27886269	3	ver/dev	HilA , regulates the expression of phoH .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sopE	regulator	33691799	0	ver/dev	As a T3SS effector protein , the expression of sopE SPI1 T3SS is tightly regulated by its central activators HilD .	345	As a T3SS effector protein , the expression of sopE and other SPI1 T3SS is tightly regulated by its central activators HilA and HilD , which are activated by ferric uptake regulator ( Fur ) [ 49 ] .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NarP	gene	narP	regulator	17906148	5	ver/dev	NarP did not appear to play a role in the regulation of this gene , since b-galactosidase activity in the narP strain was not significantly different from wild-type levels .	276	NarP did not appear to play a role in the regulation of this gene , since b-galactosidase activity in the narP strain was not significantly different from wild-type levels ( Table 5 ) .	8	REGULATION OF HYA BY NITRATE	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CsrA	gene	hilD	repressor	23676436	19	ver/dev	This CsrA-mediated repression of hilD is caused by binding of CsrA to Dalgarno sequence of hilD mRNA .	409	This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine -- Dalgarno sequence of hilD mRNA ( Martınez et al. , 2011 ) .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilD	repressor	23676436	19	ver/dev	This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine .	409	This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine -- Dalgarno sequence of hilD mRNA ( Martınez et al. , 2011 ) .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	repressor	30682134	50	ver/dev	Consistent with previous work , CsrA repressed expression of hilD .	393	Consistent with previous work , CsrA repressed expression of hilD , which is required for induction of SPI-1 ( Fig 8B ) .	15	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	hilD	repressor	31017982	24	ver/dev	SL1 , however , binds to CsrA , further shifting the balance of control towards the repression of hilD when in the presence of this global regulatory protein .	219	SL1 , however , binds to CsrA , further stabilizing it and shifting the balance of control towards the repression of hilD when in the presence of this global regulatory protein .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilD	repressor	31428589	7	ver/dev	CsrA , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , leading to hilD mRNA turnover .	164	CsrA , a global regulatory RNA-binding protein , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , preventing HilD translation and leading to hilD mRNA turnover ( Lucchetti-Miganeh et al. , 2008 ; Martínez et al. , 2011 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilD	repressor	31428589	7	ver/dev	CsrA , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , leading to hilD mRNA turnover .	164	CsrA , a global regulatory RNA-binding protein , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , preventing HilD translation and leading to hilD mRNA turnover ( Lucchetti-Miganeh et al. , 2008 ; Martínez et al. , 2011 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilD	repressor	31428589	7	ver/dev	CsrA , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , preventing HilD translation .	164	CsrA , a global regulatory RNA-binding protein , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , preventing HilD translation and leading to hilD mRNA turnover ( Lucchetti-Miganeh et al. , 2008 ; Martínez et al. , 2011 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilD	repressor	31428589	7	ver/dev	CsrA , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , preventing HilD translation .	164	CsrA , a global regulatory RNA-binding protein , post-transcriptionally downregulates hilD expression by binding near the translation initiation codon sequences of the hilD mRNA directly , preventing HilD translation and leading to hilD mRNA turnover ( Lucchetti-Miganeh et al. , 2008 ; Martínez et al. , 2011 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilD	repressor	33799446	9	ver/dev	two inhibitory small RNAs sequester CsrA and , thus , inhibit its repression of hilD	204	End products of metabolism and amino acid starvation stimulate csrB/C transcription of two inhibitory small RNAs that sequester CsrA and , thus , inhibit its repression of hilD .	9	3.2.4. STARVATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	hilD	repressor	33799446	9	ver/dev	two inhibitory small RNAs sequester CsrA and , thus , inhibit its repression of hilD	204	End products of metabolism and amino acid starvation stimulate csrB/C transcription of two inhibitory small RNAs that sequester CsrA and , thus , inhibit its repression of hilD .	9	3.2.4. STARVATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	hilD	repressor	34048498	24	ver/dev	Thus , our results suggest that in the absence of SirA the expression of hilA is repressed by two mechanisms : 1 -RRB- CsrA inhibits translation of the hilD mRNA	177	Thus , our results suggest that in the absence of SirA the expression of hilA is repressed by two mechanisms : 1 ) CsrA inhibits translation of the hilD mRNA and 2 ) the diminished amount of	9	HILE REPRESSES HILD-MEDIATED EXPRESSION OF SPI-1, SPI-2 AND SPI-5 GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Lrp	gene	fimA	activator	27909434	10	ver/dev	Among them , fimA are shown to be activated by Lrp .	338	Among them , fimZ and fimA are shown to be activated by Lrp and consequently allow S. Typhimurium to produce type 1 fimbriae ( McFarland et al. , 2008 ) .	25	ACETYLATION OF K36 AFFECTS THE EXPRESSION OF LRP REGULON	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	map	activator	12535071	48	att	Our results suggested that the 5 cents - ends of the two HilDdependent transcripts map to positions corresponding to 643 and 631 nucleotides upstream of the invF ORF ; 511 and 499 nucleotides upstream of the HilA-dependent +1 .	130	Our results suggested that the 5 cents - ends of the two HilDdependent transcripts map to positions corresponding to 643 and 631 nucleotides upstream of the invF ORF ; 511 and 499 nucleotides upstream of the HilA-dependent +1 .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	map	activator	12535071	58	att	The 5 cents end of the long HilA-dependent product appears to map to the A , although previous studies concluded that the HilA-dependent transcript maps to the T below the A .	165	The 5 cents end of the long HilA-dependent product appears to map to the A , although previous studies concluded that the HilA-dependent transcript maps to the T below the A .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	map	activator	12535071	58	att	The 5 cents end of the long HilA-dependent product appears to map to the A , although previous studies concluded that the HilA-dependent transcript maps to the T below the A .	165	The 5 cents end of the long HilA-dependent product appears to map to the A , although previous studies concluded that the HilA-dependent transcript maps to the T below the A .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	TU	ssrAB	regulator	27564394	8	att	Mechanistically , HilD indirectly regulates SsrB-regulated genes by antagonizing the H-NS-mediated repression of ssrAB at stationary-phase under SPI-1 inducing conditions [ 30 ] ( see also Fig 2 ) .	291	Mechanistically , HilD indirectly regulates SsrB-regulated genes by antagonizing the H-NS-mediated repression of ssrAB at stationary phase under SPI-1 inducing conditions [ 30 ] ( see also Fig 2 ) .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	TU	ssrAB	regulator	30718301	52	ver/dev	Together , these results indicate that SsrB are not involved in the coordinated regulation of ssrAB revealed in this study .	155	Together , these results indicate that PhoP and SsrB are not involved in the coordinated regulation of ssrAB revealed in this study , mediated by SlyA , HilD , and OmpR .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	NEG	New	Level 1
CsrA	gene	hilD	activator	28575106	2	ver/dev	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .	87	SPI-1 affect SPI-1 genes and/or HilA expression through HilD , including HilE ( repression of hilA by binding to and preventing HilD function ) [ 31 ] , FliZ ( activation of hilA via posttranslational regulation of HilD ) [ 32 ] , DNA adenine methylase ( activation of hilA via posttranslational regulation of HilD ) [ 33 ] , EnvZ-OmpR ( activation of hilA via HilD ) [ 34 ] , CpxA/R ( repression of hilA by decreasing the stability of HilD ) [ 35 ] , BarA/SirA ( activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ) [ 24 ] and Fur ( activation of hilA via an unknown regulation of HilD ) [ 26 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
NsrR	gene	hmpA	repressor	21833325	0	ver/dev	Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- S -RSB- cluster is reversibly inactivated by NO .	258	Expression of hmpA is under the control of the redox active repressor NsrR ( Bang et al. , 2006 ) , whose [ Fe -- S ] cluster is reversibly inactivated by NO .	12	INDUCIBLE DETOXIFICATION OF RNS ENZYMATIC DETOXIFICATION OF NO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	hmpA	repressor	21833325	0	ver/dev	Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- Fe is reversibly inactivated by NO .	258	Expression of hmpA is under the control of the redox active repressor NsrR ( Bang et al. , 2006 ) , whose [ Fe -- S ] cluster is reversibly inactivated by NO .	12	INDUCIBLE DETOXIFICATION OF RNS ENZYMATIC DETOXIFICATION OF NO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	hmpA	repressor	24021902	0	att	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	77	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	hmpA	repressor	24021902	0	ver/dev	murine macrophages _ causing downregulation of hmpA other NsrR-repressed genes	77	Soon after infection of macrophages , the nsrR gene is upregulated inside murine macrophages causing downregulation of hmpA and several other NsrR-repressed genes ( yeaR , ygbA , yftE , STM1808 ) [ 19,20 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	dgoA	regulator	12438352	0	att	PmrA-regulated loci identified included dgoA and yibD and demonstrated 500 - and 2,500-fold activation by PmrA , respectively .	13	PmrA-regulated loci identified included dgoA and yibD and demonstrated 500 - and 2,500-fold activation by PmrA , respectively .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	dgoA	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	dgoA	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	dgoA	regulator	12438352	10	att	PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .	183	PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal medium supplemented with 100 M FeSO4 .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	dgoA	regulator	12438352	12	att	For further characterization of the PmrA-regulated gene mutants , the promoter regions of yibD and dgoA were analyzed for the presence of a putative PmrA-binding site , which was defined by the occurrence of the consensus binding sequence for PmrA , YTTAAK-N5-YTTAAK ( 1 ) .	190	For further characterization of the PmrA-regulated gene mutants , the promoter regions of yibD and dgoA were analyzed for the presence of a putative PmrA-binding site , which was defined by the occurrence of the consensus binding sequence for PmrA , YTTAAK-N5-YTTAAK ( 1 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	dgoA	regulator	12438352	18	att	JSG897 and JSG899 , with mutations in PmrA-regulated genes yibD and dgoA , respectively , also still possessed Ara4N modification of lipid-A in similar amounts to the parental PmrAc strain .	257	JSG897 and JSG899 , with mutations in PmrA-regulated genes yibD and dgoA , respectively , also still possessed Ara4N modification of lipid A in similar amounts to the parental PmrAc strain .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	dgoA	regulator	12438352	19	att	PmrA-regulated gene mutants JSG1525 ( yibD ) and JSG1526 ( dgoA ) were as virulent as wild-type Salmonella serovar Typhimurium , so the genes interrupted have no essential role in the infection process ( Table 4 ) .	264	PmrA-regulated gene mutants JSG1525 ( yibD ) and JSG1526 ( dgoA ) were as virulent as wild-type Salmonella serovar Typhimurium , so the genes interrupted have no essential role in the infection process ( Table 4 ) .	4	RESULTS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	dgoA	regulator	12438352	2	att	All PMs mutants identified in this study demonstrated a defect in virulence compared to wild-type Salmonella serovar Typhimurium when administered orally to mice , while the PmrA-regulated gene ( yibD and dgoA ) mutants showed normal virulence in mice .	17	All PMs mutants identified in this study demonstrated a defect in virulence compared to wild-type Salmonella serovar Typhimurium when administered orally to mice , while the PmrA-regulated gene ( yibD and dgoA ) mutants showed normal virulence in mice .	1	ABSTRACT	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Mus sp.	0.5	L3	OTHER	Investigation	OTHER	Other	Level 2
PmrA	gene	dgoA	regulator	12438352	22	att	Sequencing of the MudJ insertion site of JSG899 identified dgoA as a PmrA-regulated gene .	325	Sequencing of the MudJ insertion site of JSG899 identified dgoA as a PmrA-regulated gene .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	dgoA	regulator	12438352	23	att	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	331	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	5	DISCUSSION	nan	1	L1	SPEC	Fact	NEG	Other	Level 1
PmrA	gene	dgoA	regulator	12438352	9	att	The PmrA-regulated gene mutants JSG897 ( yibD ) and JSG899 ( dgoA ) were also analyzed for sensitivity to PM by MIC assay .	179	The PmrA-regulated gene mutants JSG897 ( yibD ) and JSG899 ( dgoA ) were also analyzed for sensitivity to PM by MIC assay .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	stiC	activator	8045891	16	att	Although RpoS is required for the P , C , and N starvation induction of sti4 and stiC , separate additional signals appear to be involved in the response to individual starvation conditions as well as other conditions that induce RpoS-dependent genes .	178	Although RpoS is required for the P , C , and N starvation induction of sti4 and stiC , separate additional signals appear to be involved in the response to individual starvation conditions as well as other conditions that induce RpoS-dependent genes .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	stiC	activator	8045891	16	ver/dev	Although RpoS is required for N starvation induction of stiC , separate additional signals appear to be involved in the response to individual starvation conditions .	178	Although RpoS is required for the P , C , and N starvation induction of sti4 and stiC , separate additional signals appear to be involved in the response to individual starvation conditions as well as other conditions that induce RpoS-dependent genes .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	stiC	activator	8045891	16	ver/dev	Although RpoS is required for N starvation induction of stiC , separate additional signals appear to be involved in other conditions .	178	Although RpoS is required for the P , C , and N starvation induction of sti4 and stiC , separate additional signals appear to be involved in the response to individual starvation conditions as well as other conditions that induce RpoS-dependent genes .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RtcR	gene	xylE	activator	30201777	14	ver/dev	To test whether MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in Δre : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin -LSB- cis-diaminedichloroplatinum -RSB- versus MMC .	158	To test whether MMC-specific nucleic acid damage , such as MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT , ΔrtcR , and ΔrecA : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin [ cis-diaminedichloroplatinum ( II ) ] versus MMC .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
RtcR	gene	xylE	activator	30201777	14	ver/dev	To test whether MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in Δrtc : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin -LSB- cis-diaminedichloroplatinum -RSB- versus MMC .	158	To test whether MMC-specific nucleic acid damage , such as MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT , ΔrtcR , and ΔrecA : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin [ cis-diaminedichloroplatinum ( II ) ] versus MMC .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
RtcR	gene	xylE	activator	30201777	14	ver/dev	To test whether MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin -LSB- cis-diaminedichloroplatinum -RSB- versus MMC .	158	To test whether MMC-specific nucleic acid damage , such as MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT , ΔrtcR , and ΔrecA : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin [ cis-diaminedichloroplatinum ( II ) ] versus MMC .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
RtcR	gene	xylE	activator	30201777	14	ver/dev	To test whether MMC-specific nucleic acid damage , is responsible for the activation of RtcR , expression of the RNA repair operon in Δre : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin -LSB- cis-diaminedichloroplatinum -RSB- versus MMC .	158	To test whether MMC-specific nucleic acid damage , such as MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT , ΔrtcR , and ΔrecA : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin [ cis-diaminedichloroplatinum ( II ) ] versus MMC .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
RtcR	gene	xylE	activator	30201777	14	ver/dev	To test whether MMC-specific nucleic acid damage , is responsible for the activation of RtcR , expression of the RNA repair operon in Δrtc : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin -LSB- cis-diaminedichloroplatinum -RSB- versus MMC .	158	To test whether MMC-specific nucleic acid damage , such as MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT , ΔrtcR , and ΔrecA : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin [ cis-diaminedichloroplatinum ( II ) ] versus MMC .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
RtcR	gene	xylE	activator	30201777	14	ver/dev	To test whether MMC-specific nucleic acid damage , is responsible for the activation of RtcR , expression of the RNA repair operon in WT : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin -LSB- cis-diaminedichloroplatinum -RSB- versus MMC .	158	To test whether MMC-specific nucleic acid damage , such as MMC-DNA adducts , is responsible for the activation of RtcR , expression of the RNA repair operon in WT , ΔrtcR , and ΔrecA : : kan S. Typhimurium xylE reporter strains was assessed following treatment with cisplatin [ cis-diaminedichloroplatinum ( II ) ] versus MMC .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
LexA	gene	cib	repressor	26439675	0	ver/dev	In S. Tm , cib expression is negatively regulated in a Fur - LexA .	218	In S. Tm , cib expression is negatively regulated in a Fur ( ferric uptake regulator ) - dependent and LexA ( locus for x-ray sensitivity A ) - dependent way ( Mankovich et al. , 1986 ; Nedialkova et al. , 2014 ) and maximally induced under iron limitation and upon exposure to DNA damaging agents .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	TU	ssrAB	repressor	30718301	53	ver/dev	OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	repressor	30718301	53	ver/dev	HilD have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	repressor	30718301	53	ver/dev	SlyA have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling .	167	SlyA , HilD , and OmpR have been involved in the expression of the ssrAB regulatory operon located in SPI-2 , HilD by antagonizing H-NS-mediated repression ( 18 , 19 ) and SlyA and OmpR by until-now unknown mechanisms , although it has been reported that the control of ssrAB expression by OmpR requires relaxation of DNA supercoiling ( 66 ) .	4	DISCUSSION	unidentified	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	ssrAB	repressor	30718301	65	ver/dev	Therefore , the expression of ssrAB would involve two steps , as follows : the relief of H-NS-mediated repression by only SlyA and the recruitment of the RNA polymerase by OmpR .	185	Therefore , the expression of ssrAB mediated by SyA , HilD , and OmpR would involve two steps , as follows : the relief of H-NS-mediated repression by SlyA and HilD or only SlyA and the recruitment of the RNA polymerase by OmpR ( Fig. 8 ) .	4	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stiC	regulator	8045891	3	ver/dev	Interestingly , the regulation of the stiB locus ( unlike that of stiC ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .	36	Interestingly , the regulation of the stiB locus ( unlike that of stiA and stiC ) was unaffected by a cya mutation , suggesting that cAMP receptor protein acts alone or with a different signal molecule in the repression of stiB ( 44 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stiC	regulator	8045891	3	ver/dev	Interestingly , the regulation of the stiB locus ( unlike that of stiC ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts alone .	36	Interestingly , the regulation of the stiB locus ( unlike that of stiA and stiC ) was unaffected by a cya mutation , suggesting that cAMP receptor protein acts alone or with a different signal molecule in the repression of stiB ( 44 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	srfN	regulator	28674150	27	ver/dev	In support of this evolutionary confinement among Salmonella , Navarre et al. suggested potential negative regulation of srfN by the histone-like nucleoid structuring protein H-NS .	323	In support of this evolutionary confinement among Salmonella , Navarre et al. suggested potential negative regulation of srfN by the histone-like nucleoid structuring protein H-NS that has an important role in regulating Salmonella virulence genes ( 26 ) .	6	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stiA	regulator	8045891	3	ver/dev	Interestingly , the regulation of the stiB locus ( unlike that of stiA ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .	36	Interestingly , the regulation of the stiB locus ( unlike that of stiA and stiC ) was unaffected by a cya mutation , suggesting that cAMP receptor protein acts alone or with a different signal molecule in the repression of stiB ( 44 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stiA	regulator	8045891	3	ver/dev	Interestingly , the regulation of the stiB locus ( unlike that of stiA ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts alone .	36	Interestingly , the regulation of the stiB locus ( unlike that of stiA and stiC ) was unaffected by a cya mutation , suggesting that cAMP receptor protein acts alone or with a different signal molecule in the repression of stiB ( 44 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SprB	gene	sipC	regulator	21168230	2	ver/dev	SprB , regulates the expression of sipC .	212	SprB , a transcriptional regulator , is encoded within the SPI1 and regulates the expression of sipC , sptP , avrA , sopB and sopE ( Eichelberg et al. , 1999 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	slrP	regulator	10861017	1	ver/dev	Similar to sspH1 , slrP expression was not regulated by either HilA .	138	Similar to sspH1 , slrP expression was not regulated by either HilA or SsrAySsrB .	5	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
MlrA	gene	mlrA	regulator	15458421	4	ver/dev	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of extracellular matrix formation in S. typhimurium .	110	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene , aggregative morphology and extracellular matrix formation in E. coli and S. typhimurium ( Brown et al. , 2001 ) .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	mlrA	regulator	15458421	4	ver/dev	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of extracellular matrix formation in E. coli .	110	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene , aggregative morphology and extracellular matrix formation in E. coli and S. typhimurium ( Brown et al. , 2001 ) .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	mlrA	regulator	15458421	4	ver/dev	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of aggregative morphology in S. typhimurium .	110	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene , aggregative morphology and extracellular matrix formation in E. coli and S. typhimurium ( Brown et al. , 2001 ) .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	mlrA	regulator	15458421	4	ver/dev	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of aggregative morphology in E. coli .	110	MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene , aggregative morphology and extracellular matrix formation in E. coli and S. typhimurium ( Brown et al. , 2001 ) .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	leuO	repressor	17908208	6	ver/dev	also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region	44	Furthermore , expression of LeuO has been found to affect the expression of several genes influenced by mutations in hns : LeuO relieved silencing of the bgl operon , the operon involved in the utilization of certain b-glucosides ( Ueguchi et al. , 1998 ) ; suppressed the effect of an hns mutation on cadC , which codes for the activator of the acid-inducible lysine decarboxylase ( Shi and Bennet , 1995 ) ; and also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene and the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region ( Chen et al. , 2001 ; 2003 ) .	3	B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	leuO	repressor	18156266	37	ver/dev	it was suggested that H-NS represses leuO expression by interacting with an AT8 region located between LeuO binding sites AT3	341	Two of these sites ( AT7 and AT3 ) were mapped upstream of the leuO promoter , whereas the third site was located downstream of the leuO gene , and it was suggested that H-NS represses leuO expression by interacting with an AT8 region located between LeuO binding sites AT7 and AT3 .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	leuO	repressor	18156266	37	ver/dev	it was suggested that H-NS represses leuO expression by interacting with an AT8 region located between LeuO binding sites AT7	341	Two of these sites ( AT7 and AT3 ) were mapped upstream of the leuO promoter , whereas the third site was located downstream of the leuO gene , and it was suggested that H-NS represses leuO expression by interacting with an AT8 region located between LeuO binding sites AT7 and AT3 .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	leuO	repressor	18156266	38	ver/dev	However , the LeuO protein interacts with the LeuO binding site located downstream of leuO , making a DNA loop to counteract repression by H-NS .	342	However , the LeuO protein interacts with the AT7 region and the LeuO binding site located downstream of leuO , making a DNA loop to counteract repression by H-NS ( 2 , 3 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	leuO	repressor	18156266	44	ver/dev	Interestingly , the results indicate that H-NS is a positive regulator of STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	354	Interestingly , the results presented here indicate that H-NS is a positive regulator of tpx and STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	leuO	repressor	22804842	6	ver/dev	the response regulator RcsB activates leuO transcription in conjunction with BglJ , counteracting H-NS repression of leuO transcription	138	Interestingly , RcsA can form heterodimers with the response regulator RcsB , which activates leuO transcription in conjunction with BglJ , counteracting H-NS repression of leuO transcription ( Stratmann et al. , 2012 ) .	6	EXTENSION OF THE LEUO REGULON	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	leuO	repressor	24354910	3	ver/dev	Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions .	27	Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions that impair H-NS-mediated silencing .	7	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	leuO	repressor	24354910	3	ver/dev	Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions .	27	Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions that impair H-NS-mediated silencing .	7	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	leuO	repressor	24354910	6	ver/dev	However , the fact that both leuO are repressed by H-NS suggests that LeuO might provide a backup mechanism for SPI-1 repression .	50	However , the fact that both leuO and SPI-1 are repressed by H-NS ( Klauck et al. , 1997 ; Lucchini et al. , 2006 ; Navarre et al. , 2006 ) suggests that LeuO might provide a backup mechanism for SPI-1 repression .	8	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	leuO	repressor	24354910	45	ver/dev	LeuO is a quiescent LTTR under standard laboratory conditions because leuO transcription is repressed by H-NS .	189	LeuO is a quiescent LTTR under standard laboratory conditions because leuO transcription is repressed by H-NS ( Klauck et al. , 1997 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	leuO	repressor	24354910	46	ver/dev	To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .	190	To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .	12	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HNS	gene	leuO	repressor	24354910	54	ver/dev	Such hypothetical conditions can be expected to activate leuO expression because leuO transcription is also repressed by H-NS .	209	Such hypothetical conditions can be expected to activate leuO expression because leuO transcription is also repressed by H-NS ( Klauck et al. , 1997 ) .	12	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	leuO	repressor	25566242	2	ver/dev	The expression of leuO is repressed by H-NS , although there are some stress conditions .	59	The expression of leuO is repressed by H-NS , although there are some stress conditions when LeuO can be detected in E. coli .	4	LEUO HISTORY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	leuO	repressor	31428589	8	ver/dev	Interestingly , H-NS also represses the promoters of leuO .	170	Interestingly , H-NS also represses the promoters of leuO and hilE , which are regarded as negative regulatory genes .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	fliZ	regulator	22479568	3	ver/dev	In addition , fliZ has been shown to regulate invasion genes through the control of HilD .	150	In addition , fliZ has been shown to regulate invasion genes through the control of the SPI1 regulator , HilD [ 29,35 ] .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	fliZ	regulator	22479568	3	ver/dev	In addition , fliZ has been shown to regulate invasion genes through the control of HilD .	150	In addition , fliZ has been shown to regulate invasion genes through the control of the SPI1 regulator , HilD [ 29,35 ] .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	fliZ	regulator	29378886	36	ver/dev	the deletion of fliZ _ encoding a strong positive regulator of HilD	281	It has been previously demonstrated that the deletion of fliZ , encoding a strong positive regulator of HilD , causes a defect in the ability of Salmonella to invade the host intestinal epithelium ( 20 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	fliZ	regulator	30941426	19	ver/dev	Further overexpression of fliZ in the lon background fully restored HilD protein level in rpsD * to the WT , presumably due to the positive autoregulation of HilD expression .	280	Further overexpression of fliZ in the lon background fully restored HilD protein level in rpsD * to the WT ( Figure 7A and B ) , presumably due to the positive autoregulation of HilD expression .	25	NON-OPTIMAL TRANSLATIONAL FIDELITY PROMOTES DEGRADATION OF HILD BY LON	nan	1	L3	SPEC	Other	OTHER	New	Level 1
HilD	gene	fliZ	regulator	30941426	29	ver/dev	Our results here indicate that an increased activity of down-regulation of fliZ are major contributors for the reduced level of HilD expression in rpsD * , although other pathways of transcriptional regulation are not completely ruled out .	313	Our results here indicate that an increased activity of Lon and down-regulation of fliZ are major contributors for the reduced level of HilD and SPI-1 expression in rpsD * , although other pathways of transcriptional regulation are not completely ruled out ( Supplementary Figure S8 ) .	26	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	fliZ	regulator	31262841	15	ver/dev	Given the effect on flagellar gene expression , we then hypothesized that PinT could also control hilA by affecting expression of the FlhDC-activated flagellar gene fliZ , encoding a major regulator of HilD protein activity .	192	Given the effect on flagellar gene expression , we then hypothesized that PinT could also control hilA by affecting expression of the FlhDC-activated flagellar gene fliZ , encoding a major regulator of HilD protein activity ( 72 , 73 , 77 ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	phoQ	activator	12218035	1	att	A mutation in the S. enterica serovar Typhimurium phoQ gene which results in a threonine residue at codon 48 being replaced with an isoleucine results in overexpression of several PhoP-activated genes ( 8 , 19 , 20 , 24 ) .	119	A mutation in the S. enterica serovar Typhimurium phoQ gene which results in a threonine residue at codon 48 being replaced with an isoleucine results in overexpression of several PhoP-activated genes ( 8 , 19 , 20 , 24 ) .	4	RESULTS	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoQ	activator	12507481	0	att	The PhoP/PhoQ two-component system governs the adaptation to low Mg2þ environments and virulence in several Gram-negative species .1 The PhoQ protein is a sensor for extra-cytoplasmic Mg2þ and Ca2þ that controls the activity of the response regulator PhoP : growth in millimolar concentrations of Mg2þ or Ca2þ represses transcription of PhoP-activated genes whereas growth in micromolar concentrations of these divalent cations results in transcription of PhoP-activated genes .2 A Salmonella phoQ null mutant exhibits the same phenotype as that of a phoP null mutant : the inability to promote transcription of PhoP -	23	The PhoP/PhoQ two-component system governs the adaptation to low Mg2þ environments and virulence in several Gram-negative species .1 The PhoQ protein is a sensor for extra-cytoplasmic Mg2þ and Ca2þ that controls the activity of the response regulator PhoP : growth in millimolar concentrations of Mg2þ or Ca2þ represses transcription of PhoP-activated genes whereas growth in micromolar concentrations of these divalent cations results in transcription of PhoP-activated genes .2 A Salmonella phoQ null mutant exhibits the same phenotype as that of a phoP null mutant : the inability to promote transcription of PhoP -	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoQ	activator	12507481	10	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 harboring plasmids expressing wild-type ( phoQ ) , mutated phoQs or plasmid vector ( vector ) .	145	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 harboring plasmids expressing wild-type ( phoQ ) , mutated phoQs or plasmid vector ( vector ) .	5	THE PUTATIVE SITE PHOSPHORYLATION OF PHOQ IS DISPENSABLE FOR REPRESSION OF PHOP-MEDIATED TRANSCRIPTION DURING GROWTH IN HIGH MG21	unidentified plasmid	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	phoQ	activator	12507481	4	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , or by strain EG5931 ( b ) , and harboring plasmids expressing plasmid vector ( vector ) , wild-type phoQ ( pphoQ ) or zhoQ ( pzhoQ ) .	56	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , or by strain EG5931 ( b ) , and harboring plasmids expressing plasmid vector ( vector ) , wild-type phoQ ( pphoQ ) or zhoQ ( pzhoQ ) .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	phoQ	activator	12507481	7	att	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , ( b ) and ( d ) or by strain EG5931 ( c ) , and harboring plasmids expressing wild-type ( pphoQ and pphoP phoQ ) , mutated phoQs or plasmid vector ( vector ) .	91	b-Galactosidase activity ( Miller units ) of a lac-gene fusion to the PhoP-activated pmrC gene produced by strain EG9461 ( a ) , ( b ) and ( d ) or by strain EG5931 ( c ) , and harboring plasmids expressing wild-type ( pphoQ and pphoP phoQ ) , mutated phoQs or plasmid vector ( vector ) .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoQ	activator	14507376	2	att	PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl . ) .	126	PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl . ) .	6	TRANSCRIPTIONAL PROFILING INDICATES ACTIVATION OF THE PHOP AND RPOS REGULONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoQ	activator	14507376	5	ver/dev	To determine whether activation of PhoP by polymyxin was dependent on the presence of PhoQ , the PhoP protein level was measured in the strain , which carries the phoQ : .	158	To determine whether activation of PhoP by polymyxin was dependent on the presence of PhoQ , the PhoP protein level was measured in the strain CS009 , which carries the phoQ : : MudJ allele .	8	PHOQ-DEPENDENT REGULATION OF PHOP-ACTIVATED GENES BY CATIONIC ANTIMICROBIAL PEPTIDES	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoQ	activator	14507376	6	ver/dev	CS022 exhibits constitutive activation of the PhoP regulon due to T48I in phoQ .	177	CS022 exhibits constitutive activation of the PhoP regulon due to a point mutation ( T48I ) in phoQ .	8	PHOQ-DEPENDENT REGULATION OF PHOP-ACTIVATED GENES BY CATIONIC ANTIMICROBIAL PEPTIDES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoQ	activator	14507376	6	ver/dev	CS022 exhibits constitutive activation of the PhoP regulon due to a point mutation in phoQ .	177	CS022 exhibits constitutive activation of the PhoP regulon due to a point mutation ( T48I ) in phoQ .	8	PHOQ-DEPENDENT REGULATION OF PHOP-ACTIVATED GENES BY CATIONIC ANTIMICROBIAL PEPTIDES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoQ	activator	14742517	4	ver/dev	Transcriptional regulation of Salmonella virulence -- a phoQ periplasmic domain mutation results in increased net phosphotransfer to PhoP .	334	Transcriptional regulation of Salmonella virulence -- a phoQ periplasmic domain mutation results in increased net phosphotransfer to PhoP .	14	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoQ	activator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	phoQ	activator	18350168	2	att	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	294	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	phoQ	activator	24449881	0	att	S. Typhimurium strains with mutations in phoQ that have variable expression of PhoP-activated genes ( pag ) were constructed to study GPL regulation .	57	S. Typhimurium strains with mutations in phoQ that have variable expression of PhoP-activated genes ( pag ) were constructed to study GPL regulation .	10	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoQ	activator	33045730	56	att	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	255	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	cysD	activator	27065993	2	att	To independently test • NO - and DksA-dependent activation of sulfur assimilation and cysteine biosynthesis in Salmonella experiencing nitrosative-stress , the cysD promoter ( PcysD ) was cloned upstream of the promoterless lacZ gene in the plasmid pQF50 .	177	To independently test • NO - and DksA-dependent activation of sulfur assimilation and cysteine biosynthesis in Salmonella experiencing nitrosative stress , the cysD promoter ( PcysD ) was cloned upstream of the promoterless lacZ gene in the plasmid pQF50 .	12	RESULTS	Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
STM0952	gene	STM2865	repressor	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to nitrosative-stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
STM0952	gene	STM2865	repressor	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to nitrosative-stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
STM0952	gene	STM2865	repressor	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
STM0952	gene	STM2865	repressor	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	TU	tatABC	activator	30716090	31	att	We asked whether the tatABC operon might be CpxR-dependent regulated in pathogenic E. coli strains or other pathogenic genera like Shigella , Yer-sinia or Legionella .	371	We asked whether the tatABC operon might be CpxR-dependent regulated in pathogenic E. coli strains or other pathogenic genera like Shigella , Yer-sinia or Legionella .	23	A CPXR MUTANT DISPLAYS INCREASED SENSITIVITY TO POLYMYXIN B	Escherichia coli	0	L1	SPEC	Other	NEG	Other	Level 1
DeoR	gene	aphA	repressor	15968063	1	ver/dev	Because the AphA enzyme is known to be important for nucleotide assimilation , it seemed reasonable that aphA might be repressed by DeoR .	184	Because the AphA enzyme removes phosphate from nucleotides and is known to be important for nucleotide assimilation ( 24 , 45 ) , it seemed reasonable that aphA might be repressed by DeoR , a regulator of genes involved in use of deoxynucleotides as carbon sources .	4	RESULTS	nan	1	L1	SPEC	Fact	OTHER	Other	Level 1
DeoR	gene	aphA	repressor	15968063	1	ver/dev	Because the AphA enzyme removes phosphate from nucleotides , it seemed reasonable that aphA might be repressed by DeoR .	184	Because the AphA enzyme removes phosphate from nucleotides and is known to be important for nucleotide assimilation ( 24 , 45 ) , it seemed reasonable that aphA might be repressed by DeoR , a regulator of genes involved in use of deoxynucleotides as carbon sources .	4	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
FliZ	gene	fliZ	repressor	25161191	4	ver/dev	FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .	119	YdiV and FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 ( Fig. 1 ) ( 10 ) .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
FliZ	gene	fliZ	repressor	25161191	4	ver/dev	YdiV are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .	119	YdiV and FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 ( Fig. 1 ) ( 10 ) .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	iraP	activator	21625519	58	att	The PhoP-activated promoters of ugtL [ 47 ] and iraP [ 48 ] harbor two PhoP binding sites , and one of the sites in each promoter overlaps with the 210 element .	202	The PhoP-activated promoters of ugtL [ 47 ] and iraP [ 48 ] harbor two PhoP binding sites , and one of the sites in each promoter overlaps with the 210 element .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	iraP	activator	27618760	0	ver/dev	Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we therefore regulate spvRABCD .	260	Since PhoP is a transcriptional activator of the iraP ( yaiB ) gene that controls RpoS protein turnover by interacting with RssB [ 39 ] , we postulate that the PhoP/PhoQ and RstA/RstB systems might coregulate iraP to control RpoS , and therefore regulate spvRABCD .	19	3.2. COMPARISON OF RSTA/RSTB AND PHOP/PHOQ REGULATED PROTEINS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	iraP	activator	27618760	0	ver/dev	Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we postulate that the RstA/RstB systems might coregulate iraP to control RpoS .	260	Since PhoP is a transcriptional activator of the iraP ( yaiB ) gene that controls RpoS protein turnover by interacting with RssB [ 39 ] , we postulate that the PhoP/PhoQ and RstA/RstB systems might coregulate iraP to control RpoS , and therefore regulate spvRABCD .	19	3.2. COMPARISON OF RSTA/RSTB AND PHOP/PHOQ REGULATED PROTEINS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	iraP	activator	27618760	0	ver/dev	Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we postulate that the PhoP/PhoQ systems might coregulate iraP to control RpoS .	260	Since PhoP is a transcriptional activator of the iraP ( yaiB ) gene that controls RpoS protein turnover by interacting with RssB [ 39 ] , we postulate that the PhoP/PhoQ and RstA/RstB systems might coregulate iraP to control RpoS , and therefore regulate spvRABCD .	19	3.2. COMPARISON OF RSTA/RSTB AND PHOP/PHOQ REGULATED PROTEINS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	siiA	activator	23419780	7	ver/dev	HilA are transcription activators of effectors downregulates siiA .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	galR	repressor	24450479	31	ver/dev	However , mutations in neither galR did not affect repression by NagC .	127	However , mutations in neither galR nor galS had any effect on chiP -- lacZ expression ( Fig. 4 ) and did not affect repression by NagC .	6	BINDING OF GALR AND GALS PROTEINS IN THE REGION UPSTREAM FROM THE E. COLI CHIP PROMOTER	nan	1	L3	OTHER	Other	NEG	New	Level 1
RstA	gene	csgD	repressor	18790861	6	ver/dev	However , low pH does not seem to produce sufficient levels of active RstA in E. coli because repression of csgD transcription occurred only upon overexpression of the RstA protein from a plasmid .	32	However , low pH does not seem to produce sufficient levels of active RstA ( i.e. , phosphorylated RstA ) in E. coli because repression of csgD transcription occurred only upon overexpression of the RstA protein from a plasmid ( 19 ) .	2	MAIN	Escherichia coli;unidentified plasmid	0.5	L2	SPEC	Other	NEG	New	Level 1
RstA	gene	csgD	repressor	18790861	6	ver/dev	However , low pH does not seem to produce sufficient levels of i.e. in E. coli because repression of csgD transcription occurred only upon overexpression of the RstA protein from a plasmid .	32	However , low pH does not seem to produce sufficient levels of active RstA ( i.e. , phosphorylated RstA ) in E. coli because repression of csgD transcription occurred only upon overexpression of the RstA protein from a plasmid ( 19 ) .	2	MAIN	Escherichia coli;unidentified plasmid	0.5	L2	SPEC	Other	NEG	New	Level 1
RpoS	gene	psiF	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , psiF are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsrA	gene	rpoS	repressor	30682134	21	ver/dev	CsrA repressed translation of rpoS 2.4-fold in LB .	234	CsrA repressed translation of rpoS 2.4-fold in LB but had no effect in mLPM ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	rpoS	repressor	30682134	38	ver/dev	In LB , CsrA also repressed expression of rpoS , regulators .	279	In LB , CsrA also repressed expression of slyA , rpoS , and soxS , regulators that contribute to resistance to oxidative stress in Salmonella [ 71,109,110 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	rpoS	repressor	30682134	40	ver/dev	In contrast , the stress resistant phenotype may be apparent in LB because CsrA represses the expression of rpoS	287	In contrast , the stress resistant phenotype may be apparent in LB because CsrA represses the expression of multiple regulators ( slyA , soxS , and rpoS ) that induce expression of	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SoxS	TU	marRAB	activator	31501286	10	att	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	A genetic background was chosen to minimize any possible regulatory cross talk between RamA ( such as SoxS-dependent activation of marRAB ) .	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	A genetic background was chosen to minimize any possible regulatory cross talk between Rob ( such as SoxS-dependent activation of marRAB ) .	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	A genetic background was chosen to minimize any possible regulatory cross talk between SoxS ( such as SoxS-dependent activation of marRAB ) .	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	A genetic background was chosen to minimize any possible regulatory cross talk between MarA ( such as SoxS-dependent activation of marRAB ) .	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	any possible regulatory cross talk between RamA ( such as SoxS-dependent activation of marRAB ) might distort the effects on expression of downstream genes	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	New	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	any possible regulatory cross talk between Rob ( such as SoxS-dependent activation of marRAB ) might distort the effects on expression of downstream genes	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	New	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	any possible regulatory cross talk between SoxS ( such as SoxS-dependent activation of marRAB ) might distort the effects on expression of downstream genes	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	New	Level 1
SoxS	TU	marRAB	activator	31501286	10	ver/dev	any possible regulatory cross talk between MarA ( such as SoxS-dependent activation of marRAB ) might distort the effects on expression of downstream genes	153	A genetic background lacking all native loci for these transcription factors was chosen to minimize any possible regulatory cross talk between MarA , SoxS , Rob , and RamA ( such as SoxS-dependent activation of marRAB ) that might distort the effects on expression of downstream genes .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	New	Level 1
SoxS	TU	marRAB	activator	32210923	1	ver/dev	Different effects of SoxS on susceptibility of Escherichia coli to CAMPs : rob-dependent CAMP induction of the marRAB operon .	837	Different effects of transcriptional regulators MarA , SoxS and Rob on susceptibility of Escherichia coli to cationic antimicrobial peptides ( CAMPs ) : rob-dependent CAMP induction of the marRAB operon .	32	TIME: 17:30 # 16	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	marRAB	activator	32210923	1	ver/dev	Different effects of SoxS on susceptibility of Escherichia coli to cationic antimicrobial peptides : rob-dependent CAMP induction of the marRAB operon .	837	Different effects of transcriptional regulators MarA , SoxS and Rob on susceptibility of Escherichia coli to cationic antimicrobial peptides ( CAMPs ) : rob-dependent CAMP induction of the marRAB operon .	32	TIME: 17:30 # 16	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	marRAB	activator	34202800	27	ver/dev	The marRAB operon is also induced by SoxS .	442	The marRAB operon is also induced by SoxS and Rob , which are MarA homologs [ 97 ] .	14	3.5. THE MARR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	STM3216	regulator	27564394	9	ver/dev	STM3216 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HilA	gene	STM3216	regulator	27564394	9	ver/dev	STM3216 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsA	gene	tolB	activator	12519186	20	att	The tolB mutation specifically promotes transcription of the ugd gene in an RcsC -- YojN -- RcsB - and RcsA-dependent manner and independently of the PhoP and PmrA proteins .	61	The tolB mutation specifically promotes transcription of the ugd gene in an RcsC -- YojN -- RcsB - and RcsA-dependent manner and independently of the PhoP and PmrA proteins .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	lacZ	activator	12535071	37	att	We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .	109	We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	unidentified plasmid;Prairie vole hantavirus	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	lacZ	activator	12535071	39	ver/dev	As expected , HilA activates lacZ expression from pVV448 up to 50-fold .	112	As expected , HilA activates lacZ expression from pVV448 up to 50-fold ( Fig. 4 , open bars ) .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	Prairie vole hantavirus	0	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	hcp	activator	23651595	12	ver/dev	Additional experiments , showed that NsrR-binding plays a major role in the induction of the hcp .	608	Additional experiments , using electrophoretic mobility shift assays , showed that NsrR-binding plays a major role in the induction of the hcp -- hcr operon and that hcp is totally dependent upon anaerobiosis and the FNR protein ( Chismon , Browning , Farrant , & Busby , 2010 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrHFIJKLM	activator	15681155	7	att	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	191	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	11	3. RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PmrA	gene	pmrHFIJKLM	activator	15681155	7	att	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	191	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	11	3. RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PmrA	gene	pmrHFIJKLM	activator	15681155	2	ver/dev	PmrA mediates induction of pmrHFIJKLM .	70	PmrA mediates induction of pmrE and pmrHFIJKLM , which encode enzymes involved in the biosynthesis of Ara4N and its addition to the 40-phosphate ( and sometimes 1-phos-phate ) of the lipid A [ 7,14 -- 17 ] .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	pmrHFIJKLM	activator	20593264	1	att	Synthesis of Ara4N and addition to the lipid-A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .	173	Synthesis of Ara4N and addition to the lipid A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .	10	5.2.2 PMRA–PMRB REGULATORY SYSTEM	Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
PmrA	gene	pmrHFIJKLM	activator	24531506	1	ver/dev	pmrHFIJKLM is activated by PhoPQ through PmrA	75	Remaining components of the L-Ara4N-LPS modification pathway are encoded within an operon , pmrHFIJKLM , which is activated by PhoPQ through PmrA [ 56 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YeiE	gene	STM1697	repressor	34098734	5	ver/dev	These data suggest that YeiE may repress the expression of the STM1697 FlhD4C2 repressor .	165	These data are similar to our observations of hypermotility for the DyeiElib suppressor mutant and suggest that YeiE may repress the expression of the STM1697 FlhD4C2 repressor .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
YeiE	gene	STM1697	repressor	34098734	8	ver/dev	These data demonstrate that YeiE regulates motility by repressing the expression of the FlhD4C2 functional repressor STM1697 .	170	These data demonstrate that YeiE regulates motility by repressing the expression of the FlhD4C2 functional repressor STM1697 ( Fig. 7 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
YeiE	gene	STM1697	repressor	34098734	9	ver/dev	Furthermore , we propose that YeiE is a repressor of STM1697 .	174	Furthermore , we link the positive effect of YeiE on cell motility with STM1697 , an anti-FlhD4C2 factor , and propose that YeiE is a repressor of STM1697 ( Fig. 7 ) .	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
YeiE	gene	STM1697	repressor	34098734	11	ver/dev	YeiE may directly repress STM1697 expression by binding to its promoter to inhibit transcription .	185	YeiE may directly repress STM1697 expression by binding to its promoter to inhibit transcription .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
YeiE	gene	STM1697	repressor	34098734	12	ver/dev	YeiE may indirectly influence STM1697 expression by regulating the expression of an activator or inhibitor of STM1697 transcription .	186	YeiE may indirectly influence STM1697 expression by regulating the expression of an activator or inhibitor of STM1697 transcription .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
YeiE	gene	STM1697	repressor	34098734	13	ver/dev	Further work is needed to establish how YeiE represses STM1697 expression in S. Typhimurium .	187	Further work is needed to establish the full YeiE regulon of S. Typhimurium and to establish how YeiE represses STM1697 expression in S. Typhimurium .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YeiE	gene	STM1697	repressor	34098734	18	ver/dev	YeiE acts as a repressor of STM1697 to promote flagellum-mediated motility .	206	YeiE acts as a repressor of STM1697 to promote flagellum-mediated motility .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YeiE	gene	STM1697	repressor	34098734	22	ver/dev	The promotility effect of STM1697 inhibition by YeiE likely facilitates initial gut colonization , whereas STM1697-mediated repression of flagellin aids immune evasion once Salmonella is located intracellularly .	216	The promotility effect of STM1697 inhibition by YeiE likely facilitates initial gut colonization , whereas STM1697-mediated repression of flagellin aids immune evasion once Salmonella is located intracellularly ( 20 ) .	5	DISCUSSION	Salmonella	1	L2	SPEC	Other	OTHER	Other	Level 1
YeiE	gene	STM1697	repressor	34098734	22	ver/dev	The promotility effect of STM1697 inhibition by YeiE likely facilitates initial gut colonization , whereas STM1697-mediated repression of flagellin aids immune evasion once Salmonella is located intracellularly .	216	The promotility effect of STM1697 inhibition by YeiE likely facilitates initial gut colonization , whereas STM1697-mediated repression of flagellin aids immune evasion once Salmonella is located intracellularly ( 20 ) .	5	DISCUSSION	Salmonella	1	L2	SPEC	Other	OTHER	Other	Level 1
YeiE	gene	STM1697	repressor	34098734	23	ver/dev	We propose that YeiE serves as a control point for flagellar regulation through inhibition of the antiFlhD4C2 factor STM1697 , although additional work is needed to establish the mechanism by which YeiE influences STM1697 expression .	220	We propose that YeiE serves as a control point for flagellar regulation through inhibition of the antiFlhD4C2 factor STM1697 , although additional work is needed to establish the mechanism by which YeiE influences STM1697 expression .	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	dinI	activator	33921732	5	att	In genes that show LexA-dependent bistability and have more than one LexA box ( recN , dinI and lexA ) , only the closest LexA box with lower HI was considered .	307	In genes that show LexA-dependent bistability and have more than one LexA box ( recN , dinI and lexA ) , only the closest LexA box with lower HI was considered .	15	3.4. INFLUENCE OF THE DISTANCE AND THE NUCLEOTIDE SEQUENCE OF THE LEXA BOX ON THE EXPRESSION PATTERNS OF SOS GENES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	spiR	regulator	26441883	35	ver/dev	Fis binds directly to the promoter regions of spiR	474	Fis binds directly to the promoter regions of spiR and ssaG ( Kelly et al. , 2004 ; Lim et al. , 2006 ) and its expression correlates with Spi-2 gene expression inside macrophages ( O Croinin et al. , 2006 ) .	10	REGULATORY CIRCUITS CONTROLLING LATER STAGES OF INFECTION AND DEFENSE SYSTEMS AGAINST THE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	dam	regulator	21984608	0	ver/dev	It is interesting to note that several regulators of HilA , were found in significantly lower levels in the dam mutant .	135	It is interesting to note that several regulators of T3SS1 , such as HilA , HilC , HilD , and InvF , were found in significantly lower levels in the dam mutant .	5	TRANSCRIPTIONAL AND TRANSLATIONAL REGULATION DURING INVASION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilA	gene	dam	regulator	24947562	0	ver/dev	However , it is important to mention that sopB , is cooperatively regulated by HilA dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control .	232	However , it is important to mention that sopB , is cooperatively regulated by InvF and HilA [ 30 ] and lowered levels of all SPI-1-encoded transcriptional regulators ( HilA , HilC , HilD , and InvF ) were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control [ 24 ] .	19	4. DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	26880544	53	att	Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .	369	Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .	16	THE IMPORTANCE OF ANTI-SILENCING IN GENE REGULATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	9	ver/dev	These results show that SsrB specifically binds to the regulatory regions of hilA .	133	These results show that SsrB specifically binds to the regulatory regions of hilD and hilA .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilA	regulator	28704543	33	ver/dev	EMSAs were performed to determine whether SsrB binds to the hilA DNA fragments in hilA-cat-35 +446 fusions .	218	EMSAs were performed to determine whether SsrB binds to the hilA DNA fragments in the hilA-cat-410 +66 ( E ) , hilA-cat-100 +6 ( F ) , hilA-cat-35 +6 ( G ) and hilA-cat-35 +446 ( H ) fusions .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L3	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	hilA	regulator	28704543	33	ver/dev	EMSAs were performed to determine whether SsrB binds to the hilA DNA fragments in the hilA-cat-410 +66 , hilA-cat-100 +6 , hilA-cat-35 +6 .	218	EMSAs were performed to determine whether SsrB binds to the hilA DNA fragments in the hilA-cat-410 +66 ( E ) , hilA-cat-100 +6 ( F ) , hilA-cat-35 +6 ( G ) and hilA-cat-35 +446 ( H ) fusions .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus;Felis catus	0	L3	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilA promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilA	regulator	32021316	7	ver/dev	SsrB directly binds to the regulatory region of hilA , it has been observed that the intestinal butyrate can inhibit the expression of hilD , encoding the T3SS-1 gene regulator .165 Salmonella utilizes butyrate and , in turn , provides fitness advantages during pathogen growth .	203	SsrB directly binds to the regulatory region of hilA and hilD and suppress it .164 Recently , it has been observed that the intestinal butyrate derived from clos-tridia can inhibit the expression of hilD , encoding the T3SS-1 gene regulator .165 Salmonella utilizes butyrate using β-oxidation and , in turn , provides fitness advantages during pathogen growth .	15	HOW TO ACTIVATE PATHOGENIC GENES	Salmonella	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SlyA	gene	fruK	activator	29857034	4	ver/dev	we determined that SlyA positively regulates the fruK gene	268	Rather than suppression , the glyco-lytic pathway was activated under H2O2 stress , and we determined that SlyA positively regulates the fruK gene that encodes the enzyme 1-phosphofructokinase , which converts fructose 1-phosphate into fructose 1,6-bisphosphate .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	fruK	activator	29857034	8	ver/dev	These results suggest that fruK is upregulated by SlyA .	284	These results suggest that fruK is upregulated by SlyA .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	fruK	activator	29857034	27	ver/dev	SlyA , thus , seems to upregulate fruK expression by directly binding to Fig. 4D .	359	SlyA , thus , seems to upregulate fruK expression by directly binding to the promoter region ( Fig. 4D ) .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	fruK	activator	29857034	27	ver/dev	SlyA , thus , seems to upregulate fruK expression by directly binding to the promoter region .	359	SlyA , thus , seems to upregulate fruK expression by directly binding to the promoter region ( Fig. 4D ) .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	emrR	regulator	30992361	11	ver/dev	In contrast to PhoP-activated slyA transcription , transcription of the emrR gene was not regulated by either PhoP/PhoQ system , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains -LRB- Fig. 3A , top panel -RRB- .	114	In contrast to PhoP-activated slyA transcription ( 5 , 21 ) , transcription of the emrR gene was not regulated by either PhoP/PhoQ system or SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains ( Fig. 3A , top panel ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
SoxS	gene	fumC	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates Mn-containing superoxide dismutase , fumC .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	fumC	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , fumC .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	fumC	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , fumC .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	fumC	activator	12886427	0	ver/dev	SoxS protein , activates sodA , fumC .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	orgBC	activator	29555922	16	ver/dev	HilD also positively regulate the expression of the orgBC SPI-1 operon .	267	HilD and PhoP also positively and independently regulate the expression of the orgBC SPI-1 operon , in SPI-1-inducing growth conditions , PhoP directly and HilD through HilA8 ,56 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cbl	gene	sbp	regulator	18957594	7	ver/dev	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources .	329	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ( Kredich , 1996 ; Stec et al. , 2006 ; Van Der Ploeg et al. , 1997 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Cbl	gene	sbp	regulator	18957594	7	ver/dev	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources .	329	In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ( Kredich , 1996 ; Stec et al. , 2006 ; Van Der Ploeg et al. , 1997 ) .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	18792679	7	ver/dev	the atypical cascade in which the PhoP protein binds to the ssrB promoter to activate ssrB transcription	171	Model illustrating the atypical cascade in which the PhoP protein binds to the ssrB promoter to activate ssrB transcription and to a yet unidentified gene z that promotes SpiR expression .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	nan	1	L3	SPEC	Other	OTHER	New	Level 1
PhoP	gene	ssrB	activator	21625519	16	ver/dev	The rationale behind this experiment was the assumption that if PhoP contributes to the expression in an SsrB-dependant manner , i.e. , the expression in the double mutant strain is likely to be similar to the expression in the ssrB background ; however , if the contribution by PhoP is independent of SsrB , then an accumulative effect is expected , leading to further reduced expression in the double mutant background .	73	The rationale behind this experiment was the assumption that if PhoP contributes to the expression in an SsrB-dependant manner , i.e. functioning upstream of SsrB in the same regulatory cascade , the expression in the double mutant strain is likely to be similar to the expression in the ssrB background ; however , if the contribution by PhoP is independent of SsrB , then an accumulative effect is expected , leading to further reduced expression in the double mutant background .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ssrB	activator	26880544	1	ver/dev	Under low osmolality , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	26880544	1	ver/dev	Under acidic pH , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	26943369	20	ver/dev	PhoP upregulates the expression of SPI-2 by directly activating transcription of ssrB , therefore PhoP is indispensible for Salmonella within phagosomes .	439	PhoP upregulates the expression of SPI-2 by directly activating transcription of ssrB , therefore PhoP is indispensible for Salmonella within phagosomes [ 46 ] .	9	ACETYLATION OF PHOP K201 IS CRITICAL FOR REGULATION OF PHOP ACTIVITY	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	32209674	10	ver/dev	In addition , PhoP is a direct transcriptional activator of the ssrB genes .	134	In addition , PhoP is a direct transcriptional activator of the ssrB ( 8 ) and slyA ( 18 , 34 ) genes .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	18	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	18	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	19	att	Thus , the defect of the ssrB mutant is neither specific to a particular PhoP-activated gene nor to the reporter used .	193	Thus , the defect of the ssrB mutant is neither specific to a particular PhoP-activated gene nor to the reporter used .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ssrB	activator	33045730	20	att	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP , resulting in transcription of PhoP-activated genes .	195	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP , resulting in transcription of PhoP-activated genes .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ssrB	activator	33045730	25	att	The ssrB-dependent activation of PhoP taking place in mildly acidic pH is necessary for PhoP-dependent gene transcription because the - galactosidase activity from the PhoP-activated pcgL-lac transcriptional-fusion was much lower in the ssrB mutant than in the isogenic ssrB + strain	202	The ssrB-dependent activation of PhoP taking place in mildly acidic pH is necessary for PhoP-dependent gene transcription because the - galactosidase activity from the PhoP-activated pcgL-lac transcriptional fusion was much lower in the ssrB mutant than in the isogenic ssrB + strain	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	28	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	28	att	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional-fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional-fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Allomonas enterica;Leucobacter iarius;Natrialba aegyptia;Mycobacterium lehmannii;Marinomonas vaga	0	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	29	att	Thus , the defect of the ssrB mutant is neither specific to a particular PhoP-activated gene nor to the reporter used .	219	Thus , the defect of the ssrB mutant is neither specific to a particular PhoP-activated gene nor to the reporter used .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ssrB	activator	33045730	30	att	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP , resulting in transcription of PhoP-activated genes .	221	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP , resulting in transcription of PhoP-activated genes .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ssrB	activator	33045730	56	att	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	255	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ssrB	activator	33045730	64	att	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	283	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	75	att	The mRNA abundance of the PhoP-activated ugtL , pagC and ssrB genes was similar among wild-type , ugtL-sifBmu mutant and ssrB null strains at 1 h post bacterial internalization by macrophages ( Figure 5B ) .	328	The mRNA abundance of the PhoP-activated ugtL , pagC and ssrB genes was similar among wild-type , ugtL-sifBmu mutant and ssrB null strains at 1 h post bacterial internalization by macrophages ( Figure 5B ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	0	ver/dev	We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP PhoQ of Salmonella enter - / S. Typhimurium in mildly acidic pH .	11	We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP PhoQ of Salmonella enter - / ica serovar Typhimurium ( S. Typhimurium ) in mildly acidic pH , which S. Typhimurium experiences inside macrophages .	2	ABSTRACT	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	0	ver/dev	We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP PhoQ of Salmonella enter - / ica serovar Typhimurium in mildly acidic pH .	11	We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP PhoQ of Salmonella enter - / ica serovar Typhimurium ( S. Typhimurium ) in mildly acidic pH , which S. Typhimurium experiences inside macrophages .	2	ABSTRACT	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	20	ver/dev	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP .	195	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP , resulting in transcription of PhoP-activated genes .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ssrB	activator	33045730	24	ver/dev	These results demonstrate that ssrB is necessary to activate PhoP when the PhoQ-activating condition is mildly acidic pH.	201	These results demonstrate that ssrB is necessary to activate PhoP when the PhoQ-activating condition is mildly acidic pH.	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	25	ver/dev	The ssrB-dependent activation of PhoP is necessary for PhoP-dependent gene transcription because the - galactosidase activity from the PhoP-activated pcgL-lac transcriptional-fusion was much lower in the ssrB mutant than in strain	202	The ssrB-dependent activation of PhoP taking place in mildly acidic pH is necessary for PhoP-dependent gene transcription because the - galactosidase activity from the PhoP-activated pcgL-lac transcriptional fusion was much lower in the ssrB mutant than in the isogenic ssrB + strain	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	25	ver/dev	The ssrB-dependent activation of PhoP is necessary for PhoP-dependent gene transcription because the - galactosidase activity from the PhoP-activated pcgL-lac transcriptional-fusion was much lower in the ssrB mutant than in the isogenic ssrB	202	The ssrB-dependent activation of PhoP taking place in mildly acidic pH is necessary for PhoP-dependent gene transcription because the - galactosidase activity from the PhoP-activated pcgL-lac transcriptional fusion was much lower in the ssrB mutant than in the isogenic ssrB + strain	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	30	ver/dev	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP .	221	Taken together , the results in this section indicate that when S. Typhimurium experiences mildly acidic pH , the horizontally acquired ssrB gene activates the ancestral regulator PhoP , resulting in transcription of PhoP-activated genes .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ssrB	activator	33045730	101	ver/dev	That is , the S. Typhimurium-specific ssrB gene is necessary for activation of the widespread PhoP protein in mildly acidic pH .	429	That is , the S. Typhimurium-specific ssrB gene is necessary for activation of the widespread PhoP protein in mildly acidic pH ( Figure 2 ) .	36	THE GENETIC BASIS FOR PHENOTYPIC DIFFERENCES AMONG SALMONELLA SPECIES AND SEROVARS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	33045730	105	ver/dev	The horizontally acquired ssrB gene activates the ancestral regulator PhoP at late times inside macrophages .	444	The horizontally acquired ssrB gene activates the ancestral regulator PhoP at late times inside macrophages .	37	DIFFERENT HORIZONTALLY ACQUIRED GENES ENABLE ESCHERICHIA COLI TO ACTIVATE PHOP/PHOQ IN MILDLY ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	activator	33751923	10	ver/dev	In vitro studies demonstrated that OmpR P stimulates expression of ssrA , whereas PhoP P activates ssrB .	412	In vitro studies demonstrated that OmpR P stimulates expression of ssrA , whereas PhoP P activates ssrB ( Liew et al. 2019 ) .	10	SSRAB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrB	activator	34202800	20	ver/dev	As a result , PhoP activate transcription of ssrB genes .	390	As a result , OmpR and PhoP activate transcription of ssrA and ssrB genes , leading to the formation of SsrA and SsrB .	11	3.3.4. THE ENVZ/OMPR SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipC	regulator	31017982	5	att	We tested a single-copy chromosomal sipC : : lacZY reporter fusion as a representative HilD-regulated gene within SPI-1 , and found it to be increased by 4 - to 6-fold in these mutants ( Fig 2A ) .	91	We tested a single-copy chromosomal sipC : : lacZY reporter fusion as a representative HilD-regulated gene within SPI-1 , and found it to be increased by 4 - to 6-fold in these mutants ( Fig 2A ) .	7	ACTIVATING MUTATIONS OF HILD OCCUR IN ITS 5’ REGION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	lpxR	regulator	27886269	3	ver/dev	InvF , regulates the expression of lpxR .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	10844688	7	ver/dev	Recent studies indicate that HilA binds to specific sequences in the invF promoters .	270	Recent studies indicate that HilA binds to specific sequences in the prgH and invF promoters that are necessary for expression of these SPI1 genes , suggesting that HilA directly activates these promoters ( Lostroh et al. , 2000 ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	regulator	10844688	20	ver/dev	By placing invF encoding the secretion machinery under direct control of HilA , S. typhimurium ensures that secreted the secretion apparatus are produced simultaneously .	307	By placing invF and genes encoding the secretion machinery under direct control of HilA , S. typhimurium ensures that secreted effectors and the secretion apparatus are produced simultaneously .	16	MODELS FOR INVASION GENE REGULATION IN VIVO	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	10844688	20	ver/dev	By placing invF encoding the secretion machinery under direct control of HilA , S. typhimurium ensures that secreted effectors are produced simultaneously .	307	By placing invF and genes encoding the secretion machinery under direct control of HilA , S. typhimurium ensures that secreted effectors and the secretion apparatus are produced simultaneously .	16	MODELS FOR INVASION GENE REGULATION IN VIVO	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	11705895	0	att	HilA-regulated genes include invF , which encodes a transcriptional regulator of the AraC family and is located within SPI-1 ( 37 ) , and the components of the secretion machinery ( 3 , 4 ) .	29	HilA-regulated genes include invF , which encodes a transcriptional regulator of the AraC family and is located within SPI-1 ( 37 ) , and the components of the secretion machinery ( 3 , 4 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	12535071	98	ver/dev	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilC to activate invF .	282	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD and HilC to bind upstream of and activate invF .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	invF	regulator	12535071	98	ver/dev	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilC to bind upstream of .	282	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD and HilC to bind upstream of and activate invF .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	invF	regulator	12535071	98	ver/dev	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD to activate invF .	282	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD and HilC to bind upstream of and activate invF .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	invF	regulator	12535071	98	ver/dev	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD to bind upstream of .	282	It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD and HilC to bind upstream of and activate invF .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	invF	regulator	15661008	1	ver/dev	HilA activates invF operon expression by binding to the invF promoter .	42	HilA belongs to OmpR/ToxR family and activates invF operon expression by binding to the invF promoter ( Bajaj et al. , 1995 ; Lostroh et al. , 2000 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	16045614	54	ver/dev	Transcription of invF is primarily regulated by HilA	390	Transcription of invF is primarily regulated by HilA , but HilD , HilC and RtsA are each capable of partially activating invF ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Akbar et al. , 2003 ; Ellermeier and Slauch , 2003 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	20008574	6	ver/dev	Dam-dependent regulation of invF was still observed in HilA	152	In an analogous fashion , Dam-dependent regulation of invF was still observed in HilA , HilC , and RtsA backgrounds , and no information was obtained in a HilD background ( Figure 3 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	23419780	2	ver/dev	In the case of Fig. 1C , pGY16 contained the binding site for HilA , responsible for regulation of invF .	139	In the case of the invF promoter ( Fig. 1C ) , the original library reporter construct ( pGY16 ) contained the binding site for a known activator , HilA , responsible for regulation of various virulence genes including invF ( Lostroh et al. , 2000 ) .	13	3.2. MAPPING DNA REGIONS NECESSARY FOR TRANSCRIPTION MODULATION BY RIFAMPICIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	23419780	2	ver/dev	In the case of Fig. 1C , the original library reporter construct contained the binding site for HilA , responsible for regulation of invF .	139	In the case of the invF promoter ( Fig. 1C ) , the original library reporter construct ( pGY16 ) contained the binding site for a known activator , HilA , responsible for regulation of various virulence genes including invF ( Lostroh et al. , 2000 ) .	13	3.2. MAPPING DNA REGIONS NECESSARY FOR TRANSCRIPTION MODULATION BY RIFAMPICIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	23419780	2	ver/dev	In the case of the invF promoter , pGY16 contained the binding site for HilA , responsible for regulation of invF .	139	In the case of the invF promoter ( Fig. 1C ) , the original library reporter construct ( pGY16 ) contained the binding site for a known activator , HilA , responsible for regulation of various virulence genes including invF ( Lostroh et al. , 2000 ) .	13	3.2. MAPPING DNA REGIONS NECESSARY FOR TRANSCRIPTION MODULATION BY RIFAMPICIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	23419780	2	ver/dev	In the case of the invF promoter , pGY16 contained the binding site for HilA , responsible for regulation of various virulence genes .	139	In the case of the invF promoter ( Fig. 1C ) , the original library reporter construct ( pGY16 ) contained the binding site for a known activator , HilA , responsible for regulation of various virulence genes including invF ( Lostroh et al. , 2000 ) .	13	3.2. MAPPING DNA REGIONS NECESSARY FOR TRANSCRIPTION MODULATION BY RIFAMPICIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	23419780	2	ver/dev	In the case of the invF promoter , the original library reporter construct contained the binding site for HilA , responsible for regulation of invF .	139	In the case of the invF promoter ( Fig. 1C ) , the original library reporter construct ( pGY16 ) contained the binding site for a known activator , HilA , responsible for regulation of various virulence genes including invF ( Lostroh et al. , 2000 ) .	13	3.2. MAPPING DNA REGIONS NECESSARY FOR TRANSCRIPTION MODULATION BY RIFAMPICIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	23419780	2	ver/dev	In the case of the invF promoter , the original library reporter construct contained the binding site for HilA , responsible for regulation of various virulence genes .	139	In the case of the invF promoter ( Fig. 1C ) , the original library reporter construct ( pGY16 ) contained the binding site for a known activator , HilA , responsible for regulation of various virulence genes including invF ( Lostroh et al. , 2000 ) .	13	3.2. MAPPING DNA REGIONS NECESSARY FOR TRANSCRIPTION MODULATION BY RIFAMPICIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	26662614	1	ver/dev	The invF gene is regulated by the HilA protein .	194	The invF gene is regulated by the HilA protein , which is encoded by a gene of the hil operon , SPI-1 .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	28575106	5	att	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	167	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	8	THE GENE LOIA IS THE VIRULENCE DETERMINANT IN SPI-14	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	29761161	1	ver/dev	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of effector genes .	226	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of its downstream genes , such as the SPI-1 apparatus genes prg and org , inv and spa operon genes , and effector genes .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	29761161	1	ver/dev	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of its downstream genes .	226	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of its downstream genes , such as the SPI-1 apparatus genes prg and org , inv and spa operon genes , and effector genes .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	29761161	1	ver/dev	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of such as spa operon genes .	226	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of its downstream genes , such as the SPI-1 apparatus genes prg and org , inv and spa operon genes , and effector genes .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	regulator	29761161	1	ver/dev	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of such as the SPI-1 apparatus genes prg and org , inv .	226	HilA , the key regulator of SPI-1 , combined with the promoters of AraC-like regulator genes invF and sicA , directly activates the transcription of its downstream genes , such as the SPI-1 apparatus genes prg and org , inv and spa operon genes , and effector genes .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	29857034	42	ver/dev	Additionally , HilA can bind to specific sequences in the promoter of invF , a transcriptional regulator .	462	Additionally , HilA can bind to specific sequences in the promoter of invF , a transcriptional regulator , which is necessary for the expression of a sub-group of genes related to invasion [ 48 ] .	29	4. DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilA	gene	invF	regulator	32316180	4	ver/dev	HilA binds to the invF promoters , triggering the activation of T3SE genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	32316180	4	ver/dev	HilA binds to the invF promoters , triggering the activation of T3SS genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	regulator	32323733	1	ver/dev	invF mRNA levels _ regulated by HilA	275	In addition , invF mRNA levels , regulated by HilA and Hild , were significantly downregulated in KST0555 compared with in WT , which explains why invF-dependent sipBCDA mRNA expression levels were reduced by ~ 80 % in KST0555 compared with in WT ( P < 0.001 ; Fig. 4D ) .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	mdtABC	regulator	17919284	1	att	Microarray analysis of chemostat-cultured E. coli cells demonstrated that the RpoS-controlled mdtABC operon is upregulated in response to zinc excess ( Lee et al. , 2005 ) .	291	Microarray analysis of chemostat-cultured E. coli cells demonstrated that the RpoS-controlled mdtABC operon is upregulated in response to zinc excess ( Lee et al. , 2005 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	yciG	repressor	30682134	23	ver/dev	In mLPM , CsrA repressed translation of yciG .	241	In mLPM , CsrA repressed translation of yciG , which encodes a protein of unknown function that contributes strongly to Salmonella survival under acidic conditions [ 84 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	yhjH	repressor	25153529	3	ver/dev	yhjH inhibit expression of CsgD .	130	The GGDEF/EAL domain protein STM1703 ( yciR ) and GGDEF domain proteins STM3611 ( yhjH ) and STM4264 ( yjcC ) each inhibit expression of CsgD and hence rdar morphotype development [ 57 ] .	8	GGDEF/EAL DOMAIN PROTEINS AND RDAR MORPHOTYPE DEVELOPMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilD	regulator	16045614	43	ver/dev	Our model suggests that SirA could control expression of hilD by regulating the expression of a single regulator .	243	Our model ( Fig. 1 ) suggests that SirA could control expression of hilC , hilD and rtsA by either independently activating each gene or by regulating the expression of a single regulator .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SirA	gene	hilD	regulator	16045614	43	ver/dev	Our model suggests that SirA could control expression of hilD by either independently activating each gene .	243	Our model ( Fig. 1 ) suggests that SirA could control expression of hilC , hilD and rtsA by either independently activating each gene or by regulating the expression of a single regulator .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SirA	gene	hilD	regulator	16045614	50	ver/dev	SirA apparently controls hilD at the level of the mRNA ; overproduction of SirA increased hilD expression in a HilD-independent fashion .	295	SirA apparently controls hilD at the level of the mRNA ; overproduction of SirA increased hilD expression in a HilD-independent fashion .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SirA	gene	hilD	regulator	16045614	79	ver/dev	This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds the hilD .	550	This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both the hilC and hilA , but not the hilD , promoters ( Teplitski et al. , 2003 ) .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilD	regulator	17208038	20	ver/dev	Conversely , previously published gel-shift data suggested that SirA is able to bind to that of hilD .	121	Conversely , previously published gel-shift data [ 44 ] suggested that SirA is able to bind to the promoters of hilC and hilA , but not to that of hilD .	8	BARA/SIRA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	metE	repressor	31479952	0	ver/dev	In pr reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE levels in the rich media .	17	In an anaerobic environment , the metE : : lacZ ( pr ) fusion gene and reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE + mRNA levels in the rich media .	0	Unknown	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
FNR	gene	metE	repressor	31479952	0	ver/dev	In pr fusion gene identified that FnrS and/or FNR negatively regulate metE levels in the rich media .	17	In an anaerobic environment , the metE : : lacZ ( pr ) fusion gene and reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE + mRNA levels in the rich media .	0	Unknown	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
FNR	gene	metE	repressor	31479952	0	ver/dev	In lacZ reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE levels in the rich media .	17	In an anaerobic environment , the metE : : lacZ ( pr ) fusion gene and reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE + mRNA levels in the rich media .	0	Unknown	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
FNR	gene	metE	repressor	31479952	0	ver/dev	In lacZ fusion gene identified that FnrS and/or FNR negatively regulate metE levels in the rich media .	17	In an anaerobic environment , the metE : : lacZ ( pr ) fusion gene and reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE + mRNA levels in the rich media .	0	Unknown	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
PhoP	gene	macA	regulator	16359323	3	ver/dev	In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	regulator	16359323	3	ver/dev	In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	regulator	16359323	3	ver/dev	In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	regulator	16359323	3	ver/dev	In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .	339	In low Mg2 + environments , PhoP binds to the intergenic region between the macA and the somA genes , resulting in downregulation of macAB and expression of somA .	13	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	regulator	19230852	10	ver/dev	PhoP binds to the upstream region of the macA gene , resulting in regulation of macAB .	349	PhoP binds to the upstream region of the macA gene , resulting in regulation of macAB .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	macA	regulator	19230852	10	ver/dev	PhoP binds to the upstream region of the macA gene , resulting in regulation of macAB .	349	PhoP binds to the upstream region of the macA gene , resulting in regulation of macAB .	9	6. REGULATION OF DRUG EFFLUX PUMPS IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	hilA	repressor	16905537	8	ver/dev	The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both relA spoT strain , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of Lrp was not due to repression by these of a hilA-lacZ fusion in relA spoT strains .	185	The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both the wild type and relA spoT strain , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of Dps , Lrp , and RtsA/B on the expression in the relA spoT strain was not due to repression by these of a hilA-lacZ fusion in the wild type and relA spoT strains .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus;Leiostomus xanthurus;Leiostomus xanthurus	0	L2	SPEC	Investigation	NEG	Other	Level 1
Lrp	gene	hilA	repressor	16905537	8	ver/dev	The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both the wild type , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of Lrp was not due to repression by these of a hilA-lacZ fusion in the wild types .	185	The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both the wild type and relA spoT strain , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of Dps , Lrp , and RtsA/B on the expression in the relA spoT strain was not due to repression by these of a hilA-lacZ fusion in the wild type and relA spoT strains .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus	0	L2	SPEC	Investigation	NEG	Other	Level 1
Lrp	gene	hilA	repressor	19074398	35	ver/dev	Lrp tightly represses hilA expression .	498	Lrp binds strongly to PhilA and tightly represses hilA expression .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	hilA	repressor	19074398	44	ver/dev	It is possible that Lrp acts as a master repressor for the expression of hilA .	511	It is possible that Lrp precedes other regulators and acts as a master repressor for the expression of hilA .	6	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Lrp	gene	hilA	repressor	22291968	0	ver/dev	For instance , Lrp , reduces SPI-1 expression by repressing transcription of hilA .	42	For instance , the leucine-responsive regulatory protein , Lrp , reduces SPI-1 expression by repressing transcription of hilA and invF [ 20 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12068808	6	ver/dev	In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress , mediating the reciprocal osmotic control of ompF .	69	In E. coli , OmpR is clearly involved in the cellular response to osmotic stress , mediating the reciprocal osmotic control of ompC and ompF ( Hall and Silhavy , 1981 ; Slauch and Silhavy , 1989 ; Tate et al. , 1988 ; Lan and Igo , 1998 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	regulator	12068808	45	ver/dev	Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompF is not clearly understood .	233	Phosphorylation of OmpR induces a conformational change in the protein ( Kenney et al. , 1995 ) , but how this change influ-ences OmpR control of ompC and ompF is not clearly understood ( Head et al. , 1998 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	regulator	12068808	61	ver/dev	Harlocker , Inouye , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	457	Harlocker , S.L. , Bergstrom , L. , and Inouye , M. ( 1995 ) Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12068808	61	ver/dev	Harlocker , S.L. , Bergstrom , L. , , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	457	Harlocker , S.L. , Bergstrom , L. , and Inouye , M. ( 1995 ) Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12080060	6	ver/dev	In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress , mediating the reciprocal osmotic control of ompF .	69	In E. coli , OmpR is clearly involved in the cellular response to osmotic stress , mediating the reciprocal osmotic control of ompC and ompF ( Hall and Silhavy , 1981 ; Slauch and Silhavy , 1989 ; Tate et al. , 1988 ; Lan and Igo , 1998 ) .	6	ACID, BUT NOT OSMOTIC, STRESS INDUCES OMPR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	regulator	12080060	45	ver/dev	Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompF is not clearly understood .	233	Phosphorylation of OmpR induces a conformational change in the protein ( Kenney et al. , 1995 ) , but how this change influ-ences OmpR control of ompC and ompF is not clearly understood ( Head et al. , 1998 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	regulator	12080060	61	ver/dev	Harlocker , Inouye , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	457	Harlocker , S.L. , Bergstrom , L. , and Inouye , M. ( 1995 ) Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12080060	61	ver/dev	Harlocker , S.L. , Bergstrom , L. , , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	457	Harlocker , S.L. , Bergstrom , L. , and Inouye , M. ( 1995 ) Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12753201	51	ver/dev	Harlocker , Inouye , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	414	Harlocker , S.L. , Bergstrom , L. , and Inouye , M. ( 1995 ) Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12753201	51	ver/dev	Harlocker , S.L. , Bergstrom , L. , , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	414	Harlocker , S.L. , Bergstrom , L. , and Inouye , M. ( 1995 ) Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12753201	57	ver/dev	The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner .	461	Rampersaud , A. , Harlocker , S.L. , and Inouye , M. ( 1994 ) The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	12753201	57	ver/dev	The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner .	461	Rampersaud , A. , Harlocker , S.L. , and Inouye , M. ( 1994 ) The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	15126450	5	ver/dev	Expression of ompF genes in S. enterica serovar Typhi is under the control of OmpR .	23	Expression of the ompC and ompF genes in S. enterica serovar Typhi is under the control of EnvZ and OmpR , a two-compo-nent signal transduction system encoded by the ompB ( ompR envZ ) locus .	2	MAIN	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	regulator	15126450	34	ver/dev	Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	445	Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	21	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	16339942	27	ver/dev	Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	477	Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .	21	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	18361683	1	ver/dev	The two-component regulatory system OmpR = EnvZ regulates the porin genes ompF to osmolarity changes in Salmonella .	257	The two-component regulatory system OmpR = EnvZ regulates the porin genes ompF and ompC in response to osmolarity changes in Salmonella ( Mills et al. , 1998 ) .	12	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	19759044	4	ver/dev	Transcription regulation of ompF by OmpR .	646	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	27	290–2.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	24720747	4	ver/dev	These results support the model where the LtrR protein directly induces ompR expression , upon which OmpR binds to the regulatory region of ompF to induce their synthesis in S. Typhi IMSS-1 .	100	These results support the model where the LtrR protein directly induces ompR expression , upon which OmpR binds to the regulatory region of ompC and ompF to induce their synthesis in S. Typhi IMSS-1 .	5	DETERMINATION OF THE LTRR-OMPR-OMPC-OMPF CASCADE FOR PORIN SYNTHESIS IN S. TYPHI	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompF	regulator	25875623	0	att	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .	18	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ompF	regulator	28553268	14	ver/dev	Transcription regulation of ompF by OmpR .	2120	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	34	ACKNOWLEDGMENTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-2 genes by SsrB resembles the reciprocal control of ompF transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-1 genes by SsrB resembles the reciprocal control of ompF transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	30524381	22	att	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( a SPI-2 structural gene ) .	271	Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( a SPI-2 structural gene ) .	20	OMPR IS AN IMPORTANT GLOBAL REGULATOR OF THE BACTERIAL RESPONSE TO	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ompF	regulator	30524381	27	att	Three of these were ompF , ompC and tppB , i.e. , known OmpR-regulated genes .	295	Three of these were ompF , ompC and tppB , i.e. , known OmpR-regulated genes .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	gene	ompF	regulator	33751923	31	ver/dev	Transcription regulation of ompF by OmpR .	2518	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	204	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	regulator	33854491	20	ver/dev	Transcription regulation of ompF by OmpR .	582	Transcription regulation of ompF and ompC by a single transcription factor , OmpR .	25	THIS WORK WAS SUPPORTED BY GRANTS FROM THE DIRECCIÓN GENERAL AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB.2021.657404/ DE ASUNTOS DEL PERSONAL ACADÉMICO, DGAPA/UNAM (IN203618 FULL#SUPPLEMENTARY-MATERIAL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	hilD	activator	11123690	22	ver/dev	However , if Fis regulates hilD , it might be expected that activation of the hilD promoter in pJB1 could not occur in the fis background .	157	However , if Fis regulates hilD , it might be expected that activation of the hilD promoter in pJB1 could not occur in the fis background .	9	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
AraC	gene	invF	regulator	11705895	0	ver/dev	invF encodes a transcriptional regulator of the AraC family	29	HilA-regulated genes include invF , which encodes a transcriptional regulator of the AraC family and is located within SPI-1 ( 37 ) , and the components of the secretion machinery ( 3 , 4 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	invF	regulator	12453229	6	ver/dev	Within SPI-1 , HilA controls invF , which encodes a transcriptional regulator of the AraC family .	65	Within SPI-1 , HilA controls invF , which encodes a transcriptional regulator of the AraC family ( Kaniga et al. , 1994 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	parE	repressor	28874380	3	ver/dev	These data indicate that CRP represses expression of parE .	147	These data indicate that CRP represses expression of parC and parE and suggest that the sustained expression of parCE in SL1344 : Δcrp could alter the supercoiling state of DNA in Δcrp mutant cells .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	hfq	activator	22336758	15	ver/dev	Consequently , we conclude that besides upregulation of RpoS , other Hfq-dependent factor are required to restore rdar morphotype expression in the hfq mutant of UMR1 .	130	Consequently , we conclude that besides upregulation of RpoS , other Hfq-dependent factor ( s ) are required to restore csgD and rdar morphotype expression in the hfq mutant of UMR1 .	2	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CadC	gene	ompR	repressor	29214489	4	ver/dev	These findings reveal a previously un recognized regulatory mechanism by which CadC represses autoinduction of the ompR gene .	36	These findings reveal a previously un recognized regulatory mechanism by which CadC represses autoinduction of the ompR gene .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CadC	gene	ompR	repressor	29214489	6	ver/dev	S. enterica serovar Typhimurium CadC is known to act as a repressor of ompR transcription during acid adaptation .	96	S. enterica serovar Typhimurium CadC is known to act as a repressor of ompR transcription during acid adaptation ( Lee et al. , 2007 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Fact	OTHER	Other	Level 3
CadC	gene	ompR	repressor	29214489	9	ver/dev	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to RNA polymerase .	107	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase .	13	CADC INTERACTS DIRECTLY WITH OMPR	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	ompR	repressor	29214489	9	ver/dev	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter .	107	Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase .	13	CADC INTERACTS DIRECTLY WITH OMPR	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	ompR	repressor	29214489	12	ver/dev	Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of motility , at least during acid adaptation .	134	Since our data clearly demonstrated CadCmediated repression of ompR gene expression ( Fig. 1 ) , we speculated that CadC may be involved in the control of fla-gellation and motility , at least during acid adaptation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	ompR	repressor	29214489	12	ver/dev	Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of fla-gellation , at least during acid adaptation .	134	Since our data clearly demonstrated CadCmediated repression of ompR gene expression ( Fig. 1 ) , we speculated that CadC may be involved in the control of fla-gellation and motility , at least during acid adaptation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	ompR	repressor	29214489	16	ver/dev	a possible mechanism _ underlying the CadC-mediated repression of ompR autoinduction	168	Our data demonstrate a specific interaction between DNA-binding transcription factors , CadC and OmpR , and suggest that this direct interaction may be a possible mechanism underlying the CadC-mediated repression of ompR autoinduction .	14	CONCLUSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	srfA	regulator	16113260	0	att	srfA was identified in a screen for SsrB-regulated genes , although its function inside of macrophage cells is not known ( 76 ) .	175	srfA was identified in a screen for SsrB-regulated genes , although its function inside of macrophage cells is not known ( 76 ) .	4	RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
OxyR	gene	mntH	activator	24596096	4	ver/dev	Besides the negative regulation , mntH transcription is activated through the H2O2-sensing regulator OxyR .	51	Besides the negative regulation , mntH transcription is activated through the H2O2-sensing regulator OxyR , which binds to the OxyR-binding site in the promoter ( 11 , 19 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	lacZ	regulator	18389060	1	ver/dev	As demonstrated in Figure 6A , zirTS : : lacZ expression was found to be about 2.3 fold higher in the DoxyR background than P ,0.0001 , suggesting that OxyR is involved in the regulation of these genes .	210	As demonstrated in Figure 6A , zirTS : : lacZ expression was found to be about 2.3 fold higher in the DoxyR background than the wild-type strain ( P ,0.0001 ) , suggesting that OxyR is involved in the regulation of these genes .	8	ZIRS AND ZIRT COMPOSE A NOVEL SECRETION SYSTEM IN SALMONELLA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	lacZ	regulator	18389060	1	ver/dev	As demonstrated in Figure 6A , zirTS : : lacZ expression was found to be about 2.3 fold higher in the DoxyR background than the wild-type strain , suggesting that OxyR is involved in the regulation of these genes .	210	As demonstrated in Figure 6A , zirTS : : lacZ expression was found to be about 2.3 fold higher in the DoxyR background than the wild-type strain ( P ,0.0001 ) , suggesting that OxyR is involved in the regulation of these genes .	8	ZIRS AND ZIRT COMPOSE A NOVEL SECRETION SYSTEM IN SALMONELLA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	gtgE	activator	17379730	5	ver/dev	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA .	362	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA , which is also involved in the regulation of virulence genes such as mig-14 , sopD2 and virK ( Brumell et al. , 2003 ; Ho et al. , 2002 ; Navarre et al. , 2005 ) .	14	GIFSY-1 AND GIFSY-2 PROPHAGES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Sigma28	gene	flgH	activator	9765570	0	att	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	10998173	1	ver/dev	OmpR , in response to a drop in pH , induces the expression of ssrA ± ssr .	365	OmpR , in response to a drop in pH , induces the expression of ssrA ± ssrB , which in turn serve as transcriptional regulators of SPI2 expression ( Lee et al. , 2000 ) .	14	SALMONELLA DISRUPTION OF THE EPITHELIAL CELL ENDOCYTIC SYSTEM IS MEDIATED BY A SUBSET OF SPI2-TRANSLOCATED PROTEINS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	activator	12753201	29	att	The b-galac-tosidase activity of ssrA -- lacZ in J774 mouse macrophages ( from Fig. 2A ) is also included in the rightmost columns ( n = 6 ) for a comparison of OmpR-dependent ssrA activation observed in Salmonella-infected macrophages but not in Salmonella cultures in-vitro .	195	The b-galac-tosidase activity of ssrA -- lacZ in J774 mouse macrophages ( from Fig. 2A ) is also included in the rightmost columns ( n = 6 ) for a comparison of OmpR-dependent ssrA activation observed in Salmonella-infected macrophages but not in Salmonella cultures in vitro .	9	PHOSPHORYLATION OF OMPR INCREASES ITS AFFINITY FOR SSRA	Mus musculus;Salmonella;Salmonella;Salmonella	0.5	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ssrA	activator	12753201	29	att	The b-galac-tosidase activity of ssrA -- lacZ in J774 mouse macrophages ( from Fig. 2A ) is also included in the rightmost columns ( n = 6 ) for a comparison of OmpR-dependent ssrA activation observed in Salmonella-infected macrophages but not in Salmonella cultures in-vitro .	195	The b-galac-tosidase activity of ssrA -- lacZ in J774 mouse macrophages ( from Fig. 2A ) is also included in the rightmost columns ( n = 6 ) for a comparison of OmpR-dependent ssrA activation observed in Salmonella-infected macrophages but not in Salmonella cultures in vitro .	9	PHOSPHORYLATION OF OMPR INCREASES ITS AFFINITY FOR SSRA	Mus musculus;Salmonella;Salmonella;Salmonella	0.5	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ssrA	activator	12753201	7	att	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	73	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	2	ver/dev	A previous study discovered that transcription of SPI-2 genes , was induced in macrophages , whereas a more recent study reported that OmpR was the regulator responsible for activation of ssrA .	46	A previous study discovered that transcription of SPI-2 genes , including ssrA and ssaH , was induced in macrophages ( Cirillo et al. , 1998 ) , whereas a more recent study reported that OmpR was the regulator responsible for activation of ssrA ( Lee et al. , 2000 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	2	ver/dev	A previous study discovered that ssaH , was induced in macrophages , whereas a more recent study reported that OmpR was the regulator responsible for activation of ssrA .	46	A previous study discovered that transcription of SPI-2 genes , including ssrA and ssaH , was induced in macrophages ( Cirillo et al. , 1998 ) , whereas a more recent study reported that OmpR was the regulator responsible for activation of ssrA ( Lee et al. , 2000 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	2	ver/dev	A previous study discovered that ssrA , was induced in macrophages , whereas a more recent study reported that OmpR was the regulator responsible for activation of ssrA .	46	A previous study discovered that transcription of SPI-2 genes , including ssrA and ssaH , was induced in macrophages ( Cirillo et al. , 1998 ) , whereas a more recent study reported that OmpR was the regulator responsible for activation of ssrA ( Lee et al. , 2000 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	7	ver/dev	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	73	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	8	ver/dev	OmpR appears to function as an activator of ssrA , as reported previously	75	Thus , OmpR appears to function as an activator of ssrA , as reported previously ( Lee et al. , 2000 ) , and SsrB also appears to activate ssrA , although the mechanism of regulation remains to be determined .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssrA	activator	12753201	10	ver/dev	As we observed with OmpR activation of ssrA , activation of ssrB by OmpR also depends upon the kinase EnvZ .	80	As we observed with OmpR activation of ssrA , activation of ssrB by OmpR also depends upon the kinase EnvZ .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	11	ver/dev	L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	93	1134 X. Feng , R. Oropeza and L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrA	activator	12753201	11	ver/dev	R. Oropeza suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	93	1134 X. Feng , R. Oropeza and L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrA	activator	12753201	11	ver/dev	1134 X. Feng suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	93	1134 X. Feng , R. Oropeza and L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrA	activator	12753201	20	ver/dev	Is ssrA activation by OmpR ?	153	Is ssrA activation by OmpR osmoregulated ?	7	DNASE I FOOTPRINTING WITH OMPR AND OMPR-P AT THE SSRA/SSRB LOCUS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	24	ver/dev	In contrast to our observations in-vitro , in Salmonella-infected macrophages , the activation of ssrA was substantially dependent on OmpR .	160	In contrast to our observations in vitro , in Salmonella-infected macrophages , the activation of ssrA was substantially dependent on OmpR ( > 80 % ; Fig. 2A and Fig. 7 , columns 11 -- 12 ) .	7	DNASE I FOOTPRINTING WITH OMPR AND OMPR-P AT THE SSRA/SSRB LOCUS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	12753201	40	ver/dev	Given the location of the OmpR binding sites , we would predict that , at low-osmolarity , the ssrA-1 binding site upstream of the transcriptional start site would be occupied , leading to activation of ssrA .	233	Given the location of the OmpR binding sites reported in the present study , we would predict that , at low osmolarity , the ssrA-1 binding site ( s ) upstream of the transcriptional start site would be occupied , leading to activation of ssrA ( see Fig. 1 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
OmpR	gene	ssrA	activator	12753201	42	ver/dev	The activation of ssrA by OmpR reported in the previous study could result from differences between 14028s .	237	The activation of ssrA by OmpR and its osmoregulated expression in vitro reported in the previous study could result from differences between Salmo-nella strains SL1344 and 14028s ( Lee et al. , 2000 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrA	activator	12753201	42	ver/dev	The activation of ssrA by OmpR reported in the previous study could result from differences between Salmo-nella strains SL1344 .	237	The activation of ssrA by OmpR and its osmoregulated expression in vitro reported in the previous study could result from differences between Salmo-nella strains SL1344 and 14028s ( Lee et al. , 2000 ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	0.5	L1	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ssrA	activator	12753201	43	ver/dev	It is of interest , however , that OmpR activation of ssrA in the present study was only observed in Salmonella-infected macrophages and not in Salmonella cultures in-vitro .	238	It is of interest , however , that OmpR activation of ssrA in the present study was only observed in Salmonella-infected macrophages ( Figs 2A and 7 ) and not in Salmonella cultures in vitro .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	Salmonella;Salmonella;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	ssrA	activator	12753201	44	ver/dev	How does OmpR activate expression of ssrA ?	240	How does OmpR activate expression of ssrA and ssrB ?	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ssrA	activator	15491370	3	ver/dev	More recently , it was shown that OmpR was responsible for the activation of ssrA .	35	More recently , it was shown that OmpR was responsible for the activation of ssrA ( Lee et al. , 2000 ; Feng et al. , 2003 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	26880544	1	ver/dev	Under low osmolality , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	26880544	1	ver/dev	Under acidic pH , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	33751923	10	ver/dev	In vitro studies demonstrated that OmpR P stimulates expression of ssrA , whereas PhoP P activates ssrB .	412	In vitro studies demonstrated that OmpR P stimulates expression of ssrA , whereas PhoP P activates ssrB ( Liew et al. 2019 ) .	10	SSRAB	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssrA	activator	34202800	20	ver/dev	As a result , OmpR activate transcription of ssrA genes .	390	As a result , OmpR and PhoP activate transcription of ssrA and ssrB genes , leading to the formation of SsrA and SsrB .	11	3.3.4. THE ENVZ/OMPR SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	11755416	21	ver/dev	H-NS may directly repress PhilA because repression of hilA in E. coli requires both the upstream .	261	H-NS may bind to and directly repress PhilA because repression of hilA in E. coli requires both the upstream repressing sequences and H-NS .	8	6. P AS A LOCUS OF SIGNAL INTEGRATION HILA	Escherichia coli	0	L1	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	hilA	repressor	11755416	23	ver/dev	Thus , H-NS appears to be important for hilA repression by osmolarity .	263	Thus , H-NS appears to be important for hilA repression by osmolarity but not important for repression by oxygen .	8	6. P AS A LOCUS OF SIGNAL INTEGRATION HILA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	19074398	37	ver/dev	The small nucleoid-bind-ing protein H-NS represses hilA in response to low-osmolarity .	501	The small nucleoid-bind-ing protein H-NS represses hilA in response to low osmolarity ( 84 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	21680637	21	ver/dev	In exponential phase cells , the results provided evidence that H-NS repress hilA expression .	209	In exponential phase cells , the results obtained provided evidence that H-NS and Hha repress hilA expression .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HNS	gene	hilA	repressor	21680637	44	ver/dev	Interestingly , a partial inhibition of H-NS activity in cells resulted in a signi-ficant induction of hilA expression , up to about 50 % of the expression .	267	Interestingly , a partial inhibition of H-NS activity in cells lacking IHF resulted in a signi-ficant induction of hilA expression , up to about 50 % of the expression obtained in the wt cells ( Table 2 ) .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	21680637	54	ver/dev	The increase in the degree of stimulation in the presence of H-NS indicates that in-vitro , IHF can alleviate H-NS-mediated repression of hilA transcription .	285	The increase in the degree of stimulation in the presence of H-NS indicates that in vitro , IHF can alleviate H-NS-mediated repression of hilA transcription .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	hilA	repressor	21680637	58	ver/dev	Our work shows that H-NS repress hilA under account for SPI1 gene silencing .	316	Our work shows that H-NS and Hha repress hilA under a set of well-defined environmental and physiological conditions and consequently account for SPI1 gene silencing .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	21680637	58	ver/dev	Our work shows that H-NS repress hilA under a set of physiological conditions .	316	Our work shows that H-NS and Hha repress hilA under a set of well-defined environmental and physiological conditions and consequently account for SPI1 gene silencing .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	21680637	58	ver/dev	Our work shows that H-NS repress hilA under a set of well-defined environmental .	316	Our work shows that H-NS and Hha repress hilA under a set of well-defined environmental and physiological conditions and consequently account for SPI1 gene silencing .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilA	repressor	21680637	65	ver/dev	Finally , in-vitro-transcription data show that IHF interferes with H-NS repression of hilA .	346	Finally , in vitro transcription data show that IHF interferes with H-NS repression of hilA .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	22291968	1	ver/dev	The nucleoid-associated proteins H-NS and Hha repress hilA expression by direct binding to regions located downstream the hilA promoter .	43	The nucleoid-associated proteins H-NS and Hha repress hilA expression by direct binding to regions located upstream and downstream the hilA promoter [ 21,22 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	22291968	1	ver/dev	The nucleoid-associated proteins H-NS and Hha repress hilA expression by direct binding to regions located upstream the hilA promoter .	43	The nucleoid-associated proteins H-NS and Hha repress hilA expression by direct binding to regions located upstream and downstream the hilA promoter [ 21,22 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	25135218	70	ver/dev	How HilD counteracts the H-NS-mediated repression of hilA	213	How HilD counteracts the H-NS-mediated repression of hilA and rtsA and whether HilD acts as an antagonist of H-NS with its other target genes remain to be determined .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	31182495	46	ver/dev	H-NS represses hilA expression through repression of HilD/HilC / RtsA .	212	H-NS represses hilA expression directly and through repression of HilD/HilC / RtsA .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	31182495	46	ver/dev	H-NS represses hilA expression directly .	212	H-NS represses hilA expression directly and through repression of HilD/HilC / RtsA .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	31182495	53	ver/dev	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though RtsA are still required for full stimulation of the polymerase .	227	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD , HilC , and RtsA are still required for full stimulation of the polymerase .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	31182495	53	ver/dev	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilC are still required for full stimulation of the polymerase .	227	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD , HilC , and RtsA are still required for full stimulation of the polymerase .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	31182495	53	ver/dev	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD are still required for full stimulation of the polymerase .	227	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD , HilC , and RtsA are still required for full stimulation of the polymerase .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	repressor	33119619	1	ver/dev	H-NS represses the expression mainly by binding to the regulatory region of hilA	19	In SPI-1 , H-NS represses the expression mainly by binding to the regulatory region of hilA and derepression is exercised mainly by HilD .	7	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	repressor	33119619	12	ver/dev	As a positive control , the hilA-cat transcriptional-fusion was assessed in its derivative Δhns mutan ; H-NS represses expression of hilA .	190	As a positive control , the hilA-cat transcriptional fusion was assessed in WT E. coli and its derivative Δhns mutant ; H-NS represses expression of hilA [ 52,53 ] .	21	THE INVF/SICA COMPLEX DOES NOT ACT AS AN ANTI-HNS FACTOR ON SOPB	Felis catus	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hilA	repressor	33119619	12	ver/dev	As a positive control , the hilA-cat transcriptional-fusion was assessed in WT E. coli ; H-NS represses expression of hilA .	190	As a positive control , the hilA-cat transcriptional fusion was assessed in WT E. coli and its derivative Δhns mutant ; H-NS represses expression of hilA [ 52,53 ] .	21	THE INVF/SICA COMPLEX DOES NOT ACT AS AN ANTI-HNS FACTOR ON SOPB	Felis catus;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hilA	repressor	34424033	46	ver/dev	H-NS is known to rely on high affinity binding sites to nucleate oligomerization , lowering the binding threshold of adjacent chromosomal areas equivalent to deletions of the region deep into hilA	559	H-NS is known to rely on high affinity binding sites to nucleate oligomerization , lowering the binding threshold of adjacent chromosomal areas equivalent to deletions of the region having endpoints deep into hilA , and the fact	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
TtrR	TU	ttrBCA	activator	11274105	0	ver/dev	This insertion is upstream of the kinase domain ; it appears to cause tetrathionate-independent induction of the ttrBCA operon via TtrR , since expression requires OxrA protein .	439	This insertion is upstream of the kinase domain ; it appears to cause tetrathionate-independent induction of the ttrBCA operon via TtrR , since expression requires anaerobic conditions and OxrA protein ( Table 5 , line 8 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
TtrR	TU	ttrBCA	activator	11274105	0	ver/dev	This insertion is upstream of the kinase domain ; it appears to cause tetrathionate-independent induction of the ttrBCA operon via TtrR , since expression requires anaerobic conditions .	439	This insertion is upstream of the kinase domain ; it appears to cause tetrathionate-independent induction of the ttrBCA operon via TtrR , since expression requires anaerobic conditions and OxrA protein ( Table 5 , line 8 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
TtrR	TU	ttrBCA	activator	11274105	3	ver/dev	Activated TtrR cooperates with Fnr to positively regulate expression of the ttrBCA operon .	509	Activated TtrR cooperates with the global regulator OxrA ( Fnr ) to positively regulate expression of the ttrBCA operon .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	gipA	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	rpoN	regulator	19076233	6	att	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	138	( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .	14	INACTIVATION OF RPON INDUCES PM RESISTANCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	cse1	regulator	28270274	5	ver/dev	Although the divergently transcribed cas3 genes share a 5 cents intergenic region , we found that LeuO only control cse1 expression .	607	Although the divergently transcribed cse1 and cas3 genes share a 5 cents intergenic region , we found that LRP and LeuO only control cse1 expression .	17	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	cse1	regulator	28270274	5	ver/dev	Although the divergently transcribed cse1 genes share a 5 cents intergenic region , we found that LeuO only control cse1 expression .	607	Although the divergently transcribed cse1 and cas3 genes share a 5 cents intergenic region , we found that LRP and LeuO only control cse1 expression .	17	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	18156266	49	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	403	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	19406898	26	att	LeuO antagonizes the H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	261	LeuO antagonizes the H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	23	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	19443540	4	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	51	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	15	MAIN	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	19447191	18	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	192	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	19460824	17	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	236	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	15	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	21148209	34	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	320	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	32	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	21398529	10	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	442	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	12	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	22149171	66	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	503	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	31	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	22173828	13	att	Proc Natl Acad Sci USA 97:6640 -- 6645 De la Cruz MA , Fernández-Mora M , Guadarrama C , Flores-Valdez MA , Bustamante VH , Vázquez A , Calva E ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	213	Proc Natl Acad Sci USA 97:6640 -- 6645 De la Cruz MA , Fernández-Mora M , Guadarrama C , Flores-Valdez MA , Bustamante VH , Vázquez A , Calva E ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	22	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	22343301	38	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	391	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	26	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	22752112	26	att	Proc Natl Acad Sci USA 97:6640 -- 6645 De la Cruz MA , Fernández - Mora M , Guadarrama C , Flores-Valdez MA , Bustamante VH , Vázquez A , Calva E ( 2007 ) LeuO antagonizes H -- NS and StpA-dependent repression in Salmonella enterica ompS1 .	323	Proc Natl Acad Sci USA 97:6640 -- 6645 De la Cruz MA , Fernández - Mora M , Guadarrama C , Flores-Valdez MA , Bustamante VH , Vázquez A , Calva E ( 2007 ) LeuO antagonizes H -- NS and StpA-dependent repression in Salmonella enterica ompS1 .	20	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	22804842	31	att	De la Cruz , M.A. , Fernandez-Mora , M. , Guadarrama , C. , Flores-Valdez , M.A. , Bustamante , V.H. , Vazquez , A. , et al. ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	636	De la Cruz , M.A. , Fernandez-Mora , M. , Guadarrama , C. , Flores-Valdez , M.A. , Bustamante , V.H. , Vazquez , A. , et al. ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	25	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	23040276	6	att	[ 62 ] M.A. De la Cruz , M. Fernández - Mora , C. Guadarrama , M.A. Flores-Valdez , V.H. Bustamante , A. Vázquez , et al. , LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 , Mol .	562	[ 62 ] M.A. De la Cruz , M. Fernández - Mora , C. Guadarrama , M.A. Flores-Valdez , V.H. Bustamante , A. Vázquez , et al. , LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 , Mol .	34	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	24239962	2	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	330	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	23	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	24354910	57	att	De la Cruz , M.A. , Fernandez-Mora , M. , Guadarrama , C. , Flores-Valdez , M.A. , Bustamante , V.H. , Vazquez , A. , and Calva , E. ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	386	De la Cruz , M.A. , Fernandez-Mora , M. , Guadarrama , C. , Flores-Valdez , M.A. , Bustamante , V.H. , Vazquez , A. , and Calva , E. ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	33	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	24659766	24	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	418	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	21	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	24720747	22	att	De la Cruz , M.A. , Fernández-Mora , M. , Guadarrama , C. , Flores-Valdez , M.A. , Bustamante , V.H. , Vázquez , A. , and Calva , E. ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	480	De la Cruz , M.A. , Fernández-Mora , M. , Guadarrama , C. , Flores-Valdez , M.A. , Bustamante , V.H. , Vázquez , A. , and Calva , E. ( 2007 ) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	29	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	25566242	21	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	452	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	54	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	25916986	5	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	579	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	59	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	28270274	7	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	831	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	20	9. DELTCHEVA E, CHYLINSKI K, SHARMA CM, GONZALES K, CHAO Y ET AL. CRISPR RNA MATURATION BY TRANS-ENCODED SMALL RNA AND HOST FACTOR RNASE III. NATURE 2011;471:602–607.	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	29555922	25	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	636	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	ompS1	activator	32328049	3	att	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	744	LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1 .	42	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
RcsA	gene	rcsA	activator	15469511	0	att	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	14	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsA	activator	15469511	1	att	RcsA-dependent genes include the colanic acid cps operon and the rcsA gene , and appear to be involved primarily in the production of colanic acid capsule ( Stout and Gottesman , 1990 ; Gottesman , 1995 ; Gottesman and Stout , 1991 ; Stout , 1994 ; Ebel et al. , 1997 ) .	34	RcsA-dependent genes include the colanic acid cps operon and the rcsA gene , and appear to be involved primarily in the production of colanic acid capsule ( Stout and Gottesman , 1990 ; Gottesman , 1995 ; Gottesman and Stout , 1991 ; Stout , 1994 ; Ebel et al. , 1997 ) .	3	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsA	activator	15469511	2	att	To determine whether the restoration of wild-type virulence that resulted from inactivating the rcsB gene in the rcsC11 mutant resulted from RcsA-dependent genes , we evaluated the virulence of an rcsC11 rcsA double mutant .	63	To determine whether the restoration of wild-type virulence that resulted from inactivating the rcsB gene in the rcsC11 mutant resulted from RcsA-dependent genes , we evaluated the virulence of an rcsC11 rcsA double mutant .	6	THE REGULATORY GENE RCSA AND THE CAPSULAR	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
RcsA	gene	rcsA	activator	15469511	3	att	Because RcsA-dependent genes appear to be involved primarily in the production of colanic acid capsule ( Mou-slim et al. , 2003 ) , we investigated whether inactivation of the capsular synthesis cps genes in the rcsC11 mutant might be sufficient to restore the virulence phenotype to the rcsC11 mutant , similar to that displayed by the rcsC11 rcsA mutant .	68	Because RcsA-dependent genes appear to be involved primarily in the production of colanic acid capsule ( Mou-slim et al. , 2003 ) , we investigated whether inactivation of the capsular synthesis cps genes in the rcsC11 mutant might be sufficient to restore the virulence phenotype to the rcsC11 mutant , similar to that displayed by the rcsC11 rcsA mutant .	6	THE REGULATORY GENE RCSA AND THE CAPSULAR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsA	activator	15469511	8	att	The rcsC11 rcsA mutant was more virulent than the rcsC11 strain after intraperitoneal inoculation , but it exhibited slower mouse killing kinetics than wild-type Salmo-nella or the rcsC11 rcsB mutant ( Fig. 1 ) , indicating that the attenuation phenotype results from both RcsA-dependent and - independent genes .	219	The rcsC11 rcsA mutant was more virulent than the rcsC11 strain after intraperitoneal inoculation , but it exhibited slower mouse killing kinetics than wild-type Salmo-nella or the rcsC11 rcsB mutant ( Fig. 1 ) , indicating that the attenuation phenotype results from both RcsA-dependent and - independent genes .	10	THE GENETIC BASIS FOR THE ATTENUATION PHENOTYPE OF THE RCSC11 MUTANT	Mus musculus;Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsA	activator	27558204	0	ver/dev	To better characterize the contribution of RcsA to persistence within tomatoes , rcsA genes were deleted	53	To better characterize the contribution of RcsA and RcsB to persistence within tomatoes , rcsA and rcsB genes were deleted and the abilities of the corresponding mutants to multiply in red and green tomatoes were tested ( strains and pri-mers used to construct them are listed in Supporting Information Tables S1 and S2 ) .	7	SALMONELLA RCSA AND RCSB GENES ARE INVOLVED IN PERSISTENCE WITHIN TOMATOES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	gene	rcsA	activator	33638994	3	ver/dev	Phosphorylated RcsB can act in combination with RcsA to enhance activation of the cps operon , to activate expression of the rcsA gene .	45	Phosphorylated RcsB can act in combination with RcsA to enhance activation of the cps operon , to activate expression of the rcsA gene or to repress flhDC ( 14,16 ) .	6	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SlyA	gene	spiR	regulator	33045730	4	ver/dev	Transcription of spiR genes is regulated by SlyA .	29	Transcription of the horizontally acquired ssrB and spiR genes is regulated by several ancestral regulators , including SlyA ( 20 ) , OmpR ( 6 ) , and PhoP ( 7 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	poxB	regulator	15632439	4	att	They suggested that the difference in the CFA synthase level may be the result of different rpoS alleles , since the expression of another RpoS-regulated gene , poxB , was lower in FT1 than ZK126 ( Wang & Cronan , 1994 ) .	430	They suggested that the difference in the CFA synthase level may be the result of different rpoS alleles , since the expression of another RpoS-regulated gene , poxB , was lower in FT1 than ZK126 ( Wang & Cronan , 1994 ) .	11	DISCUSSION	Cell fusing agent virus	0	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	fliZ	repressor	32571967	10	ver/dev	Without proper assembly , flagellar regulatory systems bound to the sigma factor FliA , leading to further repression of SPI1 via decreased expression of fliZ from the FliA-dependent promoter .	216	Without proper assembly , flagellar regulatory systems are repressed by the anti-sigma factor FlgM , which remains intracellular and bound to the sigma factor FliA , leading to further repression of SPI1 via decreased expression of fliZ from the FliA-dependent promoter ( 35 , 76 , 77 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
Fis	gene	fis	activator	17784910	23	ver/dev	Expression of the fis gene was more easily induced under low-aeration conditions , confirming that other factors play a role in this low-aeration induction of the Fis protein .	388	Expression of the fis gene was more easily induced under low-aeration conditions , confirming that other factors play a role in this low-aeration induction of the Fis protein .	11	RPOS AND REPRESSION OF FIS TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompX	activator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompX	activator	18156266	19	att	Hence , the locations of two LeuO-dependent promoters ( STY3070 and ompX ) were in agreement as determined by the experimental and in silico approaches .	268	Hence , the locations of two LeuO-dependent promoters ( STY3070 and ompX ) were in agreement as determined by the experimental and in silico approaches .	5	FIG. 2	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompX	activator	18156266	30	att	Another LeuO-dependent gene reported in this work is ompX , encoding an outer membrane protein which increases E E activity when multiple copies are present ( 32 , 33 ) and which also appears to be expressed under different pH conditions ( 51 ) .	321	Another LeuO-dependent gene reported in this work is ompX , encoding an outer membrane protein which increases E E activity when multiple copies are present ( 32 , 33 ) and which also appears to be expressed under different pH conditions ( 51 ) .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
AcrR	gene	acrA	repressor	28380031	0	ver/dev	the local repressor AcrR inhibits the transcription of acrA	340	AcrAB is also regulated by the local repressor AcrR , which inhibits the transcription of acrA and acrB , and the mutation of acrR contributes to the overexpression of AcrAB and increases bacterial resistance to multiple drugs [ 21 , 22 ] .	27	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	marA	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SirA	gene	sopB	activator	11244064	13	att	SirA-dependent regulation of sopB and flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar containing kanamycin and X-Gal at 37 °C .	286	SirA-dependent regulation of sopB and flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar containing kanamycin and X-Gal at 37 °C .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	activator	11244064	5	att	SirA-dependent regulation of serovar Typhimurium sopB and flagellar regulon components during chemotaxing through three different types of 0.3 % motility agar plates ( T , TS , and LB ) at 37 °C .	101	SirA-dependent regulation of serovar Typhimurium sopB and flagellar regulon components during chemotaxing through three different types of 0.3 % motility agar plates ( T , TS , and LB ) at 37 °C .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	activator	11244064	6	att	SirA-dependent regulation of serovar Typhimurium sopB and flagellar regulon promoter fusions in shaking liquid medium .	184	SirA-dependent regulation of serovar Typhimurium sopB and flagellar regulon promoter fusions in shaking liquid medium .	6	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	activator	11244064	7	ver/dev	SirA activates the virulence gene sopB in motility agar .	209	SirA activates the virulence gene sopB in motility agar .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	activator	11244064	8	ver/dev	that SirA positively regulates sopB regardless of growth medium	216	This dem-onstrates that SirA positively regulates sopB regardless of growth medium and that the repressing effect of SirA is restricted to the flagellar fusions .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	sopB	activator	11244064	9	ver/dev	This fivefold activation of sopB is similar in magnitude to previous reports on the activation of secreted effector genes by SirA .	230	This fivefold activation of sopB is similar in magnitude to previous reports on the activation of secreted effector genes by SirA ( 2 , 32 , 44 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	sopB	activator	11244064	9	ver/dev	This fivefold activation of sopB is similar in magnitude to previous reports on the activation of secreted effector genes by SirA .	230	This fivefold activation of sopB is similar in magnitude to previous reports on the activation of secreted effector genes by SirA ( 2 , 32 , 44 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	sopB	activator	11244064	11	ver/dev	Therefore , under these conditions , the activity of SirA appears to be minimal , although the magnitude of repression of the flagellar genes mirrors the magnitude of activation of sopB .	249	Therefore , under these conditions , the activity of SirA appears to be minimal , although the magnitude of repression of the flagellar genes mirrors the magnitude of activation of sopB .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yciF	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , yciF are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilC	gene	dapZ	regulator	27601571	33	att	Moreover , while we did not detect a HilC-regulated transfrag for DapZ using Rockhopper , we did detect strong binding of HilC upstream of dapZ ( see Fig .	295	Moreover , while we did not detect a HilC-regulated transfrag for DapZ using Rockhopper , we did detect strong binding of HilC upstream of dapZ ( see Fig .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilC	gene	dapZ	regulator	27601571	33	ver/dev	Moreover , while we did not detect a HilC-regulated transfrag for DapZ , we did detect strong binding of HilC upstream of dapZ ( see Fig .	295	Moreover , while we did not detect a HilC-regulated transfrag for DapZ using Rockhopper , we did detect strong binding of HilC upstream of dapZ ( see Fig .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
LsrR	gene	invF	repressor	27920756	1	ver/dev	Inactivation of LsrR by the presence of phosphorylated AI-2 allows invF , sicA , sopB , sopE and fliC , fliD gene transcription .	84	Inactivation of LsrR by the presence of phosphorylated AI-2 allows SPI-1 ( invF , sicA , sopB , sopE ) and flagella ( fliC , fliD ) gene transcription ( Choi et al. , 2012 ) .	5	SALMONELLA TYPHIMURIUM AUTOINDUCERS AND THEIR ROLE IN VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LsrR	gene	invF	repressor	27920756	1	ver/dev	Inactivation of LsrR by the presence of phosphorylated AI-2 allows invF , sicA , sopB , sopE and flagella gene transcription .	84	Inactivation of LsrR by the presence of phosphorylated AI-2 allows SPI-1 ( invF , sicA , sopB , sopE ) and flagella ( fliC , fliD ) gene transcription ( Choi et al. , 2012 ) .	5	SALMONELLA TYPHIMURIUM AUTOINDUCERS AND THEIR ROLE IN VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	dinB	regulator	20421601	14	ver/dev	Escherichia coli where inactivation of RpoS reduced Pol IV protein levels three - to fivefold in the wild-type background , indicating that regulation of dinB expression is different in these two species	163	These results are different from those observed in Escherichia coli ( Layton and Foster 2003 ) , where inactivation of RpoS reduced Pol IV protein levels three - to fivefold in the wild-type background , indicating that regulation of dinB expression is different in these two species .	4	RESULTS	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	micF	activator	11796342	1	ver/dev	Repression of ompF by MarA is thought to occur indirectly through its activation of micF .	227	Repression of ompF by MarA is thought to occur indirectly through its activation of micF , whose RNA product interacts with ompF mRNA to prevent translation ( 4 , 18 ) .	5	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
MarA	gene	micF	activator	20237076	5	ver/dev	However , micF are also induced by stress signals in additional ways , it was suggested that S. enterica to salicylate activates MarA through binding to its repressor , MarR .	35	However , micF and acrAB are also induced by stress signals in additional ways that are not dependent on the marRAB system .17 Interestingly , antibiotics that serve as substrates of the AcrAB efflux pump are very weak inducers of the marRAB operon in E. coli and do not induce these genes in Salmonella .6,8 Based on that , it was suggested that exposure of E. coli or S. enterica to salicylate activates MarA through binding to its repressor , MarR .	5	INTRODUCTION	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	micF	activator	20237076	5	ver/dev	However , micF are also induced by stress signals in additional ways , it was suggested that exposure of E. coli activates MarA through binding to its repressor , MarR .	35	However , micF and acrAB are also induced by stress signals in additional ways that are not dependent on the marRAB system .17 Interestingly , antibiotics that serve as substrates of the AcrAB efflux pump are very weak inducers of the marRAB operon in E. coli and do not induce these genes in Salmonella .6,8 Based on that , it was suggested that exposure of E. coli or S. enterica to salicylate activates MarA through binding to its repressor , MarR .	5	INTRODUCTION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	micF	activator	20237076	7	ver/dev	These results , together with the results of the induction of micF by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	micF	activator	20237076	7	ver/dev	These results , together with the results of the induction of micF by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	micF	activator	20237076	7	ver/dev	These results , together with the results of the induction of micF by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	btuE	repressor	30682134	36	ver/dev	CsrA repressed translation of btuE 2-fold in S2 Table .	277	CsrA repressed translation of btuE 2-fold in mLPM ( S2 Table ) , which encodes a peroxidase that can use thior-edoxin or glutathione as a reductant [ 104 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	btuE	repressor	30682134	36	ver/dev	CsrA repressed translation of btuE 2-fold in mLPM .	277	CsrA repressed translation of btuE 2-fold in mLPM ( S2 Table ) , which encodes a peroxidase that can use thior-edoxin or glutathione as a reductant [ 104 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	assT	regulator	22343301	26	ver/dev	H-NS bound to the complete 5 = region of assT at a concen-8 .220.9 tration of Fig. 8B .	215	H-NS bound to the complete 5 = region of assT ( F1 ) at a concen-8 .220.9 tration of 200 nM H-NS ( Fig. 8B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	assT	regulator	22343301	26	ver/dev	H-NS bound to the complete 5 = region of assT at a concen-8 .220.9 tration of 200 nM H-NS .	215	H-NS bound to the complete 5 = region of assT ( F1 ) at a concen-8 .220.9 tration of 200 nM H-NS ( Fig. 8B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , osmolarity , DNA structure , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , osmolarity , DNA structure , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , osmolarity , DNA structure , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , osmolarity , DNA structure , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	TU	flhDC	regulator	32032766	0	ver/dev	Furthermore , the flhDC operon was reported to be regulated by RpoS , OmpR .	151	Furthermore , the flhDC operon was reported to be activated during the stationary phase under high osmolarity stress and regulated by several regulators ( such as , RpoS , OmpR , and Fis ) [ 17,24 ] .	17	3.2. EXPRESSION AND REGULATION OF ASFD IN S. TYPHI	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	TU	flhDC	regulator	32032766	3	ver/dev	Furthermore , we utilized qRT-PCR to investigate the regulation of RpoS on the flhDC operon .	194	Furthermore , we utilized qRT-PCR to investigate the regulation of RpoS , OmpR , Fis , and Hfq on AsfD and the flhDC operon .	20	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rrs	activator	29739882	25	att	Effects of low Mg2 + , acidic pH , and PhoP-dependent transcription of the lpxT gene on polymyxin B resistance ( A ) Quantification of the indicated transcripts at different times after switching WT Salmonella ( 14028s ) from high Mg2 + at pH 7.7 to high Mg2 + at pH 4.9 , normalized to the rrs transcript .	677	Effects of low Mg2 + , acidic pH , and PhoP-dependent transcription of the lpxT gene on polymyxin B resistance ( A ) Quantification of the indicated transcripts at different times after switching WT Salmonella ( 14028s ) from high Mg2 + at pH 7.7 to high Mg2 + at pH 4.9 , normalized to the rrs transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	SPEC	Analysis	OTHER	New	Level 1
LeuO	gene	cat	activator	18156266	17	att	Transcriptional profiles of the LeuO-dependent genes fused to the cat reporter gene .	260	Transcriptional profiles of the LeuO-dependent genes fused to the cat reporter gene .	5	FIG. 2	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	cat	activator	21398529	0	att	PCR fragments that contained the entire casA regulatory region as well as the 10 substitutions were fused to the cat reporter gene , a Transcriptional values for the LeuO-dependent casABCDE12-CRISPR operon were determined in MA medium .	119	PCR fragments that contained the entire casA regulatory region as well as the 10 substitutions were fused to the cat reporter gene , a Transcriptional values for the LeuO-dependent casABCDE12-CRISPR operon were determined in MA medium .	4	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	yoaE	activator	31915212	4	ver/dev	In conclusion , it was shown for the first time that CpxR positively regulated the transcription of yoaE .	15	In conclusion , it was shown for the first time that CpxR positively regulated the transcription of yoaE , which was indispensable for survival of Salmonella Enteritidis in egg white .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	yoaE	activator	31915212	10	ver/dev	CpxR positively regulated the expression of gene yoaE .	77	CpxR positively regulated the expression of gene yoaE .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	yoaE	activator	31915212	12	ver/dev	This result indicates that CpxR positively regulated the expression of yoaE gene in egg white .	84	This result indicates that CpxR positively regulated the expression of yoaE gene in egg white .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NsrR	gene	nsrR	activator	24021902	1	att	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	78	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	nsrR	activator	24021902	1	ver/dev	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of the other NsrR-dependent genes .	78	At eight hours post-infection , transcription of nsrR is reduced , leading to the upregulation of hmpA , STM1808 and the other NsrR-dependent genes .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	regulator	11796342	2	ver/dev	Two-stage control of the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS gene .	374	Two-stage control of an oxidative stress regulon : the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS gene .	18	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SoxR	gene	soxS	regulator	18984645	9	ver/dev	Two-stage control of the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene .	385	Two-stage control of an oxidative stress regulon : the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene .	21	DRUGS 2004; 64: 159–204.	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SoxR	gene	soxS	regulator	9068629	6	ver/dev	Two-stage control of the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS gene .	704	Two-stage control of an oxidative stress regulon : the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS gene .	33	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	ybfE	regulator	30201777	18	att	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	194	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Escherichia coli	0.5	L3	OTHER	Other	NEG	Other	Level 1
SsrB	gene	csgD	regulator	26880544	53	att	Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .	369	Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .	16	THE IMPORTANCE OF ANTI-SILENCING IN GENE REGULATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	csgD	regulator	26880544	7	ver/dev	AFM imaging revealed that unphosphorylated SsrB was able to bind to the csgD regulatory region	72	Moreover , AFM imaging revealed that unphosphorylated SsrB was able to bind to the csgD regulatory region and binding was sufficient to relieve H-NS-mediated repression and favor formation of S. Typhimurium biofilms .	3	INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SsrB	gene	csgD	regulator	26880544	15	ver/dev	SsrB differentially regulate csgD expression	215	SsrB and H-NS differentially regulate csgD expression	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	csgD	regulator	26880544	24	ver/dev	Unphosphorylated SsrB binds to the csgD regulatory region	267	Unphosphorylated SsrB binds to the csgD regulatory region	11	UNPHOSPHORYLATED SSRB BINDS TO THE CSGD REGULATORY REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	csgD	regulator	26880544	26	ver/dev	Surprisingly , we observed binding of SsrB , D56A SsrB and SsrBc to distinct regions of the csgD regulatory region .	271	Surprisingly , we observed binding of SsrB , D56A SsrB and SsrBc to distinct regions of the csgD regulatory region ( Figure 5B and Figure 5 -- figure supplement 1A and B ) .	11	UNPHOSPHORYLATED SSRB BINDS TO THE CSGD REGULATORY REGION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	csgD	regulator	26880544	27	ver/dev	Binding showed that unphosphorylated SsrB was capable of binding csgD .	272	Binding occured at low protein concentrations , suggesting high affinity interactions and showed that unphosphorylated SsrB was capable of binding csgD .	11	UNPHOSPHORYLATED SSRB BINDS TO THE CSGD REGULATORY REGION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	csgD	regulator	26880544	29	ver/dev	Closer examination revealed a sharp curvature at the regions where SsrB was bound to csgD .	274	Closer examination revealed a sharp curvature at the regions where SsrB was bound to csgD ( Figure 5B , arrows ) .	11	UNPHOSPHORYLATED SSRB BINDS TO THE CSGD REGULATORY REGION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	csgD	regulator	26880544	39	ver/dev	Thus , unphosphorylated SsrB can bind to the csgD regulatory region when it has been coated with the repressor H-NS .	309	Thus , unphosphorylated SsrB can bind to the csgD regulatory region when it has been coated with the repressor H-NS .	13	DOI: 10.7554/ELIFE.10747.023	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SsrB	gene	csgD	regulator	26880544	60	ver/dev	complexes _ formed by the binding of SsrB and/or H-NS to the csgD regulatory region	594	Electrophoretic mobility assay using the LightShift Chemiluminescent EMSA kit ( THERMO Scientific ) was modified to detect complexes formed by the binding of SsrB and/or H-NS to the csgD regulatory region .	35	ELECTROPHORETIC MOBILITY SUPER SHIFT ASSAY	nan	1	L3	OTHER	Other	NEG	New	Level 1
NhaR	gene	sdiA	repressor	22149171	46	ver/dev	Conversely , NhaR overexpression decreases sdiA expression -LRB- Fig .	334	Conversely , NhaR overexpression decreases sdiA expression ( Fig .	18	ILVY, NHAR, AND FUR ARE INDIRECT ACTIVATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	11755416	25	att	Little is known about the significance of HilC-dependent hilA expression versus HilD-dependent hilA expression to pathogenesis .	273	Little is known about the significance of HilC-dependent hilA expression versus HilD-dependent hilA expression to pathogenesis .	9	7. FUTURE DIRECTIONS IN REGULATION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilC	gene	hilA	activator	11755416	31	ver/dev	Two reports have shown that prgH expression , can be upregulated by artificially expressing high levels of HilC even in the absence of hilA .	558	Two reports have shown that invF expression , but not prgH expression , can be upregulated by artificially expressing high levels of HilC ( SirC , SprA ) even in the absence of hilA ( figure 1B , blue arrow ) [ 50 , 51 ] .	16	REFERENCES	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	11755416	31	ver/dev	Two reports have shown that invF expression , can be upregulated by artificially expressing high levels of HilC even in the absence of hilA .	558	Two reports have shown that invF expression , but not prgH expression , can be upregulated by artificially expressing high levels of HilC ( SirC , SprA ) even in the absence of hilA ( figure 1B , blue arrow ) [ 50 , 51 ] .	16	REFERENCES	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	15661008	22	ver/dev	To understand how Lon negatively regulates the key regulator hilA , we have focused on two activators of HilC .	257	To understand how Lon negatively regulates the expression of SPI1 genes , including the key regulator hilA , we have focused on two activators of hilA , HilC and HilD .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	15661008	23	ver/dev	HilC can independently activate the hilA promoter .	267	HilC and HilD can independently bind and activate the hilA promoter ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ) .	9	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilA	activator	15765064	16	ver/dev	These data suggest that HilC may activate hilA expression in response to a set of signals .	103	These data suggest that HilC and RtsA may activate hilA expression in response to a set of signals that are not present in laboratory conditions .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	hilA	activator	16045614	24	ver/dev	We wanted to determine if HilC could induce expression of hilA in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
HilC	gene	hilA	activator	16045614	26	ver/dev	The data in Fig. 2 demonstrate that HilC are able to induce expression of hilA in the absence of the other regulators .	127	The data in Fig. 2 demonstrate that RtsA , HilC and HilD are able to induce expression of hilA in the absence of the other regulators .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	16045614	34	ver/dev	RtsA , HilC each contribute to activating hilA in-vitro	144	RtsA, HilC and HilD each contribute to activating hilA in vitro	6	RTSA, HILC AND HILD EACH CONTRIBUTE TO ACTIVATING HILA IN VITRO	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilC	gene	hilA	activator	16045614	51	ver/dev	SirA induction of invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA	299	SirA induction of hilA and invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA and thus the entire SPI1 TTSS	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	16045614	51	ver/dev	SirA induction of hilA requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA	299	SirA induction of hilA and invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA and thus the entire SPI1 TTSS	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	16045614	69	ver/dev	We show that HilC can each independently activate expression of the hilA genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilA	activator	16045614	70	ver/dev	However , HilC normally act in concert to activate hilA .	466	However , HilD , HilC and RtsA normally act in concert to activate hilA .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	16045614	96	ver/dev	Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC .	762	Olekhnovich , I.N. , and Kadner , R.J. ( 2004 ) Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC and HilD .	27	REFERENCES	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	16045614	96	ver/dev	Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC .	762	Olekhnovich , I.N. , and Kadner , R.J. ( 2004 ) Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC and HilD .	27	REFERENCES	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	16443238	2	ver/dev	8,13,14 HilC can activate expression of hilA .	39	Three homologous proteins , 8,13,14 HilC , HilD , and RtsA , which belong to the AraC/XylS family of transcription factors can activate expression of hilA and some of its target genes .	5	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	hilA	activator	16443238	35	ver/dev	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .	625	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD .	50	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	16443238	35	ver/dev	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .	625	Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD .	50	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	17208038	10	ver/dev	The mechanism by which HilC activate expression of hilA	85	The mechanism by which HilC , HilD and RtsA activate expression of hilA ( and possibly of each other ) apparently involves counteracting silencing by the nucleoid protein Hns [ 30,31 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	17675384	3	ver/dev	That means that at least hilA are induced by HilC .	43	That means that at least hilA and rtsA are induced by HilD , HilC , and RtsA proteins .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	17675384	15	ver/dev	Under high-osmolarity conditions , HilC activate SPI1 genes indirectly through hilA .	288	Under high-osmolarity conditions , HilD , HilC , and RtsA activate SPI1 genes directly and indirectly through hilA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	17675384	15	ver/dev	Under high-osmolarity conditions , HilC activate SPI1 genes directly through hilA .	288	Under high-osmolarity conditions , HilD , HilC , and RtsA activate SPI1 genes directly and indirectly through hilA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	17675384	24	ver/dev	C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .	548	C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD .	19	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	17993530	13	ver/dev	HilC are each capable of activating hilA transcription .	86	HilD , HilC , and RtsA are each capable of activating hilA transcription .	3	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	19537165	3	ver/dev	Earlier work on mathematical modeling of regulation of expression of hilA by HilC was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .	44	Earlier work on mathematical modeling of regulation of expression of hilA by HilC , HilD and RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop [ Maithreye and Mande , 2007 ] .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	20008574	1	ver/dev	Transcriptional activation by HilC relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha .	36	Transcriptional activation by HilC and HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	23676436	1	ver/dev	HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; Schechter et al. ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	23676436	1	ver/dev	HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; 2001 ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	23676436	1	ver/dev	HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lee ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	23676436	1	ver/dev	HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas ,	31	HilC , HilD and RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas & Lee , 2001 ; Schechter et al. ,	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	25375226	29	ver/dev	hilA expression is induced by three transcriptional activators , HilC .	402	hilA expression is induced by three transcriptional activators , HilC , HilD and RtsA [ 70 ] .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	25991823	0	ver/dev	Transcription of hilA is directly activated by HilC .	24	Transcription of hilA is directly activated by HilC and HilD , both members of the AraC/XylS family of transcriptional regulators ( Schechter and Lee 2001 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	26386070	1	ver/dev	Inducible expression HilC protein was sufficient to activate hilA following growth at 42 °C .	84	Inducible expression of either HilC or RtsA protein , but not of Fur , FliZ , or HilD , was sufficient to activate hilA following growth at 42 °C .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	27404739	1	ver/dev	HilC , activate directly the expression of hilA , independently of HilA .	131	Two additional regulators , HilC and HilD , activate directly the expression of hilA and the invF operon , independently of HilA ( Dieye et al. , 2007 ) .	6	SPI-1 RELATED GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	28335027	10	ver/dev	H-NS repression of hilA counteracts transcriptional activation by HilC	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	29378886	1	ver/dev	Transcriptional activation of hilA is dependent upon three AraC-like proteins , HilC , .	45	Transcriptional activation of hilA is dependent upon three AraC-like proteins , HilD , HilC , and RtsA , which bind to the same sites upstream of activated promoters ( 11 , 12 ) .	3	KEYWORDS SALMONELLA, SPI1, HILD, HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	30077369	0	ver/dev	hilA expression is directly activated by three AraC-like regulators : SPI-1-encoded HilC and HilD	43	hilA expression is directly activated by three AraC-like regulators : SPI-1-encoded HilC and HilD , and RtsA encoded outside of SPI-1 [ 9 ] .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	31182495	4	ver/dev	The hilA gene is transcriptionally activated by three AraC-like regulatory proteins , HilC , .	33	The hilA gene is transcriptionally activated by three AraC-like regulatory proteins , HilD , HilC , and RtsA , each of which can activate expression of the hilD , hilC , rtsA , and hilA genes , creating a complex feed-forward regulatory loop ( Fig. 1 ) ( 8 , 12 , 18 ) .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilC activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilC activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	31182495	53	ver/dev	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilC are still required for full stimulation of the polymerase .	227	This suggests that H-NS does repress directly at the hilA promoter in 441 fusions , though HilD , HilC , and RtsA are still required for full stimulation of the polymerase .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of rtsA .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilA	activator	31182495	56	ver/dev	FIG 8 HilC activate hilA expression independently of H-NS .	246	FIG 8 HilD , HilC , and RtsA activate hilA expression independently of H-NS .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	31262841	0	ver/dev	Expression of hilA is activated by HilC , .	9	Expression of hilA is activated by HilD , HilC , and RtsA , which act in a complex feed-forward regulatory loop .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	31262841	2	ver/dev	HilC , activate transcription of hilA by binding the promoter .	39	Three AraC-like proteins , HilD , HilC , and RtsA , activate transcription of hilA by binding the promoter ( 15 ) .	3	KEYWORDS PHOPQ, SPI1, SALMONELLA, SRNA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	32041797	5	ver/dev	HilC activate transcription of hilA , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilA	activator	32571967	0	ver/dev	Transcription of hilA , is activated by three AraC-like regulators , HilC , .	8	Transcription of hilA , encoding the transcriptional activator of the SPI1 structural genes , is activated by three AraC-like regulators , HilD , HilC , and RtsA , that act in a complex feed-forward loop .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	32571967	2	ver/dev	The hilA gene is directly activated by three AraC-like regulators , HilC , .	36	The hilA gene is directly activated by three AraC-like regulators , HilD , HilC , and RtsA , which act in a feed-forward loop to activate expression of themselves , each other , and hilA ( Fig. 1 ) ( 2 ) .	3	KEYWORDS BAM, RCSCDB, SPI1, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilA	activator	33593291	10	ver/dev	HilC can independently activate hilA expression	100	HilD also activates two additional transcription factors , HilC and RtsA , that can independently activate hilA expression .	6	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
ArgR	gene	argR	regulator	26944792	0	ver/dev	Putative regulation by ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of argR .	261	Putative regulation by the global regulators RcsB , Fur and ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of rcsDBC , fur and argR .	8	REGULATION OF TCF EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
RstA	gene	leuS	activator	30763640	30	att	B ) Alignment of the RstA consensus motif identified in other RstA-dependent genes like ybiL ( Ec ) , nohB ( Ec ) , modA ( Ec ) and leuS ( Ec ) genes , with the STM1485 promoter sequences .	169	B ) Alignment of the RstA consensus motif identified in other RstA-dependent genes like ybiL ( Ec ) , nohB ( Ec ) , modA ( Ec ) and leuS ( Ec ) genes , with the STM1485 promoter sequences .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	gatY	regulator	27956522	11	ver/dev	These data showed that cAMP-CRP binds to the promoters of gatY , .	180	These data showed that cAMP-CRP binds to the promoters of gatY , gatZ , and gatR , confirming that the expression of galactitol degradation is subject to catabolite repression .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DksA	gene	livJ	activator	33975942	5	att	These findings suggest that DnaK does not bind directly to DksA irrespectively of the redox state of the latter and provide a reasonable explanation for the inability of DnaK alone to support the DksA-dependent activation of livJ transcription ( Fig. 5A and C ) .	193	These findings suggest that DnaK does not bind directly to DksA irrespectively of the redox state of the latter and provide a reasonable explanation for the inability of DnaK alone to support the DksA-dependent activation of livJ transcription ( Fig. 5A and C ) .	2	KEYWORDS SALMONELLA TYPHIMURIUM, DKSA, DNAK, DNAJ, CHAPERONE, STRINGENT RESPONSE, OXIDATIVE STRESS, REDOX, HYDROGEN PEROXIDE	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
DksA	gene	livJ	activator	33975942	5	ver/dev	These findings suggest that DnaK does not bind directly to DksA irrespectively of the redox state of the latter and provide a reasonable explanation for the inability of DnaK alone to support the DksA-dependent activation of livJ transcription .	193	These findings suggest that DnaK does not bind directly to DksA irrespectively of the redox state of the latter and provide a reasonable explanation for the inability of DnaK alone to support the DksA-dependent activation of livJ transcription ( Fig. 5A and C ) .	2	KEYWORDS SALMONELLA TYPHIMURIUM, DKSA, DNAK, DNAJ, CHAPERONE, STRINGENT RESPONSE, OXIDATIVE STRESS, REDOX, HYDROGEN PEROXIDE	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
OmpR	gene	ssrB	repressor	12753201	41	ver/dev	conditions under which either ssrB was repressed by OmpR	236	However , in the present study , we did not find conditions under which either ssrA or ssrB was repressed by OmpR ( see below ) .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	acrB	regulator	27199934	14	ver/dev	Our finding that CpxR can influence the susceptibility of S. enterica serovar Typhimurium to β-lactam in both △ acrB backgrou also supports the second suggestion .	366	Our finding that CpxR can influence the susceptibility of S. enterica serovar Typhimurium to aminoglycosides and β-lactams in both acrB and △ acrB backgrounds also supports the second suggestion .	16	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	acrB	regulator	27199934	14	ver/dev	Our finding that CpxR can influence the susceptibility of S. enterica serovar Typhimurium to aminoglycosides in both △ acrB backgrou also supports the second suggestion .	366	Our finding that CpxR can influence the susceptibility of S. enterica serovar Typhimurium to aminoglycosides and β-lactams in both acrB and △ acrB backgrounds also supports the second suggestion .	16	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	mgtBC	regulator	12492857	0	ver/dev	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( examples include mgtBC ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtBC	regulator	12492857	0	ver/dev	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag include mgtBC ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
MntR	gene	mntH	activator	24596096	6	att	Expression of Salmonella mntH gene is regulated by both MntR-dependent and - independent mechanisms .	183	Expression of Salmonella mntH gene is regulated by both MntR-dependent and - independent mechanisms .	5	MATERIALS AND METHODS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Mlc	gene	hilE	regulator	17993530	59	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	613	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	23	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	19074398	47	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	924	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	38	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	21829349	0	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	464	Lim S , Yun J , Yoon H , Park C , Kim B , et al. ( 2007 ) Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	17	AUTHOR CONTRIBUTIONS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	22383560	0	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	546	Lim S , et al. ( 2007 ) Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	7	EXPERIMENTAL PROCEDURES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	24079299	14	ver/dev	Lim S , Yun J , Yoon H , Park C , Kim B , Jeon B , Kim D , Ryu S : Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	577	Lim S , Yun J , Yoon H , Park C , Kim B , Jeon B , Kim D , Ryu S : Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	24	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	24354910	61	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	452	Lim , S. , Yun , J. , Yoon , H. , Park , C. , Kim , B. , Jeon , B. , et al. ( 2007 ) Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	41	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	24835993	1	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	382	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	20	31621	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	25547794	35	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	432	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	27	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	25991823	25	ver/dev	Lim , S. , J. Yun , H. Yoon , C. Park , B. Kim et al. , 2007 Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	568	Lim , S. , J. Yun , H. Yoon , C. Park , B. Kim et al. , 2007 Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	40	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	28575106	19	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	726	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	33	1	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	30077369	4	ver/dev	S. Lim , J. Yun , H. Yoon , C. Park , B. Kim , B. Jeon , D. Kim , S. Ryu , Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression , Nucleic Acids Res .	259	[ 14 ] S. Lim , J. Yun , H. Yoon , C. Park , B. Kim , B. Jeon , D. Kim , S. Ryu , Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression , Nucleic Acids Res .	27	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	31428589	5	ver/dev	Mlc downregulates hilE expression by binding to the hilE P3 promoter .	160	Mlc downregulates hilE expression by binding to the hilE P3 promoter ( Lim et al. , 2007 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	31428589	18	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	579	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	6	AUTHOR CONTRIBUTIONS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	33563986	10	ver/dev	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	892	Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	25	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	regulator	33593291	23	ver/dev	Lim S , Yun J , Yoon H , Park C , Kim B , Jeon B , Kim D , Ryu S. Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	303	Lim S , Yun J , Yoon H , Park C , Kim B , Jeon B , Kim D , Ryu S. Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .	22	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	yqjA	activator	15225317	13	att	The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .	156	The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	yqjA	activator	15225317	20	att	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	185	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	yqjA	activator	15225317	20	att	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	185	Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	csgD	repressor	25153529	7	ver/dev	As a consequence , CpxR would start inhibiting expression of csgD .	377	As a consequence , CpxR would become phosphorylated and start inhibiting expression of csgD as well as csgA .	10	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	csgD	repressor	32604994	9	ver/dev	Repressive Effect of CpxR on csgD Transcription Is Alleviated During Growth To examine the effects of Cpx-mediated repression of csgD transcription in more detail , we monitoTreodexgaemne t a f c c i r i , i ineextphereesfsfieocns ionf aCp ∆ xc-pmxeRdimteudtarnetprbeascsikognroounsdg .	160	Repressive Effect of CpxR on csgD Transcription Is Alleviated During Growth To examine the effects of Cpx-mediated repression of csgD transcription in more detail , we monitoTreodexgaemne t a f c c i r i , i ineextphereesfsfieocns ionf aCp ∆ xc-pmxeRdimteudtarnetprbeascsikognroounsdg .	11	3.1. OSMOLARITY HAS NO EFFECT ONCE CSGD TRANSCRIPTION IS ACTIVATED	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CpxR	gene	csgD	repressor	32604994	10	ver/dev	the ∆ cpxR stra , which was consistent with CpxR being a repressor of csgD transcripti	174	s c , c i s r siroenseFnigcuerof2nAon + - sinudpupcele ) mAenteexdpemteeddiapx ( FPigexuprrees2sBo ) n. Twhaseroeffwinasthaelso capxsRligthatinincrease in the ∆ cpxR strain , which was consistent with CpxR being a repressor of csgD transcription .	11	3.1. OSMOLARITY HAS NO EFFECT ONCE CSGD TRANSCRIPTION IS ACTIVATED	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	csgD	repressor	32604994	10	ver/dev	the ∆ cpxR stra , which was consistent with CpxR being a repressor of csgD transcripti	174	s c , c i s r siroenseFnigcuerof2nAon + - sinudpupcele ) mAenteexdpemteeddiapx ( FPigexuprrees2sBo ) n. Twhaseroeffwinasthaelso capxsRligthatinincrease in the ∆ cpxR strain , which was consistent with CpxR being a repressor of csgD transcription .	11	3.1. OSMOLARITY HAS NO EFFECT ONCE CSGD TRANSCRIPTION IS ACTIVATED	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	csgD	repressor	32604994	10	ver/dev	the ∆ cpxR stra , which was consistent with CpxR being a repressor of csgD transcripti	174	s c , c i s r siroenseFnigcuerof2nAon + - sinudpupcele ) mAenteexdpemteeddiapx ( FPigexuprrees2sBo ) n. Twhaseroeffwinasthaelso capxsRligthatinincrease in the ∆ cpxR strain , which was consistent with CpxR being a repressor of csgD transcription .	11	3.1. OSMOLARITY HAS NO EFFECT ONCE CSGD TRANSCRIPTION IS ACTIVATED	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	csgD	repressor	32604994	10	ver/dev	the ∆ cpxR stra , which was consistent with CpxR being a repressor of csgD transcripti	174	s c , c i s r siroenseFnigcuerof2nAon + - sinudpupcele ) mAenteexdpemteeddiapx ( FPigexuprrees2sBo ) n. Twhaseroeffwinasthaelso capxsRligthatinincrease in the ∆ cpxR strain , which was consistent with CpxR being a repressor of csgD transcription .	11	3.1. OSMOLARITY HAS NO EFFECT ONCE CSGD TRANSCRIPTION IS ACTIVATED	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssaM	regulator	17630976	0	att	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	14	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	2	SUMMARY	synthetic construct	0	L3	OTHER	Analysis	OTHER	New	Level 2
CadC	gene	STM4538	repressor	23066934	2	ver/dev	In addition , deletional inactivation of STM4538 in the wild-type background leads to the impaired proteolytic cleavage of CadC .	14	In addition , deletional inactivation of STM4538 in the wild-type background leads to the impaired proteolytic cleavage of CadC .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CadC	gene	STM4538	repressor	23066934	7	ver/dev	Inactivation of STM4538 prevents proteolytic cleavage of CadC	154	Inactivation of STM4538 prevents proteolytic cleavage of CadC	14	INACTIVATION OF STM4538 PREVENTS PROTEOLYTIC CLEAVAGE OF CADC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CadC	gene	STM4538	repressor	23066934	14	ver/dev	In particular , we demonstrated that inactivation of STM4538 impaired the proteolytic processing of CadC .	222	In particular , we demonstrated that inactivation of STM4538 impaired the proteolytic processing of CadC ( Fig. 2 ) .	17	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	pmrG	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrG	activator	23019341	0	att	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	16	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrG	activator	23019341	0	ver/dev	These PmrA-dependent activities are produced by activation of pmrG transcription .	16	These PmrA-dependent activities are produced by activation of ugd , pbgPE , pmrC , cpta , and pmrG transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	siiA	repressor	27601571	18	ver/dev	scription activation of protein-coding genes outside SPI-1 overlap Table S1 -RRB- , suggesting that failure to detect binding of InvF by regions _ bound by H-NS -LRB- HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites , , siiA , mcpC , epitope tags	210	scription activation of protein-coding genes outside SPI-1 overlap Table S1 ) , suggesting that failure to detect binding of InvF by regions that are likely bound by H-NS ( HilD/HilC/RtsA binding ChIP-seq might be due to partial inactivation of the protein by the sites associated with regulation of lpxR , STM14_5184 , siiA , mcpC , epitope tags .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	katE	activator	23651595	1	ver/dev	Activated OxyR induces katE , dps ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katE	activator	23651595	1	ver/dev	Activated OxyR induces katE , dps lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katE	activator	23651595	1	ver/dev	Activated OxyR induces katE , DNA-protection ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katE	activator	23651595	1	ver/dev	Activated OxyR induces katE , DNA-protection lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	gene	fliA	regulator	16430704	0	ver/dev	In turn , fliA is positively controlled by FlhC .	79	In turn , fliA is positively controlled by the gene products FlhD and FlhC , which are encoded by the sole operon lying at the apex of the hierarchy .	5	THE SALMONELLA DNAK MUTANT IS DEFECTIVE IN FLAGELLUM BIOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	gene	invG	repressor	15469511	10	ver/dev	In agreement with the inability of the rcsA mutation to restore invasion to the rcsC11 mutant , the inhibition of transcription of the invG gene was RcsA Fig. 3D .	290	In agreement with the inability of the rcsA mutation to restore invasion to the rcsC11 mutant ( Table 2 ) , the inhibition of transcription of the invG gene was RcsA independent ( Fig. 3D ) .	12	A ROLE FOR THE RCSC/YOJN/RCSB SYSTEM IN THE CONTROL OF INVASION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	gene	invG	repressor	15469511	10	ver/dev	In agreement with the inability of the rcsA mutation to restore invasion to the rcsC11 mutant , the inhibition of transcription of the invG gene was RcsA independent .	290	In agreement with the inability of the rcsA mutation to restore invasion to the rcsC11 mutant ( Table 2 ) , the inhibition of transcription of the invG gene was RcsA independent ( Fig. 3D ) .	12	A ROLE FOR THE RCSC/YOJN/RCSB SYSTEM IN THE CONTROL OF INVASION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	soxR	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CpxR	gene	cpxR	activator	30107570	0	ver/dev	CpxR overexpression increases the susceptibility of cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin	2	CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	cpxR	activator	32620947	21	ver/dev	CpxR overexpression increases the susceptibility of cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin .	341	CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin .	21	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	cpxR	activator	33300449	0	ver/dev	CpxR overexpression increases the susceptibility of cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin .	489	CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin .	54	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilD	activator	25135218	29	ver/dev	As shown in Fig. 2 , induction of the dominant negative H-NSQ92am domain , but not of WT H-NS , restored the expression of the ssrB-cat 302 / 478 fusion in the hilD mutant .	119	As shown in Fig. 2 , induction of the dominant negative H-NSQ92am domain , but not of WT H-NS , restored the expression of the ssrB-cat 302 / 478 fusion in the hilD mutant .	4	RESULTS	Felis catus	0	L3	OTHER	Analysis	NEG	New	Level 1
HNS	gene	hilD	activator	31484980	31	ver/dev	WT H-NS , increased the activity of sprB-cat in the ∆ hilD mutant , at similar levels to o tho .	160	Expression of H-NSG113D , but not WT H-NS , increased the activity of sprB-cat in the ∆ hilD mutant , at similar levels to those reached by this fusion in the WT strain ( Fig. 7A ) .	3	RESULTS	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilD	activator	32571967	12	ver/dev	H-NS contributes to silencing of hilD	223	Rcs could , for example , be functioning through H-NS , which contributes to silencing of hilD , hilC , rtsA , and hilA ( 33 , 78 -- 80 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilD	activator	34424033	3	ver/dev	a putative H-NS nucleation site mutation of which abrogates H-NS-mediated silencing to activate the hilD promoter	32	We identify a putative H-NS nucleation site , mutation of which abrogates H-NS-mediated silencing to activate the hilD promoter .	2	MAIN	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HNS	gene	hilD	activator	34424033	32	ver/dev	Thus , interfering with H-NS oligomerization causes significant induction of the hilD promoter .	397	Thus , interfering with H-NS oligomerization using the dominant negative allele ( 46 ) causes significant induction of the hilD promoter .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
RpoS	gene	topA	activator	21276095	16	att	In E. coli , the RpoS-activated promoter Px1 is the primary driver of topA transcription during stationary-phase , and it may compete with and repress the exponential-growth promoter P4 ( Qi et al. , 1997 ) .	235	In E. coli , the RpoS-activated promoter Px1 is the primary driver of topA transcription during stationary phase , and it may compete with and repress the exponential growth promoter P4 ( Qi et al. , 1997 ) .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	Escherichia coli	0	L1	SPEC	Analysis	OTHER	Other	Level 1
HdfR	gene	stdA	regulator	33475482	1	ver/dev	The promoter expression was evaluated in five mutants of known regulators of std in RosE , HdfR , in seven mutants of predicted regulators of the S. Typhi stdA promoter region .	114	The promoter expression was evaluated in five mutants of known regulators of std in S. Typhimurium ( RosE , HdfR , Dam , SeqA and StdE ) , in seven mutants of predicted regulators of the S. Typhi stdA promoter region , and in 41 mutants of regulators of global virulence or metabolism ( Table 1 ) .	8	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HdfR	gene	stdA	regulator	33475482	1	ver/dev	The promoter expression was evaluated in five mutants of known regulators of std in RosE , HdfR , in seven mutants of predicted regulators of the S. Typhi stdA promoter region .	114	The promoter expression was evaluated in five mutants of known regulators of std in S. Typhimurium ( RosE , HdfR , Dam , SeqA and StdE ) , in seven mutants of predicted regulators of the S. Typhi stdA promoter region , and in 41 mutants of regulators of global virulence or metabolism ( Table 1 ) .	8	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sopE2	repressor	29857034	6	ver/dev	This suggests that SlyA might downregulate sopE2 in all conditions .	277	This suggests that SlyA might downregulate sopE2 in all conditions .	23	3.2. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER H2O2 TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	sopE2	repressor	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopE2 were negatively regulated by SlyA , with DslyA expression increased five-times , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sopE2	repressor	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopE2 were negatively regulated by SlyA , with DslyA expression increased two , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	gene	garR	regulator	24272778	16	att	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	222	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	ogt	regulator	25281378	0	ver/dev	The ogt gene is regulated by RpoS .	158	The ogt gene is regulated by the alternative sigma factor S ( RpoS ) and is involved in the survival of bacteria under starvation or stress conditions ( 41 ) , which can be encountered in the reproductive tract .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ymdF	regulator	30373755	13	ver/dev	However , ymdF genes do not appear to contain YncC boxes in data not shown ; H-NS does not seem to bind coding regions of the ymdF gene , although it is shown to bind the upstream region of .	253	However , the STM14_1829 and ymdF genes do not appear to contain YncC boxes in their upstream regions ( data not shown ) ; H-NS does not seem to bind neighboring or coding regions of the ymdF gene , although it is shown to bind the upstream region of STM14_1829 ( 67 , 68 ) .	5	DISCUSSION	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	ymdF	regulator	30373755	13	ver/dev	However , ymdF genes do not appear to contain YncC boxes in their upstream regions ; H-NS does not seem to bind coding regions of the ymdF gene , although it is shown to bind the upstream region of .	253	However , the STM14_1829 and ymdF genes do not appear to contain YncC boxes in their upstream regions ( data not shown ) ; H-NS does not seem to bind neighboring or coding regions of the ymdF gene , although it is shown to bind the upstream region of STM14_1829 ( 67 , 68 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
HNS	gene	ymdF	regulator	30373755	13	ver/dev	However , the do not appear to contain YncC boxes in data not shown ; H-NS does not seem to bind coding regions of the ymdF gene , although it is shown to bind the upstream region of .	253	However , the STM14_1829 and ymdF genes do not appear to contain YncC boxes in their upstream regions ( data not shown ) ; H-NS does not seem to bind neighboring or coding regions of the ymdF gene , although it is shown to bind the upstream region of STM14_1829 ( 67 , 68 ) .	5	DISCUSSION	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	ymdF	regulator	30373755	13	ver/dev	However , the do not appear to contain YncC boxes in their upstream regions ; H-NS does not seem to bind coding regions of the ymdF gene , although it is shown to bind the upstream region of .	253	However , the STM14_1829 and ymdF genes do not appear to contain YncC boxes in their upstream regions ( data not shown ) ; H-NS does not seem to bind neighboring or coding regions of the ymdF gene , although it is shown to bind the upstream region of STM14_1829 ( 67 , 68 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
HilD	gene	hilC	repressor	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	STM0459	activator	15681155	9	att	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	206	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	11	3. RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	STM0459	activator	15681155	31	ver/dev	In addition , the lack of consensus PmrA-binding sites in the promoters of STM0459 suggested that these genes may be indirectly activated by PmrA .	339	In addition , the lack of consensus PmrA-binding sites in the promoters of STM1257 , STM3968 , STM4568 and STM0459 suggested that these genes may be indirectly activated by PmrA .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
MarA	TU	marRAB	regulator	11229910	0	ver/dev	The marRAB operon , controls multiple antibiotic resistance in E. coli by production of MarA , a 127-amino-acid protein of the XylS/AraC family of transcriptional activator proteins .	26	The marRAB operon , which is located at min 34.8 of the chromosomal map of E. coli K-12 ( 20 ) , controls multiple antibiotic resistance in E. coli by production of MarA ( 12 , 17 , 27 ) , a 127-amino-acid protein of the XylS/AraC family of transcriptional activator proteins , which alters the expression of several target genes ( 1 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	regulator	20237076	3	ver/dev	further _ activated when MarA binds marbox in the operator of marRAB .7 MarA	29	The expression of MarA is further activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes involved in adaptation to stress conditions , such as oxidative stress , heavy metals or antimicrobials .10	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	regulator	32468234	7	ver/dev	The marRAB operon encodes MarR family and MarA regulators , which control the marRAB operon by positive regulation , respectively .	128	The marRAB operon encodes MarR ( MarR family ) and MarA ( AraC/XylS family ) regulators , which control the marRAB operon by negative and positive regulation , respectively ( Sulavik et al. 1997 ) ( Fig. 2 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	TU	marRAB	regulator	32468234	7	ver/dev	The marRAB operon encodes MarR family and MarA regulators , which control the marRAB operon by negative regulation , respectively .	128	The marRAB operon encodes MarR ( MarR family ) and MarA ( AraC/XylS family ) regulators , which control the marRAB operon by negative and positive regulation , respectively ( Sulavik et al. 1997 ) ( Fig. 2 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	csgD	repressor	27206164	10	ver/dev	The biofilm master regulatory gene csgD is repressed upon RcsB phosphorylation .	66	The biofilm master regulatory gene csgD is activated by unphosphorylated RcsB , but repressed upon RcsB phosphorylation ( Latasa et al. , 2012 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrB	regulator	12898222	1	ver/dev	In electro-phoretic mobility-shift assays , Fis was found to bind to both gyrB promoters of S. enterica , despite the strong divergence from the E. coli sequence on the part of the former .	9	In electro-phoretic mobility shift assays , Fis was found to bind to both the gyrA and gyrB promoters of S. enterica , despite the strong divergence from the E. coli sequence on the part of the former .	1	ABSTRACT	Salmonella;Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrB	regulator	16999831	13	ver/dev	Fis also binds to and represses the promoters of the gyrB genes in both E. coli and S. Typhimurium , resulting in reduced levels of DNA supercoiling .	142	Fis also binds to and represses the promoters of the gyrA and gyrB genes in both E. coli ( Schneider et al. , 1999 ) and S. Typhimurium ( Keane and Dorman , 2003 ) , resulting in reduced levels of DNA supercoiling .	12	FIS LEVELS INFLUENCE DNA SUPERCOILING AND THE SSRA PROMOTER	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	gyrB	regulator	21276095	2	ver/dev	In E. coli , FIS binds the gyrB promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrB .	40	In E. coli , FIS binds the gyrA and gyrB promoters to repress their expression ( Schneider et al. , 1999 ) ; similarly , FIS has been found to repress S. enterica gyrA and gyrB ( Keane and Dorman , 2003 ) .	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrB	regulator	21276095	8	ver/dev	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrB might differ between the two species .	179	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of the genes responsible for supercoiling ( gyrA , gyrB and topA ) might differ between the two species .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	gyrB	regulator	21276095	8	ver/dev	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrB might differ between the two species .	179	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of the genes responsible for supercoiling ( gyrA , gyrB and topA ) might differ between the two species .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	gyrB	regulator	21276095	10	ver/dev	FIS control of gyrB .	184	FIS control of gyrA , gyrB and topA gene expression .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	cpxR	activator	14643403	28	ver/dev	RpoS is also required for the expression of MlrA and , at the same time activates the repressor cpxR .	209	RpoS is also required for the expression of MlrA and , at the same time activates the repressor cpxR [ 7,32 ] .	20	6.5. MLRA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	regulator	25182488	9	ver/dev	The role of HilD in the regulation of slrP were further studied at the protein level .	242	The role of Lon , LeuO , and HilD in the regulation of slrP and the relationships between the three regulators were further studied at the protein level using strains expressing SlrP-3 FLAG ( Fig. 5 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	regulator	27886269	26	ver/dev	Similarly , the expression of slrP , also encoding an effector protein , is controlled by HilD in SPI-1-inducing conditions .	165	Similarly , the expression of slrP , also encoding an effector protein secreted through both T3SS-1 and T3SS-2 , is controlled by HilD in SPI-1-inducing conditions and by the response regulator PhoP in SPI-2-inducing conditions32 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	regulator	29555922	18	ver/dev	Additionally , HilD independently regulate the expression of the slrP gene .	270	Additionally , HilD and PhoP positively and independently regulate the expression of the slrP gene , in SPI-1-inducing growth conditions , PhoP directly and HilD by an unknown mechanism37 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	zntA	regulator	24858080	10	att	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	336	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	zntA	regulator	24858080	3	att	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	264	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	hfq	activator	22336758	11	ver/dev	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 background showed a clear downregulation of slightly reduced CsgD levels , whereby	122	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 which shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype ( Fig. 3B ) and slightly reduced CsgD levels , whereby	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	activator	22336758	11	ver/dev	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 background showed a clear downregulation of Fig. 3B , whereby	122	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 which shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype ( Fig. 3B ) and slightly reduced CsgD levels , whereby	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	hfq	activator	22336758	11	ver/dev	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 background showed a clear downregulation of the rdar morphotype , whereby	122	Interestingly , overexpression of CsgD induced RpoS synthesis , most likely through a positive feedback-loop which includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 which shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype ( Fig. 3B ) and slightly reduced CsgD levels , whereby	2	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	STM1344	regulator	25437188	48	ver/dev	STM3611 , as a class III flagellar gene , is indirectly regulated by STM1344 via FliA .	556	STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC , STM1344 and STM1697 via FliA ( Figure 2 ) .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sirA	regulator	16949866	3	ver/dev	However , DNA sequence analysis suggest that the regulation of sirA by CRP is probably indirect .	17	However , gel mobility shift experiments and DNA sequence analysis suggest that the regulation of sirA by CRP is probably indirect .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	sirA	regulator	16949866	3	ver/dev	However , gel mobility-shift experiments suggest that the regulation of sirA by CRP is probably indirect .	17	However , gel mobility shift experiments and DNA sequence analysis suggest that the regulation of sirA by CRP is probably indirect .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	sirA	regulator	16949866	27	ver/dev	To test the hypothesis that the CRP binds directly to the sirA promoter , we used in-vitro gel mobility-shift assays .	445	To test the hypothesis that the CRP -- cAMP complex binds directly to the sirA promoter , we used in vitro gel mobility shift assays ( Fig. 7 ) .	18	SIRA DOES NOT AUTOREGULATE	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
CRP	gene	sirA	regulator	16949866	29	ver/dev	that the regulation of sirA by CRP is indirect	449	This suggests that the regulation of sirA by CRP -- cAMP is indirect or that CRP binding to the sirA promoter region is either very weak or requires another factor that was not present in the gel shift assays .	18	SIRA DOES NOT AUTOREGULATE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sirA	regulator	16949866	42	ver/dev	Based on these observations , it seems unlikely that CRP directly controls sirA expression .	514	Based on these observations , it seems unlikely that CRP -- cAMP directly controls sirA expression .	19	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	New	Level 1
CRP	gene	sirA	regulator	23370732	1	ver/dev	CRP functions as crp is necessary for SPI-1 genes expression by binding to its regulator sirA .	130	CRP functions as a transcriptional activator , and crp is necessary for SPI-1 genes expression by binding to its regulator sirA .	7	VACCINES OF SPI-1 MUTANTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	sirA	regulator	23370732	1	ver/dev	CRP functions as a transcriptional activator is necessary for SPI-1 genes expression by binding to its regulator sirA .	130	CRP functions as a transcriptional activator , and crp is necessary for SPI-1 genes expression by binding to its regulator sirA .	7	VACCINES OF SPI-1 MUTANTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	acrA	regulator	30448437	3	ver/dev	As BaeR does not bind to the promoter region of acrA ,6 binding of BaeR to these two promoter regions was performed to serve as positive controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L3	OTHER	Other	NEG	Other	Level 1
BaeR	gene	acrA	regulator	30448437	3	ver/dev	As BaeR does not bind to the promoter region of acrA ,6 binding of BaeR to these two promoter regions was performed to serve as positive controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L3	OTHER	Other	NEG	Other	Level 1
BaeR	gene	acrA	regulator	30448437	3	ver/dev	As BaeR does not bind to the promoter region of acrA ,6 binding of BaeR to these two promoter regions was performed to serve as negative controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L3	OTHER	Other	NEG	Other	Level 1
BaeR	gene	acrA	regulator	30448437	3	ver/dev	As BaeR does not bind to the promoter region of acrA ,6 binding of BaeR to these two promoter regions was performed to serve as negative controls , respectively .	123	As BaeR does not bind to the promoter region of acrA but can bind to that of acrD ,6 binding of BaeR to these two promoter regions was performed to serve as negative and positive controls , respectively .	15	EXPRESSION OF STM3031 BUT NOT STM3030 IS REGULATED BY BAER OF THE TCS BAESR	nan	1	L3	OTHER	Other	NEG	Other	Level 1
BaeR	gene	acrA	regulator	30448437	5	ver/dev	Binding of BaeR to the promoter regions of acrA was performed to serve as positive controls , respectively .	191	Binding of BaeR to the promoter regions of acrA and acrD was performed to serve as negative and positive controls , respectively .	16	STM3030 AND STM3031 INTERACT WITH EACH OTHER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	acrA	regulator	30448437	5	ver/dev	Binding of BaeR to the promoter regions of acrA was performed to serve as negative controls , respectively .	191	Binding of BaeR to the promoter regions of acrA and acrD was performed to serve as negative and positive controls , respectively .	16	STM3030 AND STM3031 INTERACT WITH EACH OTHER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	crl	activator	17293430	9	ver/dev	During early stationary-phase , the absence of activation by Crl resulted in a slightly delayed expression of genes in the crl mutant .	242	During early stationary phase , the absence of activation by Crl resulted in a slightly delayed expression of genes in the crl mutant ( Fig. 3B ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilE	activator	17208038	27	ver/dev	Data _ suggesting that PhoP represses SPI1 by activating hilE expression	149	Data suggesting that PhoP represses SPI1 by activating hilE expression has also been presented [ 53 ] .	10	HILE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	prgH	activator	34424033	39	ver/dev	Introduction of the H-NS DN caused significant induction of the prgH promoter .	446	Introduction of the H-NS DN caused significant induction of the prgH promoter ( Fig. 8B ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
FNR	gene	tag	regulator	19690172	0	ver/dev	Mutation in glnP , the glutamine-binding protein , results in the inability to grow on proline Mutation in glnP results in an inability to grow on L-glutamate Many E. coli K12 strains harbor a thermolabilespecific aldolase involved in galactitol degradation FNR i.e. anaerobiosis-dependent expression of ansB ( L-asparagine II ) occurs in E. coli but not Salmonella -- The pdu operon is present in Salmonella but absent in E. coli ApeE , an outer membrane esterase present in Salmonella , allows hydrolysis of naphthyl esters ApeE , an outer membrane esterase present in Salmonella , allows hydrolysis of naphthyl esters Genes for ribitol catabolism missing in E. coli K12 The cit/tcu operon is absent in most E. coli but enables citrate utilization in Salmonella The cit/tcu operon , absent in E. coli , is also responsible for metabolism of the structurally related tricarballylic-acid The hpa operon required for catabolism of 4-HPA is present in Salmonella but missing in E. coli K12 strains The hpa operon required for catabolism of 4-HPA is present in Salmonella but missing in E. coli K12 -- The deoQKPX operon , absent from E. coli , is required for the uptake , phosphorylation , and regulation of 2-deoxy-D-ribose utilization The presence of tag genes in the gat ( galactitol ) operon enables degradation of D-tagatose in Salmonella -- In Salmonella , tyramine utilization as a carbon source results from its oxidative deamination by the cell membrane-bound tyramine oxidase ( TynA/MaoA ) to 4-HPA , requiring the hpa operon , which is absent from E. coli K12 The ebg operon required for lactulose utilization is absent in Salmonella Tartrate dehydrogenase , yeaU or ttuC , required for the breakdown of D-malate , is present in E. coli but absent from Salmonell	181	Mutation in glnP , the glutamine-binding protein , results in the inability to grow on proline ( 29 ) Mutation in glnP results in an inability to grow on L-glutamate ( 29 ) Many E. coli K12 strains harbor a thermolabilespecific aldolase involved in galactitol degradation ( 51 ) FNR i.e. anaerobiosis-dependent expression of ansB ( L-asparagine II ) occurs in E. coli but not Salmonella ( 37 ) -- The pdu operon is present in Salmonella but absent in E. coli ( 38 , 52 ) ApeE , an outer membrane esterase present in Salmonella , allows hydrolysis of naphthyl esters ( 53 , 54 ) ApeE , an outer membrane esterase present in Salmonella , allows hydrolysis of naphthyl esters ( 53 , 54 ) Genes for ribitol catabolism missing in E. coli K12 ( 55 , 56 ) The cit/tcu operon is absent in most E. coli but enables citrate utilization in Salmonella ( 57 ) The cit/tcu operon , absent in E. coli , is also responsible for metabolism of the structurally related tricarballylic acid ( 58 ) The hpa operon required for catabolism of 4-HPA is present in Salmonella but missing in E. coli K12 strains ( 39 ) The hpa operon required for catabolism of 4-HPA is present in Salmonella but missing in E. coli K12 ( 39 ) -- The deoQKPX operon , absent from E. coli , is required for the uptake , phosphorylation , and regulation of 2-deoxy-D-ribose utilization ( 59 ) The presence of tag genes in the gat ( galactitol ) operon enables degradation of D-tagatose in Salmonella -- In Salmonella , tyramine utilization as a carbon source results from its oxidative deamination by the cell membrane-bound tyramine oxidase ( TynA/MaoA ) to 4-HPA , requiring the hpa operon , which is absent from E. coli K12 ( 60 ) The ebg operon required for lactulose utilization is absent in Salmonella ( 61 , 62 ) Tartrate dehydrogenase , yeaU or ttuC , required for the breakdown of D-malate , is present in E. coli ( 22 , 63 ) but absent from Salmonell	3	EXPERIMENTAL PROCEDURES	Escherichia coli;Escherichia coli;Salmonella;Salmonella;Escherichia coli;Salmonella;Salmonella;Escherichia coli;Escherichia coli;Salmonella;Escherichia coli;Salmonella;Escherichia coli;Salmonella;Escherichia coli;Escherichia coli;Salmonella;Salmonella;Escherichia coli;Salmonella;Escherichia coli	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	katE	activator	15790293	4	ver/dev	While initially defined as an activator of the catalase gene katE , RpoS seems to participate in the ATRs	233	While initially defined as an activator of the catalase gene katE , RpoS seems to participate in the ATRs ( Audia et al. , 2001 ) , and inactivation of rpoS leads to avirulence in the mouse salmonellosis model ( Fang et al. , 1992 ) .	14	ALTERNATIVE R-FACTORS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	katE	activator	19843227	49	att	Tanaka , K. , Handel , K. , Loewen , P.C. , and Takahashi , H. ( 1997 ) Identification and analysis of the RpoS-dependent promoter of katE , encoding catalase HPII in Escherichia coli .	582	Tanaka , K. , Handel , K. , Loewen , P.C. , and Takahashi , H. ( 1997 ) Identification and analysis of the RpoS-dependent promoter of katE , encoding catalase HPII in Escherichia coli .	40	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	katE	activator	22275872	7	att	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	326	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	10	VALIDATION OF MICROARRAY ANALYSIS USING LAC FUSIONS	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	katE	activator	22356617	4	att	Further , a mutation in the fliZ gene in E. coli has recently been shown to cause premature expression of RpoS-dependent genes ( Pesavento et al. , 2008 ) and in Salmonella overproduction of FliZ decreases expression of the RpoS-dependent genes , katE and sodCII ( Chubiz et al. , 2010 ) .	342	Further , a mutation in the fliZ gene in E. coli has recently been shown to cause premature expression of RpoS-dependent genes ( Pesavento et al. , 2008 ) and in Salmonella overproduction of FliZ decreases expression of the RpoS-dependent genes , katE and sodCII ( Chubiz et al. , 2010 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	katE	activator	25549217	1	att	RpoS-dependent katE transcription in SG .	135	RpoS-dependent katE transcription in SG .	6	STATISTICAL ANALYSIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	activator	25549217	2	att	RpoS-dependent katE transcription in SG .	156	RpoS-dependent katE transcription in SG .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	activator	30414454	3	ver/dev	Previous research showed that katE is induced by RpoS in S. typhimurium .	230	Previous research showed that katE is induced by RpoS in S. typhimurium [ 32 ] and that RpoS is involved in VBNC resuscitation in E. coli [ 33 ] .	20	3.5. CAT GENE IS REGULATED BY RPOS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	katE	activator	33799446	0	att	The katE gene , encoding the HPII catalase , is considered to be RpoS-dependent in Salmonella [ 38,39 ] , and it also contributes to the prevention of oxidative-stress [ 40 ] .	98	The katE gene , encoding the HPII catalase , is considered to be RpoS-dependent in Salmonella [ 38,39 ] , and it also contributes to the prevention of oxidative stress [ 40 ] .	4	1. INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	glpF	activator	19843227	42	att	( ii ) Regulation of CRP-cAMP-dependent genes ( e.g. glpF , dctA , mglA ) is restricted to the late exponential phase .	302	( ii ) Regulation of CRP-cAMP-dependent genes ( e.g. glpF , dctA , mglA ) is restricted to the late exponential phase .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	glpF	activator	19843227	22	ver/dev	glpF , are activated by CRP-cAMP in Table S1 .	139	Many of these genes , including mglAB , aspA and glpF , are involved in the catabolism of carbohydrates and are activated by CRP-cAMP in E. coli ( Gosset et al. , 2004 ) ( Table S1 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	glpF	activator	19843227	22	ver/dev	glpF , are activated by CRP-cAMP in E. coli .	139	Many of these genes , including mglAB , aspA and glpF , are involved in the catabolism of carbohydrates and are activated by CRP-cAMP in E. coli ( Gosset et al. , 2004 ) ( Table S1 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	gtgE	regulator	27886269	0	ver/dev	protein-DNA interaction assays showed regulation by HilD for six of these genes : gtgE , phoH , sinR , SL1263 -LRB- lpxR -RRB- were regulated directly , whereas SL1896 was regulated indirectly .	10	Expression analyses and protein-DNA interaction assays showed regulation by HilD for six of these genes : gtgE , phoH , sinR , SL1263 ( lpxR ) and SL4247 were regulated directly , whereas SL1896 was regulated indirectly .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	gtgE	regulator	27886269	0	ver/dev	Expression analyses showed regulation by HilD for six of these genes : gtgE , phoH , sinR , SL1263 -LRB- lpxR -RRB- were regulated directly , whereas SL1896 was regulated indirectly .	10	Expression analyses and protein-DNA interaction assays showed regulation by HilD for six of these genes : gtgE , phoH , sinR , SL1263 ( lpxR ) and SL4247 were regulated directly , whereas SL1896 was regulated indirectly .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	gtgE	regulator	27886269	3	ver/dev	HilD , regulates the expression of gtgE .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	gtgE	regulator	27886269	11	ver/dev	that HilD directly controls the expression of the gtgE genes	94	Thus , these data strongly support that HilD directly controls the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly , through a regulator found in S. Typhimurium but not in E. coli MC4100 , that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	gtgE	regulator	27886269	12	ver/dev	HilD binds to the regulatory regions of gtgE .	110	HilD binds to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	gtgE	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of gtgE is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	gtgE	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of gtgE is direct , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	gtgE	regulator	27886269	16	ver/dev	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the gtgE genes .	120	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	gtgE	regulator	27886269	17	ver/dev	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : gtgE .	125	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes that are co-expressed with SPI-1 were identified : gtgE , phoH , sinR , SL1028 , lpxR , SL1896 , SL3812 , SL4247 and SL4433 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Escherichia coli	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of gtgE .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Salmonella;Salmonella	0.5	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	gtgE	regulator	27886269	21	ver/dev	Thus , HilD directly regulates the expression of the gtgE genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	gtgE	regulator	27886269	25	ver/dev	Therefore , the expression of gtgE is controlled by HilD in SPI-1-inducing conditions .	164	Therefore , the expression of gtgE is controlled by HilD in SPI-1-inducing conditions and probably by another regulator in SPI-2-inducing conditions , which would coordinate the secretion of GtgE through the T3SS-1 and T3SS-2 , respectively .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	gtgE	regulator	27886269	25	ver/dev	Therefore , the expression of gtgE is controlled by HilD by another regulator in SPI-2-inducing conditions .	164	Therefore , the expression of gtgE is controlled by HilD in SPI-1-inducing conditions and probably by another regulator in SPI-2-inducing conditions , which would coordinate the secretion of GtgE through the T3SS-1 and T3SS-2 , respectively .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	gtgE	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the gtgE genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	gtgE	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the gtgE genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	gtgE	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the gtgE genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	gtgE	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the gtgE genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	gtgE	regulator	27886269	31	ver/dev	HilD binds to the regulatory region of gtgE .	177	HilD binds to the regulatory region of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	asr	regulator	18790861	53	ver/dev	the E. coli asr gene where the RstA protein bound at a site between 68 upstream of the asr promoter	268	Considering the binding position , the Salmonella RstA protein is likely to act as a class I transcription factor for feoAB transcription as proposed for the E. coli asr gene , where the RstA protein bound at a site between 55 and 68 upstream of the asr promoter and activated its transcription ( 19 ) .	5	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	asr	regulator	18790861	53	ver/dev	the E. coli asr gene where the RstA protein bound at a site between 55 upstream of the asr promoter	268	Considering the binding position , the Salmonella RstA protein is likely to act as a class I transcription factor for feoAB transcription as proposed for the E. coli asr gene , where the RstA protein bound at a site between 55 and 68 upstream of the asr promoter and activated its transcription ( 19 ) .	5	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	asr	regulator	30763640	25	att	The alignment of asr and STM1485 RstA-regulated sequences displays 92.89 % identity ( Fig .	159	The alignment of asr and STM1485 RstA-regulated sequences displays 92.89 % identity ( Fig .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	wzzB	activator	27206164	24	att	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	rpoA	repressor	25107963	1	ver/dev	Besides overall transcriptional decreases for genes , lower transcript abundances were observed in rpoA ( encoding DNA-directed RNA polymerase subunit alpha ) , DNA-binding protein Fis .	186	Besides overall transcriptional decreases for genes related to translation , lower transcript abundances were observed for genes involved in transcription and in replication , recombination , and repair , such as rpoA ( encoding DNA-directed RNA polymerase subunit alpha ) , gyrA ( DNA gyrase subunit A ) , fis ( DNA-binding protein Fis ) , and priB ( primosomal replication protein N ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhD	gene	fliA	regulator	16430704	0	ver/dev	In turn , fliA is positively controlled by the gene products FlhD .	79	In turn , fliA is positively controlled by the gene products FlhD and FlhC , which are encoded by the sole operon lying at the apex of the hierarchy .	5	THE SALMONELLA DNAK MUTANT IS DEFECTIVE IN FLAGELLUM BIOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtcR	gene	STM0571	activator	27583250	4	ver/dev	Further characterization of RtcR activation of STM0571 will give a clearer picture of how bEBPs can alter the lifestyle of other pathogens to improve their chances of survival during the infection process .	281	Further characterization of RtcR activation by nucleic acid damage/modi fication and of the three currently uncharacterized bEBPs ( STM0571 , STM0652 , and STM2361 ) will give a clearer picture of how bEBPs can alter the lifestyle of S. Typhimurium and other pathogens to improve their chances of survival during the infection process .	16	CONCLUSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtcR	gene	STM0571	activator	27583250	4	ver/dev	Further characterization of RtcR activation of STM0571 will give a clearer picture of how bEBPs can alter the lifestyle of S. Typhimurium to improve their chances of survival during the infection process .	281	Further characterization of RtcR activation by nucleic acid damage/modi fication and of the three currently uncharacterized bEBPs ( STM0571 , STM0652 , and STM2361 ) will give a clearer picture of how bEBPs can alter the lifestyle of S. Typhimurium and other pathogens to improve their chances of survival during the infection process .	16	CONCLUSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	STM1485	activator	30763640	60	att	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	NEG	Other	Level 1
SdiA	TU	PSLT025	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	ptsN	regulator	33853321	5	ver/dev	These suggest that CRP might control ptsN transcription in response to glucose concentrations .	120	These suggest that CRP might control ptsN transcription in response to glucose concentrations .	3	SI SUPPORTING INFORMATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	ptsN	regulator	33853321	8	ver/dev	In vitro binding of CRP protein to the ptsN promoter with diverse concentrations of cAMP .	130	( C ) In vitro binding of CRP protein to the ptsN promoter with diverse concentrations of cAMP .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	ptsN	regulator	33853321	12	ver/dev	To examine whether CRP directly controls ptsN transcription by binding to the regulatory region , purified CRP proteins were incubated with ptsN promoter DNA fragments .	156	To examine whether CRP directly controls ptsN transcription by binding to the regulatory region , purified CRP proteins were incubated with ptsN promoter DNA fragments .	3	SI SUPPORTING INFORMATION	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
CRP	gene	ptsN	regulator	33853321	13	ver/dev	In the presence of suficient cAMP , purified CRP binds to the ptsN promoter in-vitro .	157	In the presence of suficient cAMP , purified CRP binds to the ptsN promoter in vitro ( Figure 3C ) .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	ptsN	regulator	33853321	14	ver/dev	In agreement with the glucose-dependent control of the ptsN gene , CRP binding to the ptsN promoter requires cAMP .	158	In agreement with the glucose-dependent control of the ptsN gene ( Figure 3B ) , CRP binding to the ptsN promoter requires cAMP ( Figure 3C ) .	3	SI SUPPORTING INFORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	tpx	repressor	18156266	11	ver/dev	The proteomic data revealed that LeuO represses the expression of tpx .	240	The proteomic data mentioned above also revealed that LeuO represses the expression of tpx , ompX , and STY1978 .	5	FIG. 2	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	tpx	repressor	18156266	31	ver/dev	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code during biofilm formation .	323	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme that is induced under several pH conditions ( 51 ) , in the exponential growth phase , and during biofilm formation ( 22 ) .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	tpx	repressor	18156266	31	ver/dev	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code in the exponential-growth-phase .	323	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme that is induced under several pH conditions ( 51 ) , in the exponential growth phase , and during biofilm formation ( 22 ) .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	tpx	repressor	18156266	31	ver/dev	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme .	323	The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme that is induced under several pH conditions ( 51 ) , in the exponential growth phase , and during biofilm formation ( 22 ) .	6	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	feoA	regulator	18790861	52	ver/dev	the RstA protein bound to the feoA promoter	267	Indeed , the RstA protein bound to the feoA promoter , and mutation of this putative site prevented RstA binding ( Fig. 2C ) , which in turn abolished the RstA-mediated activation of feoAB transcription ( Fig. 2A ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	feoA	regulator	18790861	58	ver/dev	When activated under iron-replete conditions by unknown signal , the RstA protein binds to the feoA promoter to activate transcription of the feoAB operon .	284	When activated under iron-replete conditions by unknown signal ( s ) , the RstA protein binds to the feoA promoter to activate transcription of the feoAB operon encoding the Fe ( II ) transporter FeoB .	5	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	New	Level 3
Lrp	gene	invF	repressor	19074398	14	ver/dev	Transcription of the hilA , invF is repressed by Lrp .	276	Transcription of the hilA , invF , and ssrA genes is repressed by Lrp .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	invF	repressor	22291968	0	ver/dev	For instance , Lrp , reduces SPI-1 expression by repressing transcription of invF .	42	For instance , the leucine-responsive regulatory protein , Lrp , reduces SPI-1 expression by repressing transcription of hilA and invF [ 20 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoB	gene	phoB	regulator	29693629	0	ver/dev	Furthermore , proteomic analysis of a mutant lacking phoB ( that encodes a key regulator of Pi shortage response ) suggested that only a small subset of the altered proteins upon Pi limitation was PhoB-dependent .	10	Furthermore , proteomic analysis of a mutant lacking phoB ( that encodes a key regulator of Pi shortage response ) suggested that only a small subset of the altered proteins upon Pi limitation was PhoB-dependent .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	hilA	regulator	22004521	11	ver/dev	Moreover , studies have shown that FliZ , under the control of FlhDC , positively regulates hilA expression by controlling HilD post-translationally , through a mechanism independent of the Lon protease .	326	Moreover , studies have shown that FliZ , under the control of FlhDC , positively regulates hilA expression by controlling HilD post-translationally , through a mechanism independent of the Lon protease ( 50 ) .	25	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	invG	repressor	25028458	29	ver/dev	Although we demonstrated that this phenotype results from strong repression of invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes .	322	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	slrP	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilC independently of InvF .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	slrP	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilC independently of both HilA .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	slrP	activator	25182488	3	ver/dev	In this context , slrP is induced by overexpression of HilC independently of the central SPI1 regulator HilA , with RtsA .	38	In this context , slrP is induced by overexpression of HilC , HilD , and RtsA independently of the central SPI1 regulator HilA , with RtsA being the best inducer .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hns	activator	15256548	15	ver/dev	These included the cold-shock-responsive hns gene previously shown to be activated by Fis and -LRB- like H-NS -RRB- regulates several virulence genes in response to temperature .	667	These included the cold-shock-responsive hns gene previously shown to be activated by Fis ( Dersch et al. , 1994 ; Falconi et al. , 1996 ) , the hha gene whose product can form heteromeric complexes with H-NS and ( like H-NS ) regulates several virulence genes in response to temperature ( Madrid et al. , 2002 ; Nieto et al. , 2002 ) , and the stpA gene that encodes a paralogue of H-NS and can also form heteromers with it ( Deighan et al. , 2003 ; Free et al. , 2001 ; Johansson et al. , 2001 ; Williams et al. , 1996 ) .	15	STRESS RESPONSE GENES AND GLOBAL REGULATORS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsA	gene	ugd	activator	12519186	20	att	The tolB mutation specifically promotes transcription of the ugd gene in an RcsC -- YojN -- RcsB - and RcsA-dependent manner and independently of the PhoP and PmrA proteins .	61	The tolB mutation specifically promotes transcription of the ugd gene in an RcsC -- YojN -- RcsB - and RcsA-dependent manner and independently of the PhoP and PmrA proteins .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsA	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes promoted by various signals -- the RcsA protein .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsA	gene	ugd	activator	12519186	41	ver/dev	Likewise , ugd transcription is co-ordinately induced with that of the cps genes by the RcsA protein , possibly because of its role in col-anic acid capsule synthesis .	125	Likewise , ugd transcription is co-ordinately induced with that of the cps genes by the RcsC -- YojN -- RcsB system and the RcsA protein ( Fig. 3 ) , possibly because of its role in col-anic acid capsule synthesis .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsA	gene	ugd	activator	12519186	42	ver/dev	Transcriptional activation of the ugd gene by the RcsC -- YojN -- RcsA protein	130	Transcriptional activation of the ugd gene by the RcsC -- YojN -- RcsB system and RcsA protein	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsA	gene	ugd	activator	12519186	43	ver/dev	We have established that the tolB-promoted expression of the ugd gene occurs by activation of the RcsA proteins	131	We have established that the tolB-promoted expression of the ugd gene occurs by activation of the RcsB and RcsA proteins and is independent of the PhoP -- PhoQ and	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	yjdB	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	12675803	1	ver/dev	Transcription of the flhDC operon is known to be regulated by signals from a network of CRP .	44	Transcription of the flhDC operon is known to be regulated by signals from a network of cell components including CRP , OmpR , H-NS and the DnaK-DnaJ-GrpE system ( Yokota and Gots , 1970 ; Shi et al. , 1992 ; Bertin et al. , 1994 ; Kutsukake , 1997 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CRP	TU	flhDC	regulator	17074910	2	ver/dev	Transcription of the flhDC promoter is regulated by Crp , LrhA .	60	Transcription of the flhDC promoter is regulated by Crp , OmpR , H-NS , HdfR , QseBC , FliA and LrhA , and also by DNA supercoiling , temperature , growth phase and cell cycle ( Chilcott & Hughes , 2000 ; Clarke & Sperandio , 2005 ; Kutsukake , 1997 ; Soutourina et al. , 1999 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	17074910	2	ver/dev	Transcription of the flhDC promoter is regulated by Crp , FliA .	60	Transcription of the flhDC promoter is regulated by Crp , OmpR , H-NS , HdfR , QseBC , FliA and LrhA , and also by DNA supercoiling , temperature , growth phase and cell cycle ( Chilcott & Hughes , 2000 ; Clarke & Sperandio , 2005 ; Kutsukake , 1997 ; Soutourina et al. , 1999 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	17074910	2	ver/dev	Transcription of the flhDC promoter is regulated by Crp , QseBC .	60	Transcription of the flhDC promoter is regulated by Crp , OmpR , H-NS , HdfR , QseBC , FliA and LrhA , and also by DNA supercoiling , temperature , growth phase and cell cycle ( Chilcott & Hughes , 2000 ; Clarke & Sperandio , 2005 ; Kutsukake , 1997 ; Soutourina et al. , 1999 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	17074910	2	ver/dev	Transcription of the flhDC promoter is regulated by Crp , HdfR .	60	Transcription of the flhDC promoter is regulated by Crp , OmpR , H-NS , HdfR , QseBC , FliA and LrhA , and also by DNA supercoiling , temperature , growth phase and cell cycle ( Chilcott & Hughes , 2000 ; Clarke & Sperandio , 2005 ; Kutsukake , 1997 ; Soutourina et al. , 1999 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	17074910	2	ver/dev	Transcription of the flhDC promoter is regulated by Crp , H-NS .	60	Transcription of the flhDC promoter is regulated by Crp , OmpR , H-NS , HdfR , QseBC , FliA and LrhA , and also by DNA supercoiling , temperature , growth phase and cell cycle ( Chilcott & Hughes , 2000 ; Clarke & Sperandio , 2005 ; Kutsukake , 1997 ; Soutourina et al. , 1999 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	17074910	2	ver/dev	Transcription of the flhDC promoter is regulated by Crp , OmpR .	60	Transcription of the flhDC promoter is regulated by Crp , OmpR , H-NS , HdfR , QseBC , FliA and LrhA , and also by DNA supercoiling , temperature , growth phase and cell cycle ( Chilcott & Hughes , 2000 ; Clarke & Sperandio , 2005 ; Kutsukake , 1997 ; Soutourina et al. , 1999 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	flhDC	regulator	25161191	1	ver/dev	The cAMP-CRP complex also regulates the transcription of the flhDC operon in S. enterica , although YdiV apparently masks the effect , at least under the conditions .	35	The cAMP-CRP complex also regulates the transcription of the flhDC operon in S. enterica ( 9 ) , although YdiV apparently masks the effect , at least under the conditions in which these experiments were performed .	2	MAIN	Salmonella;Salmonella	1	L2	OTHER	Other	OTHER	New	Level 1
CRP	TU	flhDC	regulator	32909667	1	ver/dev	The cAMP -- CRP regulon controls flagellar master operon flhDC in S. enterica .	165	The cAMP -- CRP regulon controls the flagellar gene cluster I and flagellar master operon flhDC in S. enterica [ 26 ] .	10	D‐ARABINOSE − +++ +	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	TU	flhDC	regulator	34202800	1	ver/dev	In S. Typhimurium , flhDC expression is regulated by CRP receptor protein , Fur , proteins binding Fis nucleoid , histone-like protein .	191	In S. Typhimurium , flhDC expression is regulated by several factors such as cAMP ( CRP ) receptor protein , Fur , proteins binding Fis nucleoid , histone-like protein structuring the ( H-NS ) nucleoids , and SlyA [ 63 ] .	5	2. SALMONELLA PATHOGENESIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	entF	regulator	33638994	17	ver/dev	By nuclease assays , we confirmed that RcsB binds , in a phosphorylation dependent way , specifically to the intergenic region between the 3 ′ end of entF to n -LRB- sequence from -1 to , protecting against DNAse I e I the re .	394	By nuclease assays , we confirmed that RcsB binds , in a phosphorylation dependent way , specifically to the intergenic region between the 3 ′ end of entF to 5 ′ fepE gene start codon ( sequence from -1 to -249 ) , protecting against DNAse I the region that includes the RcsB consensus sequence ( Supplementary Figure S11 ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	entF	regulator	33638994	17	ver/dev	By nuclease assays , we confirmed that RcsB binds , in a phosphorylation dependent way , specifically to the intergenic region between the 3 ′ end of entF to o 5 ′ fepE gene start c , protecting against DNAse I e I the re .	394	By nuclease assays , we confirmed that RcsB binds , in a phosphorylation dependent way , specifically to the intergenic region between the 3 ′ end of entF to 5 ′ fepE gene start codon ( sequence from -1 to -249 ) , protecting against DNAse I the region that includes the RcsB consensus sequence ( Supplementary Figure S11 ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FimZ	gene	fimA	activator	11133935	14	ver/dev	Instead , FimW may function by influencing the ability of FimZ to activate transcription from this promoter , either by inhibiting the binding of FimZ to the fimA promoter or by inhibiting activation by FimZ once this protein has bound .	361	Instead , FimW may function by influencing the ability of FimZ to activate transcription from this promoter , either by inhibiting the binding of FimZ to the fimA promoter or by inhibiting activation by FimZ once this protein has bound .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
FimZ	gene	fimA	activator	11911183	4	ver/dev	Consistent with the role of FimZ as an activator of S. typhimurium fimA expression , fimZ mutants exhibit only low levels of fimA expression .	31	Consistent with the role of FimZ as an activator of S. typhimurium fimA expression , fimZ mutants are non-fimbriate and exhibit only low levels of fimA expression ( 40 ) .	2	KEY WORDS: SALMONELLA TYPHIMURIUM, TYPE 1 FIMBRIAE, ACTIVATOR	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	activator	11911183	4	ver/dev	Consistent with the role of FimZ as an activator of S. typhimurium fimA expression , fimZ mutants are non-fimbriate .	31	Consistent with the role of FimZ as an activator of S. typhimurium fimA expression , fimZ mutants are non-fimbriate and exhibit only low levels of fimA expression ( 40 ) .	2	KEY WORDS: SALMONELLA TYPHIMURIUM, TYPE 1 FIMBRIAE, ACTIVATOR	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	fimA	activator	24462182	31	ver/dev	Since FimZ are both required to activate fimA , it is possible that these two proteins form a complex to bind the promoter of fimA .	245	Since FimY and FimZ are both required to activate fimA ( Swenson and Clegg , 1992 ) , it is possible that these two proteins form a complex to bind the promoter of fimA .	17	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
FimZ	gene	fimA	activator	31139165	8	att	The authors suggested that FimW may have a modulatory role in FimZ-induced activation of the T1F fimA promoter by preventing FimZ binding to PfimA .	114	The authors suggested that FimW may have a modulatory role in FimZ-induced activation of the T1F fimA promoter by preventing FimZ binding to PfimA .	4	DIRECT REGULATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FimZ	gene	fimA	activator	31139165	3	ver/dev	Activation of the fimA promoter by FimZ requires the presence of a second regulator -- FimY .	98	Activation of the fimA promoter by FimZ requires the presence of a second regulator -- FimY ( Yeh et al. , 1995 ) , which acts upstream of FimZ in the regulatory pathway , but does not interact directly with either FimZ or FimW ( Zeiner et al. , 2013 ) .	4	DIRECT REGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	activator	31139165	8	ver/dev	The authors suggested that FimW may have a modulatory role in FimZ-induced activation of the T1F fimA promoter by preventing FimZ binding to PfimA .	114	The authors suggested that FimW may have a modulatory role in FimZ-induced activation of the T1F fimA promoter by preventing FimZ binding to PfimA .	4	DIRECT REGULATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FimZ	gene	fimA	activator	8550478	0	ver/dev	We demonstrated that FimZ is a transcriptional activator of fimA .	88	We have recently characterized the fimZ mutant of S. typhimurium LB5010 and demonstrated that FimZ is a transcriptional activator of fimA ( 24 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fur	gene	sodB	activator	17208038	23	att	Another ` Fur-activated ' gene , sodB , is controlled at the level of translation by the small RNA ryhB , with the help of the RNA binding protein Hfq , in Escherichia coli [ 45 -- 48 ] .	131	Another ` Fur-activated ' gene , sodB , is controlled at the level of translation by the small RNA ryhB , with the help of the RNA binding protein Hfq , in Escherichia coli [ 45 -- 48 ] .	9	FUR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sodB	activator	17993530	11	att	One such `` Fur-activated '' gene is sodB ( 15 ) , which encodes the superoxide dismutase with an Fe cofactor in E. coli .	55	One such `` Fur-activated '' gene is sodB ( 15 ) , which encodes the superoxide dismutase with an Fe cofactor in E. coli .	2	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sodB	activator	17993530	27	att	Known `` Fur-activated '' genes , like sodB , are regulated at the level of translation initiation and/or mRNA stability .	218	Known `` Fur-activated '' genes , like sodB , are regulated at the level of translation initiation and/or mRNA stability .	4	RESULTS	nan	1	L2	OTHER	Other	NEG	Other	Level 1
OmpR	gene	atpB	activator	25875623	11	ver/dev	The transcript for atpB was up-regulated -LRB- 2.1-fold -RRB- in the WT strain , suggesting a role for OmpR in activation of S9B Fig .	285	The transcript for atpB was up-regulated ( 2.1-fold ) in the WT strain , suggesting a role for OmpR in activation of atpB ( S9B Fig ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	atpB	activator	25875623	11	ver/dev	The transcript for atpB was up-regulated -LRB- 2.1-fold -RRB- in the WT strain , suggesting a role for OmpR in activation of atpB .	285	The transcript for atpB was up-regulated ( 2.1-fold ) in the WT strain , suggesting a role for OmpR in activation of atpB ( S9B Fig ) .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	atpB	activator	29103680	0	ver/dev	The authors further showed that , in addition to repression of the cadBA genes , OmpR was apparently also involved in activation of the atpB gene , encoding the α F0 subunit of the ATP synthase , thereby maintaining the cytoplasmic acidification in media at pH 5.6 .	173	The authors further showed that , in addition to repression of the cadBA genes which would consume protons , OmpR was apparently also involved in activation of the atpB gene , encoding the α F0 subunit of the ATP synthase , thereby maintaining the cytoplasmic acidification in media at pH 5.6 .	18	4. DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
NsrR	gene	hcp	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
LacI	gene	lacI	regulator	21134969	7	att	In our case , the regulatable repression element is arabinose-regulated lacI , and the regulatable promoter is LacI-regulated Ptrc .	327	In our case , the regulatable repression element is arabinose-regulated lacI , and the regulatable promoter is LacI-regulated Ptrc .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LacI	gene	lacI	regulator	25362512	1	ver/dev	LacI expression in 14028 was also under the control of its native promoter by inserting both lacI gene sequence to pACYC184 .	67	LacI expression in 14028 was also under the control of its native promoter by inserting both lacI promoter and lacI gene sequence to pACYC184 .	5	BACTERIAL STRAINS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LacI	gene	lacI	regulator	25362512	1	ver/dev	LacI expression in 14028 was also under the control of its native promoter by inserting both lacI promoter to pACYC184 .	67	LacI expression in 14028 was also under the control of its native promoter by inserting both lacI promoter and lacI gene sequence to pACYC184 .	5	BACTERIAL STRAINS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompR	activator	30663891	7	ver/dev	H-NS in turn increases ompR transcription	292	After these findings , it was suggested that the acid stress alters DNA supercoiling in the ompR promoter , allowing OmpR-P to bind and displace H-NS , which in turn increases ompR transcription ( Audia et al. , 2001 ) .	11	4.2.1 ACID TOLERANCE RESPONSE (ATR)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompR	activator	30663891	7	ver/dev	H-NS in turn increases ompR transcription	292	After these findings , it was suggested that the acid stress alters DNA supercoiling in the ompR promoter , allowing OmpR-P to bind and displace H-NS , which in turn increases ompR transcription ( Audia et al. , 2001 ) .	11	4.2.1 ACID TOLERANCE RESPONSE (ATR)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimY	gene	fimZ	regulator	24462182	0	ver/dev	FimY of Salmonella enterica serovar Typhimurium binds the fimZ promoter	3	FimY of Salmonella enterica serovar Typhimurium functions as a DNA-binding protein and binds the fimZ promoter	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimY	gene	fimZ	regulator	31139165	14	ver/dev	FimY of Salmonella enterica serovar Typhimurium binds the fimZ promoter .	1208	FimY of Salmonella enterica serovar Typhimurium functions as a DNA-binding protein and binds the fimZ promoter .	18	TIME: 14:52 # 17	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
DnaA	gene	seqA	regulator	20132031	0	ver/dev	the control of the DnaA binding to oriC can be related with the partial reestablishment of the replication asynchrony _ observed at every seqA mutant	275	However , Makise et al. ( 2002 ) have reported that UFAs increase membrane fluidity , which may be important for the control of the DnaA binding to oriC in vitro and can be related with the partial reestablishment of the replication asynchrony observed at every seqA and dam mutant ( Lobner-Olesen and Von Freiesleben , 1996 ) .	14	MEMBRANE PHL COMPOSITION OF S. ENTERICA SEROVAR TYPHIMURIUM: EFFECTS OF SEQA AND DAM MUTATIONS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
DnaA	gene	seqA	regulator	20132031	0	ver/dev	the control of the DnaA binding to oriC in-vitro _ observed at every seqA mutant	275	However , Makise et al. ( 2002 ) have reported that UFAs increase membrane fluidity , which may be important for the control of the DnaA binding to oriC in vitro and can be related with the partial reestablishment of the replication asynchrony observed at every seqA and dam mutant ( Lobner-Olesen and Von Freiesleben , 1996 ) .	14	MEMBRANE PHL COMPOSITION OF S. ENTERICA SEROVAR TYPHIMURIUM: EFFECTS OF SEQA AND DAM MUTATIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	aldB	repressor	15256548	8	ver/dev	The aldB gene was repressed by Fis in agreement with previous data from E. coli .	641	The aldB gene was repressed by Fis ( Table 4 ) in agreement with previous data from E. coli ( Xu & Johnson , 1995a , b ) .	14	GENES INVOLVED IN METABOLISM AND TRANSPORT	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
MlrA	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of MlrA to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
MlrA	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of MlrA to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	sipC	activator	26039089	12	att	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary-phase ( Fig 5 ) .	214	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary phase ( Fig 5 ) .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sipC	activator	26039089	12	att	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary-phase ( Fig 5 ) .	214	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary phase ( Fig 5 ) .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sipC	activator	26039089	13	att	This may suggest a mechanism whereby sipC and possibly other SPI1 encoded gene expression could remain ` buffered ' against rapid changes in RNAP distribution caused by alternative sigma factors such as RpoS , thus potentially optimising a balance between the RpoS-dependent stationary-phase stress response and invasion .	218	This may suggest a mechanism whereby sipC and possibly other SPI1 encoded gene expression could remain ` buffered ' against rapid changes in RNAP distribution caused by alternative sigma factors such as RpoS , thus potentially optimising a balance between the RpoS-dependent stationary phase stress response and invasion .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sipC	activator	26039089	12	ver/dev	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC .	214	The sigma factor competition model would predict that overexpression of RpoS may result in reduced expression of the SPI1 effector gene sipC , due to the inferred redistribution of RNAP to RpoS-dependent promoter sites rather than SPI1 promoter sites and consistent with this , we confirmed that ectopic induction of RpoS resulted in severely reduced sipC : : lacZ activity compared to the parent strain during stationary phase ( Fig 5 ) .	13	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FimZ	TU	flhDC	regulator	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliT , FimZ .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	fur	repressor	18790861	18	att	We next examined transcription of the two Fur-repressed genes in the strain that carried deletions of the rstA and fur genes and harbored either the RstA expression plasmid or the plasmid vector ; analysis determined that the mRNA levels of fhuA and fhuF were similar to those in the fur deletion strain regardless of RstA expression ( Fig. 1B ) .	154	We next examined transcription of the two Fur-repressed genes in the strain that carried deletions of the rstA and fur genes and harbored either the RstA expression plasmid or the plasmid vector ; analysis determined that the mRNA levels of fhuA and fhuF were similar to those in the fur deletion strain regardless of RstA expression ( Fig. 1B ) .	4	RESULTS	unidentified plasmid;unidentified plasmid	1	L3	OTHER	Investigation	NEG	Other	Level 1
Fur	gene	fur	repressor	18790861	19	att	Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB-medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .	155	Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	h-NS	repressor	32209674	62	auto	C. Ueguchi , M. Kakeda , T. Mizuno , Autoregulatory expression of the Escherichia coli hns gene encoding a nucleoid protein : H-NS functions as a repressor of its own transcription .	740	C. Ueguchi , M. Kakeda , T. Mizuno , Autoregulatory expression of the Escherichia coli hns gene encoding a nucleoid protein : H-NS functions as a repressor of its own transcription .	6	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RhaS	gene	rhaT	regulator	24391637	2	ver/dev	The transcriptional regulator RhaS in E. coli controls the L-Rha transporter rhaT .	156	The transcriptional regulator RhaS in E. coli belongs to the AraC protein family and controls the L-Rha transporter rhaT and the catabolic operon rhaBADU ( Egan and Schleif , 1993 ; Via et al. , 1996 ) .	12	L-RHAMNOSE CATABOLIC REGULONS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	parC	repressor	28874380	3	ver/dev	These data indicate that CRP represses expression of parC .	147	These data indicate that CRP represses expression of parC and parE and suggest that the sustained expression of parCE in SL1344 : Δcrp could alter the supercoiling state of DNA in Δcrp mutant cells .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	activator	16045614	14	att	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	68	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	4	INTRODUCTION	unidentified	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	activator	16045614	14	ver/dev	Mutations in a previously unidentified PhoP-activated gene lead to increased hilA expression .	68	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	4	INTRODUCTION	unidentified	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	activator	26441883	0	att	The response regulator PhoP represses hilA and the prg ( PhoP-repressed genes ) genes ( Pegues et al. , 1995 ; Bajaj et al. , 1996 ) , whereas transcription of PhoP-activated genes ( pag ) required for survival within macrophages is activated ( Miller et al. , 1989 ; Belden and Miller , 1994 ) .	72	The response regulator PhoP represses hilA and the prg ( PhoP-repressed genes ) genes ( Pegues et al. , 1995 ; Bajaj et al. , 1996 ) , whereas transcription of PhoP-activated genes ( pag ) required for survival within macrophages is activated ( Miller et al. , 1989 ; Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	activator	31182495	10	att	This demonstrates that PhoP represses expression of hilA independently of any of these PhoP-activated regulatory systems .	78	This demonstrates that PhoP represses expression of hilA independently of any of these PhoP-activated regulatory systems .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	activator	31182495	6	ver/dev	Here , we show that PhoP acts by directly blocking activation of the hilA promoter .	50	Here , we show that PhoP acts by affecting expression of the upstream regulators RtsA and HilD , by directly blocking activation of the hilA promoter and by controlling expression of the small RNA ( sRNA ) PinT ( 46 ) .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	activator	31262841	4	ver/dev	We have shown that the PhoP represses hilA transcription by blocking activation of the promoter , providing mechanistic insight into how the SPI1 system is shut off after invasion .	54	We have shown that the PhoP represses hilA transcription by blocking activation of the promoter and also indirectly affects hilD and rtsA transcription , providing mechanistic insight into how the SPI1 system is shut off after invasion ( 60 ) .	3	KEYWORDS PHOPQ, SPI1, SALMONELLA, SRNA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	activator	31262841	11	ver/dev	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both hilA ( and hilD ) .	169	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both hilA and rtsA ( and hilD ) ( 60 ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	activator	33751923	1	ver/dev	Besides , PhoP can block hilA activation by binding to the promoter on a region .	344	Besides , PhoP can block hilA activation by binding to the promoter on a region that overlaps with HilD , HilC , and RtsA binding sites ( Palmer et al. 2019 ) .	7	PHOPQ	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SoxR	gene	acnA	activator	23637460	9	ver/dev	The activation of acnA expression by SoxR indicate that these are conserved regulatory features in both bacteria .	241	The activation of acnA expression by CRP and SoxR and repression by FNR are in accord with observations reported for the E. coli acnA promoter ( Cunningham et al. , 1997 ; Fig. 3b ) and indicate that these are conserved regulatory features in both bacteria .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxR	gene	acnA	activator	23637460	9	ver/dev	The activation of acnA expression by SoxR are in accord with observations .	241	The activation of acnA expression by CRP and SoxR and repression by FNR are in accord with observations reported for the E. coli acnA promoter ( Cunningham et al. , 1997 ; Fig. 3b ) and indicate that these are conserved regulatory features in both bacteria .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM3388	repressor	16629664	20	ver/dev	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 25 ± 11 after ( Fig. .	229	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed ( 156 ± 17 % ) at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 h and 25 ± 11 % after 24 h ( Fig. 5B ) .	10	REGULATION OF CSGD EXPRESSION BY CHROMOSOMALLY EXPRESSED GGDEF–EAL DOMAIN PROTEINS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM3388	repressor	16629664	20	ver/dev	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 25 ± 11 after r 24 .	229	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed ( 156 ± 17 % ) at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 h and 25 ± 11 % after 24 h ( Fig. 5B ) .	10	REGULATION OF CSGD EXPRESSION BY CHROMOSOMALLY EXPRESSED GGDEF–EAL DOMAIN PROTEINS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM3388	repressor	16629664	20	ver/dev	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 after ( Fig. .	229	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed ( 156 ± 17 % ) at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 h and 25 ± 11 % after 24 h ( Fig. 5B ) .	10	REGULATION OF CSGD EXPRESSION BY CHROMOSOMALLY EXPRESSED GGDEF–EAL DOMAIN PROTEINS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM3388	repressor	16629664	20	ver/dev	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 after r 24 .	229	In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed ( 156 ± 17 % ) at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 h and 25 ± 11 % after 24 h ( Fig. 5B ) .	10	REGULATION OF CSGD EXPRESSION BY CHROMOSOMALLY EXPRESSED GGDEF–EAL DOMAIN PROTEINS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MetR	gene	metE	repressor	21768276	4	ver/dev	Role of the MetR regulatory system in vitamin-B12-mediated repression of the Salmonella typhimurium metE gene .	1407	Role of the MetR regulatory system in vitamin B12-mediated repression of the Salmonella typhimurium metE gene .	44	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	ptsG	activator	23935052	1	ver/dev	Mlc is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli .	608	A global repressor ( Mlc ) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	fliA	repressor	18350168	3	att	According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .	295	According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	fliA	repressor	18350168	5	att	Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .	335	Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .	19	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
DksA	gene	sipC	regulator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at LSP according to measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	regulator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP according to measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	bfr	regulator	17302823	0	ver/dev	Thus , the S. Typhimu-rium bfr are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	virK	repressor	15225317	5	ver/dev	Candidate genes for this activity include virK because inactivation of these PhoP-activated genes results in strains .	35	Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .	3	2 ND POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	virK	repressor	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	mcpC	repressor	33441540	17	ver/dev	These data indicate that the region between − 79 to − , and support a derepression model by which HilD binding displaces a repressor of mcpC expression , i.e. if the upstream region is rem , then HilD binding is no longer required .	107	These data indicate that the region between − 79 to − 387 , which contains the HilD-binding site , has a repressing effect on mcpC expression and support a derepression model by which HilD binding displaces a repressor of mcpC expression , i.e. if the upstream region is removed , then HilD binding is no longer required .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Lrp	TU	ilvIH	regulator	11591661	2	ver/dev	In the presence of leucine , binding of Lrp is reduced , resulting in reduced transcriptional activation of ilvIH expression .	50	In the presence of leucine , binding of Lrp is reduced , resulting in reduced transcriptional activation of ilvIH expression ( references 60 and 61 and references therein ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	TU	ilvIH	regulator	12882514	4	ver/dev	It has been known that ilvIH promoter activity is under the positive control of Lrp .	281	It has been known that ilvIH promoter activity is under the positive control of Lrp ( leucine-responsive regulatory protein ) ( 57 , 65 ) .	31	III. A NEW EXPLANATION FOR THE OLD PHENOMENON, THE SUPPRESSION OF LEU-500 MUTATION IN SALMONELLA TYPHIMURIUM TOPA MUTANTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
Lrp	TU	ilvIH	regulator	19074398	4	att	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	25	Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .	2	MAIN	Salmonella;unidentified plasmid;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	srgB	regulator	29276700	0	ver/dev	The last two ORFs of srgB , encode a transcriptional regulator of the AraC family respectively .	110	The last two ORFs of the operon , srgB and srgC , encode a putative lipoprotein and a transcriptional regulator of the AraC family respectively .	3	FROM THE PEFI-SRGC OPERON TO THE REGULATION OF RCK EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	hilA	repressor	15469511	9	ver/dev	a putative RcsB binding site in the promoter region of the hilA gene _ suggesting that the transcriptional repression of the sipC genes observed in the rcsC11 mutant might result from reduced levels of hilA expression	289	Consistent with this notion , we identified a putative RcsB binding site in the promoter region of the hilA gene , suggesting that the transcriptional repression of the invG , invF and sipC genes observed in the rcsC11 mutant might result from reduced levels of hilA expression .	12	A ROLE FOR THE RCSC/YOJN/RCSB SYSTEM IN THE CONTROL OF INVASION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	hilA	repressor	15469511	9	ver/dev	a putative RcsB binding site in the promoter region of the hilA gene _ suggesting that the transcriptional repression of the invF genes observed in the rcsC11 mutant might result from reduced levels of hilA expression	289	Consistent with this notion , we identified a putative RcsB binding site in the promoter region of the hilA gene , suggesting that the transcriptional repression of the invG , invF and sipC genes observed in the rcsC11 mutant might result from reduced levels of hilA expression .	12	A ROLE FOR THE RCSC/YOJN/RCSB SYSTEM IN THE CONTROL OF INVASION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	hilA	repressor	15469511	9	ver/dev	a putative RcsB binding site in the promoter region of the hilA gene _ suggesting that the transcriptional repression of the invG genes observed in the rcsC11 mutant might result from reduced levels of hilA expression	289	Consistent with this notion , we identified a putative RcsB binding site in the promoter region of the hilA gene , suggesting that the transcriptional repression of the invG , invF and sipC genes observed in the rcsC11 mutant might result from reduced levels of hilA expression .	12	A ROLE FOR THE RCSC/YOJN/RCSB SYSTEM IN THE CONTROL OF INVASION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of inner membrane proteins i.e. AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of inner membrane proteins i.e. TolC with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of inner membrane proteins i.e. OmpD with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of inner membrane proteins i.e. OmpW with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of inner membrane proteins i.e. OmpC with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of inner membrane proteins i.e. OmpF with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer membrane proteins i.e. AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer membrane proteins i.e. TolC with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer membrane proteins i.e. OmpD with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer membrane proteins i.e. OmpW with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer membrane proteins i.e. OmpC with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	STM1530	activator	32468234	9	ver/dev	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer membrane proteins i.e. OmpF with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	144	It has been found that CpxR overexpression in S. Typhimurium results in reduced expression of outer and inner membrane proteins i.e. OmpF , OmpC , OmpW , OmpD , TolC , and AcrB with concomitant upregulation of outer membrane proteins i.e. STM1530 and STM3031 .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	clpX	activator	12675803	3	ver/dev	Turnover of FlhDC by ClpXP protease 445 was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpX .	87	Turnover of FlhDC by ClpXP protease 445 was not changed , in contrast to the marked increase of bgalactosidase levels expressed from the fliC-lac fusion , by mutations in either clpX or clpP ( Tomoyasu et al. , 2002 ) .	6	LEVELS OF MASTER REGULATORS, FLHD AND FLHC, IN THE CLPXP PROTEASE-DEPLETED MUTANT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	TU	flhDC	repressor	30373755	1	ver/dev	By comparing the gene expression profiles between the wild-type and strains via RNA sequencing , we found that the gene is upregulated in the mutant , suggesting the indirect repression of the flhDC operon by the activated PhoP .	13	By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing , we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant , suggesting the indirect repression of the flhDC operon by the activated PhoP .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	TU	flhDC	repressor	30373755	6	ver/dev	PhoP consequently downregulates the transcription of the flhDC operon and , subsequently , of fliC	61	Genetic and phenotypic analyses indicated that STM14_1829 is a key small protein required for full motility and that a swimming motility defect in a ΔSTM14_1829 mutant is due to the increased activity of PhoP , which consequently downregulates the transcription of the flhDC operon and , subsequently , of downstream flagellum genes such as fliC .	3	KEYWORDS SMALL PROTEINS, INTRINSICALLY DISORDERED PROTEINS, FLAGELLA, MOTILITY, SALMONELLA, PHOP	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	TU	flhDC	repressor	30373755	6	ver/dev	PhoP consequently downregulates the transcription of the flhDC operon and , subsequently , of downstream flagellum genes	61	Genetic and phenotypic analyses indicated that STM14_1829 is a key small protein required for full motility and that a swimming motility defect in a ΔSTM14_1829 mutant is due to the increased activity of PhoP , which consequently downregulates the transcription of the flhDC operon and , subsequently , of downstream flagellum genes such as fliC .	3	KEYWORDS SMALL PROTEINS, INTRINSICALLY DISORDERED PROTEINS, FLAGELLA, MOTILITY, SALMONELLA, PHOP	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	TU	flhDC	repressor	30373755	6	ver/dev	PhoP consequently downregulates the transcription of the flhDC operon and , subsequently , of fliC	61	Genetic and phenotypic analyses indicated that STM14_1829 is a key small protein required for full motility and that a swimming motility defect in a ΔSTM14_1829 mutant is due to the increased activity of PhoP , which consequently downregulates the transcription of the flhDC operon and , subsequently , of downstream flagellum genes such as fliC .	3	KEYWORDS SMALL PROTEINS, INTRINSICALLY DISORDERED PROTEINS, FLAGELLA, MOTILITY, SALMONELLA, PHOP	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	TU	flhDC	repressor	30373755	6	ver/dev	PhoP consequently downregulates the transcription of the flhDC operon and , subsequently , of downstream flagellum genes	61	Genetic and phenotypic analyses indicated that STM14_1829 is a key small protein required for full motility and that a swimming motility defect in a ΔSTM14_1829 mutant is due to the increased activity of PhoP , which consequently downregulates the transcription of the flhDC operon and , subsequently , of downstream flagellum genes such as fliC .	3	KEYWORDS SMALL PROTEINS, INTRINSICALLY DISORDERED PROTEINS, FLAGELLA, MOTILITY, SALMONELLA, PHOP	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	ompS1	repressor	17908208	4	ver/dev	H-NS , negatively regulates ompS1 expression by binding upstream of position -88 .	34	H-NS , a nucleoid protein of 137 amino acids ( ~ 15 kDa ) , negatively regulates ompS1 expression by binding upstream of position -88 ( Flores-Valdez et al. , 2003 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	repressor	17908208	32	ver/dev	H-NS negatively regulates ompS1 expression in both S. Typhimurium .	96	H-NS negatively regulates ompS1 expression in both S. Typhi and S. Typhimurium ( Flores-Valdez et al. , 2003 ) .	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	repressor	17908208	32	ver/dev	H-NS negatively regulates ompS1 expression in both S. Typhi .	96	H-NS negatively regulates ompS1 expression in both S. Typhi and S. Typhimurium ( Flores-Valdez et al. , 2003 ) .	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	repressor	18156266	0	ver/dev	Expression of ompS1 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	12	Expression of ompS1 , assT , and STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx and STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	ompS1	repressor	18156266	28	ver/dev	The transcriptional profile was consistent with the hypothesis that H-NS represses the expression of ompS1 , .	298	The transcriptional profile obtained was consistent with the hypothesis that H-NS represses the expression of ompS1 ( 5 ) ( Fig. 2c ) , assT ( Fig. 2b ) , and STY307O ( Fig. 2a ) , suggesting that the STY3070-STY3064 operon also belongs to the H-NS regulon .	5	FIG. 2	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HNS	gene	ompS1	repressor	18156266	42	ver/dev	The results of our experiments concur with the concept that H-NS represses the expression of ompS1 in Salmonella serovar Typhi .	351	The results of our experiments concur with the concept that H-NS represses the expression of STY3070 , assT , and ompS1 in Salmonella serovar Typhi ( Fig. 2a to c ) .	6	DISCUSSION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	repressor	18156266	43	ver/dev	Previous studies also showed that ompS1 are repressed by H-NS in Salmo-nella serovar Typhimurium .	352	Previous studies also showed that assT and ompS1 are repressed by H-NS in Salmo-nella serovar Typhimurium and Salmonella serovar Typhi , respectively ( 13 , 37 ) .	6	DISCUSSION	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	repressor	19406898	2	ver/dev	an H-NS paralogue , was found to repress ompS1 in an hns background ; and a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	repressor	19406898	2	ver/dev	an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	repressor	19406898	17	ver/dev	a model where the derepression is due to the lowering of the affinity of these two silencing proteins by the change in DNA curvature of the ompS1 regulatory region that the effect of the introduced mutations is indeed on the alteration of the binding of H-NS to its nucleation site	169	These data are in accord with a model where the derepression observed with the pRO310-mt fusion ( Fig. 2 ) is due to the lowering of the affinity of these two silencing proteins by the change in DNA curvature of the ompS1 regulatory region , and with the notion that the effect of the introduced mutations is indeed on the DNA curvature and not on the alteration of the binding of H-NS to its nucleation site .	11	EFFECT OF CURVATURE ON H-NS, STPA AND LEUO BINDING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	repressor	19406898	23	ver/dev	We previously accounted for the repression of ompS1 expression by the formation of an H-NS nucleofilament .	223	We previously accounted for the repression of ompS1 expression by the formation of an H-NS nucleofilament ( De la Cruz et al. , 2007 ) .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
EutR	gene	ssrB	regulator	26565973	8	ver/dev	that EutR influenced expression of ssrB targets	176	The genetic data indicated that EutR influenced expression of ssrB and downstream targets , but that EutR did not impact ssrA expression ( Fig 4B and S8 Fig ) , indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EutR	gene	ssrB	regulator	26565973	8	ver/dev	S8 Fig _ indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter	176	The genetic data indicated that EutR influenced expression of ssrB and downstream targets , but that EutR did not impact ssrA expression ( Fig 4B and S8 Fig ) , indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	regulator	26565973	8	ver/dev	Fig 4B _ indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter	176	The genetic data indicated that EutR influenced expression of ssrB and downstream targets , but that EutR did not impact ssrA expression ( Fig 4B and S8 Fig ) , indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	regulator	26565973	9	ver/dev	EMSAs indicated that EutR directly binds the ssrB promoter to activate expression of Fig 4C .	178	Electrophoretic mobility shift assays ( EMSAs ) indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 ( Fig 4C ) .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	regulator	26565973	9	ver/dev	EMSAs indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 .	178	Electrophoretic mobility shift assays ( EMSAs ) indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 ( Fig 4C ) .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	regulator	26565973	9	ver/dev	Electrophoretic mobility-shift assays indicated that EutR directly binds the ssrB promoter to activate expression of Fig 4C .	178	Electrophoretic mobility shift assays ( EMSAs ) indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 ( Fig 4C ) .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	regulator	26565973	9	ver/dev	Electrophoretic mobility-shift assays indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 .	178	Electrophoretic mobility shift assays ( EMSAs ) indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 ( Fig 4C ) .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EutR	gene	ssrB	regulator	26565973	12	ver/dev	To test our findings within the complexities of the in-vivo environment , we assessed EutR-dependent regulation of ssrB using single strain infections .	208	To test our findings within the complexities of the in vivo environment , we assessed EutR-dependent regulation of ssrB using single strain infections and purified S. Typhimurium RNA from harvested spleens .	11	EUTR SIGNALING DURING SYSTEMIC INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
EutR	gene	ssrB	regulator	28357338	3	ver/dev	In vitro assays revealed that EutR directly binds the ssrB promoter to activate SPI-2 expression .	66	In vitro assays using purified EutR in conjunction with in vivo assays revealed that EutR directly binds the ssrB promoter to activate SPI-2 expression .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	dam	regulator	21984608	0	ver/dev	It is interesting to note that several regulators of HilD , were found in significantly lower levels in the dam mutant .	135	It is interesting to note that several regulators of T3SS1 , such as HilA , HilC , HilD , and InvF , were found in significantly lower levels in the dam mutant .	5	TRANSCRIPTIONAL AND TRANSLATIONAL REGULATION DURING INVASION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
LexA	gene	recN	activator	33921732	5	att	In genes that show LexA-dependent bistability and have more than one LexA box ( recN , dinI and lexA ) , only the closest LexA box with lower HI was considered .	307	In genes that show LexA-dependent bistability and have more than one LexA box ( recN , dinI and lexA ) , only the closest LexA box with lower HI was considered .	15	3.4. INFLUENCE OF THE DISTANCE AND THE NUCLEOTIDE SEQUENCE OF THE LEXA BOX ON THE EXPRESSION PATTERNS OF SOS GENES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	acnA	regulator	23637460	0	ver/dev	that acnA expression was regulated by CRP , glucose-starvation .	17	that acnA expression was regulated by the cyclic-AMP receptor protein ( CRP , glucose starvation ) , the fumarate nitrate reduction regulator ( FNR , oxygen starvation ) , the ferric uptake regulator ( Fur , iron starvation ) and the superoxide response protein ( SoxR , oxidative stress ) .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PspC	gene	bla	regulator	18458067	0	ver/dev	We evaluated the utilities of these vectors by fusing PspC , to C-terminal peptide of - bla SS CT on Asd plasmids under the control of the Ptrc promoter .	12	We evaluated the utilities of these vectors by fusing two different antigens , the - helix domains of pneumococcal surface protein A ( PspA ) and pneumococcal surface protein C ( PspC ) , to the signal sequences of - lactamase ( bla SS ) , ompA , and phoA and the signal sequence and C-terminal peptide of - lactamase ( bla SS CT ) on Asd plasmids under the control of the Ptrc promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PspC	gene	bla	regulator	18458067	0	ver/dev	We evaluated the utilities of these vectors by fusing PspC , to C-terminal peptide of - bla SS CT on Asd plasmids under the control of the Ptrc promoter .	12	We evaluated the utilities of these vectors by fusing two different antigens , the - helix domains of pneumococcal surface protein A ( PspA ) and pneumococcal surface protein C ( PspC ) , to the signal sequences of - lactamase ( bla SS ) , ompA , and phoA and the signal sequence and C-terminal peptide of - lactamase ( bla SS CT ) on Asd plasmids under the control of the Ptrc promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cra	gene	csgD	regulator	25437188	23	ver/dev	Although the O1-site downstream of the transcriptional start site appears to be the most important for csgD expression , binding of Cra to operators O3 located upstream commonly appears to be important for maximal transcription .	287	Although the O1-site downstream of the transcriptional start site appears to be the most important for csgD expression , binding of Cra to operators O2 and O3 located upstream commonly appears to be important for maximal transcription [ 90 ] .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Cra	gene	csgD	regulator	25437188	23	ver/dev	Although the O1-site downstream of the transcriptional start site appears to be the most important for csgD expression , binding of Cra to operators O2 upstream commonly appears to be important for maximal transcription .	287	Although the O1-site downstream of the transcriptional start site appears to be the most important for csgD expression , binding of Cra to operators O2 and O3 located upstream commonly appears to be important for maximal transcription [ 90 ] .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	acnA	repressor	23637460	7	ver/dev	This lowering of acnA transcription was not observed when b-galactosidase activity from PacnA-lacZ was measured in anaerobic cultures of the S. Typhimurium fnr mutant , suggesting that FNR represses acnA expression .	232	This lowering of acnA transcription was not observed when b-galactosidase activity from PacnA-lacZ was measured in anaerobic cultures of the S. Typhimurium fnr mutant , suggesting that FNR represses acnA expression ( Fig. 3a ) .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsB	gene	asr	regulator	30763640	53	ver/dev	In spite of this , our results suggest that asr genes are controlled in the same way by the RcsB regulator .	275	In spite of this , our results suggest that asr and STM1485 genes are controlled in the same way by the RcsB regulator .	16	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcdA	gene	csgD	regulator	25437188	17	ver/dev	A DNAseI footprinting assay demonstrated that the TetR-type transcriptional regulator RcdA binds to four high-affinity sites between -308 upstream of the csgD transcription start site .	207	A DNAseI footprinting assay demonstrated that the TetR-type transcriptional regulator RcdA ( formerly YbjK ) binds to four high-affinity sites between -192 and -308 upstream of the csgD transcription start site which expanded to cover a region from -20 to -308 at higher concentration ( Figure 3 ; Table 1 ) .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcdA	gene	csgD	regulator	25437188	17	ver/dev	A DNAseI footprinting assay demonstrated that the TetR-type transcriptional regulator RcdA binds to four high-affinity sites between -192 upstream of the csgD transcription start site .	207	A DNAseI footprinting assay demonstrated that the TetR-type transcriptional regulator RcdA ( formerly YbjK ) binds to four high-affinity sites between -192 and -308 upstream of the csgD transcription start site which expanded to cover a region from -20 to -308 at higher concentration ( Figure 3 ; Table 1 ) .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CysB	gene	cysN	activator	25637663	4	att	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	39	An additional sulfate assimilation pathway that might be involved in H2S production , includes cysN , cysD , cysC and cysJIH operon which shown to be expressed in a CysB-dependent manner [ 13e16 ] .	6	MAIN	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	hilE	repressor	24354910	5	ver/dev	However , we provide evidence that LeuO mainly exerts SPI-1 repression by an indirect mechanism , hitherto unsuspected : LeuO activates transcription of the hilE gene .	48	However , we provide evidence that LeuO mainly exerts SPI-1 repression by an indirect mechanism , hitherto unsuspected : LeuO activates transcription of the hilE gene , which is located outside SPI-1 and encodes a SPI-1 repressor ( Fahlen et al. , 2000 ; Baxter et al. , 2003 ) .	8	INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
LeuO	gene	hilE	repressor	24354910	11	ver/dev	LeuO downregulates SPI-1 expression via hilE	70	LeuO downregulates SPI-1 expression via hilE and hilD	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	hilE	repressor	24354910	20	ver/dev	Furthermore , even though a hilD mutation was epistatic over hilE , moderate repression of SPI-1 by LeuO was still observed in a HilD − HilE − background .	94	Furthermore , even though a hilD mutation was epistatic over hilE , moderate repression of SPI-1 by LeuO was still observed in a HilD − HilE − background ( Fig. 4 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	ssrA	regulator	29751061	2	ver/dev	IHF , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated .	236	Other SPI-2 regulators , such as YdgT , Hha and IHF , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated [ 21,24,25 ] .	19	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Lrp	gene	argR	regulator	22941081	0	ver/dev	trolled by the argR repressor , while the biosynthesis genes of the other amino-acids are controlled by the transcription factors Lrp .	242	trolled by the argR repressor , while the biosynthesis genes of the other amino acids are controlled by the transcription factors Lrp and TrpR ( 17 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sipB	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sipB	regulator	14633100	3	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	190	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	sipB	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilD	activator	24354910	16	att	Because HilE is a negative regulator of hilD ( Baxter et al. , 2003 ) , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level , which in turn might inhibit HilD activity .	83	Because HilE is a negative regulator of hilD ( Baxter et al. , 2003 ) , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level , which in turn might inhibit HilD activity .	9	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilD	gene	dsbA	repressor	32571967	8	ver/dev	Because repression of SPI1 expression is partially independent because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through rtsA transcription .	145	Because repression of SPI1 expression caused by loss of bamB is partially independent of FliZ ( Fig. 3B ) and because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD , hilC , or rtsA transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	dsbA	repressor	32571967	8	ver/dev	Because repression of SPI1 expression is partially independent because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilC .	145	Because repression of SPI1 expression caused by loss of bamB is partially independent of FliZ ( Fig. 3B ) and because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD , hilC , or rtsA transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	dsbA	repressor	32571967	8	ver/dev	Because repression of SPI1 expression is partially independent because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD .	145	Because repression of SPI1 expression caused by loss of bamB is partially independent of FliZ ( Fig. 3B ) and because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD , hilC , or rtsA transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	scsB	activator	29866803	9	att	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper-stress .	211	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper stress .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CspC	gene	cspD	activator	24056458	0	ver/dev	this effect was reflected by induction of cspD and proteins ( CspC ) in response to preadaptation to cold-stress	146	Cold stress genes and proteins regulate membrane fluidity and resume protein synthesis ( 18 ) , and this effect was reflected by induction of cold stress genes ( cspB and cspD ) and proteins ( CspA , CspE , and CspC ) in response to preadaptation to cold stress .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	fliA	regulator	26441883	22	ver/dev	Temperature-dependent regulation of the flagellar genes appears to occur through σ28 / FliA , as a rapid reduction of fliA mRNA was observed at a temperatureupshift , whereas the flhDC master operon is transcribed in a temperature-independent manner .	381	Temperature-dependent regulation of the flagellar genes appears to occur through σ28 / FliA , as a rapid reduction of fliA mRNA was observed at a temperatureupshift , whereas the flhDC master operon is transcribed in a temperature-independent manner ( Kapatral et al. , 2004 ; Nuss et al. , 2015 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	fliA	regulator	8206838	1	ver/dev	These results indicate that the fliA operon itself is under the positive control of FliA .	117	These results indicate that the fliA operon itself is under the positive control of FliA and under the negative control of FlgM .	7	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	fliA	regulator	8631681	1	att	In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	6	In this investigation , we observed that ( i ) the in vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	OTHER	Other	OTHER	Other	Level 1
Sigma70	TU	flhDC	activator	17997077	0	att	The early genes , flhDC , encode the FlhDC master regulator complex which dictates the s70-dependent transcription of the middle genes .	333	The early genes , flhDC , encode the FlhDC master regulator complex which dictates the s70-dependent transcription of the middle genes .	11	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	tnpA	repressor	28335027	5	ver/dev	The fact that tnpA inhibited InvF protein expression at an early growth phase while not affecting invF mRNA levels suggests that translation inhibition is invF pairing .	730	The fact that tnpA inhibited InvF protein expression at an early growth phase ( Figure 4E ) while not affecting invF mRNA levels ( Figure 6E ) suggests that translation inhibition is at least one consequence of tnpA -- invF pairing .	22	RIBONUCLEOLYTIC PROCESSING OF TNPA MRNA GENERATES SRNA REGULATORS OF INVF EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	tnpA	repressor	28335027	5	ver/dev	The fact that tnpA inhibited InvF protein expression at an early growth phase while not affecting invF mRNA levels suggests that translation inhibition is at least one consequence of tnpA .	730	The fact that tnpA inhibited InvF protein expression at an early growth phase ( Figure 4E ) while not affecting invF mRNA levels ( Figure 6E ) suggests that translation inhibition is at least one consequence of tnpA -- invF pairing .	22	RIBONUCLEOLYTIC PROCESSING OF TNPA MRNA GENERATES SRNA REGULATORS OF INVF EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	hilA	regulator	25028458	29	att	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	322	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	TU	araBAD	repressor	24272778	3	ver/dev	In the absence-of-arabinose , AraC represses transcription of araBAD by forming a repression loop .	15	In the absence of arabinose , AraC represses transcription of araBAD and araC by forming a repression loop mediated by dimerization of distally bound AraC monomers ( 5 , 6 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	TU	araBAD	repressor	24272778	44	ver/dev	Although arabinose-dependent repression by AraC has not been observed before , there are clear parallels with arabinose-de-pendent activation of araBAD transcription .	412	Although arabinose-dependent repression by AraC has not been observed before , there are clear parallels with arabinose-de-pendent activation of araBAD transcription .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
AraC	TU	araBAD	repressor	24272778	45	ver/dev	Thus , arabinose-dependent repression of ydeNM by AraC would use the same mechanism as arabinose-dependent activation of araBAD .	421	Thus , arabinose-dependent repression of ydeNM by AraC would use the same mechanism as arabinose-dependent activation of araBAD .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	virK	activator	18270203	71	att	This form of regulation is in striking parallel to that controlling expression of the ugtL gene ( 23 ) , and it may apply to other PhoP - and SlyA-dependent genes , such as mig-14 and virK ( which also seem to have been horizontally acquired ) , because the PhoP protein has been shown to bind to their respective promoters in-vitro and in-vivo ( 26 ) .3	296	This form of regulation is in striking parallel to that controlling expression of the ugtL gene ( 23 ) , and it may apply to other PhoP - and SlyA-dependent genes , such as mig-14 and virK ( which also seem to have been horizontally acquired ) , because the PhoP protein has been shown to bind to their respective promoters in vitro and in vivo ( 26 ) .3	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Zur	gene	znuA	regulator	24858080	12	att	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	408	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Zur	gene	znuA	regulator	24858080	4	ver/dev	at least three loci _ controlled by the Zn-responsive Zur repressor in the presence of CuSO4 , znuA , zinT and	266	The transcriptome analysis revealed the activation of at least three loci controlled by the Zn-responsive Zur repressor in the presence of CuSO4 , znuA , zinT and rpmE2-rpmJ_1 ( Fig. 1 , Tables S3 and S4 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	gtgE	regulator	27886269	3	ver/dev	InvF , regulates the expression of gtgE .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ytfK	regulator	33638994	19	ver/dev	These assays confirmed binding of phosphorylated RcsB to ytfK promoters .	398	These assays confirmed binding of phosphorylated RcsB to fepE , osmB and ytfK promoters and to flgA and nlpD Intra-CDS sequences ( Figure 7A and C ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	cas	activator	33854491	12	att	Interestingly , the presence of OmpF was evident in these cas mutants , supporting the notion that OmpF is not only OmpR-dependent , and that other transcriptional factors are able to induce OmpF expression .	276	Interestingly , the presence of OmpF was evident in these cas mutants , supporting the notion that OmpF is not only OmpR-dependent , and that other transcriptional factors are able to induce OmpF expression .	19	DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	pmrA	activator	23690578	2	att	The pmrA mutant displayed heightened expression of SsrB-dependent genes and faster Spi/Ssa-dependent macrophage killing than wild-type Salmonella .	9	The pmrA mutant displayed heightened expression of SsrB-dependent genes and faster Spi/Ssa-dependent macrophage killing than wild-type Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	dps	regulator	25028458	9	att	As shown in Fig. 1 ( a , b ) , we found a sequence homologous to the RcsB-binding site present in other well-characterized RcsB-regulated genes , located 272 nt upstream from the previously described dps	110	As shown in Fig. 1 ( a , b ) , we found a sequence homologous to the RcsB-binding site present in other well-characterized RcsB-regulated genes , located 272 nt upstream from the previously described dps	5	IDENTIFICATION OF DPS AS A MEMBER OF THE RCSB REGULON	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	dps	regulator	25028458	11	ver/dev	Taken together , our results confirm that RcsB promotes dps expression by directly binding to the promoter region of dps .	118	Taken together , our results confirm that RcsB promotes dps expression by directly binding to the promoter region of dps .	5	IDENTIFICATION OF DPS AS A MEMBER OF THE RCSB REGULON	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	dps	regulator	25028458	17	ver/dev	To determine which of the RcsB phosphorylation pathway is involved in the control of dps expression , levels of b-galactosidase : : lacZYA was determined in tolB P double rcsB mutants .	141	To determine which of the RcsB phosphorylation pathway is involved in the control of dps expression , levels of b-galactosidase produced from pPdps : : lacZYA was determined in tolB rcsB , tolB PrcsDB and tolB P double rcsB mutants .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	dps	regulator	25028458	17	ver/dev	To determine which of the RcsB phosphorylation pathway is involved in the control of dps expression , levels of b-galactosidase : : lacZYA was determined in tolB rcsB , tolB PrcsDB .	141	To determine which of the RcsB phosphorylation pathway is involved in the control of dps expression , levels of b-galactosidase produced from pPdps : : lacZYA was determined in tolB rcsB , tolB PrcsDB and tolB P double rcsB mutants .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	dps	regulator	25028458	34	ver/dev	Although Yoo et al. reported that dps expression is induced during the stationary-phase by the Fur regulator , our results demonstrated that this gene is also regulated by RcsB .	334	Although Yoo et al. ( 2007 ) reported that dps expression is induced during the stationary phase by the Fur regulator , our results demonstrated that this gene is also regulated by RcsB but during the exponential phase of growth .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YdgT	gene	ssrA	regulator	29751061	2	ver/dev	YdgT , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated .	236	Other SPI-2 regulators , such as YdgT , Hha and IHF , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated [ 21,24,25 ] .	19	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
TorR	TU	torCAD	activator	32413972	0	ver/dev	In E. coli , TorR activates the transcription of torCAD	665	In E. coli , TorR activates the transcription of torCAD [ 113 ] , which encodes proteins required for anaerobic respiration [ 114 -- 116 ]	13	3.63..6S.TSRATRIN I T AINSPSPECEICFIFCICITIYY	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
TorR	TU	torCAD	activator	33751923	18	ver/dev	TorR Asp53 -RRB- inducing transcription of the torCAD operon .	576	TorR Asp53 ) inducing transcription of the torCAD operon ( Jourlin et al. 1996 ) .	20	TORSR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	bfr	repressor	17302823	2	att	One possible reason for the detrimental effects of bfr overexpression in strains carrying an intact Fur repressor is titration of the Fur-repressed small RNA RyhB by bfr mRNA .	261	One possible reason for the detrimental effects of bfr overexpression in strains carrying an intact Fur repressor is titration of the Fur-repressed small RNA RyhB by bfr mRNA .	14	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Fur	gene	bfr	repressor	17302823	2	att	One possible reason for the detrimental effects of bfr overexpression in strains carrying an intact Fur repressor is titration of the Fur-repressed small RNA RyhB by bfr mRNA .	261	One possible reason for the detrimental effects of bfr overexpression in strains carrying an intact Fur repressor is titration of the Fur-repressed small RNA RyhB by bfr mRNA .	14	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Fur	gene	bfr	repressor	17302823	1	ver/dev	Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
Fur	gene	bfr	repressor	17302823	1	ver/dev	Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA .	233	Similar to E. coli ( Masse and Gottesman , 2002 ; McHugh et al. , 2003 ) , the S. Typhimurium bfr and ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA , RyhB .	14	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
LexA	gene	ant	regulator	12399494	10	ver/dev	ant does not appear to be regulated by LexA	416	The genome of P22 lacks a tum homologue but encodes another antirepressor ( ant ) that does not appear to be regulated by LexA ( 49 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RcsA	TU	flhDC	regulator	27206164	12	ver/dev	In E. coli flagellar motility is negatively regulated by RcsA binding to the RcsAB box of the promoter of the flagellar master regulator flhDC .	71	In E. coli flagellar motility is negatively regulated by RcsB and RcsA binding to the RcsAB box of the promoter of the flagellar master regulator flhDC ( Francez-Charlot et al. , 2003 ) .	4	INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	TU	flhDC	regulator	27206164	50	ver/dev	In Salmonella , however , RcsB-mediated regulation of the flagellar master operon flhDC has been described to be independent from RcsA .	269	In Salmonella , however , RcsB-mediated regulation of the flagellar master operon flhDC has been described to be independent from RcsA ( Wang et al. , 2007 ) .	11	DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	spvR	regulator	25217722	0	ver/dev	It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvR	regulator	25217722	0	ver/dev	It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .	270	It is possible that the upregulation of spvR and the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression but a negative regulator of sefA expression ( Chen et al. , 1995 ; Edwards et al. , 2001 ; Kowarz et al. , 1994 ) .	21	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	spiC	regulator	12753201	32	ver/dev	spiC is regulated by both OmpR	205	spiC is regulated by both OmpR and SsrB	9	PHOSPHORYLATION OF OMPR INCREASES ITS AFFINITY FOR SSRA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hupB	regulator	10767604	12	ver/dev	Since a Tn5 insertion in this region disrupts the negative regulation by FIS we currently do not know if the transposon insertion decreases normal expression of hupB .	297	Since a Tn5 insertion in this region disrupts the positive regulation of hupB by crp-cAMP as well as the negative regulation by FIS we currently do not know if the transposon insertion increases or decreases normal expression of hupB .	18	4. DISCUSSION	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
Fis	gene	hupB	regulator	10767604	12	ver/dev	Since a Tn5 insertion in this region disrupts the negative regulation by FIS we currently do not know if the transposon insertion increases normal expression of hupB .	297	Since a Tn5 insertion in this region disrupts the positive regulation of hupB by crp-cAMP as well as the negative regulation by FIS we currently do not know if the transposon insertion increases or decreases normal expression of hupB .	18	4. DISCUSSION	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
SsrB	gene	sifB	regulator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sifB by both relief of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SsrB	gene	sifB	regulator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sifB by both direct activation of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	slsA	activator	26561851	1	att	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	159	For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .	7	THE PRIMARY TRANSCRIPTOME OF INTRA-MACROPHAGE S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rho	regulator	33939833	0	ver/dev	The here-observed strong association of this RpoS-dependent stationary-phase specific sRNA lends support to a previously proposed activity of SraL as a ProQ dependent regulator of rho mRNA .	241	The here-observed strong association of this RpoS-dependent stationary-phase specific sRNA ( 54,55 ) lends support to a previously proposed activity of SraL as a ProQ dependent regulator of rho mRNA ( 56 ) .	20	FINP AND REPX ARE THE MAJOR LIGANDS OF FINO INDEPENDENT OF GROWTH STAGE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ssrA	regulator	15491370	2	ver/dev	Results from DNase-I-protection assays provide direct evidence that SsrB binds at ssrA , although the binding sites lie within the .	17	Results from DNase I protection assays provide direct evidence that SsrB binds at ssrA and ssrB , although the binding sites lie within the transcribed regions .	3	SUMMARY	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
SsrB	gene	ssrA	regulator	20660761	2	ver/dev	SsrB C203D allele bound to the ssrA promoter with affinity apparently similar that of Fig. 3D .	131	SsrB C203D allele , the C203S variant bound to the ssrA promoter with affinity apparently similar that of the wild-type protein ( Fig. 3D ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SsrB	gene	ssrA	regulator	20660761	2	ver/dev	SsrB C203D allele bound to the ssrA promoter with affinity apparently similar that of the wild-type protein .	131	SsrB C203D allele , the C203S variant bound to the ssrA promoter with affinity apparently similar that of the wild-type protein ( Fig. 3D ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SsrB	gene	ssrA	regulator	24643535	0	ver/dev	In addition , the SsrB regulator also directly binds and autoregulates the ssrA promoters to activate their expression .	20	In addition , the SsrB regulator also directly binds and autoregulates the ssrA and ssrB promoters to activate their expression ( 7 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssrA	regulator	30524381	18	ver/dev	Apart from ssrA , none of the other SPI-2 genes have been shown to be direct targets of OmpR regulation , although many of them are directly regulated by SsrB .	246	Apart from ssrA and ssrB , none of the other SPI-2 genes have been shown to be direct targets of OmpR regulation ( Lee et al. , 2000 ; Feng et al. , 2003 , 2004 ) , although many of them are directly regulated by SsrB ( Feng et al. , 2004 ; Walthers et al. , 2007 , 2011 ) .	18	COMPARISON OF OSMOLYTES IN THE OMPR S. TYPHIMURIUM TRANSCRIPTOME- SALT VS.	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxS	gene	fpr	regulator	19917752	0	ver/dev	SoxS _ regulated , including fpr	266	Among the genes that were upregulated in 104-cip , a number were SoxS regulated , including acnA , fpr , ribA , sodA , lpxC , and soxS itself .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	purB	regulator	33045730	55	ver/dev	SsrB promotes phoP transcription by binding to the purB cod - ing region upstream of the phoP promoter	254	SsrB promotes phoP transcription by binding to the purB cod- ing region upstream of the phoP promoter	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	purB	regulator	33045730	69	ver/dev	SsrB promotes phoP transcription by binding to the purB .	299	SsrB promotes phoP transcription by binding to the purB coding region upstream of the phoP promoter .	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	purB	regulator	33045730	108	ver/dev	SsrB also increases phoP transcription by directly binding to the purB .	451	SsrB also increases phoP transcription by directly binding to the purB coding region upstream of the phoP promoter region .	37	DIFFERENT HORIZONTALLY ACQUIRED GENES ENABLE ESCHERICHIA COLI TO ACTIVATE PHOP/PHOQ IN MILDLY ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssrB	activator	23690578	23	att	S1 ) and that the ssrB promoter mutation had no effect on the expression of the PmrA-activated pmrC gene ( Fig. 5C ) .	92	S1 ) and that the ssrB promoter mutation had no effect on the expression of the PmrA-activated pmrC gene ( Fig. 5C ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	ssrB	activator	23690578	43	att	Whereas PmrA-dependent LPS modi cations can reduce the risk of Salmonella detection by the fi Toll-like receptor-4 in a mammalian host ( 15 , 45 ) , its role in ssrB repression may reduce expression of Spi/Ssa-secreted effectors that dampen the host immune response ( 46 , 47 ) .	166	Whereas PmrA-dependent LPS modi cations can reduce the risk of Salmonella detection by the fi Toll-like receptor-4 in a mammalian host ( 15 , 45 ) , its role in ssrB repression may reduce expression of Spi/Ssa-secreted effectors that dampen the host immune response ( 46 , 47 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ssrB	activator	23690578	49	att	Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .	182	Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ssrB	activator	23690578	49	att	Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .	182	Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ssrB	activator	23690578	48	ver/dev	a posttranslational activator of PmrA represses ssrB transcription	179	However , it promotes expression of PmrD , a posttranslational activator of PmrA ( 34 ) , which represses ssrB transcription ( Fig. 2 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , stationary-phase , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , stationary-phase , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , RpoS , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , RpoS , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , stationary-phase , DnaJ , DnaK , GrpE .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	10972838	1	ver/dev	The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , stationary-phase , heat-shock .	122	The flhDC master operon is influenced by a number of global regulatory signals , including catabolite repression ( c-AMP , CAP ) , temperature , cell cycle , osmolarity ( OmpR ) , DNA structure ( H-NS ) , stationary phase ( RpoS ) , heat shock ( DnaJ , DnaK , GrpE ) and membrane biosynthesis ( Silverman and Simon , 1974Komeda et al. , 1975 ; Shi et al. , 1992 , 1993a , b ; Amsler et al. , 1993 ; Bertin et al. , 1994 ; Kitamura et al. , 1994 ; Miziyama et al. , 1995 ; Mizushima et al. , 1995 , 1997 ; Shin and Park , 1995 ; PruÈû and Matsumura , 1996 , 1997 ; PruÈû et al. , 1997 ) .	4	ISOLATION OF T-POP-INDUCED FLHDC EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	flhDC	regulator	12675803	1	ver/dev	Transcription of the flhDC operon is known to be regulated by signals from a network of H-NS .	44	Transcription of the flhDC operon is known to be regulated by signals from a network of cell components including CRP , OmpR , H-NS and the DnaK-DnaJ-GrpE system ( Yokota and Gots , 1970 ; Shi et al. , 1992 ; Bertin et al. , 1994 ; Kutsukake , 1997 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	TU	flhDC	regulator	17074910	23	ver/dev	Multiple control of flagellum biosynthesis in Escherichia coli : role of H-NS protein -- catabolite activator protein complex in transcription of the flhDC master operon .	693	Multiple control of flagellum biosynthesis in Escherichia coli : role of H-NS protein and the cyclic AMP -- catabolite activator protein complex in transcription of the flhDC master operon .	65	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	flhDC	regulator	28973452	3	ver/dev	H-NS also regulate cell motility by interacting with the flhDC promoter .	29	RcsB , H-NS and RtsB also regulate cell motility by interacting with the flhDC promoter ( 11 -- 13 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	marA	regulator	27199934	12	ver/dev	To our knowledge , the influence of CpxR on the mRNA levels of marA genes has not been demonstrated .	362	To our knowledge , the influence of CpxR on the mRNA levels of marA and soxS genes has not been demonstrated .	16	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
Crl	gene	bcsA	activator	16707690	10	ver/dev	Together , these results demonstrated that Crl plays a role in the transcription activation of bcsA genes required for developing a typical rdar morphotype in Salmo-nella .	297	Together , these results demonstrated that Crl plays a role in the transcription activation of the csgD , csgB , adrA , and bcsA genes required for developing a typical rdar morphotype in Salmo-nella .	4	RESULTS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	slyA	activator	15208313	15	att	The Regulatory Gene slyA Is Essential for Transcription of the PhoP-activated ugtL Gene -- We analyzed the 536-bp region upstream of the ugtL coding region but did not find an obvious PhoP box sequence resembling the ( T/G ) GTTTA-N5 - ( T / G ) GTTTA motif at an equivalent position as the PhoP box present in the promoter region of other PhoP-activated genes characterized in E. coli ( 14 , 15 , 30 ) and Salmonella ( 13 ) .	102	The Regulatory Gene slyA Is Essential for Transcription of the PhoP-activated ugtL Gene -- We analyzed the 536-bp region upstream of the ugtL coding region but did not find an obvious PhoP box sequence resembling the ( T/G ) GTTTA-N5 - ( T / G ) GTTTA motif at an equivalent position as the PhoP box present in the promoter region of other PhoP-activated genes characterized in E. coli ( 14 , 15 , 30 ) and Salmonella ( 13 ) .	4	RESULTS	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	slyA	activator	15208313	35	att	As expected for a PhoP-activated gene , there was no slyA transcription when bacteria were grown under PhoP-repress-ing conditions ( i.e. 10 mM Mg2 ) , regardless of the presence of a functional phoP gene ( Fig. 4A ) .	150	As expected for a PhoP-activated gene , there was no slyA transcription when bacteria were grown under PhoP-repress-ing conditions ( i.e. 10 mM Mg2 ) , regardless of the presence of a functional phoP gene ( Fig. 4A ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	slyA	activator	15208313	51	att	The arrow corresponds to the slyA transcription start site that is PhoP-dependent and designated as P2 in Ref .	190	The arrow corresponds to the slyA transcription start site that is PhoP-dependent and designated as P2 in Ref .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyA	activator	17259627	6	ver/dev	In addition , slyA itself is activated under low-Mg conditions by the PhoP protein , 2 + .	48	In addition , slyA itself is activated under low-Mg conditions by the PhoP protein , 2 + which binds directly to the slyA promoter region ( Norte et al. , 2003 ; Shi et al. , 2004 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyA	activator	18715828	1	ver/dev	Interestingly , slyA of S. Typhi-murium has been shown to be induced via the PhoP / PhoQ two-component system following internalization of the bacteria by macrophages .	363	Interestingly , slyA of S. Typhi-murium has been shown to be induced via the PhoP / PhoQ two-component system following internalization of the bacteria by macrophages ( Buchmeier et al. , 1997 ; Norte et al. , 2003 ; Shi et al. , 2004 ) .	24	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	slyA	activator	19091955	23	ver/dev	Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by PhoP because the mRNA level of transcripts is reduced significantly in the slyA mutants grown in low-Mg2 conditions -LRB- Fig .	147	Our results from primer extension demonstrate that transcriptions of the identified loci are activated by PhoP and SlyA because the mRNA level of transcripts is reduced significantly in the phoP and slyA mutants grown in low-Mg2 conditions ( Fig .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	synthetic construct	0	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	slyA	activator	19229334	2	ver/dev	slyA transcriptional activation by PhoP has been reported .	409	slyA transcriptional activation by PhoP has been reported [ 63,64 ] .	13	SLYA CAN COMPLEMENT OTHER REGULATORS FOR SPI-2 EXPRESSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	slyA	activator	30992361	11	att	In contrast to PhoP-activated slyA transcription ( 5 , 21 ) , transcription of the emrR gene was not regulated by either PhoP/PhoQ system or SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains ( Fig. 3A , top panel ) .	114	In contrast to PhoP-activated slyA transcription ( 5 , 21 ) , transcription of the emrR gene was not regulated by either PhoP/PhoQ system or SlyA , since the levels of emrR transcripts were similar in the wild-type , ΔphoP , and ΔslyA strains ( Fig. 3A , top panel ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	slyA	activator	30992361	0	ver/dev	further _ supported by the observations that i.e. , the PhoP / PhoQ two-component system , activated transcription of the slyA gene	50	This characterization was further supported by the observations that a master virulence regulator , i.e. , the PhoP / PhoQ two-component system , activated transcription of the slyA gene ( 5 , 21 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	slyA	activator	30992361	2	ver/dev	Actually , the PhoP protein acts not only as the transcriptional activator of the slyA gene .	52	Actually , the PhoP protein acts not only as the transcriptional activator of the slyA gene but also as one of two transcriptional activators ( the other activator being SlyA ) for a subset of horizontally acquired gene clusters , including several divergent operons ( 5 , 23 ) .	2	MAIN	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	slyA	activator	32209674	10	ver/dev	In addition , PhoP is a direct transcriptional activator of the slyA genes .	134	In addition , PhoP is a direct transcriptional activator of the ssrB ( 8 ) and slyA ( 18 , 34 ) genes .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	slyA	activator	33045730	97	ver/dev	PhoP is a direct transcriptional activator of the slyA genes	413	And second , SsrB activation of PhoP is likely to have genome-wide effects , beyond the genes directly controlled by PhoP because : ( i ) PhoP is a direct transcriptional activator of the rstA and slyA genes , which specify DNA binding regulatory proteins ( 63,64,68,69 ) ; ( ii ) PhoP activates the transcriptional regulator PmrA post-translationally ( 70,71 ) ; ( iii ) PhoP promotes degradation of the gene silencer H-NS ( 72 ) ; and ( iv ) PhoP reduces proteolysis by different proteases that target pleiotropic regulators ( 73 -- 75 ) .	35	CONTROL OF THE VIRULENCE REGULATOR PHOP BY THE SSRB PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	csrB	regulator	16045614	11	ver/dev	The transcription of csrB is regulated by SirA .	59	The transcription of csrB and csrC is regulated by UvrY ( SirA ) ( Suzuki et al. , 2002 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	csrB	regulator	16949866	16	ver/dev	In E. coli , SirA directly regulates csrB .	300	In both Salmonella and E. coli , SirA directly regulates csrB , a gene encoding a small regulatory RNA that inhibits the activity of the RNA-binding protein CsrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	regulator	16949866	16	ver/dev	In both Salmonella , SirA directly regulates csrB .	300	In both Salmonella and E. coli , SirA directly regulates csrB , a gene encoding a small regulatory RNA that inhibits the activity of the RNA-binding protein CsrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	regulator	16949866	19	ver/dev	To test the hypothesis that csrC is directly regulated by SirA , in-vitro gel mobility-shift assays were performed as previously described for csrB .	337	To test the hypothesis that csrC is directly regulated by SirA , in vitro gel mobility shift assays were performed as previously described for csrB ( Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SirA	gene	csrB	regulator	16949866	32	ver/dev	SirA of Salmonella both control the csr system by directly binding the csrB gene .	458	SirA of Salmonella and UvrY of E. coli both control the csr system by directly binding and activating the csrB gene ( Pernestig et al. , 2001 ; Teplitski et al. , 2003 ) .	19	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	regulator	16949866	36	ver/dev	These two reports suggest that in contrast to csrB , the regulation of csrC by SirA may be indirect .	487	These two reports taken together suggest that in contrast to csrB , the regulation of csrC by SirA may be indirect .	19	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	ssrB	repressor	33045730	18	ver/dev	because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains	192	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	24	NON-PATHOGENIC S. BONGORI HARBORS A FUNCTIONAL UGTL VIRU- LENCE GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	repressor	33045730	28	ver/dev	because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains	218	The ssrB gene is required for normal transcription of other PhoP-activated genes because the ssrB mutant exhibited lower expression of PhoP-activated genes in strains harboring a lac transcriptional fusion to the ugtL gene ( Supplemental Figure S4A ) , gfp transcriptional fusions to the phoP , pmrD , and mig-14 genes ( Supplemental Figure S4B ) , and also when examining the mRNA amounts of the mgtC , ugtL , pcgL , pagC and pagD genes ( Supplemental Figure S4C ) , than the isogenic ssrB + strain ( 40,42,46 ) .	25	PHOP ACTIVATION IN MILDLY ACIDIC PH REQUIRES THE REGULATORY GENE SSRB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrB	repressor	33045730	56	ver/dev	because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain	255	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	narZ	repressor	31563538	5	ver/dev	These results indicated that the RcsB regulator could mediate the repression of narZ gene expression once it is activated under high glucose concentration .	189	These results indicated that the RcsB regulator could mediate the repression of narZ gene expression once it is activated under high glucose concentration .	12	3.3. EFFECT OF RCSCDB SUGAR-ACTIVATION ON NARZ GENE EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	osmC	regulator	19389776	1	ver/dev	Interplay between global regulators of Escherichia coli : effect of RpoS on the transcription of the gene osmC .	493	Interplay between global regulators of Escherichia coli : effect of RpoS , Lrp and H-NS on the transcription of the gene osmC .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	osmC	regulator	19843227	46	ver/dev	Gutierrez , C. Interplay between global regulators of Escherichia coli : effect of RpoS on transcription of the gene osmC .	469	Bouvier , J. , Gordia , S. , Kampmann , G. , Lange , R. , Hengge-Aronis , R. , and Gutierrez , C. ( 1998 ) Interplay between global regulators of Escherichia coli : effect of RpoS , Lrp and H-NS on transcription of the gene osmC .	32	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	osmC	regulator	21311887	1	ver/dev	Among the 38 genes , osmC were previously reported to be regulated by RpoS .	120	Among the 38 genes , four ( osmC , osmY , osmB , and otsBA ) were previously reported to be regulated by RpoS [ 4 , 7 , 10 , 12 , 16 , 37 ] .	9	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	osmC	regulator	33638994	1	ver/dev	In this context , phosphorylated RcsB activates expression of cps operon ; rprA ; osmC , two genes also regulated by RpoS ; and , the cell division gene ftsZ , among others .	43	In this context , phosphorylated RcsB activates expression of the capsule ( cps ) operon ( 10 ) ; rprA , which encodes the small RNA RprA ( 11 ) ; osmC and osmB , two genes also regulated by RpoS ( 12 ) ; and , the cell division gene ftsZ ( 13 ) , among others .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmC	regulator	33638994	1	ver/dev	In this context , phosphorylated RcsB activates expression of the capsule operon ; rprA ; osmC , two genes also regulated by RpoS ; and , the cell division gene ftsZ , among others .	43	In this context , phosphorylated RcsB activates expression of the capsule ( cps ) operon ( 10 ) ; rprA , which encodes the small RNA RprA ( 11 ) ; osmC and osmB , two genes also regulated by RpoS ( 12 ) ; and , the cell division gene ftsZ ( 13 ) , among others .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hilC	repressor	17675384	1	ver/dev	The data show that all three genes , hilC , were repressed by H-NS and/or Hha .	10	The data show that all three genes , hilD , hilC , and rtsA , were repressed by H-NS and/or Hha .	1	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsA	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , mutation of the putative RcsB binding site in the ugd promoter abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RcsA	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , Fig. 2B abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , yojN genes abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , rcsC genes abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsA	gene	rcsA	repressor	12519186	39	ver/dev	The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , rcsB genes abolished tolB-promoted ugd transcription .	122	The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay , and by the RcsA protein because inactivation of the rcsA , rcsB , rcsC or yojN genes ( Fig. 2B ) or mutation of the putative RcsB binding site in the ugd promoter ( Fig. 5 ) abolished tolB-promoted ugd transcription .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	10816543	0	ver/dev	The constitutive phoP gene was placed under the control of an arabinose-inducible promoter to examine the kinetics of PhoP-activated gene induction .	10	The constitutive phoP gene was placed under the control of an arabinose-inducible promoter to examine the kinetics of PhoP-activated gene induction and the resultant modifications of LPS .	1	ABSTRACT	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	11918812	1	ver/dev	A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence .	249	A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence ( Miller and Mekalanos , 1990 ) .	8	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	11918812	1	ver/dev	A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence .	249	A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence ( Miller and Mekalanos , 1990 ) .	8	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	12492857	0	ver/dev	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( examples include genes ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	regulator	12492857	0	ver/dev	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag include genes ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	regulator	14507376	2	att	PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl . ) .	126	PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl . ) .	6	TRANSCRIPTIONAL PROFILING INDICATES ACTIVATION OF THE PHOP AND RPOS REGULONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	14563863	10	att	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	125	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	14563863	16	ver/dev	PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL .	155	PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL , and pmrC genes but not to the promoter region of phoN , pagC , or mgtC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	15208313	7	att	The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .	30	The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	15225317	0	att	In Salmonella enterica , the PhoP -- PhoQ two-component system governs resistance to structurally different antimicrobial peptides including the alphahelical magainin 2 , the b-sheet defensins and the cyclic lipopeptide polymyxin B. To identify the PhoP-regulated determinants mediating peptide resistance , we prepared a plasmid library from a phoP mutant , introduced it into a phoP mutant and selected for magainin-resistant clones .	10	In Salmonella enterica , the PhoP -- PhoQ two-component system governs resistance to structurally different antimicrobial peptides including the alphahelical magainin 2 , the b-sheet defensins and the cyclic lipopeptide polymyxin B. To identify the PhoP-regulated determinants mediating peptide resistance , we prepared a plasmid library from a phoP mutant , introduced it into a phoP mutant and selected for magainin-resistant clones .	1	SUMMARY	Salmonella;Salmonella enterica;Salmonella;unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	15225317	15	att	Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .	169	Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	regulator	15225317	22	att	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	192	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	8	UGTL IS AN INNER MEMBRANE PROTEIN THAT PROMOTES THE FORMATION OF MONOPHOSPHORYLATED LIPID A	Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	15225317	4	att	A phoP mutant is > 20 times more polymyxin B sensitive than a pmrA mutant when bacteria are grown in low Mg2 + and > 20 times more sensitive than wild-type Salmonella when bacteria are grown in the presence of Fe3 + ( Wosten et al. , 2000 ) , indicating that a PhoP-regulated PmrA-independent gene ( s ) participate ( s ) in polymyxin B resistance .	34	A phoP mutant is > 20 times more polymyxin B sensitive than a pmrA mutant when bacteria are grown in low Mg2 + and > 20 times more sensitive than wild-type Salmonella when bacteria are grown in the presence of Fe3 + ( Wosten et al. , 2000 ) , indicating that a PhoP-regulated PmrA-independent gene ( s ) participate ( s ) in polymyxin B resistance .	3	2 ND POLYMYXIN B	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	15225317	6	att	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid-A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	37	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	3	2 ND POLYMYXIN B	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	15225317	7	att	To identify PhoP-regulated genes mediating magainin 2 resistance , we prepared a genomic library from the phoP mutant strain MS7953s in the multicopy number plasmid pUC19 ( Norrander et al. , 1983 ) , introduced the library into the same phoP mutant and exposed the transformants to magainin 2 ( see Experimental procedures ) .	48	To identify PhoP-regulated genes mediating magainin 2 resistance , we prepared a genomic library from the phoP mutant strain MS7953s in the multicopy number plasmid pUC19 ( Norrander et al. , 1983 ) , introduced the library into the same phoP mutant and exposed the transformants to magainin 2 ( see Experimental procedures ) .	5	A SURVIVAL ENRICHMENT STRATEGY FOR RECOVERING PEPTIDE RESISTANCE GENES	Methanosarcina barkeri;unidentified plasmid;Cloning vector pUC19	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	phoP	regulator	15225317	8	att	This strategy was based on the premise that PhoP-regulated genes might be expressed from the lac promoter in pUC19 and confer magainin 2 resistance upon the phoP mutant .	49	This strategy was based on the premise that PhoP-regulated genes might be expressed from the lac promoter in pUC19 and confer magainin 2 resistance upon the phoP mutant .	5	A SURVIVAL ENRICHMENT STRATEGY FOR RECOVERING PEPTIDE RESISTANCE GENES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	15703297	19	att	These results were unexpected because acid resistance genes were not identified as PhoP-regulated genes in two previous microarray experiments that compared expression of wild-type and phoP Escherichia coli strains ( 14 , 35 ) nor had mutations in phoP been uncovered in screenings for acid regulatory genes in Escherichia coli .	153	These results were unexpected because acid resistance genes were not identified as PhoP-regulated genes in two previous microarray experiments that compared expression of wild-type and phoP Escherichia coli strains ( 14 , 35 ) nor had mutations in phoP been uncovered in screenings for acid regulatory genes in Escherichia coli .	4	RESULTS	Escherichia coli;Escherichia coli	0	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	phoP	regulator	15703297	3	att	For example , one of the profiles encompassed promoters that belong to the same expression ( E1 ) , PhoP box submotif ( M2 ) , and promoter class ( P1 ) ( Fig. 1H ) and harbored not only the prototypical PhoP-regulated phoP and mgtA promoters ( 13 , 14 ) but also the yhiW promoter , which was not known to be under PhoP control .	97	For example , one of the profiles encompassed promoters that belong to the same expression ( E1 ) , PhoP box submotif ( M2 ) , and promoter class ( P1 ) ( Fig. 1H ) and harbored not only the prototypical PhoP-regulated phoP and mgtA promoters ( 13 , 14 ) but also the yhiW promoter , which was not known to be under PhoP control .	4	RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PhoP	gene	phoP	regulator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	18792679	20	att	PhoQlPhoP 's sole role in the PmrD-mediated pathway is to promote PmrD expression because transcription of the pmrD gene from a heterologous promoter renders production of PmrA-activated mRNAs phoP - and phoQ-independent .42 Moreover , the PhoP-regulated PmrD protein functions at a posttranslationallevel because expression ofPmrA-activared genes was still phoP - andpmrD-dependent when thepmrA andpmrBgenes were expressed using a heterologous promoter and ribosome-binding site .	234	PhoQlPhoP 's sole role in the PmrD-mediated pathway is to promote PmrD expression because transcription of the pmrD gene from a heterologous promoter renders production of PmrA-activated mRNAs phoP - and phoQ-independent .42 Moreover , the PhoP-regulated PmrD protein functions at a posttranslationallevel because expression ofPmrA-activared genes was still phoP - andpmrD-dependent when thepmrA andpmrBgenes were expressed using a heterologous promoter and ribosome-binding site .	9	PHOP AS A CO-ACTIVATOR PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	19202096	1	ver/dev	pagC was downregulated almost 100-fold in the phoP mutant , validating this method for investigating gene regulation by PhoP inside macrophages .	317	pagC was downregulated almost 100-fold in the phoP mutant , validating this method for investigating gene regulation by PhoP inside macrophages ( Fig. 6b ) .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	20396961	4	att	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	209	To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .	11	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	25972862	3	ver/dev	In contrast , intracellular induction was not observed in a phoP null mutant , giving additional support to the conclusion that PhoP is a positive regulator of the expression of sseK1 .	387	In contrast , intracellular induction was not observed in a phoP null mutant , giving additional support to the conclusion that PhoP is a positive regulator of the expression of sseK1 .	21	SYNTHESIS AND TRANSLOCATION INTO MAMMALIAN CELLS OF SSEK1 UNDER SPI1 AND	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	phoP	regulator	26943369	1	att	Subsequently , the phosphoryl of PhoQ is transferred to the conserved aspartyl of PhoP , and then the phosphorylated PhoP activates the transcription of phoP itself and PhoP-regulated genes .	44	Subsequently , the phosphoryl of PhoQ is transferred to the conserved aspartyl of PhoP , and then the phosphorylated PhoP activates the transcription of phoP itself and PhoP-regulated genes .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	26943369	11	att	The qPCR assay demonstrated that both K201Q and K201A mutations led to significant transcriptional reduction of phoP and PhoP-regulated genes compared with the wild type strain , while K201R mimicking non-acetylated lysine residue activated the transcription of these genes dramatically ( Fig 3C ) , suggesting acetylation of K201 is involved in regulating the binding of PhoP to its DNA site and thus its ability to regulate its regulon in S. Typhimurium in-vivo .	174	The qPCR assay demonstrated that both K201Q and K201A mutations led to significant transcriptional reduction of phoP and PhoP-regulated genes compared with the wild type strain , while K201R mimicking non-acetylated lysine residue activated the transcription of these genes dramatically ( Fig 3C ) , suggesting acetylation of K201 is involved in regulating the binding of PhoP to its DNA site and thus its ability to regulate its regulon in S. Typhimurium in vivo .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	26943369	17	att	It has been shown that the transcription of phoP and PhoP-regulated genes were completely inhibited by 10 mM magnesium [ 41 ] , which caused about one third of PhoP K201 was acetylated , suggesting low acetylation proportion of PhoP K201 is required for PhoP activity .	269	It has been shown that the transcription of phoP and PhoP-regulated genes were completely inhibited by 10 mM magnesium [ 41 ] , which caused about one third of PhoP K201 was acetylated , suggesting low acetylation proportion of PhoP K201 is required for PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	26943369	19	att	The underlying reason is that PhoP K201R kept the ability to activate phoP transcription initiated from P1 promoter and PhoP-regulated gene transcription during infection , while PhoP K201Q inhibited these genes transcription due to its low DNA-binding affinity .	437	The underlying reason is that PhoP K201R kept the ability to activate phoP transcription initiated from P1 promoter and PhoP-regulated gene transcription during infection , while PhoP K201Q inhibited these genes transcription due to its low DNA-binding affinity .	9	ACETYLATION OF PHOP K201 IS CRITICAL FOR REGULATION OF PHOP ACTIVITY	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	26943369	2	att	Acetylation of lysine residue located in the DNA-binding motif inhibits DNA-binding ability of PhoP , and further alters the transcription of phoP and PhoP-regulated genes .	63	Acetylation of lysine residue located in the DNA-binding motif inhibits DNA-binding ability of PhoP , and further alters the transcription of phoP and PhoP-regulated genes .	5	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	phoP	regulator	26943369	21	att	It has been shown that PhoP phosphorylation is required for activation of transcription of phoP and PhoP-regulated genes [ 7 ] .	447	It has been shown that PhoP phosphorylation is required for activation of transcription of phoP and PhoP-regulated genes [ 7 ] .	9	ACETYLATION OF PHOP K201 IS CRITICAL FOR REGULATION OF PHOP ACTIVITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	26943369	3	att	Acetylation inhibits the transcription of phoP and PhoP-regulated genes	81	Acetylation inhibits the transcription of phoP and PhoP-regulated genes	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	26943369	5	att	The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .	84	The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	regulator	26943369	5	att	The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .	84	The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	regulator	26943369	6	att	We next ask whether deletion of pat increases the transcription of phoP and PhoP-regulated genes in-vivo .	86	We next ask whether deletion of pat increases the transcription of phoP and PhoP-regulated genes in vivo .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Other	OTHER	New	Level 1
PhoP	gene	phoP	regulator	26943369	7	att	mRNA levels of phoP and PhoP-regulated genes in the pat deletion mutant were also elevated significantly compared with the wild type strain in macrophage cells ( Fig 2C ) .	99	mRNA levels of phoP and PhoP-regulated genes in the pat deletion mutant were also elevated significantly compared with the wild type strain in macrophage cells ( Fig 2C ) .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	26943369	8	att	( C ) The transcription levels of phoP and PhoP-regulated genes of S. Typhimurium in macrophage cells .	125	( C ) The transcription levels of phoP and PhoP-regulated genes of S. Typhimurium in macrophage cells .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	26943369	9	ver/dev	EMSA was used to test the binding of the indicated concentrations of PhoP to 6 ' - FAM-labeled phoP promoter .	151	EMSA was used to test the binding of the indicated concentrations of PhoP ( lanes 2 to 5 , 7 to 10 , 12 to 15 , 17 -- 20 ) to 6 ' - FAM-labeled phoP promoter .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	26943369	14	ver/dev	EMSA was used to test the binding of PhoP at indicated concentrations to 6 ' - FAM-labeled phoP promoter .	206	EMSA was used to test the binding of PhoP at indicated concentrations ( lanes 2 to 5 and lanes 7 to 10 ) to 6 ' - FAM-labeled phoP promoter .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	29739882	23	ver/dev	PhoP promotes lpxT transcription directly by binding to the lpxT promoter Quantification of lpxT transcripts by qRT-PCR before phoP mutant Salmonella high Mg2 ; normalized to the 16S ribosomal RNA transcript .	647	PhoP promotes lpxT transcription directly by binding to the lpxT promoter ( A ) Quantification of lpxT transcripts by qRT-PCR before and 60 min after switching wildtype ( WT , 14028s ) and pmrA ( EG7139 ) , phoP ( MS7953s ) , and phoP pmrA ( EG12443 ) mutant Salmonella high Mg2 + medium ( 10 mM MgCl2 ) to low Mg2 + medium ( 10 µM MgCl2 ) at pH 7.7 ; normalized to the rrs ( 16S ribosomal RNA ) transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	29739882	23	ver/dev	PhoP promotes lpxT transcription directly by binding to the lpxT promoter Quantification of lpxT transcripts by qRT-PCR before phoP mutant Salmonella high Mg2 ; normalized to the rrs transcript .	647	PhoP promotes lpxT transcription directly by binding to the lpxT promoter ( A ) Quantification of lpxT transcripts by qRT-PCR before and 60 min after switching wildtype ( WT , 14028s ) and pmrA ( EG7139 ) , phoP ( MS7953s ) , and phoP pmrA ( EG12443 ) mutant Salmonella high Mg2 + medium ( 10 mM MgCl2 ) to low Mg2 + medium ( 10 µM MgCl2 ) at pH 7.7 ; normalized to the rrs ( 16S ribosomal RNA ) transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	29739882	23	ver/dev	PhoP promotes lpxT transcription directly by binding to the lpxT promoter Quantification of lpxT transcripts by qRT-PCR before phoP pmrA mutant Salmonella high Mg2 ; normalized to the 16S ribosomal RNA transcript .	647	PhoP promotes lpxT transcription directly by binding to the lpxT promoter ( A ) Quantification of lpxT transcripts by qRT-PCR before and 60 min after switching wildtype ( WT , 14028s ) and pmrA ( EG7139 ) , phoP ( MS7953s ) , and phoP pmrA ( EG12443 ) mutant Salmonella high Mg2 + medium ( 10 mM MgCl2 ) to low Mg2 + medium ( 10 µM MgCl2 ) at pH 7.7 ; normalized to the rrs ( 16S ribosomal RNA ) transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	29739882	23	ver/dev	PhoP promotes lpxT transcription directly by binding to the lpxT promoter Quantification of lpxT transcripts by qRT-PCR before phoP pmrA mutant Salmonella high Mg2 ; normalized to the rrs transcript .	647	PhoP promotes lpxT transcription directly by binding to the lpxT promoter ( A ) Quantification of lpxT transcripts by qRT-PCR before and 60 min after switching wildtype ( WT , 14028s ) and pmrA ( EG7139 ) , phoP ( MS7953s ) , and phoP pmrA ( EG12443 ) mutant Salmonella high Mg2 + medium ( 10 mM MgCl2 ) to low Mg2 + medium ( 10 µM MgCl2 ) at pH 7.7 ; normalized to the rrs ( 16S ribosomal RNA ) transcript .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	regulator	30373755	8	att	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	regulator	30967459	8	att	If the regulation of PhoP-regulated genes by EIIANtr is due to altered phoP transcription , heterologous expression of phoP from a plasmid should abolish the effect of EIIANtr on the expression of those genes .	140	If the regulation of PhoP-regulated genes by EIIANtr is due to altered phoP transcription , heterologous expression of phoP from a plasmid should abolish the effect of EIIANtr on the expression of those genes .	3	RESULTS	unidentified plasmid	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	30967459	8	ver/dev	If the regulation of PhoP-regulated genes by EIIANtr is due to altered phoP transcription , heterologous expression of phoP from a plasmid should abolish the effect of EIIANtr on the expression of those genes .	140	If the regulation of PhoP-regulated genes by EIIANtr is due to altered phoP transcription , heterologous expression of phoP from a plasmid should abolish the effect of EIIANtr on the expression of those genes .	3	RESULTS	unidentified plasmid	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	phoP	regulator	31447308	1	att	However , PhoP-regulated genes were not highly counter-selected in our study , and a phoP mutant had only a modest competitive disadvantage in humanized mice .	151	However , PhoP-regulated genes were not highly counter-selected in our study , and a phoP mutant had only a modest competitive disadvantage in humanized mice .	5	DISCUSSION	Mus sp.	0	L3	OTHER	Investigation	NEG	Other	Level 1
SoxS	gene	tolC	activator	11036033	1	ver/dev	Like marRAB , tolC are positively regulated by SoxS .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	tolC	activator	16842216	0	ver/dev	SoxS are primarily responsible for activation of tolC transcription .	343	The global regulatory proteins MarA , SoxS and Rob are primarily responsible for activation of acrAB and tolC transcription .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	tolC	activator	18984645	1	ver/dev	8 -- 13 _ shown that SoxS , play a role in antimicrobial resistance by activating tolC	21	Studies in Escherichia coli have 8 -- 13 shown that transcriptional activators , such as MarA , SoxS and Rob , play a role in antimicrobial resistance by activating transcription of efflux pumps , including acrAB and tolC .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	tolC	activator	34202800	6	ver/dev	SoxS , , are involved in activating tolC expression .	254	Three homologous transcriptional activators , RamA , SoxS , and MarA , controlled by RamR , SoxR , and MarR , are involved in activating acrB and tolC expression [ 68 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	rob	regulator	22752112	4	ver/dev	The expression of rob is negatively regulated by MarA in response to sodium salicylate and paraquat , respectively .	29	The expression of rob is negatively regulated by MarA and SoxS in response to sodium salicylate and paraquat , respectively ( Pomposiello et al. 2001 ; Michán et al. 2002 ; Schneiders and Levy 2006 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	rob	regulator	22752112	9	ver/dev	rob is negatively regulated by MarA	200	rob is negatively regulated by MarA and SoxS	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	rob	regulator	22752112	13	ver/dev	MarA bind the promoter region of rob	231	MarA and SoxS bind the promoter region of rob	16	MARA AND SOXS BIND THE PROMOTER REGION OF ROB	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	rob	regulator	22752112	21	ver/dev	other studies _ performed in E. coli where rob was shown to be negatively regulated by both MarA by a direct interaction with its promoter region	304	Our results are in agreement with other studies performed in E. coli where rob was shown to be negatively regulated by both MarA and SoxS by a direct interaction with its promoter region ( Schneiders and Levy 2006 ; Michán et al. 2002 ) .	17	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	rob	regulator	22752112	22	ver/dev	EMSAs _ demonstrating that MarA bind to the promoter region of rob , indicating that the repression exerted by MarA is due to a direct interaction with the DNA	308	DNA-protein interaction was confirmed by EMSAs demonstrating that MarA and SoxS bind to the promoter region of rob ( Fig. 4b , c ) , indicating that the repression exerted by MarA and SoxS is due to a direct interaction with the DNA ( Table 3 ) .	17	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsB	TU	flhDC	regulator	15256548	20	ver/dev	Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon .	678	Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon ( Ellermeier & Slauch , 2003 ) .	15	STRESS RESPONSE GENES AND GLOBAL REGULATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsB	TU	flhDC	regulator	16988271	0	ver/dev	RtsB have also been shown to regulate SPI-1 genes and flhDC , respectively .	357	RtsA and RtsB have also been shown to regulate SPI-1 genes and flhDC ( which direct flagellum biosynthesis ) , respectively ( 16 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsB	TU	flhDC	regulator	27601571	2	ver/dev	However , unlike HilD , RtsB is a negative regulator of flhDC .	63	However , unlike HilD , RtsB is a negative regulator of flhDC ( 10 , 19 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsB	TU	flhDC	regulator	28973452	3	ver/dev	RtsB also regulate cell motility by interacting with the flhDC promoter .	29	RcsB , H-NS and RtsB also regulate cell motility by interacting with the flhDC promoter ( 11 -- 13 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsB	TU	flhDC	regulator	31262841	12	ver/dev	We have previously shown that RtsB regulates flagellar gene expression by repressing the transcription of flhDC , encoding the master regulator of the flagellar regulon .	180	We have previously shown that RtsB regulates flagellar gene expression by repressing the transcription of flhDC , encoding the master regulator of the flagellar regulon ( 19 , 70 , 71 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtcR	gene	rtcB	activator	30201777	3	ver/dev	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcB were measured in a WT strai .	103	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcA or rtcB were measured in a ΔrtcR mutant and a WT strain ( Fig. 3 ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcB	activator	30201777	3	ver/dev	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcB were measured in a ΔrtcR mutan .	103	To determine whether the upregulation of RNA repair operon expression under these three stress conditions is dependent on RtcR , transcript levels for rtcA or rtcB were measured in a ΔrtcR mutant and a WT strain ( Fig. 3 ) .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcB	activator	30201777	13	ver/dev	Since RtcR appears to be activated by the RecA-dependent SOS response following MMC treatment , it is surprising that peroxide stress , did not activate RtcR to stimulate expression of rtcB .	152	Since RtcR appears to be activated by the RecA-dependent SOS response following MMC treatment , it is surprising that peroxide stress , which also induces the SOS response , did not activate RtcR to stimulate expression of rtcB .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express Fig. 3B , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcB was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for ΔrpoN strai .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express Fig. 3B , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcB was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for Δrtc .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express Fig. 3B , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcB was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcB was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for ΔrpoN strai .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcB was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for Δrtc .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rtcB was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for ΔrpoN strai .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for Δrtc .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
RtcR	gene	rtcB	activator	30201777	15	ver/dev	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT .	168	To examine the second proposed reason for why the 1 mM H2O2 treatment did not activate RtcR to express rtcB ( Fig. 3B ) , i.e. , the level of DNA damage from this peroxide treatment was not sufficient to generate the SOS-dependent signal for activation of RtcR , expression of rsr , rtcB , and rtcA was measured by qRT-PCR after a 20 min treatment with 7 mM H2O2 for WT , ΔrtcR , and ΔrpoN strains .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
OmpR	gene	atpB	repressor	29103680	0	ver/dev	The authors further showed that , in addition to repression of the cadBA genes , OmpR was apparently also involved in activation of the atpB gene , encoding the α F0 subunit of the ATP synthase , thereby maintaining the cytoplasmic acidification in media at pH 5.6 .	173	The authors further showed that , in addition to repression of the cadBA genes which would consume protons , OmpR was apparently also involved in activation of the atpB gene , encoding the α F0 subunit of the ATP synthase , thereby maintaining the cytoplasmic acidification in media at pH 5.6 .	18	4. DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
StpA	gene	ugtL	repressor	19843227	36	att	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	262	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sipC	repressor	26386070	2	ver/dev	These data demonstrated that the expression of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	262	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	rck	regulator	25080967	36	ver/dev	The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS .	315	The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS ( Ono et al. , 2005 ; Navarre et al. , 2006 ) .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	STM3216	repressor	27564394	9	ver/dev	STM3216 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI4-encoded genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM3216	repressor	27564394	9	ver/dev	STM3216 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-associated genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	STM3216	repressor	27564394	9	ver/dev	STM3216 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-encoded genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
OmpR-P	gene	csgD	activator	14643403	25	ver/dev	Under microaerophilic conditions IHF occupies the IHF1 site upstream of the csgD promoter by replacing OmpR-P from the D3 -- D6 site and activation of csgD transcription .	202	Under microaerophilic conditions IHF occupies the IHF1 site upstream of the csgD promoter by replacing OmpR-P from the D3 -- D6 site and activation of csgD transcription .	20	6.5. MLRA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	galP	repressor	24450479	40	ver/dev	NagC _ participating with GalS in the repression of galP in E. coli	177	This seemed to imply another link between galactose and amino sugar metabolism as exemplified by NagC participating with GalR and GalS in the repression of galP in E. coli ( El Qaidi et al. , 2009 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	galP	repressor	24450479	40	ver/dev	NagC _ participating with GalS in the repression of galP in E. coli	177	This seemed to imply another link between galactose and amino sugar metabolism as exemplified by NagC participating with GalR and GalS in the repression of galP in E. coli ( El Qaidi et al. , 2009 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HilC	TU	ssrAB	regulator	25135218	78	ver/dev	Thus , it is possible that HilC can regulate the expression of ssrAB .	224	Thus , it is possible that the feed forward loop constituted by HilD , HilC , and RtsA can regulate the expression of ssrAB .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
AraC	gene	garD	regulator	24272778	16	att	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	222	and tdcE ) , D-glucarate/D-galactarate metabolism ( garD , garL , Novel AraC-regulated genes identified using this approach are garP , and garR ) , and tryptophan metabolism ( tnaA , tnaB , and discussed below .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	sifA	repressor	21059643	15	ver/dev	H-NS specifically repressed transcription of sifA	291	H-NS specifically repressed transcription of sifA , but this repression was antagonized by the presence of SsrB .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	csgD	repressor	26880544	17	ver/dev	This result indicated that H-NS was functioning to repress csgD .	228	This result indicated that H-NS was functioning to repress csgD ( see Discussion ) .	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	csgD	repressor	26880544	23	ver/dev	This work clearly shows that , as observed in E. coli , H-NS represses expression of csgD in Salmonella .	266	This work clearly shows that , as observed in E. coli , H-NS represses expression of csgD in Salmonella ( see Discussion ) .	10	SSRB AND H-NS DIFFERENTIALLY REGULATE CSGD EXPRESSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	repressor	26880544	34	ver/dev	our earlier observations H-NS repressed expression of csgD	290	Thus , we reaffirmed our earlier observations that H-NS repressed expression of csgD by filament formation , leading to transcriptional silencing ( Figure 4D ) .	12	SSRB BINDS AN H-NS STIFFENED NUCLEOPROTEIN FILAMENT AT CSGD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	csgD	repressor	26880544	58	ver/dev	Furthermore , we identify H-NS as a repressor of csgD in Salmonella , instead of an activator .	397	Furthermore , we identify H-NS as a repressor of csgD in Salmonella , instead of an activator ( Gerstel et al. , 2003 ) .	17	STRUCTURAL HOMOLOGY DOES NOT INDICATE FUNCTIONAL HOMOLOGY	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
CadC	gene	STM4538	activator	23066934	8	ver/dev	To assess the potential role of STM4538 in the proteolytic activation of CadC , we performed an immunoblot analysis of total protein extracts from DSTM4538 strains .	155	To assess the potential role of STM4538 in the proteolytic activation of CadC , we performed an immunoblot analysis of total protein extracts from the S. Typhimurium wild-type and DSTM4538 strains harboring pACYC184-HA-CadC .	14	INACTIVATION OF STM4538 PREVENTS PROTEOLYTIC CLEAVAGE OF CADC	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
CadC	gene	STM4538	activator	23066934	8	ver/dev	To assess the potential role of STM4538 in the proteolytic activation of CadC , we performed an immunoblot analysis of total protein extracts from the S. Typhimurium wild-type .	155	To assess the potential role of STM4538 in the proteolytic activation of CadC , we performed an immunoblot analysis of total protein extracts from the S. Typhimurium wild-type and DSTM4538 strains harboring pACYC184-HA-CadC .	14	INACTIVATION OF STM4538 PREVENTS PROTEOLYTIC CLEAVAGE OF CADC	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	OTHER	Analysis	OTHER	Other	Level 1
CadC	gene	STM4538	activator	23066934	9	ver/dev	These results suggest that the PTS permease STM4538 is required for the proteolytic activation of CadC signaling in S. Typhimurium .	159	These results suggest that the PTS permease STM4538 is required for the proteolytic activation of CadC signaling in S. Typhimurium .	14	INACTIVATION OF STM4538 PREVENTS PROTEOLYTIC CLEAVAGE OF CADC	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	STM4538	activator	23066934	12	ver/dev	PTS permease STM4538 is involved in the proteolytic activation of CadC .	214	PTS permease STM4538 is involved in the proteolytic activation of CadC .	16	S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CadC	gene	STM4538	activator	23066934	18	ver/dev	The identi-fication of STM4538 as a positive modulator of CadC function provides important information for uncovering the molecular basis of the proteolytic activation of CadC .	237	The identi-fication of STM4538 as a positive modulator of CadC function provides important information for uncovering the molecular basis of the proteolytic activation of CadC .	17	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	sirA	activator	33162952	0	ver/dev	Expression studies indicates that CRP-cAMP , in contrast to its role , positively regulate the expression of CsrC via upregulation of sirA .	51	Expression studies using S. enterica cultures on solid media indicates that CRP-cAMP , in contrast to its role described in E. coli , positively regulate the expression of CsrB and CsrC via upregulation of sirA ( Teplitski et al. , 2006 ) .	4	NTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	sirA	activator	33162952	0	ver/dev	Expression studies indicates that CRP-cAMP , in contrast to its role , positively regulate the expression of CsrC via upregulation of sirA .	51	Expression studies using S. enterica cultures on solid media indicates that CRP-cAMP , in contrast to its role described in E. coli , positively regulate the expression of CsrB and CsrC via upregulation of sirA ( Teplitski et al. , 2006 ) .	4	NTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	sirA	activator	33162952	0	ver/dev	Expression studies indicates that CRP-cAMP , in contrast to its role , positively regulate the expression of CsrB via upregulation of sirA .	51	Expression studies using S. enterica cultures on solid media indicates that CRP-cAMP , in contrast to its role described in E. coli , positively regulate the expression of CsrB and CsrC via upregulation of sirA ( Teplitski et al. , 2006 ) .	4	NTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	sirA	activator	33162952	0	ver/dev	Expression studies indicates that CRP-cAMP , in contrast to its role , positively regulate the expression of CsrB via upregulation of sirA .	51	Expression studies using S. enterica cultures on solid media indicates that CRP-cAMP , in contrast to its role described in E. coli , positively regulate the expression of CsrB and CsrC via upregulation of sirA ( Teplitski et al. , 2006 ) .	4	NTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	invF	activator	10692170	0	ver/dev	HilA , is believed to directly activate expression from the invF promoters in SPI1 .	59	HilA , encoded within SPI1 , is a ToxR/OmpR-type regulator and is believed to directly activate expression from the invF and prgH promoters in SPI1 .	4	MAIN	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilA	gene	invF	activator	10692170	3	ver/dev	HilA activates the expression of the regulatory gene invF , the first gene of the large SPI1 inv ± spa ± sip gene cluster .	63	HilA activates the expression of the regulatory gene invF , the first gene of the large SPI1 inv ± spa ± sip gene cluster .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	activator	10826713	0	ver/dev	HilA may activate invF , by interacting	28	HilA may activate expression of invasion genes , including invF , by interacting	3	MAIN	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	invF	activator	11123690	0	ver/dev	HilA is a member of the ToxR/OmpR-like family of transcriptional regulatory proteins and is required for induction of the SPI-1 prg operon , and is also required for optimal expression of invF .	41	HilA is a member of the ToxR/OmpR-like family of transcriptional regulatory proteins and is required for induction of the SPI-1 prg operon , which encodes components of the type III secretion apparatus , and is also required for optimal expression of invF , which encodes an AraC-like transcriptional regulator of additional SPI-1 invasion genes ( Kaniga et al. , 1994 ; Bajaj et al. , 1995 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	activator	11755416	33	att	Overexpression of HilD appears to directly activate a promoter well upstream of the previously characterized HilA-dependent invF promoter .	560	Overexpression of HilD appears to directly activate a promoter well upstream of the previously characterized HilA-dependent invF promoter .	16	REFERENCES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	invF	activator	11755416	1	ver/dev	The straight , solid-headed arrows show that HilA protein directly activates the expression of invF .	67	The straight , solid-headed arrows show that HilA protein directly activates the expression of structural genes such as the prgs and another regulatory gene , invF .	4	2. ROLES OF SPI1 IN PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	25	att	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	84	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	25	att	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	84	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	34	att	HilD and HilC do not activate invF expression from the HilA-dependent invF promoter	106	HilD and HilC do not activate invF expression from the HilA-dependent invF promoter	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilA	gene	invF	activator	12535071	34	att	HilD and HilC do not activate invF expression from the HilA-dependent invF promoter	106	HilD and HilC do not activate invF expression from the HilA-dependent invF promoter	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilA	gene	invF	activator	12535071	36	att	We considered that HilD and HilC might also bind upstream of invF and directly activate transcription from the HilA-activated invF promoter .	108	We considered that HilD and HilC might also bind upstream of invF and directly activate transcription from the HilA-activated invF promoter .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L1	SPEC	Other	OTHER	New	Level 1
HilA	gene	invF	activator	12535071	36	att	We considered that HilD and HilC might also bind upstream of invF and directly activate transcription from the HilA-activated invF promoter .	108	We considered that HilD and HilC might also bind upstream of invF and directly activate transcription from the HilA-activated invF promoter .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L1	SPEC	Other	OTHER	New	Level 1
HilA	gene	invF	activator	12535071	37	att	We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .	109	We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	unidentified plasmid;Prairie vole hantavirus	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	37	att	We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .	109	We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	unidentified plasmid;Prairie vole hantavirus	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	4	att	Our studies show that HilD and HilC activate transcription of invF from a promoter that is far upstream of its HilA-dependent promoter .	16	Our studies show that HilD and HilC activate transcription of invF from a promoter that is far upstream of its HilA-dependent promoter .	2	ABSTRACT	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	42	att	A HilD- and HilC-dependent invF transcription start site lies far upstream of the HilA-dependent transcription start site	115	A HilD- and HilC-dependent invF transcription start site lies far upstream of the HilA-dependent transcription start site	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	45	att	The location of ebe17 hybridization is close to that of primer invF-RT , which we used previously to determine the HilA-dependent transcription start site ( +1 ) of invF ( Lostroh et al. , 2000 ) .	120	The location of ebe17 hybridization is close to that of primer invF-RT , which we used previously to determine the HilA-dependent transcription start site ( +1 ) of invF ( Lostroh et al. , 2000 ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	synthetic construct	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	46	att	Genetic studies indicate that the longer product corresponds to the physiologically relevant HilA-dependent +1 of invF ( Lostroh et al. , 2000 ) .	122	Genetic studies indicate that the longer product corresponds to the physiologically relevant HilA-dependent +1 of invF ( Lostroh et al. , 2000 ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	12535071	48	att	Our results suggested that the 5 cents - ends of the two HilDdependent transcripts map to positions corresponding to 643 and 631 nucleotides upstream of the invF ORF ; 511 and 499 nucleotides upstream of the HilA-dependent +1 .	130	Our results suggested that the 5 cents - ends of the two HilDdependent transcripts map to positions corresponding to 643 and 631 nucleotides upstream of the invF ORF ; 511 and 499 nucleotides upstream of the HilA-dependent +1 .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	invF	activator	12535071	50	att	pVV448 contains the 447 bp from upstream of invF ( -319 to +128 , relative to HilA-dependent +1 position .	138	pVV448 contains the 447 bp from upstream of invF ( -319 to +128 , relative to HilA-dependent +1 position .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Prairie vole hantavirus	0	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	66	att	Instead , there appears to be a single HilD - and HilC-dependent promoter in this region corresponding to the predicted transcription start site located 631 bp upstream of the invF ORF ; 499 bp upstream of the HilA-dependent +1 .	180	Instead , there appears to be a single HilD - and HilC-dependent promoter in this region corresponding to the predicted transcription start site located 631 bp upstream of the invF ORF ; 499 bp upstream of the HilA-dependent +1 .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	12535071	75	att	pSA7 contains the 919 bp from upstream of invF ( -791 to +128 , relative to HilA-dependent +1 position ) .	191	pSA7 contains the 919 bp from upstream of invF ( -791 to +128 , relative to HilA-dependent +1 position ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	78	att	pSA7 contains the 919 bp from upstream of invF ( -791 to +128 , relative to HilA-dependent +1 position ) .	208	pSA7 contains the 919 bp from upstream of invF ( -791 to +128 , relative to HilA-dependent +1 position ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	95	att	In the meantime , HilD/C could directly activate invF expression , which , by bypassing the HilA-dependent pathway , would shorten the time leading to expression of the secreted effectors .	279	In the meantime , HilD/C could directly activate invF expression , which , by bypassing the HilA-dependent pathway , would shorten the time leading to expression of the secreted effectors .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Other	OTHER	New	Level 1
HilA	gene	invF	activator	12535071	96	att	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	280	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	12535071	2	ver/dev	HilA activates invF .	12	HilA activates invF as well as SPI1 genes that encode components of the TTS apparatus .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	6	ver/dev	By binding upstream of invF , HilA directly activates expression of the invF operons that encode the components of the TTS apparatus .	34	By binding upstream of invF and prgH , HilA directly activates expression of the invF and prgH operons that encode the components of the TTS apparatus ( Lostroh et al. , 2000 ; Lostroh and Lee , 2001 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	35	ver/dev	Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .	107	Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box ( Lostroh et al. , 2000 ) .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	35	ver/dev	Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .	107	Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box ( Lostroh et al. , 2000 ) .	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	12535071	81	ver/dev	HilA activates transcription of invF from a start site .	231	HilA activates transcription of invF from a start site that is 132 nucleotides upstream of the invF ORF ( Lostroh et al. , 2000 ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	12535071	96	ver/dev	Thus , by the time HilA-dependent activation of invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be ready to be secreted .	280	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	12535071	96	ver/dev	Thus , by the time HilA-dependent activation of invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed .	280	Thus , by the time HilA-dependent activation of prgH and invF leads to the expression and formation of a functional TTS apparatus , effector proteins would already be expressed and ready to be secreted .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	14977940	1	ver/dev	HilA activates invF .	274	HilA activates invF as well as other SPI1 genes and therefore plays a key role in coordinating the expression of the SPI1-encoded type III secretion system .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	15661008	1	ver/dev	HilA activates invF operon expression by binding to the invF promoter .	42	HilA belongs to OmpR/ToxR family and activates invF operon expression by binding to the invF promoter ( Bajaj et al. , 1995 ; Lostroh et al. , 2000 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	15661008	1	ver/dev	HilA activates invF operon expression by binding to the invF promoter .	42	HilA belongs to OmpR/ToxR family and activates invF operon expression by binding to the invF promoter ( Bajaj et al. , 1995 ; Lostroh et al. , 2000 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	15765064	5	ver/dev	Apparently , HilA activates the expression of invF .	58	Apparently , HilA activates the expression of invF and sicA , whose genes respectively encode an AraC/XylS transcriptional activator and a chaperone , that together activate transcription of the sip operon .	3	THE HILA REGULATOR	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilA	gene	invF	activator	15790293	12	att	Genetic analyses on SPI1 regulation have revealed a second promoter upstream the HilA-dependent one in front of invF that responds to over-expression of HilC , another AraC/XylS-like protein coded for by SPI1 , and of HilD ( Akbar et al. , 2003 ) .	307	Genetic analyses on SPI1 regulation have revealed a second promoter upstream the HilA-dependent one in front of invF that responds to over-expression of HilC , another AraC/XylS-like protein coded for by SPI1 , and of HilD ( Akbar et al. , 2003 ) .	16	TWO-COMPONENT RESPONSE REGULATOR SYSTEMS AS REGULON COMPONENTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	16045614	6	att	These proteins also act independently of HilA to activate expression of the invF operon , albeit at significantly lower levels than HilA-dependent activation ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Akbar et al. , 2003 ; Ellermeier and Slauch , 2003 ) .	43	These proteins also act independently of HilA to activate expression of the invF operon , albeit at significantly lower levels than HilA-dependent activation ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Akbar et al. , 2003 ; Ellermeier and Slauch , 2003 ) .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilA	gene	invF	activator	16253373	0	ver/dev	invF genes where the HilA transcriptional regulator induces invF -LRB- as well genes -RRB-	251	The expression of the SPI-1 genes is controlled by a regulatory cascade involving the SPI-1-encoded hilA and invF genes where the HilA transcriptional regulator induces invF ( as well genes that encode components of the type III secretion apparatus ) , and the InvF protein then turns on the expression of other SPI-1 genes including the sip genes ( Eichelberg and Galan , 1999 ) .	18	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	17060472	5	ver/dev	Moreover , HilA indirectly regulates the expression of secreted proteins by activating the transcription of the SPI-1 invF gene .	428	Moreover , HilA indirectly regulates the expression of secreted proteins by activating the transcription of the SPI-1 invF gene , encoding an AraC family transcriptional regulator .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	21573071	1	ver/dev	HilA , directly activates the expression of the invF operons .	32	The main regulator of SPI1 , HilA , directly activates the expression of the invF and prgH operons , which encode the components of the T3SS apparatus [ 6,7 ] .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	21722794	2	att	Fur also positively regulates other HilA-dependent genes ( invF and sipC ) involved in invasion , by repressing the expression of H-NS ( Troxell et al. , 2011 ) .	444	Fur also positively regulates other HilA-dependent genes ( invF and sipC ) involved in invasion , by repressing the expression of H-NS ( Troxell et al. , 2011 ) .	11	3.1. TRANSCRIPTIONAL REGULATION BY FUR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	activator	22479568	1	ver/dev	HilA also induces the expression of the transcriptional regulator invF .	32	HilA also induces the expression of the transcriptional regulator invF , encoding a member of the AraC family that activates the expression of genes encoding effector proteins within and outside SPI1 [ 13,14 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	24500522	0	ver/dev	HilA in the invasion pathway independently activate the expression of invF .	164	HilA and HilC/D in the invasion pathway independently activate the expression of invF regulated by invF-1 and invF-2 promoters , respectively ( Lim et al. 2012 ) .	19	VIABILITY AND MOTILITY OF S. TYPHIMURIUM EXPOSED TO THE SIMULATED INTESTINAL CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	26386070	2	att	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	262	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	27404739	0	ver/dev	One of the operons directly activated by HilA contains invF gene .	120	One of the operons directly activated by HilA contains invF gene , which in turn stimulates the expression of TTSS-1 effectors encoded both inside and outside SPI-1 ( 32 ) .	6	SPI-1 RELATED GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	27549210	1	ver/dev	By binding upstream of invF , HilA directly activates the expression of invF .	363	By binding upstream of invF , HilA directly activates the expression of invF .	21	DISSCUSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	27549210	1	ver/dev	By binding upstream of invF , HilA directly activates the expression of invF .	363	By binding upstream of invF , HilA directly activates the expression of invF .	21	DISSCUSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	27886269	5	ver/dev	invF is positively regulated by HilD through HilA	65	As a control , the expression of a cat transcriptional fusion of invF , which is positively regulated by HilD through HilA , was also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	invF	activator	28333132	0	ver/dev	HilA , in turn , directly activates the expression of invF encoding T3SS .	45	HilA , in turn , directly activates the expression of invF and the genes encoding T3SS and also indirectly induces the transcription of SPI-4 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	28335027	12	att	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	770	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	28335027	3	ver/dev	As HilA is a transcriptional activator of invF , the ΔhilA strain provides a measure of uninduced invF expression .	368	As HilA is a transcriptional activator of invF , the ΔhilA strain provides a measure of uninduced invF expression .	17	REPRESSION OF SPI-1 ENCODED GENES BY TNPA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	invF	activator	28335027	9	ver/dev	This threshold for activation would ensure that InvF is only synthesized once there is a sufficiently high transcriptional activation of the invF promoter by HilA .	765	This threshold for activation would ensure that InvF is only synthesized once there is a sufficiently high transcriptional activation of the invF promoter by HilA .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilA	gene	invF	activator	28439039	1	att	It is also reported that HilD is able to activate the transcription of invF from a promoter that is far upstream of its HilA-dependent promoter ( 6 ) .	97	It is also reported that HilD is able to activate the transcription of invF from a promoter that is far upstream of its HilA-dependent promoter ( 6 ) .	4	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	28439039	7	att	Furthermore , it was reported HilD is able to activate the transcription of invF from a promoter that is far upstream of its HilA-dependent promoter .	296	Furthermore , it was reported HilD is able to activate the transcription of invF from a promoter that is far upstream of its HilA-dependent promoter .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilA	gene	invF	activator	31428589	2	ver/dev	HilA directly activates the expression of invF .	151	HilA directly activates the expression of two SPI-1 genes ( invF and sicA ) that encode SPI-1 T3SS apparatus components .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	32316180	3	ver/dev	HilA , in turn , activates transcription of the regulator invF .	395	HilA , in turn , activates transcription of the regulator invF and acts directly at the T3SS and T3SE gene promoters .	14	3.7. AT NUCLEOTIDE CONTENT AND THE EVOLUTION OF TRANSCRIPTIONAL CONTROL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	32316180	4	ver/dev	HilA binds to the invF promoters , triggering the activation of T3SE genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	32316180	4	ver/dev	HilA binds to the invF promoters , triggering the activation of T3SS genes .	398	HilA binds to the invF and prgH promoters , triggering the activation of T3SS and T3SE genes [ 81 -- 83 ] .	15	3.8. EVOLUTION OF TRANSCRIPTIONAL CONTROL: ACQUISITION OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	invF	activator	33101243	4	ver/dev	HilA , induces the expression of the AraC-like regulator genes invF and sicA .	234	HilA , the critical regulator of SPI-1 , induces the expression of the AraC-like regulator genes invF and sicA , encoding the inv/spa , prg/org , and sic/sip operons ( Ellermeier et al. , 2005 ; Golubeva et al. , 2012 ) .	24	MYRICANOL INHIBITS THE T3SS MAINLY BY LOWERING THE LEVEL OF HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CytR	gene	udp	activator	16949866	46	ver/dev	Role of multiple CytR binding sites on induction at the E. coli udp promoter .	648	Role of multiple CytR binding sites on cooperativity , competition , and induction at the E. coli udp promoter .	42	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	regulator	10998173	0	ver/dev	SpvR regulates the spvABCD operon	255	SpvR regulates the spvABCD operon , and both are encoded in an 8 kb locus on the large virulence plasmid pSLT2 ( Guiney et al. , 1995 ) .	10	DISRUPTION OF A PSLT-ENCODED TRANSCRIPTIONAL REGULATOR RESULTS IN A MODERATE REDUCTION IN LGP-TUBULE FREQUENCY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	regulator	11207562	0	ver/dev	the spvABCD genes _ regulated by the SpvR protein	42	The Salmonella spv genes are organized as an operon , with expression of the spvABCD genes regulated by the SpvR protein ( Fang et al. , 1991 ; Krause et al. , 1992 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SpvR	gene	spvABCD	regulator	11207562	2	ver/dev	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , that of the spvABCD operon .	44	SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	mcpC	regulator	33441540	5	ver/dev	HilD regulates mcpC by derepression of H-NS .	66	HilD regulates mcpC by derepression of H-NS .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	mcpC	regulator	33441540	13	ver/dev	HilD specifically bind to the regulatory region of mcpC	78	Thus , HilD and H-NS specifically bind to the regulatory region of mcpC and HilD is an antagonist of H-NS binding .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	mcpC	regulator	33441540	19	ver/dev	Purified maltose-binding protein HilD fusion protein bound to the full-length 387 bp mcpC promoter .	109	Purified maltose-binding protein HilD fusion protein ( MBP-HilD ) bound to the full-length 387 bp mcpC promoter ( PmcpC-387 , Fig. 2e ) but not to the shortened 79 bp regulatory region ( PmcpC-79 , Fig. 2f ) or the promoter region of another chemoreceptor ( PmcpB-333 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	csgD	repressor	14643403	1	ver/dev	CsgD transcription remained unchanged in buffered medium whereas in unbuffered rich-medium csgD activity was repressed by our unpublished data .	102	CsgD transcription remained unchanged in buffered medium whereas in unbuffered rich medium csgD activity was repressed by glucose ( our unpublished data ) [ 14 ] .	11	4.3. TEMPERATURE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	csgD	repressor	14643403	1	ver/dev	CsgD transcription remained unchanged in buffered medium whereas in unbuffered rich-medium csgD activity was repressed by glucose .	102	CsgD transcription remained unchanged in buffered medium whereas in unbuffered rich medium csgD activity was repressed by glucose ( our unpublished data ) [ 14 ] .	11	4.3. TEMPERATURE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ssrA	regulator	15491370	19	ver/dev	SlyA also regulates ssrA	322	SlyA also regulates ssrA	10	SLYA ALSO REGULATES SSRA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ssrA	regulator	15491370	20	ver/dev	Our recent observations indicate that SlyA exerts a direct effect by binding at ssrA .	360	Our recent observations indicate that SlyA exerts a direct effect by binding at ssrA and ssrB ( D. Walthers et al. , in preparation ) .	10	SLYA ALSO REGULATES SSRA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ssrA	regulator	17259627	0	ver/dev	the ssrA , indicating that SlyA is directly involved in the regulation of SPI-2 gene expression .	11	the ssrA promoter , indicating that SlyA is directly involved in the regulation of SPI-2 gene expression .	0	Unknown	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ssrA	regulator	17259627	10	ver/dev	We show that the SlyA protein binds directly to the ssrA promoter .	65	We show that the SlyA protein binds directly to the ssrA promoter .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ssrA	regulator	17259627	34	ver/dev	We have shown that SlyA controls ssrA transcription directly by binding to the ssrA promoter .	344	We have shown that SlyA controls ssrA transcription directly by binding to the ssrA promoter .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ssrA	regulator	17259627	34	ver/dev	We have shown that SlyA controls ssrA transcription directly by binding to the ssrA promoter .	344	We have shown that SlyA controls ssrA transcription directly by binding to the ssrA promoter .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ssrA	regulator	17259627	34	ver/dev	We have shown that SlyA controls ssrA transcription directly by binding to the ssrA promoter .	344	We have shown that SlyA controls ssrA transcription directly by binding to the ssrA promoter .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ssrA	regulator	17259627	41	ver/dev	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators SsrB .	367	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators OmpR and SsrB .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	ssrA	regulator	17259627	41	ver/dev	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators OmpR .	367	Similarly , in the case of ssrA , the binding of SlyA might change the local nucleoprotein structure of the chromosome by competing with the negative action of repressors ( such as H-NS ) , and enabling activation of ssrA by response regulators OmpR and SsrB .	12	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
CsgD	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the master biofilm regulator CsgD on fliF operons ; .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the master biofilm regulator CsgD on fliE ; .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the master biofilm regulator CsgD on fliA ; .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	cueR	activator	23645605	0	att	cueR was introduced into L the chromosome of the S. Typhimurium 14028 strain replacing wild-type cueR , and the expression of the CueR-dependent copA : : lacZ reporter in cells grown in Luria-Bertani ( LB ) medium was determined in the presence or absence of either 40 M AuHCl4 or 1 mM CuSO4 ( Fig. 1B ) .	87	cueR was introduced into L the chromosome of the S. Typhimurium 14028 strain replacing wild-type cueR , and the expression of the CueR-dependent copA : : lacZ reporter in cells grown in Luria-Bertani ( LB ) medium was determined in the presence or absence of either 40 M AuHCl4 or 1 mM CuSO4 ( Fig. 1B ) .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	spvR	repressor	30682134	15	ver/dev	CsrA repressed spvR translation 4-fold in mLPM	218	CsrA repressed spvR translation 4-fold in mLPM , but levels of this mRNA were insufficient for analysis in LB ( S2 Table ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	spvR	repressor	30682134	20	ver/dev	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM encoded effectors , slyA in LB .	227	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM and repressing the regulator of SPI-2 encoded effectors , slyA in LB .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	Salmonella;unidentified plasmid	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	prgH	repressor	20002188	0	ver/dev	Comparison of the INP0403-sensitive transcriptome to the HilA regulon indicated that prgH in the HilA regulon was significantly -LRB- at least twofold -RRB- repressed , suggesting that inhibition of T3SS-1 by INP0403 may occur in a HilA-independent manner .	169	Comparison of the INP0403-sensitive transcriptome to the HilA regulon ( De Keersmaecker et al. , 2005 ; Thijs et al. , 2007 ) indicated that only one gene ( prgH ) in the HilA regulon was significantly ( at least twofold ) repressed , suggesting that inhibition of T3SS-1 by INP0403 may occur in a HilA-independent manner .	20	EFFECT OF INP0403 ON TRANSCRIPTION OF KNOWN T3SS-1 REGULATORS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
AcrR	gene	soxS	activator	28650690	2	ver/dev	Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	soxS	activator	28650690	2	ver/dev	Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	soxS	activator	28650690	2	ver/dev	Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	soxS	activator	28650690	2	ver/dev	Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	cpxP	activator	31611347	3	att	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ-transcriptional-fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	94	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ transcriptional fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	dinF	repressor	12399494	4	ver/dev	a two-gene operon -LRB- with dinF -RRB- is repressed by LexA protein	22	In both bacteria , lexA is the first gene in a two-gene operon ( with dinF ) that is repressed by LexA protein .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	hilD	regulator	11755416	13	ver/dev	This pstS mutation only reduces hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilD .	218	This pstS mutation only reduces hilC and hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC or hilD ( R. Lucas and C. Lee , unpublished observations ) .	7	5. SIGNALS AND SIGNAL TRANSDUCERS INVOLVED IN TTSS-1 REGULATION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoB	gene	hilD	regulator	11755416	13	ver/dev	This pstS mutation only reduces hilC expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilD .	218	This pstS mutation only reduces hilC and hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC or hilD ( R. Lucas and C. Lee , unpublished observations ) .	7	5. SIGNALS AND SIGNAL TRANSDUCERS INVOLVED IN TTSS-1 REGULATION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with Venus , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with Venus , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with yfp , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with yfp , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with Venus , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with Venus , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with yfp , akin to the work of coworkers .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	fliC	repressor	31501286	12	ver/dev	To identify which classes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of fliC with yfp , akin to the work of Koirala .	168	To identify which classes of flagellar genes are subject to repression by MarA homologs , we constructed single-copy promoter fusions of flhDC ( class I ) , flhB ( class II ) , and fliC ( class III ) with yfp ( Venus ) , akin to the work of Koirala and coworkers ( 70 , 71 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	sprB	activator	27601571	22	ver/dev	InvF , sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - .	222	InvF , sopB ( sigD ) , sicA , and sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - ( 14 , 46 ) ( note that sopE is not present in the strain we used but that a close homologue , sopE2 , is present ) .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	sprB	activator	27601571	22	ver/dev	InvF , sigD , sicA , , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - .	222	InvF , sopB ( sigD ) , sicA , and sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - ( 14 , 46 ) ( note that sopE is not present in the strain we used but that a close homologue , sopE2 , is present ) .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	sprB	activator	27601571	22	ver/dev	InvF , sopB , sicA , , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - .	222	InvF , sopB ( sigD ) , sicA , and sopE , have been described previously HilD and HilC positively regulate sprB , most likely cotrans - ( 14 , 46 ) ( note that sopE is not present in the strain we used but that a close homologue , sopE2 , is present ) .	3	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	ugtL	activator	33045730	67	att	SsrB-dependent activation of the ugtL gene is necessary for virulence	286	SsrB-dependent activation of the ugtL gene is necessary for virulence	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	72	att	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	316	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	30	B	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	76	att	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	333	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	77	att	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	340	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	2	ver/dev	SsrB also increases ugtL transcription by binding to the ugtL promoter region , where it overcomes gene silencing by the heat-stable nucleoid structuring protein H-NS , enhancing virulence .	13	SsrB also increases ugtL transcription by binding to the ugtL promoter region , where it overcomes gene silencing by the heat-stable nucleoid structuring protein H-NS , enhancing virulence .	2	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SsrB	gene	ugtL	activator	33045730	7	ver/dev	S. Typhimurium acquired the ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter , enables activation of virulence .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ugtL	activator	33045730	7	ver/dev	S. Typhimurium acquired the spiR genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter , enables activation of virulence .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ugtL	activator	33045730	7	ver/dev	S. Typhimurium acquired the ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in purple , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ugtL	activator	33045730	7	ver/dev	S. Typhimurium acquired the ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ugtL	activator	33045730	7	ver/dev	S. Typhimurium acquired the spiR genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in purple , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ugtL	activator	33045730	7	ver/dev	S. Typhimurium acquired the spiR genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL genes ) .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ugtL	activator	33045730	67	ver/dev	SsrB-dependent activation of the ugtL gene is necessary for virulence	286	SsrB-dependent activation of the ugtL gene is necessary for virulence	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	72	ver/dev	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence for transcription of PhoP-activated genes inside macrophages .	316	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	30	B	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	72	ver/dev	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice .	316	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	30	B	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	77	ver/dev	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence for transcription of PhoP-activated genes inside macrophages .	340	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	77	ver/dev	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice .	340	SsrB-dependent activation of ugtL transcription is required for S. Typhimurium virulence in mice and for transcription of PhoP-activated genes inside macrophages .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ugtL	activator	33045730	79	ver/dev	Thus , we wondered whether the SsrB activation of ugtL is retained in S. enterica serovars with different host ranges .	350	Thus , we wondered whether the SsrB activation of ugtL is retained in S. enterica serovars with different host ranges .	32	THE SSRB BINDING SITE IN THE UGTL PROMOTER IS CONSERVED AMONG S. ENTERICA SEROVARS THAT INFECT WARM-BLOODED ANIMALS	Salmonella;Salmonella	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	TU	marRAB	activator	15073288	0	ver/dev	while transcription of acrAB is activated by bile , this activation is independent of marRAB , as well as Rob , RpoS or PhoP -- PhoQ	17	In S. typhimurium , acrAB is required for bile resistance , but while transcription of acrAB is activated by bile , this activation is independent of marRAB , as well as Rob , RpoS or PhoP -- PhoQ .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	phoP	regulator	17725620	1	att	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	247	These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .	20	LF1036 4.49 LF1037 7.58	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LysR	gene	STM2372	regulator	12406731	7	ver/dev	The ydcI gene encodes a putative transcriptional regulator of the LysR family , while the STM2372 gene is predicted to encode a putative membrane transporter .	203	The ydcI gene encodes a putative transcriptional regulator of the LysR family , while the STM2372 gene is predicted to encode a putative membrane transporter .	5	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	prgI	repressor	19202096	2	ver/dev	prgI are known to be repressed , respectively , by the active form of PhoP .	332	pagC and prgI are known to be activated and repressed , respectively , by the active form of PhoP , and were used as controls .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	prgI	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilC	regulator	12535071	89	ver/dev	Although HilC regulate two promoters upstream of hilC , they activate one and repress the other , such that overall HilC appear to have no effect on hilC expression .	252	Although HilD and HilC regulate two promoters upstream of hilC , they activate one and repress the other , such that overall HilD and HilC appear to have no effect on hilC expression ( Olekhnovich and Kadner , 2002 ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
HilC	gene	hilC	regulator	15661008	15	ver/dev	These results indicate that Lon is involved in the autoregulation of hilC transcription by modulating amounts of HilC .	181	These results indicate that Lon is involved in the autoregulation of hilC and hilD transcription by modulating amounts of HilC and HilD .	7	LEVEL OF HILC AND HILD TRANSCRIPTION IN WILD-TYPE AND LON-DISRUPTED MUTANT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	hilC	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilC by HilC .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	hilC	regulator	17675384	4	ver/dev	The HilC proteins bind to the common DNA sites at hilC promoters .	44	The HilD and HilC proteins bind to the common DNA sites at the hilA , hilD , and hilC promoters ( 37 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	hilC	regulator	22479568	0	ver/dev	HilC can activate expression of hilC of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
FNR	gene	nirB	activator	10816454	1	ver/dev	the nirB promoter _ known to be activated by Fnr under anaerobic conditions as found in the intestinal environment or intracellularly	289	For this , we used the nirB promoter , known to be activated by Fnr under anaerobic conditions as found in the intestinal environment or intracellularly ( 12 , 27 , 57 ) .	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
STM2748	gene	pgtP	regulator	33563986	0	ver/dev	Upon investigating the regulatory functions of 18 putative regulatory proteins , we identified STM2748 -LRB- named VrpA , viru-lence-related regulatory protein A -RRB- as a potential positive regulator of pgtP , as the other three genes in the pgt gene cluster was downregulated in the vrpA mutant .	178	Upon investigating the regulatory functions of 18 putative regulatory proteins that present in STM but absent in Escherichia coli ( Supplementary Table 3 ) by transcriptome analysis , we identified STM2748 ( named VrpA , viru-lence-related regulatory protein A ) as a potential positive regulator of pgtP , as the transcription of pgtP and the other three genes in the pgt gene cluster was downregulated in the vrpA mutant ( NCBI SRA accession : PRJNA561041 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
STM2748	gene	pgtP	regulator	33563986	0	ver/dev	Upon investigating the regulatory functions of 18 putative regulatory proteins , we identified STM2748 -LRB- named VrpA , viru-lence-related regulatory protein A -RRB- as a potential positive regulator of pgtP , as the transcription of pgtP was downregulated in the vrpA mutant .	178	Upon investigating the regulatory functions of 18 putative regulatory proteins that present in STM but absent in Escherichia coli ( Supplementary Table 3 ) by transcriptome analysis , we identified STM2748 ( named VrpA , viru-lence-related regulatory protein A ) as a potential positive regulator of pgtP , as the transcription of pgtP and the other three genes in the pgt gene cluster was downregulated in the vrpA mutant ( NCBI SRA accession : PRJNA561041 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
STM2748	gene	pgtP	regulator	33563986	0	ver/dev	Upon investigating the regulatory functions of 18 putative regulatory proteins , we identified STM2748 -LRB- named VrpA , viru-lence-related regulatory protein A -RRB- as a potential positive regulator of pgtP , as the other three genes in the pgt gene cluster was downregulated in PRJNA561041 .	178	Upon investigating the regulatory functions of 18 putative regulatory proteins that present in STM but absent in Escherichia coli ( Supplementary Table 3 ) by transcriptome analysis , we identified STM2748 ( named VrpA , viru-lence-related regulatory protein A ) as a potential positive regulator of pgtP , as the transcription of pgtP and the other three genes in the pgt gene cluster was downregulated in the vrpA mutant ( NCBI SRA accession : PRJNA561041 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
STM2748	gene	pgtP	regulator	33563986	0	ver/dev	Upon investigating the regulatory functions of 18 putative regulatory proteins , we identified STM2748 -LRB- named VrpA , viru-lence-related regulatory protein A -RRB- as a potential positive regulator of pgtP , as the other three genes in the pgt gene cluster was downregulated in NCBI SRA accession .	178	Upon investigating the regulatory functions of 18 putative regulatory proteins that present in STM but absent in Escherichia coli ( Supplementary Table 3 ) by transcriptome analysis , we identified STM2748 ( named VrpA , viru-lence-related regulatory protein A ) as a potential positive regulator of pgtP , as the transcription of pgtP and the other three genes in the pgt gene cluster was downregulated in the vrpA mutant ( NCBI SRA accession : PRJNA561041 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
STM2748	gene	pgtP	regulator	33563986	0	ver/dev	Upon investigating the regulatory functions of 18 putative regulatory proteins , we identified STM2748 -LRB- named VrpA , viru-lence-related regulatory protein A -RRB- as a potential positive regulator of pgtP , as the transcription of pgtP was downregulated in PRJNA561041 .	178	Upon investigating the regulatory functions of 18 putative regulatory proteins that present in STM but absent in Escherichia coli ( Supplementary Table 3 ) by transcriptome analysis , we identified STM2748 ( named VrpA , viru-lence-related regulatory protein A ) as a potential positive regulator of pgtP , as the transcription of pgtP and the other three genes in the pgt gene cluster was downregulated in the vrpA mutant ( NCBI SRA accession : PRJNA561041 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
STM2748	gene	pgtP	regulator	33563986	0	ver/dev	Upon investigating the regulatory functions of 18 putative regulatory proteins , we identified STM2748 -LRB- named VrpA , viru-lence-related regulatory protein A -RRB- as a potential positive regulator of pgtP , as the transcription of pgtP was downregulated in NCBI SRA accession .	178	Upon investigating the regulatory functions of 18 putative regulatory proteins that present in STM but absent in Escherichia coli ( Supplementary Table 3 ) by transcriptome analysis , we identified STM2748 ( named VrpA , viru-lence-related regulatory protein A ) as a potential positive regulator of pgtP , as the transcription of pgtP and the other three genes in the pgt gene cluster was downregulated in the vrpA mutant ( NCBI SRA accession : PRJNA561041 ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	aceA	regulator	12791144	9	ver/dev	Conversely , two glyoxyate shunt genes under the positive control of CsrA in E. coli , aceA , were induced twofold in the S. typhimu-rium csrA mutant .	221	Conversely , two glyoxyate shunt genes under the positive control of CsrA in E. coli , aceA and aceB , were induced twofold in the S. typhimu-rium csrA mutant .	9	REGULATION OF CARBON METABOLISM BY CSRA	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
MntR	gene	cdtB	regulator	17555437	0	ver/dev	( tldD ) transcripts _ suggesting that MntR may also act upstream of tldD in the control of cdtB gene expression	118	Moreover , constitutive expression of sty0876 ( mntR ) led to a slight reduction in the levels of sty3548 ( tldD ) transcripts ( Fig. 3 ) , suggesting that Sty0876 ( MntR ) may also act upstream of sty3548 ( tldD ) in the control of cdtB gene expression .	5	IDENTIFICATION OF S. TYPHI GENES THAT CONTROL CDTB EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MntR	gene	cdtB	regulator	17555437	0	ver/dev	( tldD ) transcripts _ suggesting that MntR may also act upstream of sty3548 in the control of cdtB gene expression	118	Moreover , constitutive expression of sty0876 ( mntR ) led to a slight reduction in the levels of sty3548 ( tldD ) transcripts ( Fig. 3 ) , suggesting that Sty0876 ( MntR ) may also act upstream of sty3548 ( tldD ) in the control of cdtB gene expression .	5	IDENTIFICATION OF S. TYPHI GENES THAT CONTROL CDTB EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MntR	gene	cdtB	regulator	17555437	0	ver/dev	( tldD ) transcripts _ suggesting that MntR may also act upstream of tldD in the control of cdtB gene expression	118	Moreover , constitutive expression of sty0876 ( mntR ) led to a slight reduction in the levels of sty3548 ( tldD ) transcripts ( Fig. 3 ) , suggesting that Sty0876 ( MntR ) may also act upstream of sty3548 ( tldD ) in the control of cdtB gene expression .	5	IDENTIFICATION OF S. TYPHI GENES THAT CONTROL CDTB EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MntR	gene	cdtB	regulator	17555437	0	ver/dev	( tldD ) transcripts _ suggesting that MntR may also act upstream of sty3548 in the control of cdtB gene expression	118	Moreover , constitutive expression of sty0876 ( mntR ) led to a slight reduction in the levels of sty3548 ( tldD ) transcripts ( Fig. 3 ) , suggesting that Sty0876 ( MntR ) may also act upstream of sty3548 ( tldD ) in the control of cdtB gene expression .	5	IDENTIFICATION OF S. TYPHI GENES THAT CONTROL CDTB EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CysB	gene	cysK	regulator	18957594	2	att	With the exception of cysK and sbp , mutants in all other CysB-regulated genes showed little or no activity on swim plates .	233	With the exception of cysK and sbp , mutants in all other CysB-regulated genes showed little or no activity on swim plates .	7	CYSTEINE AUXOTROPHS HAVE ALTERED SWARM COLONY MORPHOLOGY	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
CysB	gene	cysK	regulator	24659766	26	ver/dev	Stoichiometry of binding of CysB to cysK .	559	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	44	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysK	regulator	27530757	0	ver/dev	In this regard , it has been reported that expression of cysK in E. coli is under the control of CysB .	264	In this regard , it has been reported that expression of cysK in E. coli is under the control of CysB , a LysR-family transcription factor .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CysB	gene	cysK	regulator	27530757	4	ver/dev	Stoichiometry of binding of CysB to cysK .	315	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	18	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysK	regulator	30538683	0	ver/dev	Previous literature has characterized binding of CysB to the promoter regions of cysK .	52	Previous literature has characterized binding of CysB to the promoter regions of cysK [ encodes O-acetylserine ( thiol ) - lyase , EC 2.5.1.47 ] , cysJIH ( encode sulfite reductase , EC 1.8.7.1 ) , cysP ( encodes thiosulfatebinding protein ) , and to cysB ( encodes a LysR regulator ) ( Monroe et al. , 1990 ; Hryniewicz and Kredich , 1991 , 1994 ; Ostrowski and Kredich , 1991 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysK	regulator	30538683	1	ver/dev	Transcription of cysK is upregulated upon binding of CysB .	65	Transcription of cysJIH and cysK is upregulated upon binding of CysB and acetyl-serine .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysK	regulator	30538683	3	ver/dev	Transcription of cysK is upregulated upon binding of CysB .	91	Transcription of cysJIH and cysK is upregulated upon binding of CysB and acetyl-serine .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysK	regulator	30538683	11	ver/dev	Stoichiometry of binding of CysB to cysK .	444	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	26	FUNDING	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoB	gene	phoH	activator	16574345	0	att	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	179	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	15	3.1. MICROARRAY ANALYSIS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilA	gene	sipB	regulator	20634977	0	ver/dev	HilA is a master regulator of SPI1 genes like sipB , sipC , sopD , sopB etc. .	222	HilA is a master regulator of SPI1 genes like sipB , sipC , sopD , sopB etc. ( 24 ) .	19	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sipB	regulator	28575106	5	att	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	167	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	8	THE GENE LOIA IS THE VIRULENCE DETERMINANT IN SPI-14	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	hns	regulator	33524062	9	ver/dev	Analysis of binding of FNR to hns promoters .	595	Analysis of binding of FNR and ArcA to rnc , rng , and hns promoters .	33	ENO LEVELS WERE SET TO 1. FOR (B) AND (C), M; SIZE MARKER. (TIF)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	cse1	activator	28270274	2	ver/dev	Since LeuO positively regulates the cas3-divergent cse1 gene , we evaluated the role of this LysR regulator in cas3 expression .	209	Since LeuO positively regulates the cas3-divergent cse1 gene , we evaluated the role of this LysR regulator in cas3 expression .	15	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	yjbE	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	sodCII	regulator	16697686	0	att	The down-regulation of sodCII transcription in-vivo is surprising , given that this gene is under the control of alternative sigma factor s ( RpoS ) [ 14 ] ( data not s shown ) and that RpoS-controlled genes are thought to be expressed inside host cells .	400	The down-regulation of sodCII transcription in vivo is surprising , given that this gene is under the control of alternative sigma factor s ( RpoS ) [ 14 ] ( data not s shown ) and that RpoS-controlled genes are thought to be expressed inside host cells .	23	4. DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	sodCII	regulator	18362154	2	ver/dev	only sodCII is regulated by RpoS	314	Both sodCI and sodCII are maximally expressed in stationary phase during in vitro growth in rich medium ( 16 , 18 , 21 ) , but only sodCII is regulated by the alternative sigma factor s ( RpoS ) ( 16 , 18 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	agn43	activator	18681797	0	att	Wallecha A , Munster V , Correnti J , Chan T , van der Woude M. Dam - and OxyR-dependent phase variation of agn43 : essential elements and evidence for a new role of DNA methylation .	126	Wallecha A , Munster V , Correnti J , Chan T , van der Woude M. Dam - and OxyR-dependent phase variation of agn43 : essential elements and evidence for a new role of DNA methylation .	11	REFERENCES	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
OxyR	gene	agn43	activator	19717610	0	att	Dam - and OxyR-dependent phase variation of agn43 : essential elements and evidence for a new role of DNA methylation .	653	Dam - and OxyR-dependent phase variation of agn43 : essential elements and evidence for a new role of DNA methylation .	34	REFERENCES	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
OxyR	gene	agn43	activator	25462918	2	att	Dam - and OxyR-dependent phase variation of agn43 : essential elements andevidence for a new role of DNA methylation .	664	Dam - and OxyR-dependent phase variation of agn43 : essential elements andevidence for a new role of DNA methylation .	38	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	agn43	activator	26687718	2	att	The same is true for other OxyR-dependent phase variation systems such as agn43 ( 47 ) and gtr ( 15 ) .	344	The same is true for other OxyR-dependent phase variation systems such as agn43 ( 47 ) and gtr ( 15 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	agn43	activator	26687718	3	ver/dev	A DNA bend is induced by OxyR in agn43 .	381	A DNA bend is induced by OxyR in agn43 ( 47,56 ) , another phase variation locus regulated by Dam methylation and OxyR .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	copA	regulator	12023084	1	ver/dev	CueR is known to be a copper-responsive transcriptional regulator of the copA gene .	91	CueR is known to be a copper-responsive transcriptional regulator of the copA gene [ 4 ] , which encodes a copper-inducible P-type ATPase , and yacK [ 12 ] , which encodes a putative copper e ¥ ux oxidase .	11	3.2. AMINO ACID SEQUENCE ANALYSIS OF SCTR	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CueR	gene	copA	regulator	17768242	0	ver/dev	copA is shown here to be transcriptionally controlled by CueR	9	In contrast , the pathogenic bacterium Salmonella harbours only the cue regulon , including copA , which is shown here to be transcriptionally controlled by CueR .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	regulator	17768242	2	ver/dev	Expression of copA in Salmonella is directly controlled by CueR	135	Expression of copA in Salmonella is directly controlled by CueR	8	EXPRESSION OF COPA IN SALMONELLA IS DIRECTLY CONTROLLED BY CUER	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	copA	regulator	17768242	7	ver/dev	To confirm that copA transcription in Salmonella is controlled directly by the transcriptional regulator CueR , we first mapped the transcription start site of the gene by primer-extension analysis , using RNA .	192	To confirm that copA transcription in Salmonella is controlled directly by the transcriptional regulator CueR , we first mapped the transcription start site of the gene by primer extension analysis , using RNA isolated from wildtype or DcueR mutant cells grown in the presence or absence of CuSO4 .	8	EXPRESSION OF COPA IN SALMONELLA IS DIRECTLY CONTROLLED BY CUER	Salmonella;synthetic construct	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	regulator	17768242	10	ver/dev	CueR binds to the promoter region of copA .	230	CueR binds to the promoter region of copA .	8	EXPRESSION OF COPA IN SALMONELLA IS DIRECTLY CONTROLLED BY CUER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	copA	regulator	17919284	0	att	Among these , we identified the GolS-target operators from the golTS operon and the golB gene ( Checa et al. , 2007 ) , as well as the CueR-controlled operators from cueO and copA genes ( Kim et al. , 2002 ; Espariz et al. , 2007 ) .	66	Among these , we identified the GolS-target operators from the golTS operon and the golB gene ( Checa et al. , 2007 ) , as well as the CueR-controlled operators from cueO and copA genes ( Kim et al. , 2002 ; Espariz et al. , 2007 ) .	8	THE SALMONELLA-SPECIFIC CBA EFFLUX SYSTEM IS PART OF THE GOL REGULON	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	regulator	24858080	10	att	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	336	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	copA	regulator	24858080	3	att	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	264	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	copA	regulator	28924031	0	ver/dev	CueR regulates copA .	67	CueR regulates copA , cueO , and cueP ( 28 -- 30 ) .	3	KEYWORDS COPPER EFFLUX, SALMONELLA, SODC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	copA	regulator	34125582	5	ver/dev	detoxification genes copA _ regulated by CueR	249	As expected , the known copper efflux and detoxification genes copA , cueO , and cusCFBA , regulated by CueR and CusR , are upregulated in E. coli during growth in copper-supplemented media .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	dctA	repressor	33593945	0	ver/dev	that activation of RpoS results in the repression of dctA , encoding the primary dicarboxylate importer	9	We demonstrate that activation of RpoS results in the repression of dctA , encoding the primary dicarboxylate importer , and that constitutive expression of dctA induces growth .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	lacZ	activator	15491370	10	ver/dev	srfH -- lacZ activity 20-fold _ mimicking the effect we observed with SsrB stimulation of srfH in Salmonella-infected macrophages	115	However , addition of ssrB on an arabinose-inducible plasmid in the presence of arabinose stimulated srfH -- lacZ activity 20-fold , mimicking the effect we observed with SsrB stimulation of srfH in Salmonella-infected macrophages ( Fig. 3 ) .	7	SSRB AND OMPR ACTIVATE SRFH	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	TU	ssrAB	regulator	20221735	2	ver/dev	The expression of ssrAB is , in turn , regulated by SlyA .	308	The expression of ssrAB is , in turn , regulated by the OmpR-EnvZ two-component system and SlyA .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	TU	ssrAB	regulator	27886269	28	ver/dev	SlyA cooperate to directly control the expression of ssrAB in our unpublished results .	170	HilD and SlyA cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions ( our unpublished results ) , which could also apply for lpxR .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	TU	ssrAB	regulator	27886269	28	ver/dev	SlyA cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions .	170	HilD and SlyA cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions ( our unpublished results ) , which could also apply for lpxR .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	TU	ssrAB	regulator	29857034	17	ver/dev	SlyA involvement in TCS regulation has been previously discussed , suggesting that SlyA regulates the locus of ssrAB in SPI-2 .	317	SlyA involvement in two-component system ( TCS ) regulation has been previously discussed , suggesting that SlyA regulates the locus of ssrAB , a TCS that is responsible for controlling genes present in SPI-2 [ 7,34 ] .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	TU	ssrAB	regulator	29857034	17	ver/dev	SlyA involvement in two-component system regulation has been previously discussed , suggesting that SlyA regulates the locus of ssrAB in SPI-2 .	317	SlyA involvement in two-component system ( TCS ) regulation has been previously discussed , suggesting that SlyA regulates the locus of ssrAB , a TCS that is responsible for controlling genes present in SPI-2 [ 7,34 ] .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	TU	ssrAB	regulator	30718301	69	ver/dev	FIG 8 Model for the regulation of ssrAB by SlyA .	211	FIG 8 Model for the regulation of ssrAB by SlyA , HilD , OmpR , and H-NS .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	crp	regulator	19843227	43	ver/dev	Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli .	303	Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli ( Johansson et al. , 2000 ) .	15	DISCUSSION	Escherichia coli	0	L2	SPEC	Other	OTHER	Other	Level 1
FimZ	gene	fimA	regulator	11133935	14	ver/dev	Instead , FimW may function by influencing the ability of FimZ to activate transcription from this promoter , either by inhibiting the binding of FimZ to the fimA promoter or by inhibiting activation by FimZ once this protein has bound .	361	Instead , FimW may function by influencing the ability of FimZ to activate transcription from this promoter , either by inhibiting the binding of FimZ to the fimA promoter or by inhibiting activation by FimZ once this protein has bound .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
FimZ	gene	fimA	regulator	11911183	0	ver/dev	FimZ Binds the Salmonella typhimurium fimA	2	FimZ Binds the Salmonella typhimurium fimA	0	Unknown	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	regulator	11911183	7	ver/dev	Also , since FimZ regulates S. typhimurium fimA expression , we constructed a fimZ-lacZ fusion to investigate the expression of this important regulator of the fimbrial system .	39	Also , since FimZ regulates S. typhimurium fimA expression and is related to a family of sensory regulators , we constructed a fimZ-lacZ fusion to investigate the expression of this important regulator of the fimbrial system .	2	KEY WORDS: SALMONELLA TYPHIMURIUM, TYPE 1 FIMBRIAE, ACTIVATOR	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	fimA	regulator	11911183	7	ver/dev	Also , since FimZ regulates S. typhimurium fimA expression , we constructed a fimZ-lacZ fusion to investigate the expression of this important regulator of the fimbrial system .	39	Also , since FimZ regulates S. typhimurium fimA expression and is related to a family of sensory regulators , we constructed a fimZ-lacZ fusion to investigate the expression of this important regulator of the fimbrial system .	2	KEY WORDS: SALMONELLA TYPHIMURIUM, TYPE 1 FIMBRIAE, ACTIVATOR	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	fimA	regulator	11911183	20	ver/dev	this , along with our previous reports of FimZ , indicates that FimZ can bind to the fimA promoter region	184	Examination of the amino acid sequence of the C-terminal domain of FimZ reveals a helix-turn-helix motif and this , along with our previous reports of FimZ affecting fimA expression ( 33 , 40 ) , indicates that FimZ can bind to the fimA promoter region .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FimZ	gene	fimA	regulator	11911183	24	ver/dev	However , our in-vitro results indicate that FimZ alone will bind to the fimA promoter .	195	However , our in vitro results indicate that FimZ alone will bind to the fimA promoter .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FimZ	gene	fimA	regulator	11911183	25	ver/dev	However , when FimZ binds in-vitro to the fimA promoter , many molecules of FimZ are associated with the DNA fragments , creating a large DNA-pro-tein complex .	201	However , when FimZ binds in vitro to the fimA promoter , many molecules of FimZ are associated with the DNA fragments , creating a large DNA-pro-tein complex that has difficulty entering the gel .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimZ	gene	fimA	regulator	17074910	25	ver/dev	FimZ binds the Salmonella typhimurium fimA promoter .	750	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	79	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	regulator	21852351	0	ver/dev	FimZ binds the Salmonella typhimurium fimA promoter .	628	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	62	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	regulator	22778099	0	ver/dev	FimZ binds the Salmonella typhimu-rium fimA promoter .	527	FimZ binds the Salmonella typhimu-rium fimA promoter region and may regulate its own expression with FimY .	27	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	regulator	24462182	6	ver/dev	FimZ was shown to bind the fimA promoter to activate fimbrial expression .	34	FimZ was shown to bind the fimA promoter to activate fimbrial expression ( Yeh et al. , 2002 ) .	4	1. INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FimZ	gene	fimA	regulator	25547794	39	ver/dev	FimZ binds the Salmonella Typhimu-rium fimA promoter .	525	FimZ binds the Salmonella Typhimu-rium fimA promoter region and may regulate its own expression with FimY .	37	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	regulator	31139165	1	ver/dev	three major regulatory proteins , FimZ ( each ) control fim operon expression primarily through regulation of the fimA promotor	84	In Salmonella , there are three major regulatory proteins , FimZ , FimY , and FimW ( each expressed under its own promoter ) , that control fim operon expression primarily through regulation of the fimA promotor ( PfimA ; Yeh et al. , 1995 , 2002b ; Tinker and Clegg , 2000 , 2001 ) .	4	DIRECT REGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	gene	fimA	regulator	31139165	2	ver/dev	FimZ , is able to bind the region upstream of the fimA transcription initiation site , similar to other classical activators .	90	FimZ , which is thought to be a dominant activator of T1F expression , has high homology to a family of DNA binding proteins associated with response regulators of two-component regulatory systems and is able to bind the region upstream ( from -- 47 to -- 98 nucleotides ) of the fimA transcription initiation site , similar to other classical activators ( Yeh et al. , 2002b ) .	4	DIRECT REGULATION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
FimZ	gene	fimA	regulator	31139165	15	ver/dev	FimZ binds the Salmonella typhimurium fimA promoter .	1246	FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .	18	TIME: 14:52 # 17	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	TU	flhDC	repressor	30355489	5	ver/dev	Although we found that purified HilD bound equally well to SBG flhDC promoters , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa , thus ruling out a competitive inhibition by SsrB .	97	Although we found that purified HilD bound equally well to the STM and SBG flhDC promoters ( Figure S3B ) , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa ( Figure S3C ) , thus ruling out a competitive inhibition by SsrB .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	TU	flhDC	repressor	30355489	5	ver/dev	Although we found that purified HilD bound equally well to the STM , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa , thus ruling out a competitive inhibition by SsrB .	97	Although we found that purified HilD bound equally well to the STM and SBG flhDC promoters ( Figure S3B ) , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa ( Figure S3C ) , thus ruling out a competitive inhibition by SsrB .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SsrB	TU	flhDC	repressor	30355489	7	ver/dev	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC .	115	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC ( Figure S3D ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	TU	flhDC	repressor	30355489	14	ver/dev	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC .	143	Consistent with the previous binding experiments , the 827 +83 fragment showed SsrB-dependent repression of flhDC ( Figure S3D ) .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YdcR	gene	ydcR	regulator	28674150	2	att	Herein we quantitatively studied the protein expression of a Salmonella mutant lacking ydcR ( ydcR ) within host cells in comparison to that of its parental strain , which provides a powerful means to uncover potential YdcR-regulated proteins under physiological conditions .	40	Herein we quantitatively studied the protein expression of a Salmonella mutant lacking ydcR ( ydcR ) within host cells in comparison to that of its parental strain , which provides a powerful means to uncover potential YdcR-regulated proteins under physiological conditions .	2	YANHUA LIU‡ , QIAN LIU§ , LINLU QI‡, TAO DING‡, ZHEN WANG‡, JIAQI FU‡, MO HU‡, MIN LI§, JEONGMIN SONG¶**, AND XIAOYUN LIU‡‡‡	Salmonella	1	L1	OTHER	Analysis	OTHER	Other	Level 1
YdcR	gene	ydcR	regulator	28674150	5	att	Experimental Design and Statistical Rationale -- To uncover potential YdcR-regulated proteins , we performed proteomic analyses of the intracellular ydcR mutant at 18 hpi , whereas the wild-type strain was used as a control .	57	Experimental Design and Statistical Rationale -- To uncover potential YdcR-regulated proteins , we performed proteomic analyses of the intracellular ydcR mutant at 18 hpi , whereas the wild-type strain was used as a control .	3	EXPERIMENTAL PROCEDURES	nan	1	L1	OTHER	Analysis	OTHER	Other	Level 1
YdcR	gene	ydcR	regulator	28674150	6	att	To uncover YdcR-regulated proteins , we exploited quantitative proteomics to compare intracellular Sal-monella protein expression between the wild-type and the isogenic ydcR strains .	154	To uncover YdcR-regulated proteins , we exploited quantitative proteomics to compare intracellular Sal-monella protein expression between the wild-type and the isogenic ydcR strains .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
YdcR	gene	ydcR	regulator	28674150	13	ver/dev	In contrast , the expression level of PipB did not differ significantly for Salmonella strains chromosomally expressing 3 FLAG-tagged PipB in ydcR deletion backgrounds , indicating the specific regulation of SrfN by YdcR .	228	In contrast , the expression level of PipB did not differ significantly for Salmonella strains chromosomally expressing 3 FLAG-tagged PipB in the wild-type and ydcR deletion backgrounds ( Fig. 5B ) , indicating the specific regulation of SrfN by YdcR .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	Salmonella;Iris germanica	0.5	L2	SPEC	Analysis	NEG	New	Level 1
LysR	gene	tdcA	activator	29018419	1	ver/dev	tdcA Transcriptional activator of LysR family	148	tdcA Transcriptional activator of tdc operon ( LysR family )	5	MOTILITY, CHEMOTAXIS, AND ADHERENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	norV	regulator	22039967	0	ver/dev	These genes are regulated by the cytoplasmic NO-responsive transcription factors NsrR and NorR -LRB- norV -RRB- ,	114	These genes are regulated by the cytoplasmic NO-responsive transcription factors NsrR ( hmp and hcp ) and NorR ( norV ) ,	8	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	invI	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR-P	gene	ompS2	regulator	15126450	23	ver/dev	In this respect , in the footprinting experiments , OmpR-P bound to the ompS2 regulatory region at 0.8 M , similar to what was observed for the footprinting of OmpR-P on ssrA box A1 boxes .	272	In this respect , in the footprinting experiments , OmpR-P bound to the ompS2 regulatory region at 0.8 M ( Fig. 8 ) , similar to what was observed for the footprinting of OmpR-P on ssrA box A1 , which has been considered just below the highest affinity F1 and C1 boxes ( 15 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR-P	gene	ompS2	regulator	15126450	30	ver/dev	Thus , OmpR-P would then be allowed to bind at and around the consensus OmpR-binding box , permitting ompS2 expression mostly at high-osmolarity .	297	Thus , OmpR-P would then be allowed to bind at and around the consensus OmpR-binding box , permitting ompS2 expression mostly at high osmolarity , where there is a higher abundance of OmpR-P ( 41 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
BasR	gene	csgD	regulator	25437188	22	ver/dev	In E. coli , BasR binds directly to the csgD promoter to activate transcription .	214	In E. coli , BasR binds directly to the csgD promoter to activate transcription [ 89 ] .	8	REGULATION OF CSGD TRANSCRIPTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
IHF	gene	dps	activator	10618525	1	ver/dev	The dps promoter is activated by IHF S in stationary-phase .	303	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	dps	activator	10874730	6	ver/dev	1994 The dps promoter is activated by IHF in stationary-phase .	375	1994 The dps promoter is activated by OxyR during growth and by IHF and ss in stationary phase .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	dps	activator	14742565	1	ver/dev	The dps promoter is activated by IHF S in stationary-phase .	133	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase .	4	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	dps	activator	15790293	15	ver/dev	The dps promoter is activated by IHF in stationary-phase .	385	The dps promoter is activated by OxyR during growth and by IHF and ss in stationary phase .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	dps	activator	19223478	1	att	In E. coli , dps transcription is regulated in a sigma S - and IHF-dependent manner , and the IHF protein has been shown to bind upstream of the dps promoter ( 3 ) .	358	In E. coli , dps transcription is regulated in a sigma S - and IHF-dependent manner , and the IHF protein has been shown to bind upstream of the dps promoter ( 3 ) .	5	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	dps	activator	19223478	2	ver/dev	The dps promoter is activated by IHF S in stationary-phase .	427	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase .	8	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that both subunits of IHF protein ( IHFR	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an direct role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Wrb	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Tre	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Dp	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	21563813	1	ver/dev	A previous microarray study showed that IHF had an auxiliary role in the activation of dps Interestingly , we found that many IHF/RpoS coregulated proteins ( Osm	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IHF	gene	dps	activator	25028458	48	ver/dev	The dps promoter is activated by IHF in stationary-phase .	415	The dps promoter is activated by OxyR during growth and by IHF and s in stationary phase .	11	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	dps	activator	32900812	5	att	The dps gene is transcribed on entry into stationary-phase using RpoS , the stress-and-stationary-phase sigma factor of RNA polymerase , although this can be overridden during oxidative-stress when dps is transcribed using RpoD in an OxyR - and IHF-dependent mechanism ( 56 , 57 ) .	70	The dps gene is transcribed on entry into stationary phase using RpoS , the stress-and-stationary-phase sigma factor of RNA polymerase , although this can be overridden during oxidative stress when dps is transcribed using RpoD in an OxyR - and IHF-dependent mechanism ( 56 , 57 ) .	2	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	STM1344	regulator	19376870	35	ver/dev	STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad .	384	STM1344 is an integral part of the sessility-motility switch but not the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA ( K. Jonas , A. N. Edwards , I. Ahmad , A. Lamprokostopoulou , T. Romeo , U. Römling , and Ö .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NtrC	gene	glnL	activator	32265871	1	ver/dev	However , the correlation of activation of NtrBC two-component system [ encoded by glnL and glnG ( NtrC ) genes ] need to be further .	314	However , the correlation of activation of NtrBC two-component system [ encoded by glnL ( NtrB ) and glnG ( NtrC ) genes ] need to be further validated .	23	THE DELETION OF GLNA ACTIVATES TRANSCRIPTION OF NTRBC TWO-COMPONENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NtrC	gene	glnL	activator	32265871	1	ver/dev	However , the correlation of activation of NtrBC two-component system [ encoded by glnL and glnG ( NtrC ) genes ] need to be further .	314	However , the correlation of activation of NtrBC two-component system [ encoded by glnL ( NtrB ) and glnG ( NtrC ) genes ] need to be further validated .	23	THE DELETION OF GLNA ACTIVATES TRANSCRIPTION OF NTRBC TWO-COMPONENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sipC	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sipC	regulator	14633100	3	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	190	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	sipC	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
FruR	gene	pps	regulator	19136587	16	ver/dev	In vitro binding of FruR , to the fru , pps , ace , pts of Salmonella typhimurium .	551	In vitro binding of the pleiotropic transcriptional regulatory protein , FruR , to the fru , pps , ace , pts and icd operons of Esche-richia coli and Salmonella typhimurium .	20	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
FruR	gene	pps	regulator	19136587	16	ver/dev	In vitro binding of FruR , to the fru , pps , ace , pts of Esche-richia coli .	551	In vitro binding of the pleiotropic transcriptional regulatory protein , FruR , to the fru , pps , ace , pts and icd operons of Esche-richia coli and Salmonella typhimurium .	20	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	csrB	regulator	12453229	2	ver/dev	csrB binds CsrA , thereby reducing the level of free CsrA protein .	40	csrB binds CsrA , titrating it and thereby reducing the level of free CsrA protein ( Liu et al. , 1997 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	csrB	regulator	12453229	2	ver/dev	csrB binds CsrA , titrating it .	40	csrB binds CsrA , titrating it and thereby reducing the level of free CsrA protein ( Liu et al. , 1997 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	csrB	regulator	12791144	3	ver/dev	CsrA also activates transcription of csrB , possibly through indirect regulation of a transcription factor .	32	CsrA also activates transcription of csrB , possibly through indirect regulation of a transcription factor ( Gudapaty et al. , 2001 ) .	4	INTRODUCTION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CspE	gene	uspA	activator	17081727	1	ver/dev	The CspE proteins increase stability of uspA mRNA facilitating steady-state expression .	37	The CspC and CspE proteins increase stability of uspA mRNA facilitating steady-state expression but are not involved in uspA induction during physiological stress [ 16 ] .	3	1. INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SirA	TU	flhDC	repressor	11244064	15	ver/dev	The simplest hypothesis is that SirA represses the master regulator of the flagellar regulon flhDC gene fusions .	304	The simplest hypothesis is that SirA represses the master regulator of the flagellar regulon flhDC , which leads to decreased expression of all the flagellar gene fusions examined in this study .	7	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
Fis	gene	gyrB	repressor	12898222	2	ver/dev	Fis represses transcription of the gyrB genes in E. coli .	18	Fis represses transcription of the gyrA and gyrB genes in E. coli ( Schneider et al. 1999 ) .	3	INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	gyrB	repressor	12898222	7	ver/dev	Given the strong sequence similarity between the S. enterica gyrB gene , we anticipated that its promoter would show evidence of repression by Fis to a similar degree to approximately 1.5-fold .	144	Given the strong sequence similarity between the S. enterica gyrB gene and that of E. coli , we anticipated that its promoter would show evidence of repression by Fis to a similar degree to that ( approximately 1.5-fold ) reported previously for E. coli gyrB ( Schneider et al. 1999 ) .	14	EXPRESSION OF GYRA IN A FIS KNOCK-OUT MUTANT	Salmonella;Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	gyrB	repressor	12898222	7	ver/dev	Given the strong sequence similarity between the S. enterica gyrB gene , we anticipated that its promoter would show evidence of repression by Fis to a similar degree to that .	144	Given the strong sequence similarity between the S. enterica gyrB gene and that of E. coli , we anticipated that its promoter would show evidence of repression by Fis to a similar degree to that ( approximately 1.5-fold ) reported previously for E. coli gyrB ( Schneider et al. 1999 ) .	14	EXPRESSION OF GYRA IN A FIS KNOCK-OUT MUTANT	Salmonella;Salmonella	1	L1	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	gyrB	repressor	16999831	1	ver/dev	the Fis protein is a repressor of gyrB transcription	44	Second , the Fis protein is a repressor of gyrA and gyrB transcription ( Schneider et al. , 1999 ; Keane and Dorman , 2003 ) and it is an activator of topA , at least under certain conditions ( Weinstein-Fischer et al. , 2000 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrB	repressor	21276095	2	ver/dev	In E. coli , FIS binds the gyrB promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrB .	40	In E. coli , FIS binds the gyrA and gyrB promoters to repress their expression ( Schneider et al. , 1999 ) ; similarly , FIS has been found to repress S. enterica gyrA and gyrB ( Keane and Dorman , 2003 ) .	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	phoP	regulator	19091955	24	ver/dev	As suggested by our previous study , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the phoP mutants in low-Mg2 conditions .	150	As suggested by our previous study ( 14 ) , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS , which antagonizes the functions of SlyA and PhoP ; thus the mRNA level is reduced greatly in the phoP or slyA mutants in PhoP-activating ( low-Mg2 ) conditions but remains high in PhoP-repressing ( high-Mg2 ) conditions in the hns mutant ( Fig. 4B ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	phoP	regulator	19091955	24	ver/dev	As suggested by our previous study , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the phoP mutants in PhoP-activating conditions .	150	As suggested by our previous study ( 14 ) , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS , which antagonizes the functions of SlyA and PhoP ; thus the mRNA level is reduced greatly in the phoP or slyA mutants in PhoP-activating ( low-Mg2 ) conditions but remains high in PhoP-repressing ( high-Mg2 ) conditions in the hns mutant ( Fig. 4B ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	pagC	activator	18270203	32	ver/dev	Promoters -- The H-NS protein has been shown to impede tranWe determined that the predicted PhoP box in the pagC pro- scriptional activation by at least two mechanisms : 1 ) H-NS moter is a bona fide PhoP-binding site , because the PhoP pro- binding to a promoter may hinder recruitment of RNA polytein footprinted Fig. 3B .	202	Promoters -- The H-NS protein has been shown to impede tranWe determined that the predicted PhoP box in the pagC pro- scriptional activation by at least two mechanisms : 1 ) H-NS moter is a bona fide PhoP-binding site , because the PhoP pro- binding to a promoter may hinder recruitment of RNA polytein footprinted this region ( Fig. 3B ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	pagC	activator	18270203	32	ver/dev	Promoters -- The H-NS protein has been shown to impede tranWe determined that the predicted PhoP box in the pagC pro- scriptional activation by at least two mechanisms : 1 ) H-NS moter is a bona fide PhoP-binding site , because the PhoP pro- binding to a promoter may hinder recruitment of RNA polytein footprinted this region .	202	Promoters -- The H-NS protein has been shown to impede tranWe determined that the predicted PhoP box in the pagC pro- scriptional activation by at least two mechanisms : 1 ) H-NS moter is a bona fide PhoP-binding site , because the PhoP pro- binding to a promoter may hinder recruitment of RNA polytein footprinted this region ( Fig. 3B ) .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	pagC	activator	31333620	5	ver/dev	Similarly , transcription of pagC -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS in .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	pagC	activator	31333620	5	ver/dev	Similarly , transcription of pagC -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS high Mg2 + .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	pagC	activator	31333620	5	ver/dev	Similarly , transcription of pagC -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS low + .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	pagC	activator	31333620	5	ver/dev	Similarly , transcription of pagC -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS Figures 2B , data not shown .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	gene	pagC	activator	31333620	5	ver/dev	Similarly , transcription of pagC -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS Figures 2B , C not shown .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	pagC	activator	31333620	6	ver/dev	It also provided an explanation for the H-NSHA-WT protein heterogeneously produced from plasmid upregulation of these PhoP/PhoQ-dependent genes due to the pUHE21-hns-HA reduced the transcription of pagC , T13 phosphorylation of H-NS .	340	It also provided an explanation for the H-NSHA-WT protein heterogeneously produced from plasmid upregulation of these PhoP/PhoQ-dependent genes due to the pUHE21-hns-HA reduced the transcription of the pcgL , pagC , T13 phosphorylation of H-NS .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	New	Level 2
HU	gene	hilA	regulator	15161921	1	ver/dev	Studies of bacteria have , to date , revealed that hilA expression is regulated by a complex array of hilC/sirC/sprA , hilD , sirA/barA , fis , csrAB , envZ / HU .	35	Studies of bacteria grown under these conditions have , to date , revealed that hilA expression is regulated by a complex array of regulatory systems including hilC/sirC/sprA ( 13 -- 15 ) , hilD ( 15 ) , sirA/barA ( 16 , 17 ) , fis ( 18 , 19 ) , csrAB ( 16 , 20 ) , envZ / ompR ( 21 ) , phoB ( 7 ) , fadD ( 7 ) , fliZ ( 7 ) , hha ( 22 ) , H-NS ( 19 ) , and HU ( 19 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hemX	activator	27564394	18	ver/dev	the hemX gene were used as positive control regions , respectively , as H-NS binds to the proV promoter .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ssaG	regulator	23690578	11	ver/dev	Taken together , these results indicate that PmrA functions as a negative regulator of ssaG .	72	Taken together , these results indicate that PmrA functions as a negative regulator of ssaG and potentially of other SPI-2 genes .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	ssaG	regulator	23690578	13	ver/dev	In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator or by furthering expression of an ssaG repressor .	74	In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator ( s ) or by furthering expression of an ssaG repressor ( s ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L1	SPEC	Other	NEG	New	Level 1
PmrA	gene	ssaG	regulator	23690578	18	ver/dev	Second , chromatin immunoprecipitation experiments revealed that an HA-tagged PmrA bound to the ssaG promoter .	85	Second , chromatin immunoprecipitation experiments revealed that an HA-tagged PmrA expressed from its normal promoter and chromosomal location bound to the ssrB promoter in vivo but not to the ssaG promoter ( Fig. 4C ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Fur	gene	fur	regulator	1624426	0	att	Consequently , a global study of the iron modulon will provide insight into the extent and nature of Fur-regulated gene expression and may offer clues to the acid-sensitive nature of fur mutants .	37	Consequently , a global study of the iron modulon will provide insight into the extent and nature of Fur-regulated gene expression and may offer clues to the acid-sensitive nature of fur mutants .	2	MAIN	nan	1	L1	SPEC	Investigation	NEG	Other	Level 1
RstA	gene	STM1485	activator	30763640	26	att	However , this percentage decreased to 89.29 % identity when the binding sequence identified in the STM1485 promoter region was aligned with the motif of other reported RstA-dependent genes ( Fig. 3B , left panel ) .	161	However , this percentage decreased to 89.29 % identity when the binding sequence identified in the STM1485 promoter region was aligned with the motif of other reported RstA-dependent genes ( Fig. 3B , left panel ) .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RstA	gene	STM1485	activator	30763640	27	att	In addition , we found a second RstA putative binding site on the STM1485 promoter , located at 38 bp of the 35 box and displays 83.93 % identity with the regulatory site of other RstA-dependent genes ( Fig. 3B , right panel ) .	163	In addition , we found a second RstA putative binding site on the STM1485 promoter , located at 38 bp of the 35 box and displays 83.93 % identity with the regulatory site of other RstA-dependent genes ( Fig. 3B , right panel ) .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
RstA	gene	STM1485	activator	30763640	30	att	B ) Alignment of the RstA consensus motif identified in other RstA-dependent genes like ybiL ( Ec ) , nohB ( Ec ) , modA ( Ec ) and leuS ( Ec ) genes , with the STM1485 promoter sequences .	169	B ) Alignment of the RstA consensus motif identified in other RstA-dependent genes like ybiL ( Ec ) , nohB ( Ec ) , modA ( Ec ) and leuS ( Ec ) genes , with the STM1485 promoter sequences .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RstA	gene	STM1485	activator	30763640	58	att	However , this binding site displayed a large number of nucleotides position conserved in the alignment between STM1485 promoter and those from other RstA-dependent genes ( Fig. 3B ) , suggesting that could acts as RstA regulatory site .	284	However , this binding site displayed a large number of nucleotides position conserved in the alignment between STM1485 promoter and those from other RstA-dependent genes ( Fig. 3B ) , suggesting that could acts as RstA regulatory site .	16	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	STM1485	activator	30763640	38	ver/dev	These data suggest that , at physiological pH , RstA is required to induce STM1485 expression to reach wild type levels .	184	These data suggest that , at physiological pH , RstA is required to induce STM1485 expression to reach wild type levels .	13	3.4. RSTA CONTROLS IN VIVO THE STM1485 GENE EXPRESSION IN S. TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	STM1485	activator	30763640	48	ver/dev	that RstA induces the expression of STM1485	217	These results confirm that RstA induces the expression of STM1485 , when it is abundant or when rcsB is absent .	14	3.5. COMBINED EFFECTS OF RCSB AND RSTA REGULATORS ON STM1485 GENE TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RstA	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RstA	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression under PhoP-dependent RstA activation was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RstA	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression under magnesium starvation conditions was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
RstA	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression under PhoP-dependent RstA activation was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RstA	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression under magnesium starvation conditions was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	NEG	Other	Level 1
SlyA	gene	sopD2	regulator	17379730	5	ver/dev	SlyA is also involved in the regulation of sopD2	362	Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA , which is also involved in the regulation of virulence genes such as mig-14 , sopD2 and virK ( Brumell et al. , 2003 ; Ho et al. , 2002 ; Navarre et al. , 2005 ) .	14	GIFSY-1 AND GIFSY-2 PROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
GalR	gene	galP	repressor	24450479	40	ver/dev	NagC _ participating with GalR in the repression of galP in E. coli	177	This seemed to imply another link between galactose and amino sugar metabolism as exemplified by NagC participating with GalR and GalS in the repression of galP in E. coli ( El Qaidi et al. , 2009 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
GalR	gene	galP	repressor	24450479	40	ver/dev	NagC _ participating with GalR in the repression of galP in E. coli	177	This seemed to imply another link between galactose and amino sugar metabolism as exemplified by NagC participating with GalR and GalS in the repression of galP in E. coli ( El Qaidi et al. , 2009 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	pocR	activator	30682134	43	ver/dev	In LB , CsrA activated the translation of genes for pocR metabolism -LRB- S2 Table -RRB- .	297	In LB , CsrA activated the translation of genes for fucose ( fucR ) , 1,2-propanediol ( pocR ) , and threonine/serine ( tdcA ) metabolism ( S2 Table ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	STM4568	activator	15681155	9	att	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	206	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	11	3. RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	STM4568	activator	15681155	31	ver/dev	In addition , the lack of consensus PmrA-binding sites in the promoters of STM4568 suggested that these genes may be indirectly activated by PmrA .	339	In addition , the lack of consensus PmrA-binding sites in the promoters of STM1257 , STM3968 , STM4568 and STM0459 suggested that these genes may be indirectly activated by PmrA .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
AcrR	gene	acrB	activator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	acrB	activator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , MarA , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	acrB	activator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , SoxS , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	acrB	activator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , RamA , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rho	activator	11673423	0	ver/dev	The E. coli proU P1 promoter was also cryptic in these cases activation of in-vivo expression was achieved either by a rho mutation during-growth at 10 ° ( affecting the nucleoid protein H-NS ) at 30 °C .	7	The E. coli proU P1 promoter was also cryptic in constructs that carried 1.2 kb of downstream proU sequence , and in these cases activation of in vivo expression was achieved either by a rho mutation during growth at 10 °C or by an hns null mutation ( affecting the nucleoid protein H-NS ) at 30 °C .	0	Unknown	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	lexA	activator	16713610	1	att	To further determine whether this induction was LexA-dependent , a lexA ( Ind ) S. enterica derivative was constructed ( Table 2 ) , and its recA expression after bacteriophage infection was also analyzed .	64	To further determine whether this induction was LexA-dependent , a lexA ( Ind ) S. enterica derivative was constructed ( Table 2 ) , and its recA expression after bacteriophage infection was also analyzed .	4	RESULTS AND DISCUSSION	Salmonella;Salmonella;Bacteriophage sp.	0.5	L3	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	lexA	activator	21102598	0	ver/dev	the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes include lexA	78	DNA damage created by quinolone antibiotics has been shown to be sufficient to stimulate umuC transcription and the SOS response .4,5 The initial response to DNA damage is the reduction in LexA protein levels and induction of LexA repressed genes , which include lexA , umuDC and dinP .2,3 ( In Escherichia .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	lexA	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	lexA	activator	33921732	5	att	In genes that show LexA-dependent bistability and have more than one LexA box ( recN , dinI and lexA ) , only the closest LexA box with lower HI was considered .	307	In genes that show LexA-dependent bistability and have more than one LexA box ( recN , dinI and lexA ) , only the closest LexA box with lower HI was considered .	15	3.4. INFLUENCE OF THE DISTANCE AND THE NUCLEOTIDE SEQUENCE OF THE LEXA BOX ON THE EXPRESSION PATTERNS OF SOS GENES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	sinR	regulator	27886269	3	ver/dev	HilA , regulates the expression of sinR .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	leuO	activator	22804842	0	ver/dev	More recently it has been shown that the leuO gene is activated by the transcriptional regulators RcsB and BglJ .	34	More recently it has been shown that the leuO gene is activated by the transcriptional regulators RcsB and BglJ and is negatively auto-regulated ( Stratmann et al. , 2012 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	leuO	activator	22804842	6	ver/dev	the response regulator RcsB activates leuO transcription in conjunction with BglJ , counteracting H-NS repression of leuO transcription	138	Interestingly , RcsA can form heterodimers with the response regulator RcsB , which activates leuO transcription in conjunction with BglJ , counteracting H-NS repression of leuO transcription ( Stratmann et al. , 2012 ) .	6	EXTENSION OF THE LEUO REGULON	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	leuO	activator	24659766	4	ver/dev	More recently , it was shown that leuO expression in E. coli can be activated by the RcsB regulators .	18	More recently , it was shown that leuO expression in E. coli can be activated by the RcsB and BglJ regulators ( 26 ) .	2	MAIN	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
RcsB	gene	leuO	activator	25566242	14	ver/dev	Also , LeuO expression was detected in a phosphate-restricted media ; and recently it was shown that the expression of the leuO gene can be activated by the RcsB regulators	115	Also , LeuO expression was detected in a phosphate-restricted media ( 98 ) ; and recently it was shown that the expression of the leuO gene can be activated by the RcsB and BglJ regulators ( 58 , 101 )	6	LEUO EXPRESSION CONDITIONS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
FliA	gene	STM1300	activator	33257526	13	att	FIG 3 FliA-dependent transcription of the STM1300 and sdiA protein-coding genes .	115	FIG 3 FliA-dependent transcription of the STM1300 and sdiA protein-coding genes .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	STM1300	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	cse1	repressor	28270274	0	ver/dev	Previously , we have determined that the cse1 promoter is repressed by the global regulators H-NS and LRP whereas LeuO participates in its positive regulation ; also , it can be expressed independently of LeuO in N-MM .	96	Previously , we have determined that the cse1 promoter is repressed by the global regulators H-NS and LRP whereas LeuO participates in its positive regulation ; also , it can be expressed independently of LeuO in N-MM [ 22 ] .	15	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
YdcR	gene	srfN	regulator	28674150	3	ver/dev	Furthermore , we found evidence that YdcR directly control its expression on the transcriptional level by binding to the promoter region of the srfN gene .	42	Furthermore , we found evidence that YdcR directly control its expression on the transcriptional level by binding to the promoter region of the srfN gene .	2	YANHUA LIU‡ , QIAN LIU§ , LINLU QI‡, TAO DING‡, ZHEN WANG‡, JIAQI FU‡, MO HU‡, MIN LI§, JEONGMIN SONG¶**, AND XIAOYUN LIU‡‡‡	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
YdcR	gene	srfN	regulator	28674150	9	ver/dev	Futhermore , - galactosidase assays were used to establish the transcriptional control of the srfN gene by YdcR .	178	Futhermore , - galactosidase assays were used to establish the transcriptional control of the srfN gene by YdcR .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YdcR	gene	srfN	regulator	28674150	10	ver/dev	Taken together , these results indicate that YdcR controls the expression of the srfN gene at the transcriptional level .	185	Taken together , these results indicate that YdcR controls the expression of the srfN gene at the transcriptional level .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
YdcR	gene	srfN	regulator	28674150	21	ver/dev	First , we used qRT-PCR to measure the transcript levels of srfN and found the regulation of YdcR on the expression of SrfN indeed occurs on the transcriptional level .	290	First , we used qRT-PCR to measure the transcript levels of srfN and found the regulation of YdcR on the expression of SrfN indeed occurs on the transcriptional level .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YdcR	gene	srfN	regulator	28674150	22	ver/dev	Further also confirmed that YdcR can mediate transcriptional regulation of srfN in bacteria .	291	Further - galactosidase assays of Sal-monella strains harboring a lacZ fusion to the promoter region of the srfN gene also confirmed that YdcR can mediate transcriptional regulation of srfN in bacteria cultured in vitro .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
YdcR	gene	srfN	regulator	28674150	22	ver/dev	galactosidase assays of Sal-monella strains also confirmed that YdcR can mediate transcriptional regulation of srfN in bacteria .	291	Further - galactosidase assays of Sal-monella strains harboring a lacZ fusion to the promoter region of the srfN gene also confirmed that YdcR can mediate transcriptional regulation of srfN in bacteria cultured in vitro .	6	DISCUSSION	Salmonella;Salmonella	1	L2	OTHER	Analysis	OTHER	New	Level 1
YdcR	gene	srfN	regulator	32708900	1	ver/dev	further biochemical assays validated the direct regulation of srfN by YdcR	81	The expression of SrfN , a known virulence factor , was found to be strictly dependent on YdcR during infection , and further biochemical assays validated the direct regulation of srfN by YdcR .	6	2.1. RESEARCH ON SALMONELLA PROTEOME DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YdcR	gene	srfN	regulator	32708900	3	ver/dev	further biochemical assays validated the direct regulation of srfN by YdcR	108	The expression of SrfN , a known virulence factor , was found to be strictly dependent on YdcR during infection , and further biochemical assays validated the direct regulation of srfN by YdcR .	6	2.1. RESEARCH ON SALMONELLA PROTEOME DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	yibJ	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , yibJ are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Fur	gene	entE	activator	24858080	11	ver/dev	To confirm this induction by an expected behaviour for a Fur-regulated locus -- we employed a strain carrying an entE : .	376	To confirm this induction as well as the repression by Fe ( II ) -- an expected behaviour for a Fur-regulated locus ( Tsolis et al. , 1995 ) -- we employed a strain carrying an entE : : MudJ transcriptional fusion ( Table S1 ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	activator	27206164	24	att	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	activator	27206164	49	att	In E. coli , it has been shown that an auxiliary regulatory protein , RcsA , enhan-ces RcsB-dependent repression of flhDC ( Francez-Charlot et al. , 2003 ) .	268	In E. coli , it has been shown that an auxiliary regulatory protein , RcsA , enhan-ces RcsB-dependent repression of flhDC ( Francez-Charlot et al. , 2003 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	activator	31563538	2	att	These results confirm that the flhDC repression produced by glucose , trehalose , mannitol and mannose occurs in a RcsB-dependent pathway , specific to RcsCDB system activation .	124	These results confirm that the flhDC repression produced by glucose , trehalose , mannitol and mannose occurs in a RcsB-dependent pathway , specific to RcsCDB system activation .	10	3.1. EFFECTS OF CARBON SOURCE ON RCSCDB SYSTEM ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	sseL	activator	21625519	13	ver/dev	Subsequently , we were interested in assessing the relative contribution of PhoP to the integrated regulation of sseL .	69	Subsequently , we were interested in assessing the relative contribution of PhoP and SsrB to the integrated regulation of sseL .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	activator	21625519	17	ver/dev	that PhoP contributes to the expression of sseL by an SsrB-independent manner	74	sseL : : lacZ expression in the phoP ssrB double mutant showed ,2 - fold lower expression compared to that in the ssrB strain ( P ,0.0001 ) supporting the possibility that PhoP and SsrB have accumulative effects on the expression of sseL , and that PhoP contributes to the expression of sseL by an SsrB-independent manner , in addition to its epistatic regulation of ssrB .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	sseL	activator	21625519	17	ver/dev	that PhoP contributes to the expression of sseL by an SsrB-independent manner	74	sseL : : lacZ expression in the phoP ssrB double mutant showed ,2 - fold lower expression compared to that in the ssrB strain ( P ,0.0001 ) supporting the possibility that PhoP and SsrB have accumulative effects on the expression of sseL , and that PhoP contributes to the expression of sseL by an SsrB-independent manner , in addition to its epistatic regulation of ssrB .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	sseL	activator	21625519	18	ver/dev	These data provided further evidence that PhoP can contribute to sseL transcription in an SsrB-independent mechanism .	78	These data provided further evidence that PhoP can contribute to sseL transcription in an SsrB-independent mechanism .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	sseL	activator	21625519	22	ver/dev	PhoP activates the expression of sseL in an SsrB-independent manner .	99	PhoP activates the expression of sseL in an SsrB-independent manner .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	activator	21625519	23	ver/dev	The results _ suggesting that sseL is activated by PhoP	113	The results suggesting that sseL is activated by PhoP have led us to search for the presence of potential PhoP binding sites .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	sseL	activator	21625519	34	ver/dev	The S. enterica PhoP , activates sseL expression	131	The S. enterica PhoP , but not an impaired ortholog from a S. bongori strain , activates sseL expression	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	activator	21625519	35	ver/dev	To further characterize the relative contribution of PhoP to the transcriptional output of sseL we sought to analyze sseL : : lacZ expression in two SsrB-free heterologous hosts , E. coli and	132	To further characterize the relative contribution of PhoP and SsrB to the transcriptional output of sseL we sought to analyze sseL : : lacZ expression in two SsrB-free heterologous hosts , E. coli and	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	activator	21625519	39	ver/dev	In agreement with the previously presented data , these results provided a further line of evidence that the S. Typhimurium PhoP can induce sseL expression independently of SsrB .	143	In agreement with the previously presented data , these results provided a further line of evidence that the S. Typhimurium PhoP can induce sseL expression independently of SsrB .	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	sseL	activator	21625519	43	ver/dev	S. Typhimurium PhoP did not seem to activate sseL expression .	159	S. Typhimurium PhoP , the S. bongori ortholog did not seem to activate sseL expression .	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	NEG	New	Level 1
PhoP	gene	sseL	activator	21625519	46	ver/dev	We concluded from this analysis that the PhoP of the S. bongori strain was unable to activate sseL expression due to a single amino-acid change at the C-terminal domain of this regulator .	167	We concluded from this analysis that the PhoP of the S. bongori strain was unable to activate sseL expression due to a single amino acid change at the C-terminal domain of this regulator .	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	sseL	activator	21625519	49	ver/dev	that the PhoP of the S. bongori strain is attenuated in activating expression of not only sseL	173	Taken together , these results suggested that the PhoP of the S. bongori strain is attenuated in activating expression of not only sseL , but also other members of the PhoP regulon , and that the valine residue at position 169 is required for the regulatory activity of PhoP .	6	PHOP BINDS DIRECTLY TO THE PROMOTER REGION OF SSEL	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	sseL	activator	21625519	51	ver/dev	Several lines of evidences indicated the ability of PhoP to promote expression of sseL in an SsrB-independent fashion : reduced expression of sseL : : lacZ was demonstrated in a phoP ssrB double mutant strain compared to diminution in the abundance of sseL transcripts in the phoP ssrB background in relation to Fig. 2B ; a PhoP-mediated induction of sseL : .	184	Several lines of evidences indicated the ability of PhoP to promote expression of sseL in an SsrB-independent fashion : ( i ) reduced expression of sseL : : lacZ was demonstrated in a phoP ssrB double mutant strain compared to the ssrB background in S. Typhimur-ium ( Fig. 2A ) ; ( ii ) diminution in the abundance of sseL transcripts in the phoP ssrB background in relation to the ssrB strain ( Fig. 2B ) ; ( iii ) a PhoP-mediated induction of sseL : : lacZ in a S. bongori SsrB-free heterologous host ( Fig. 5 ) ; ( iv ) the presence of two putative PhoP boxes in the promoter region of sseL ( Fig. 3 ) ; and ( v ) direct in-vitro binding of His-PhoP to the promoter region of sseL in a gel mobility shift assay ( Fig. 4 ) .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	sseL	activator	21625519	51	ver/dev	Several lines of evidences indicated the ability of PhoP to promote expression of sseL in an SsrB-independent fashion : reduced expression of sseL : : lacZ was demonstrated in a phoP ssrB double mutant strain compared to diminution in the abundance of sseL transcripts in the phoP ssrB background in relation to the ssrB strain ; a PhoP-mediated induction of sseL : .	184	Several lines of evidences indicated the ability of PhoP to promote expression of sseL in an SsrB-independent fashion : ( i ) reduced expression of sseL : : lacZ was demonstrated in a phoP ssrB double mutant strain compared to the ssrB background in S. Typhimur-ium ( Fig. 2A ) ; ( ii ) diminution in the abundance of sseL transcripts in the phoP ssrB background in relation to the ssrB strain ( Fig. 2B ) ; ( iii ) a PhoP-mediated induction of sseL : : lacZ in a S. bongori SsrB-free heterologous host ( Fig. 5 ) ; ( iv ) the presence of two putative PhoP boxes in the promoter region of sseL ( Fig. 3 ) ; and ( v ) direct in-vitro binding of His-PhoP to the promoter region of sseL in a gel mobility shift assay ( Fig. 4 ) .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	sseL	activator	21625519	52	ver/dev	Collectively , our data suggest that PhoP directly activates sseL by a feed-forward regulatory mechanism .	185	Collectively , our data suggest that PhoP directly activates sseL by a feed-forward regulatory mechanism .	7	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	sseL	activator	21625519	54	ver/dev	Controlling sseL expression by PhoP could be mediated either by transcription activation by counteracting nucleoid-like proteins .	188	Controlling sseL expression by PhoP could be mediated either by transcription activation per se or by counteracting nucleoid-like proteins , such as H-NS , YdgT , and Hha that were shown to bind A+T rich sequences and repress transcription of SPI-2 genes ( reviewed in [ 24 ] ) including sseL specifically [ 9 ] .	7	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
PhoP	gene	sseL	activator	21625519	66	ver/dev	Similarly , introducing PhoP into S. bongori resulted in a much higher induction of sseL expression than in S. Typhimurium background , implying the possibility that a particular sseL-negative regulator , not present in S. bongori , may play a role in S. Typhimurium .	227	Similarly , introducing SsrB or PhoP into S. bongori resulted in a much higher induction of sseL expression than in S. Typhimurium background ( Fig. 5 ) , implying the possibility that a particular sseL-negative regulator , not present in S. bongori , may play a role in S. Typhimurium .	7	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	NEG	New	Level 1
PhoP	gene	sseL	activator	23504014	36	ver/dev	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .	654	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog .	51	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	activator	25182488	30	ver/dev	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .	614	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog .	4	8	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	activator	25972862	6	ver/dev	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .	561	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog .	36	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sseL	activator	26553464	17	ver/dev	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .	501	The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog .	45	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
RtcR	gene	rtcR	activator	30201777	12	ver/dev	No predicted LexA binding site was identified in rtcR transcription is unchanged upon treatment with MMC , suggesting that the SOS response is indirectly involved in inducing the operon , perhaps generating the signal for activation of RtcR .	151	No predicted LexA binding site was identified in this region , and rtcR transcription is unchanged upon treatment with MMC ( see the RNA-seq analysis described below ) , suggesting that the SOS response is indirectly involved in inducing the operon , perhaps generating the signal for activation of RtcR .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtcR	gene	rtcR	activator	30201777	19	ver/dev	The comparative analysis of WT MMC versus WT also confirmed that expression of rtcR from the 70-type rtcRp was not significantly changed by MMC treatment , while expression of the RNA repair operon in the WT strain was highly induced , suggesting activation of RtcR to stimulate transcription from 54-dependent rsrp .	207	The comparative analysis of WT MMC versus WT also confirmed that expression of rtcR from the 70-type rtcRp was not significantly changed by MMC treatment ( 1.37-fold decrease ; q value , 0.37 ) , while expression of the RNA repair operon in the WT strain treated with MMC was highly induced ( rsr , rtcB , and rtcA increased 191 - , 158 - , and 87-fold , respectively ) , suggesting activation of RtcR to stimulate transcription from 54-dependent rsrp .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
STM0952	gene	STM4367	regulator	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to nitrosative-stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
STM0952	gene	STM4367	regulator	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to nitrosative-stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
STM0952	gene	STM4367	regulator	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
STM0952	gene	STM4367	regulator	24021902	3	ver/dev	asr STM1485 Expression avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric-oxide detoxification and virulence in mice	101	asr STM1485 Expression induced by acidic pH , essential for replication in macrophages and epithelial cells avrA STM2865 Inhibitor of the key proinflammatory NF-kB transcription factor hrg STM0952 Counteracts H2O2 stress nsrR STM4367 Key regulator of resistance to oxidative and nitrosative stress prfH STM0315 Multidrug transporter yejE STM2218 Confers resistance to AMPs protamine , polymyxin B , human defensin ( HBD ) -1 and HBD-2 yghA STM3157 Contributes to detoxification of reactive oxygen species STM1808 Contributes to nitric oxide detoxification and virulence in mice	6	INTRODUCTION	Homo sapiens;Mus sp.	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	malT	regulator	14996792	54	att	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
CRP	gene	malT	regulator	28373272	3	ver/dev	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cAMP and cAMP-receptor-protein -LRB- CRP -RRB- .	320	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT when bound by ATP and maltotriose ; transcription of malT is positively regulated by cyclic AMP ( cAMP ) and cAMP receptor protein ( CRP ) ( 58 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	malT	regulator	28373272	3	ver/dev	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cyclic AMP and cAMP-receptor-protein -LRB- CRP -RRB- .	320	These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT when bound by ATP and maltotriose ; transcription of malT is positively regulated by cyclic AMP ( cAMP ) and cAMP receptor protein ( CRP ) ( 58 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	19270312	1	ver/dev	RamA confers MDR in Salmonella Typhimurium via increased expression of acrB .	533	RamA confers MDR in Salmonella Typhimurium via increased expression of acrB which is inhibited by chlorpromazine .	21	TROP MED HYG 2004; 98: 423–30.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	acrB	activator	19759044	3	ver/dev	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .	528	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB , which is inhibited by chlorpromazine .	27	290–2.	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	21148208	25	ver/dev	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .	286	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB , which is inhibited by chlorpromazine .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	22948865	0	ver/dev	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .	124	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB , which is inhibited by chlorpromazine .	6	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	23493314	2	ver/dev	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .	257	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB , which is inhibited by chlorpromazine .	25	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	23882012	4	ver/dev	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .	719	RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB , which is inhibited by chlorpromazine .	36	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	27210311	0	ver/dev	RamA confers multidrug resistance in Sal-monella enterica via increased expression of acrB .	156	RamA confers multidrug resistance in Sal-monella enterica via increased expression of acrB , which is inhibited by chlorpromazine .	4	REFERENCES	Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	acrB	activator	34202800	6	ver/dev	RamA , , are involved in activating acrB expression .	254	Three homologous transcriptional activators , RamA , SoxS , and MarA , controlled by RamR , SoxR , and MarR , are involved in activating acrB and tolC expression [ 68 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hilD	regulator	11123690	22	ver/dev	However , if Fis regulates hilD , it might be expected that activation of the hilD promoter in pJB1 could not occur in the fis background .	157	However , if Fis regulates hilD , it might be expected that activation of the hilD promoter in pJB1 could not occur in the fis background .	9	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
FadR	gene	uspA	regulator	21715109	0	ver/dev	In E. coli uspA has been shown to be regulated by FadR .	180	In E. coli uspA has been shown to be regulated by FadR , a global regulator of fatty acid synthesis and degradation .	13	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
DksA	gene	sifA	activator	29930310	6	ver/dev	We next tested whether the stringent-response regulators DksA and ppGpp contribute to the intracellular expression of sifA .	63	We next tested whether the stringent response regulators DksA and ( p ) ppGpp contribute to the intracellular expression of sifA .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
Zur	gene	zinT	activator	24858080	6	att	Using semiquantitative RT-PCR we verified not only the repression by Zn and the Zur-dependent expression of znuA , zinT and , but also their induction by Cu ( Fig. 3 ) .	271	Using semiquantitative RT-PCR we verified not only the repression by Zn and the Zur-dependent expression of znuA , zinT and rpmE2-rpmJ_1 , but also their induction by Cu ( Fig. 3 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	NEG	New	Level 1
Zur	gene	zinT	activator	24858080	12	ver/dev	The Zur-regulated genes zinT are activated by Cu ions .	408	The Zur-regulated genes zinT , znuA and rpmE2 are activated by Cu ions .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	hmp	repressor	17024490	12	ver/dev	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp genes that PQ regulation of the hmpSt is mainly mediated by RamA .	227	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp and hmp genes and Ec St that PQ regulation of the hmpSt is mainly mediated by RamA .	16	CONCLUSIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	hmp	repressor	17024490	12	ver/dev	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp genes that PQ regulation of the hmpSt is mainly mediated by RamA .	227	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp and hmp genes and Ec St that PQ regulation of the hmpSt is mainly mediated by RamA .	16	CONCLUSIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	gatR	regulator	27956522	11	ver/dev	These data showed that cAMP-CRP binds to the promoters of gatR , .	180	These data showed that cAMP-CRP binds to the promoters of gatY , gatZ , and gatR , confirming that the expression of galactitol degradation is subject to catabolite repression .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TrpR	gene	argR	regulator	22941081	0	ver/dev	trolled by the argR repressor , while the biosynthesis genes of the other amino-acids are controlled by TrpR .	242	trolled by the argR repressor , while the biosynthesis genes of the other amino acids are controlled by the transcription factors Lrp and TrpR ( 17 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgtCBR	regulator	26231375	3	ver/dev	Then , phosphorylated PhoP binds to the promoter of the mgtCBR operon .	56	Then , phosphorylated PhoP binds to the promoter of the mgtCBR operon and activates transcription initiation .	6	REGULATION AT THE LEVEL OF TRANSCRIPTION ELONGATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtCBR	regulator	28181542	2	ver/dev	Similarly , PhoP controls transcription of the mgtCBR full-length messages .	153	Similarly , PhoP controls transcription of the mgtCBR full-length messages as well as the AmgR antisense transcript initiated from mgtC-mgtB intergenic region toward the mgtC gene15 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtCBR	regulator	28181542	3	ver/dev	Moreover , PhoP binds the promoter of the mgtCBR operon with a higher affiffinity than that of the amgR15 , gradually establishing different levels between MgtB proteins inside host cells .	158	Moreover , PhoP binds the promoter of the mgtCBR operon with a higher affiffinity than that of the amgR15 , gradually establishing different levels between MgtC and MgtB proteins inside host cells .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgtCBR	regulator	28181542	3	ver/dev	Moreover , PhoP binds the promoter of the mgtCBR operon with a higher affiffinity than that of the amgR15 , gradually establishing different levels between MgtC proteins inside host cells .	158	Moreover , PhoP binds the promoter of the mgtCBR operon with a higher affiffinity than that of the amgR15 , gradually establishing different levels between MgtC and MgtB proteins inside host cells .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagP	regulator	15225317	14	att	PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes	168	PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagP	regulator	15225317	17	att	A ugtL pagP double mutant was more sensitive than either the ugtL or pagP single mutants but still more resistant than the phoP mutant ( Fig. 2C ) , indicating that the ugtL and pagP genes participate in different pathways of magainin 2 resistance and that additional PhoP-regulated genes contribute to magainin 2 resistance .	172	A ugtL pagP double mutant was more sensitive than either the ugtL or pagP single mutants but still more resistant than the phoP mutant ( Fig. 2C ) , indicating that the ugtL and pagP genes participate in different pathways of magainin 2 resistance and that additional PhoP-regulated genes contribute to magainin 2 resistance .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagP	regulator	15225317	27	att	In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .	276	In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagP	regulator	18467098	5	att	The PhoP-regulated genes described and the modifications their products mediate are : pagP , palmitoyl transferase ; lpxO , formation of 2-hydroxy myristate ; pagL , 3-O-deacylase .	135	The PhoP-regulated genes described and the modifications their products mediate are : pagP , palmitoyl transferase ; lpxO , formation of 2-hydroxy myristate ; pagL , 3-O-deacylase .	10	PMRAB-MEDIATED LPS MODIFICATIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagP	regulator	23166721	2	att	The PhoP-regulated genes pagP and pagL encode proteins involved in addition of palmitate and 3-O-deacylation of the lipid-A , respectively .	271	The PhoP-regulated genes pagP and pagL encode proteins involved in addition of palmitate and 3-O-deacylation of the lipid A , respectively .	17	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagP	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
LeuO	gene	lacZ	activator	17908208	14	ver/dev	Interestingly , lacZ fusion was also positively regulated by LeuO .	55	Interestingly , the pRO310 ompS1 -- lacZ fusion was also positively regulated by LeuO , but at higher concentrations of IPTG than previously reported for ompS2 .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slyA	activator	27886269	36	ver/dev	slyA is positively regulated by HilD	203	Interestingly , between these genes are SL1265 and SL4248 , located in the S. Typhimurium genomic islands carrying lpxR ( SL1263 ) and SL4247 , respectively , as well as slyA that is positively regulated by HilD ( our unpublished results ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slyA	activator	27886269	36	ver/dev	slyA is positively regulated by HilD	203	Interestingly , between these genes are SL1265 and SL4248 , located in the S. Typhimurium genomic islands carrying lpxR ( SL1263 ) and SL4247 , respectively , as well as slyA that is positively regulated by HilD ( our unpublished results ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	lacZ	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	lacZ	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	lacZ	activator	33257526	5	att	To test whether novel FliA binding sites identified in the motility promoter-de-ficient strain represent active FliA-dependent promoters in a wild-type strain , transcriptional reporter fusions of 10 putative FliA-dependent promoters to lacZ were constructed .	63	To test whether novel FliA binding sites identified in the motility promoter-de-ficient strain represent active FliA-dependent promoters in a wild-type strain , transcriptional reporter fusions of 10 putative FliA-dependent promoters to lacZ were constructed .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
FliA	gene	ygaC	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrAB	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium indirectly through pmrAB .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	pmrAB	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by regulating pmrAB through other regulators .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	pmrAB	regulator	32620947	11	ver/dev	We hypothesized that the expression level of pmrAB may be regulated by CpxR through the connective protein PmrD .	93	We hypothesized that the expression level of pmrAB may be regulated by CpxR through the connective protein PmrD .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrAB	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium indirectly through pmrAB .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrAB	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of CRRGs , binding directly to pmrAB .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	pmrAB	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of colistin resistance-related genes , binding directly to pmrAB .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	yrbL	activator	15703297	16	att	( F ) Transcription of the yrbL gene is induced in low Mg2 in a PhoP-dependent fashion and repressed by Fe3 in a PmrA-dependent manner .	142	( F ) Transcription of the yrbL gene is induced in low Mg2 in a PhoP-dependent fashion and repressed by Fe3 in a PmrA-dependent manner .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	pagC	activator	19843227	18	att	Our data show that ugtL is StpA-dependent , as are other genes involved in LPS modification including pagC and pagP .	107	Our data show that ugtL is StpA-dependent , as are other genes involved in LPS modification including pagC and pagP .	8	STPA REPRESSES GENES REQUIRED FOR CELL ENVELOPE MODIFICATION AND RESISTANCE TO CATIONIC PEPTIDES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pbgP	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	pbgP	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	pbgP	activator	12519186	21	att	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	62	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB medium was determined for strains harbouring lac transcriptional fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pbgP	activator	12519186	21	att	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	62	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB medium was determined for strains harbouring lac transcriptional fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pbgP	activator	20593264	2	att	For example , despite the absence of the pmrD gene , Yersinia pestis ( Y. pestis ) can mediate PhoP-dependent modification of lipid-A with Ara4N through transcription of the pbgP and ugd genes ( Winfield et al. , 2005 ) .	226	For example , despite the absence of the pmrD gene , Yersinia pestis ( Y. pestis ) can mediate PhoP-dependent modification of lipid A with Ara4N through transcription of the pbgP and ugd genes ( Winfield et al. , 2005 ) .	12	5.3 ADDITIONAL BACTERIA CAPABLE OF MODIFYING LPS	Yersinia pestis	0	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	pbgP	activator	29739882	10	ver/dev	its pbgP promoter _ being directly activated by both the PhoP	147	For example , Yersinia pestis differs from Salmonella in lacking a pmrC gene and in its pbgP promoter being directly activated by both the PhoP and PmrA proteins ( 32 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliA	gene	sdiA	activator	33257526	0	att	We show that FliA-dependent transcription of sdiA is required for SdiA activity , highlighting a regulatory link between flagellar motility and intercellular communication .	10	We show that FliA-dependent transcription of sdiA is required for SdiA activity , highlighting a regulatory link between flagellar motility and intercellular communication .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	sdiA	activator	33257526	13	att	FIG 3 FliA-dependent transcription of the STM1300 and sdiA protein-coding genes .	115	FIG 3 FliA-dependent transcription of the STM1300 and sdiA protein-coding genes .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	sdiA	activator	33257526	18	att	We hypothesized that FliA-dependent transcription of sdiA is required for S. Typhimurium to accumulate sufficient SdiA protein to activate transcription of its target genes .	136	We hypothesized that FliA-dependent transcription of sdiA is required for S. Typhimurium to accumulate sufficient SdiA protein to activate transcription of its target genes .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	sdiA	activator	33257526	2	att	FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes , highlighting a regulatory link between flagellar motility and intercellular communication .	16	FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes , highlighting a regulatory link between flagellar motility and intercellular communication .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	sdiA	activator	33257526	23	att	We conclude that FliA-dependent transcription of sdiA is required for S. Typhimurium to accumulate sufficient SdiA protein to activate transcription of its target genes .	151	We conclude that FliA-dependent transcription of sdiA is required for S. Typhimurium to accumulate sufficient SdiA protein to activate transcription of its target genes .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	sdiA	activator	33257526	30	att	FliA-dependent transcription of sdiA may coordinate motility with interbacterial communication .	171	FliA-dependent transcription of sdiA may coordinate motility with interbacterial communication .	3	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
FliA	gene	sdiA	activator	33257526	34	att	We conclude that FliA-dependent transcription of sdiA is likely conserved in a small number of closely related genera .	182	We conclude that FliA-dependent transcription of sdiA is likely conserved in a small number of closely related genera .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	sdiA	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hdfR	activator	16763111	6	ver/dev	For example , the apparent activation of flagellar genes by H-NS most likely occurs by mediated repression of hdfR .	91	For example , the apparent activation of flagellar genes by H-NS most likely occurs by means of H-NS -- mediated repression of hdfR , a repressor of the flagellar regulators flhDC ( 1 ) .	4	6 FEBRUARY 2006; ACCEPTED 30 MAY 2006 10.1126/SCIENCE.1125878	nan	1	L2	SPEC	Other	OTHER	New	Level 1
LeuO	gene	leuO	regulator	18156266	41	ver/dev	LeuO are involved in regulation of leuO .	349	LeuO and H-NS are involved in regulation of leuO and ompS1 ( 2 , 5 ) , in addition to bgl , cadC , dsrA , and rovA ( 27 , 45 , 50 , 55 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	leuO	regulator	21398529	7	ver/dev	To determine whether LeuO is the casA activator in N-minimal-medium , the pKK-375 fusion was introduced into the IMSS-1 leuO strain : we found that LeuO does not induce casA expression in N-minimal-medium , since the activity values in the leuO-deficient strain were the same as those in the wild-type strain -LRB- data not shown -RRB- .	300	To determine whether LeuO is the casA activator in N-minimal medium , the pKK-375 fusion was introduced into the IMSS-1 leuO strain : we found that LeuO does not induce casA expression in N-minimal medium , since the activity values in the leuO-deficient strain were the same as those in the wild-type strain ( data not shown ) .	4	RESULTS	unidentified	1	L3	SPEC	Analysis	NEG	Other	Level 1
LeuO	gene	leuO	regulator	24354910	46	ver/dev	To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .	190	To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .	12	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	23040276	9	ver/dev	T. Wada , Y. Tanabe , K. Kutsukake , FliZ acts as a repressor of he ydiV gene .	624	[ 85 ] T. Wada , Y. Tanabe , K. Kutsukake , FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar typhimurium , J. Bacteriol .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25161191	2	ver/dev	FliZ directly represses ydiV transcription	37	FliZ directly represses ydiV transcription , and YdiV indirectly represses fliZ transcription through FlhD4C2 ( Fig. 1 ) ( 10 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	ydiV	repressor	25161191	4	ver/dev	FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .	119	YdiV and FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 ( Fig. 1 ) ( 10 ) .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
FliZ	gene	ydiV	repressor	25161191	4	ver/dev	YdiV are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .	119	YdiV and FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 ( Fig. 1 ) ( 10 ) .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
FliZ	gene	ydiV	repressor	25161191	9	ver/dev	FliZ acts as a repressor of the ydiV gene .	413	FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	11	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25201947	1	ver/dev	FliZ acts as a repressor of the ydiV gene .	463	FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4FlhC2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	11	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25422036	0	ver/dev	Kutsukake , K. FliZ acts as a repressor of the ydiV gene .	282	Wada , T. , Tanabe , Y. and Kutsukake , K. ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	34	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25422036	0	ver/dev	Y. , K. FliZ acts as a repressor of the ydiV gene .	282	Wada , T. , Tanabe , Y. and Kutsukake , K. ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	34	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25422036	0	ver/dev	Tanabe , K. FliZ acts as a repressor of the ydiV gene .	282	Wada , T. , Tanabe , Y. and Kutsukake , K. ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	34	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25422036	0	ver/dev	T. , K. FliZ acts as a repressor of the ydiV gene .	282	Wada , T. , Tanabe , Y. and Kutsukake , K. ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	34	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25422036	0	ver/dev	Wada , K. FliZ acts as a repressor of the ydiV gene .	282	Wada , T. , Tanabe , Y. and Kutsukake , K. ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	34	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	25972986	5	ver/dev	J Bacteriol 184:645 -- 653 Wada T , Tanabe Y , Kutsukake K FliZ acts as a repressor of the ydiV gene .	566	J Bacteriol 184:645 -- 653 Wada T , Tanabe Y , Kutsukake K ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar typhimurium .	26	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	26267246	4	ver/dev	FliZ represses transcription of ydiV .	68	FliZ represses transcription of ydiV that encodes for a posttranscriptional anti-FlhD4C2 factor [ 28 ] .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	ydiV	repressor	26441883	51	ver/dev	FliZ acts as a repressor of the ydiV gene .	1488	FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar typhimurium .	103	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	27206164	70	ver/dev	Kutsukake , K. FliZ acts as a repressor of the ydiV gene	544	Wada , T. , Tanabe , Y. , and Kutsukake , K. ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar	49	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	28593349	0	ver/dev	Wada T , Tanabe Y , Kutsukake K FliZ acts as a repressor of the ydiV gene .	428	Wada T , Tanabe Y , Kutsukake K ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	33	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	29021529	0	ver/dev	FliZ can repress ydiV expression , indirectly activating FlhD4C2 function38 .	149	FliZ can repress ydiV expression , indirectly activating FlhD4C2 function38 ; as well as increase FlhD4C2 protein levels through an unknown YdiV-independent mechanism39 ( Fig. 5 ) .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
FliZ	gene	ydiV	repressor	29021529	1	ver/dev	FliZ can counterbalance this affect by repressing ydiV expression .	192	FliZ can counterbalance this affect by repressing ydiV expression as well as increasing FlhD4C2 protein abundance in an YdiV-independent manner39 .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
FliZ	gene	ydiV	repressor	29021529	3	ver/dev	Kutsukake , K. FliZ acts as a repressor of the ydiV gene .	525	Wada , T. , Tanabe , Y. & Kutsukake , K. FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	14	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	29021529	3	ver/dev	Y. , K. FliZ acts as a repressor of the ydiV gene .	525	Wada , T. , Tanabe , Y. & Kutsukake , K. FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	14	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	29021529	3	ver/dev	Tanabe , K. FliZ acts as a repressor of the ydiV gene .	525	Wada , T. , Tanabe , Y. & Kutsukake , K. FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	14	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	29021529	3	ver/dev	T. , K. FliZ acts as a repressor of the ydiV gene .	525	Wada , T. , Tanabe , Y. & Kutsukake , K. FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	14	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	29021529	3	ver/dev	Wada , K. FliZ acts as a repressor of the ydiV gene .	525	Wada , T. , Tanabe , Y. & Kutsukake , K. FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar Typhimurium .	14	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	29369799	0	ver/dev	FliZ represses ydiV transcription .	189	FliZ increases flhDC synthesis through an unknown mechanism [ 78 ] and represses ydiV transcription .	13	3.2. MOTILITY (FLIC)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	ydiV	repressor	30862737	0	ver/dev	Wada T , Tanabe Y , Kutsukake K FliZ acts as a repressor of the ydiV gene .	359	Wada T , Tanabe Y , Kutsukake K ( 2011 ) FliZ acts as a repressor of the ydiV gene , which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar typhimurium .	7	FOR MORE DETAILED MATERIAL AND METHOD INFORMATION, SEE SI APPENDIX.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	ydiV	repressor	31488053	1	ver/dev	In addition , FliZ , represses ydiV transcription .	137	In addition , FliZ , whose expression is induced by FlhD4C2 , represses ydiV transcription [ 20 ] .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
GatR	gene	gatR	regulator	27956522	8	ver/dev	The promoters of gatR are negatively regulated by GatR .	102	The promoters of gatZ , gatY , and gatR are negatively regulated by GatR .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	csrB	activator	15130116	3	ver/dev	SirA also directly activates the evolutionarily conserved csrB gene .	166	SirA also directly activates the evolutionarily conserved csrB gene , which encodes an RNA that antagonizes the activity of the CsrA protein .	5	THE SALMONELLA SDIA SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	activator	15130116	7	ver/dev	An evolutionarily conserved function of SirA appears to be the direct activation of csrB .	220	An evolutionarily conserved function of SirA appears to be the direct activation of csrB ( carbon storage regulator ) , an RNA that antagonizes the activity of the RNA-binding protein CsrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	5	THE SALMONELLA SDIA SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	csrB	activator	16949866	1	ver/dev	SirA also directly activates the csrB regulatory RNA gene .	12	SirA also directly activates the csrB regulatory RNA gene .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	activator	16949866	17	ver/dev	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA .	301	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	nan	1	L3	OTHER	Other	NEG	New	Level 1
SirA	gene	csrB	activator	16949866	17	ver/dev	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA .	301	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	nan	1	L3	OTHER	Other	NEG	New	Level 1
SirA	gene	csrB	activator	16949866	32	ver/dev	SirA of Salmonella both control the csr system by directly activating the csrB gene .	458	SirA of Salmonella and UvrY of E. coli both control the csr system by directly binding and activating the csrB gene ( Pernestig et al. , 2001 ; Teplitski et al. , 2003 ) .	19	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	activator	17074910	0	ver/dev	In S. typhimurium , SirA activates the csrB regulatory RNAs .	9	In S. typhimurium , SirA activates the csrB and csrC carbon storage regulatory RNAs and the virulence gene regulators hilA and hilC .	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	csrB	activator	17074910	1	ver/dev	Therefore , SirA activates csrB to promote biofilm formation .	17	Therefore , SirA activates csrB , csrC and the fim operon to promote biofilm formation .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	csrB	activator	17208038	16	ver/dev	Data have shown that SirA acts by inducing expression of csrB .	109	Data have shown that SirA acts by inducing expression of two small RNA molecules , csrB and csrC [ 36,41,42,43 ] .	8	BARA/SIRA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	csrB	activator	32392214	19	att	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
SirA	gene	csrB	activator	32392214	19	ver/dev	and likely CsrC is largely responsible for SirA-dependent activation of RcsB because a plasmid complemented not only the csrB csrC double mutant but also the sirA and barA S4 Fig .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L2	SPEC	Other	NEG	Other	Level 1
SirA	gene	csrB	activator	32392214	19	ver/dev	and likely CsrC is largely responsible for SirA-dependent activation of RcsB because a plasmid complemented not only the csrB csrC double mutant but also the sirA and barA single mutants .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L2	SPEC	Other	NEG	Other	Level 1
SirA	gene	csrB	activator	32392214	19	ver/dev	CsrB is largely responsible for SirA-dependent activation of RcsB because a plasmid complemented not only the csrB csrC double mutant but also the sirA and barA S4 Fig .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L3	OTHER	Other	NEG	Other	Level 1
SirA	gene	csrB	activator	32392214	19	ver/dev	CsrB is largely responsible for SirA-dependent activation of RcsB because a plasmid complemented not only the csrB csrC double mutant but also the sirA and barA single mutants .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L3	OTHER	Other	NEG	Other	Level 1
CpxR	gene	scsA	activator	29866803	9	att	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper-stress .	211	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper stress .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	scsA	activator	29866803	9	att	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper-stress .	211	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper stress .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
STM3602	gene	phnA	regulator	28361036	0	ver/dev	JE351 JE346 phnA : : lacZY ( Nal-R , Kan-R ) JE10 .1 HA964 ∆ STM3602 : : ( Cm-R , Kan pCP20 flp recombinase ; AmpR pCLF3 .1 Template for Cm-R KO PCR product regulation of various process .	102	JE351 JE346 phnA : : lacZY ( Nal-R , Kan-R ) JE10 .1 HA964 ∆ STM3602 : : kan ( Cm-R , Kan-R ) pCP20 flp recombinase ; AmpR pCLF3 .1 Template for Cm-R KO PCR product regulation of various processes needed for STm to thrive in the intestine .	5	HA1474 HA420 ∆STM3602::KAN + PWSK29::STM3602 (KAN-R, NAL-R, AMP-R)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM3602	gene	phnA	regulator	28361036	0	ver/dev	JE351 JE346 phnA : : lacZY ( Nal-R , Kan-R ) JE10 .1 HA964 ∆ STM3602 : : : k pCP20 flp recombinase ; AmpR pCLF3 .1 Template for Cm-R KO PCR product regulation of various process .	102	JE351 JE346 phnA : : lacZY ( Nal-R , Kan-R ) JE10 .1 HA964 ∆ STM3602 : : kan ( Cm-R , Kan-R ) pCP20 flp recombinase ; AmpR pCLF3 .1 Template for Cm-R KO PCR product regulation of various processes needed for STm to thrive in the intestine .	5	HA1474 HA420 ∆STM3602::KAN + PWSK29::STM3602 (KAN-R, NAL-R, AMP-R)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM3602	gene	phnA	regulator	28361036	4	ver/dev	We hypothesized that STM3602 regulates the phnABO operon because the annotation of phnA suggests that PhnA may degrade PA. .	221	We hypothesized that STM3602 regulates the phnABO operon because the annotation of phnA suggests that PhnA may degrade PA. .	17	EXPRESSION OF PHNA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
STM3602	gene	phnA	regulator	28361036	6	ver/dev	These data suggest that STM3602 does not regulate phnA in rich-medium in the presence or absence of PA. .	225	These data suggest that STM3602 does not regulate phnA in rich medium in the presence or absence of PA. .	17	EXPRESSION OF PHNA	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
FNR	gene	hlyE	regulator	14996792	14	ver/dev	Thus , we concluded that FNR all contribute towards the regulation of hlyE expression .	83	Thus , we concluded that CRP , FNR , and H-NS all contribute towards the regulation of hlyE expression .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FNR	gene	hlyE	regulator	14996792	21	ver/dev	that during anaerobic-growth in liquid cultures in the absence of glucose , FNR is the major regulator of hlyE expression	115	This suggests that during anaerobic growth in liquid cultures in the absence of glucose , FNR is the major regulator of hlyE expression , and that CRP-mediated hlyE expression requires the presence of H-NS .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	14996792	23	ver/dev	In summary , the data suggest that FNR are positive regulators of hlyE expression in liquid culture in response to glucose-starvation , respectively .	124	In summary , the data presented here suggest that FNR and CRP are positive regulators of hlyE expression in liquid culture in response to oxygen and glucose starvation , respectively .	7	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	hlyE	regulator	14996792	23	ver/dev	In summary , the data suggest that FNR are positive regulators of hlyE expression in liquid culture in response to oxygen , respectively .	124	In summary , the data presented here suggest that FNR and CRP are positive regulators of hlyE expression in liquid culture in response to oxygen and glucose starvation , respectively .	7	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	hlyE	regulator	17259627	39	ver/dev	For example , E. coli hlyE -LRB- also known as sheA -RRB- , is regulated positively by the global transcriptional factors FNR and CRP -LRB- cAMP-receptor-protein -RRB- .	365	For example , E. coli hlyE ( also known as clyA and sheA ) , which encodes a novel pore-forming toxin , is regulated positively by the global transcriptional factors FNR ( fumarate and nitrate reduction ) and CRP ( cAMP receptor protein ) and by SlyA , and negatively by the nucleoid-structuring protein H-NS ( Wyborn et al. , 2004 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
FNR	gene	hlyE	regulator	17259627	39	ver/dev	For example , E. coli hlyE -LRB- also known as clyA -RRB- , is regulated positively by the global transcriptional factors FNR and CRP -LRB- cAMP-receptor-protein -RRB- .	365	For example , E. coli hlyE ( also known as clyA and sheA ) , which encodes a novel pore-forming toxin , is regulated positively by the global transcriptional factors FNR ( fumarate and nitrate reduction ) and CRP ( cAMP receptor protein ) and by SlyA , and negatively by the nucleoid-structuring protein H-NS ( Wyborn et al. , 2004 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
Hha	gene	pefA	regulator	31661351	17	ver/dev	While the precise mechanism of pef fimbriae regulation by Hha remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefA since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs .	344	While the precise mechanism of pef fimbriae regulation by Hha and YdgT remains to be determined , the silencing by H-NS most certainly involves a direct interaction of H-NS with the promoter regions upstream of pefB and pefA since a chromatin immu-noprecipitation-on-chip analysis identified an H-NS binding site upstream of both ORFs [ 24 ] .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	srfN	repressor	28674150	28	ver/dev	Navarre et al. can selectively silence horizontally acquired their microarray data revealed 6.7-fold repression of srfN expression by H-NS .	324	Navarre et al. found H-NS can selectively silence horizontally acquired genes and their microarray data revealed 6.7-fold repression of srfN expression by H-NS ( 26 ) .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HNS	gene	srfN	repressor	28674150	28	ver/dev	Navarre et al. can selectively silence horizontally acquired genes revealed 6.7-fold repression of srfN expression by H-NS .	324	Navarre et al. found H-NS can selectively silence horizontally acquired genes and their microarray data revealed 6.7-fold repression of srfN expression by H-NS ( 26 ) .	6	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
HNS	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB activate the expression of srfN .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB activate the expression of srfN .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB may come into play .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR activate the expression of srfN .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR activate the expression of srfN .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR may come into play .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	fis	repressor	17784910	30	ver/dev	Our data indicate that the presence of the RpoS sigma factor correlates with repression of the fis gene .	543	Our data indicate that the presence of the RpoS sigma factor correlates with repression of the fis gene .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	fis	repressor	17784910	31	ver/dev	As it is unlikely that RpoS represses the fis promoter directly , repression may involve an indirect negative effect .	545	As it is unlikely that RpoS represses the fis promoter directly , repression may involve an indirect negative effect in which RpoS upregulates an as-yet uni-dentified negative regulator of Fis .	14	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	fis	repressor	17784910	36	ver/dev	By reducing the number of RpoDcontaining holoenzymes , RpoS may downregulate that of the fis gene .	551	By reducing the number of RpoDcontaining holoenzymes , RpoS may downregulate RpoD-dependent promoters such as that of the fis gene .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	STM4118	activator	15681155	12	att	Thus , STM4118 may be a PmrA-activated gene responsible for modification of LPS core with pEtN in S. enterica serovar Typhimu-rium .	224	Thus , STM4118 may be a PmrA-activated gene responsible for modification of LPS core with pEtN in S. enterica serovar Typhimu-rium .	12	3.3. ANALYSIS OF RESISTANCE AND LPS PHENOTYPES	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	STM4118	activator	15681155	28	att	Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .	334	Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .	14	4. DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	STM4118	activator	15681155	9	att	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	206	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	11	3. RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilC	gene	dsbA	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilC independently of InvF .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	dsbA	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilC independently of both HilA .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsB	repressor	15469511	6	ver/dev	of the RcsC/YojN/RcsB regulatory system due to the rcsC11 allele in the sensor RcsC renders Salmonella that inactivation of the response regulator gene rcsB restores full virulence to the rcsC11 mutant , indicative that its attenuated phenotype results from aberrant expression of RcsB-regulated genes .	192	of the RcsC/YojN/RcsB regulatory system due to the rcsC11 allele in the sensor RcsC renders Salmonella avirulent , and that inactivation of the response regulator gene rcsB restores full virulence to the rcsC11 mutant , indicative that its attenuated phenotype results from aberrant expression of RcsB-regulated genes .	9	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsB	repressor	30510144	41	ver/dev	Taking into account that the activity of P1flhDC ensures the synthesis of the flagellum to positively control motility , P1flhDC is negatively affected by RcsB , even at basal levels , and high levels of SlyA repress the expression of rcsB from its two promoters , hence no repression of P1flhDC takes place , we here propose that SlyA activation indirectly modulates Salmonella motility in a RcsB-dependent pathway .	185	Taking into account that ( i ) the activity of P1flhDC ensures the synthesis of the flagellum to positively control motility , ( ii ) P1flhDC is negatively affected by RcsB , even at basal levels , and ( iii ) high levels of SlyA repress the expression of rcsB from its two promoters , hence no repression of P1flhDC takes place , we here propose that SlyA activation indirectly modulates Salmonella motility in a RcsB-dependent pathway .	5	DISCUSSION	Salmonella	1	L3	SPEC	Analysis	OTHER	Other	Level 1
BarA-SirA	gene	hilA	activator	16585772	0	ver/dev	Briefly , BarA-SirA , activates hilA .	19	Briefly , a two-component system , BarA-SirA , activates hilA ( 3 , 22 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	TU	araBAD	activator	10998173	3	ver/dev	The araBAD promoter is induced in the presence of arabinose by the positive regulator AraC .	420	The araBAD promoter is induced in the presence of arabinose by the positive regulator AraC and repressed in the presence of glucose .	16	INDUCIBLE, INTRACELLULAR COMPLEMENTATION OF SALMONELLA PHENOTYPES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AraC	TU	araBAD	activator	24272778	2	ver/dev	E. coli AraC activates transcription of the araBAD , araFGH , araE in the presence of its inducer , L-arabinose .	12	E. coli AraC activates transcription of the araBAD , araFGH , araE , and araJ transcripts in the presence of its inducer , L-arabinose ( 5 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
AraC	TU	araBAD	activator	24272778	44	ver/dev	Although arabinose-dependent repression by AraC has not been observed before , there are clear parallels with arabinose-de-pendent activation of araBAD transcription .	412	Although arabinose-dependent repression by AraC has not been observed before , there are clear parallels with arabinose-de-pendent activation of araBAD transcription .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
AraC	TU	araBAD	activator	24272778	45	ver/dev	Thus , arabinose-dependent repression of ydeNM by AraC would use the same mechanism as arabinose-dependent activation of araBAD .	421	Thus , arabinose-dependent repression of ydeNM by AraC would use the same mechanism as arabinose-dependent activation of araBAD .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pgtE	regulator	18096019	0	ver/dev	The expression of pgtE in the presence of PhoP / Q-inducing N-minimal-medium with a low Mg concen-21 tration was shown in some studies , although Guina et al. reported that the PhoP/PhoQ regulatory system does not account for the regulation of transport of pgtE .	135	The expression of pgtE in the presence of PhoP / Q-inducing N-minimal medium with a low Mg concen-21 tration was shown in some studies ( Kukkonen et al. , 2004 ) , although Guina et al. ( 2000 ) reported that the PhoP/PhoQ regulatory system does not account for the regulation of transcription or transport of pgtE , but plays a role in its post-transcriptional regulation .	15	IN VITRO EXPRESSION OF GFP	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pgtE	regulator	18096019	0	ver/dev	The expression of pgtE in the presence of PhoP / Q-inducing N-minimal-medium with a low Mg concen-21 tration was shown in some studies , although Guina et al. reported that the PhoP/PhoQ regulatory system does not account for the regulation of transcription of pgtE .	135	The expression of pgtE in the presence of PhoP / Q-inducing N-minimal medium with a low Mg concen-21 tration was shown in some studies ( Kukkonen et al. , 2004 ) , although Guina et al. ( 2000 ) reported that the PhoP/PhoQ regulatory system does not account for the regulation of transcription or transport of pgtE , but plays a role in its post-transcriptional regulation .	15	IN VITRO EXPRESSION OF GFP	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pgtE	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsA	gene	rcsB	activator	15469511	0	att	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	14	Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB - and RcsA-dependent colanic acid capsule synthesis cps operon .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsB	activator	15469511	2	att	To determine whether the restoration of wild-type virulence that resulted from inactivating the rcsB gene in the rcsC11 mutant resulted from RcsA-dependent genes , we evaluated the virulence of an rcsC11 rcsA double mutant .	63	To determine whether the restoration of wild-type virulence that resulted from inactivating the rcsB gene in the rcsC11 mutant resulted from RcsA-dependent genes , we evaluated the virulence of an rcsC11 rcsA double mutant .	6	THE REGULATORY GENE RCSA AND THE CAPSULAR	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
RcsA	gene	rcsB	activator	15469511	8	att	The rcsC11 rcsA mutant was more virulent than the rcsC11 strain after intraperitoneal inoculation , but it exhibited slower mouse killing kinetics than wild-type Salmo-nella or the rcsC11 rcsB mutant ( Fig. 1 ) , indicating that the attenuation phenotype results from both RcsA-dependent and - independent genes .	219	The rcsC11 rcsA mutant was more virulent than the rcsC11 strain after intraperitoneal inoculation , but it exhibited slower mouse killing kinetics than wild-type Salmo-nella or the rcsC11 rcsB mutant ( Fig. 1 ) , indicating that the attenuation phenotype results from both RcsA-dependent and - independent genes .	10	THE GENETIC BASIS FOR THE ATTENUATION PHENOTYPE OF THE RCSC11 MUTANT	Mus musculus;Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsA	gene	rcsB	activator	27558204	0	ver/dev	To better characterize the contribution of RcsA to persistence within tomatoes , rcsB genes were deleted	53	To better characterize the contribution of RcsA and RcsB to persistence within tomatoes , rcsA and rcsB genes were deleted and the abilities of the corresponding mutants to multiply in red and green tomatoes were tested ( strains and pri-mers used to construct them are listed in Supporting Information Tables S1 and S2 ) .	7	SALMONELLA RCSA AND RCSB GENES ARE INVOLVED IN PERSISTENCE WITHIN TOMATOES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	TU	marRAB	regulator	24139882	0	ver/dev	Expression of AcrAB is controlled by AcrR can also be plasmid-In this study , marRAB .	69	Expression of AcrAB is controlled by AcrR , the local repressor Quinolone resistance in Salmonella can also be plasmid-In this study , mutations in the QRDR of parE and in the regu-of AcrAB , and the global regulators MarA ( marRAB ) , SoxS ( soxRS ) and RamA .	5	GENE FOR SEQUENCING	unidentified plasmid	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	pmrCAB	regulator	12438352	26	att	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	334	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrCAB	regulator	12438352	26	ver/dev	PmrA has been shown to bind pmrCAB .	334	PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrCAB	regulator	20227482	0	att	In S. Typhimurium , the QseBC ( PreAB ) two-component system was initially described by Merighi et al. as modulating a subset of PmrA-regulated genes including pmrCAB and yibD [ 12 ] .	37	In S. Typhimurium , the QseBC ( PreAB ) two-component system was initially described by Merighi et al. as modulating a subset of PmrA-regulated genes including pmrCAB and yibD [ 12 ] .	6	1. INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	pmrCAB	regulator	20593264	0	ver/dev	In addition , PmrA can autoregulate the pmrCAB operon to increase expression of th regulatory system in response to induction signals .	165	In addition , PmrA can autoregulate the pmrCAB operon to increase expression of th regulatory system in response to induction signals ( Gunn and Miller , 1996 ) .	10	5.2.2 PMRA–PMRB REGULATORY SYSTEM	nan	1	L2	OTHER	Other	OTHER	New	Level 1
Sigma28	gene	fliB	activator	9765570	1	att	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	71	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	tolB	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	tolB	regulator	12438352	1	att	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	16	The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid A. yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .	1	ABSTRACT	nan	1	L2	SPEC	Other	NEG	Other	Level 1
PmrA	gene	tolB	regulator	12438352	23	att	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	331	While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .	5	DISCUSSION	nan	1	L1	SPEC	Fact	NEG	Other	Level 1
CRP	gene	aspA	activator	19843227	22	ver/dev	aspA , are activated by CRP-cAMP in Table S1 .	139	Many of these genes , including mglAB , aspA and glpF , are involved in the catabolism of carbohydrates and are activated by CRP-cAMP in E. coli ( Gosset et al. , 2004 ) ( Table S1 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	aspA	activator	19843227	22	ver/dev	aspA , are activated by CRP-cAMP in E. coli .	139	Many of these genes , including mglAB , aspA and glpF , are involved in the catabolism of carbohydrates and are activated by CRP-cAMP in E. coli ( Gosset et al. , 2004 ) ( Table S1 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
OmpR-P	gene	ssrA	activator	12753201	47	ver/dev	When OmpR-P levels are low , the highest affinity sites would be occupied ( ssrA-1 ) , leading to activation of ssrA .	245	When OmpR-P levels are low , the highest affinity sites would be occupied ( ssrA-1 ) , leading to activation of ssrA .	12	WHAT ARE THE SIGNALS THAT DETERMINE THE EXPRESSION OF SPI-2 GENES?	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
OmpR-P	gene	ssrA	activator	15491370	7	ver/dev	OmpR-P binds to sites downstream of the ssrA transcriptional start site , activating ssrA .	85	OmpR-P binds to sites upstream and downstream of the ssrA transcriptional start site , activating ssrA .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR-P	gene	ssrA	activator	15491370	7	ver/dev	OmpR-P binds to sites upstream of the ssrA transcriptional start site , activating ssrA .	85	OmpR-P binds to sites upstream and downstream of the ssrA transcriptional start site , activating ssrA .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	narH	regulator	29857034	19	ver/dev	narH are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PocR	gene	crp	activator	8636018	5	att	We tested the role of CRP in PocR-dependent transcription activation by constructing a strain with a deletion in the crp gene .	298	We tested the role of CRP in PocR-dependent transcription activation by constructing a strain with a deletion in the crp gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PocR	gene	crp	activator	8636018	5	ver/dev	We tested the role of CRP in PocR-dependent transcription activation by constructing a strain with a deletion in the crp gene .	298	We tested the role of CRP in PocR-dependent transcription activation by constructing a strain with a deletion in the crp gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	rstA	activator	32392214	32	att	This was also true for strains harboring gfp transcriptional-fusions to the PhoP-activated rstA gene ( S17 Fig ) and the OmpR-activated ompC gene ( S18 Fig ) .	328	This was also true for strains harboring gfp transcriptional fusions to the PhoP-activated rstA gene ( S17 Fig ) and the OmpR-activated ompC gene ( S18 Fig ) .	17	BARA IS DISPENSABLE FOR ACTIVATION OF THE REGULATORS ARCA, OMPR, AND PHOP UNDER CONDITIONS IN WHICH IT ACTIVATES RCSB	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	rcsB	regulator	12675799	6	ver/dev	These experiments indicate that the putative yojN rcsB operon requires the OmpR response regulator for expression .	229	These experiments indicate that the putative yojN rcsB operon requires the OmpR response regulator for expression .	5	IDENTIFICATION OF SPI-2 CO-EXPRESSED GENES	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	rcsB	regulator	23316043	0	ver/dev	7.10 3.33 E 51 Vi polysaccharide biosynthesis , UDP-glucose/GDP-mannose dehydrogenase t4349 tviE 280 4,659 592,697 6.96 1.28 E 49 Vi polysaccharide biosynthesis , TviE t4353 tviA 89 1,721 184,485 6.66 2.79 E 46 Vi polysaccharide biosynthesis regulator t4350 tviD 627 22,768 1,870,584 6.35 6.18 E 43 Vi polysaccharide biosynthesis t4011 yrfF 190 1,263 94,290 6.11 1.99 E 40 Putative membrane protein t4344 vexE 141 3,246 219,685 6.04 1.20 E 39 Vi polysaccharide export protein t4351 tviC 224 5,856 332,427 5.80 2.68 E 37 Vi polysaccharide biosynthesis protein , epimerase t4347 vexB 168 5,269 286,393 5.74 1.17 E 36 Vi polysaccharide export inner membrane protein t4345 vexD 218 6,661 325,843 5.59 3.05 E 35 Vi polysaccharide export inner membrane protein t4348 vexA 206 9,690 470,499 5.59 3.34 E 35 Vi polysaccharide export protein t4179 actP 94 1,216 49,412 5.23 6.59 E 32 Sodium-solute symporter family protein t4346 vexC 177 18,227 620,241 5.08 1.54 E 30 Vi polysaccharide export ATP-binding protein t4225 phoN 208 5,341 87,540 4.01 8.23 E 22 Nonspecific acid phosphatase precursor t4209 dcuB 71 2,371 39,400 4.00 9.93 E 22 Anaerobic C4-dicarboxylate transporter t1220 ihfA 8 60 2,186 3.84 1.51 E 20 Integration host factor alpha subunit t4362 246 4,107 55,798 3.73 8.40 E 20 Putative membrane protein t4004 ompR 47 272 4,392 3.59 7.64 E 19 Two-component response regulator OmpR t4356 271 5,186 60,540 3.52 2.44 E 18 Hypothetical protein t4268 169 2,629 30,184 3.47 5.12 E 18 Putative exported protein t3216 greA 32 527 5,488 3.16 5.74 E 16 Transcription elongation factor t0012 dnaK 5 14 862 3.08 1.77 E 15 DnaK protein t4005 envZ 77 602 3,708 2.44 7.98 E 12 Two-component sensor kinase EnvZ t4386 efp 51 300 1,689 2.16 2.12 E 10 Elongation factor P t2867 barA 140 1,780 8,225 2.15 2.50 E 10 Sensor protein t3205 nusA 18-108-743 2.02 1.03 E 09 L factor t4313 27-220-968 1.74 1.95 E 08 Putative membrane protein t0929 sirA 36-263-964 1.55 1.22 E 07 Invasion response regulator t3500 oxyR 66 717 1,853 1.26 1.73 E 06 Hydrogen peroxide-inducible regulon activator t3474 rpoB 5 9 159 1.25 1.87 E 06 DNA-directed RNA polymerase , beta subunit t1627 topA 66-280-591 0.86 4.06 E 05 DNA topoisomerase I , omega protein I t2325 ppiB 50 153 0.75 8.91 E 05 Peptidyl-prolyl cis-trans isomerase B t3095 parC 1 12 83 0.71 1.23 E 04 Topoisomerase IV subunit A t1238 78 788 1,284 0.64 1.96 E 04 Conserved hypothetical protein t0013 dnaJ 38-234-419 0.64 2.01 E 04 DnaJ protein t0595 rcsB 28-180-318 0.58 2.96 E 04 Regulator of capsule synthesis B component t1952 ihfB 16 2 102 183 0.49 5.32 E 04 Integration host factor beta subunit t4219 46 2 2,902 4,090 0.48 5.51 E 04 Hypothetical protein a `` Sys ID '' refers to the gene number in the sequenced S. Typhi Ty2 genome ( GenBank accession number ) .	97	7.10 3.33 E 51 Vi polysaccharide biosynthesis , UDP-glucose/GDP-mannose dehydrogenase t4349 tviE 280 4,659 592,697 6.96 1.28 E 49 Vi polysaccharide biosynthesis , TviE t4353 tviA 89 1,721 184,485 6.66 2.79 E 46 Vi polysaccharide biosynthesis regulator t4350 tviD 627 22,768 1,870,584 6.35 6.18 E 43 Vi polysaccharide biosynthesis t4011 yrfF 190 1,263 94,290 6.11 1.99 E 40 Putative membrane protein t4344 vexE 141 3,246 219,685 6.04 1.20 E 39 Vi polysaccharide export protein t4351 tviC 224 5,856 332,427 5.80 2.68 E 37 Vi polysaccharide biosynthesis protein , epimerase t4347 vexB 168 5,269 286,393 5.74 1.17 E 36 Vi polysaccharide export inner membrane protein t4345 vexD 218 6,661 325,843 5.59 3.05 E 35 Vi polysaccharide export inner membrane protein t4348 vexA 206 9,690 470,499 5.59 3.34 E 35 Vi polysaccharide export protein t4179 actP 94 1,216 49,412 5.23 6.59 E 32 Sodium-solute symporter family protein t4346 vexC 177 18,227 620,241 5.08 1.54 E 30 Vi polysaccharide export ATP-binding protein t4225 phoN 208 5,341 87,540 4.01 8.23 E 22 Nonspecific acid phosphatase precursor t4209 dcuB 71 2,371 39,400 4.00 9.93 E 22 Anaerobic C4-dicarboxylate transporter t1220 ihfA 8 60 2,186 3.84 1.51 E 20 Integration host factor alpha subunit t4362 246 4,107 55,798 3.73 8.40 E 20 Putative membrane protein t4004 ompR 47 272 4,392 3.59 7.64 E 19 Two-component response regulator OmpR t4356 271 5,186 60,540 3.52 2.44 E 18 Hypothetical protein t4268 169 2,629 30,184 3.47 5.12 E 18 Putative exported protein t3216 greA 32 527 5,488 3.16 5.74 E 16 Transcription elongation factor t0012 dnaK 5 14 862 3.08 1.77 E 15 DnaK protein t4005 envZ 77 602 3,708 2.44 7.98 E 12 Two-component sensor kinase EnvZ t4386 efp 51 300 1,689 2.16 2.12 E 10 Elongation factor P t2867 barA 140 1,780 8,225 2.15 2.50 E 10 Sensor protein t3205 nusA 18 108 743 2.02 1.03 E 09 L factor t4313 27 220 968 1.74 1.95 E 08 Putative membrane protein t0929 sirA 36 263 964 1.55 1.22 E 07 Invasion response regulator t3500 oxyR 66 717 1,853 1.26 1.73 E 06 Hydrogen peroxide-inducible regulon activator t3474 rpoB 5 9 159 1.25 1.87 E 06 DNA-directed RNA polymerase , beta subunit t1627 topA 66 280 591 0.86 4.06 E 05 DNA topoisomerase I , omega protein I t2325 ppiB 50 153 0.75 8.91 E 05 Peptidyl-prolyl cis-trans isomerase B t3095 parC 1 12 83 0.71 1.23 E 04 Topoisomerase IV subunit A t1238 78 788 1,284 0.64 1.96 E 04 Conserved hypothetical protein t0013 dnaJ 38 234 419 0.64 2.01 E 04 DnaJ protein t0595 rcsB 28 180 318 0.58 2.96 E 04 Regulator of capsule synthesis B component t1952 ihfB 16 2 102 183 0.49 5.32 E 04 Integration host factor beta subunit t4219 46 2 2,902 4,090 0.48 5.51 E 04 Hypothetical protein a `` Sys ID '' refers to the gene number in the sequenced S. Typhi Ty2 genome ( GenBank accession number NC_004631 ) .	2	MATERIALS AND METHODS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hns	repressor	26441883	25	ver/dev	d in Salmonella it has been shown that transcription of the hns gene -- which influences expression of the Spi-1-encoded invasion genes through the regulator HilD -- is repressed by the iron homeostasis regulator F	408	For instance , the H-NS modulator YmoA is preferentially degraded at 37 ◦ C by the ClpP and Lon proteases in Yersinia ( Jackson et al. , 2004 ) , and in Salmonella it has been shown that transcription of the hns gene -- which influences expression of the Spi-1-encoded invasion genes through the regulator HilD -- is repressed by the iron homeostasis regulator Fur ( Troxell et al. , 2011 ) .	9	ATTACHMENT AND INVASION OF THE INTESTINAL EPITHELIUM	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	sptP	activator	20221735	0	ver/dev	Most of these genes were induced at a higher level in the RpoS - sptP .	167	Most of these genes were induced at a higher level in the RpoS - mutant background with a few exceptions , such as sptP , sscB , sseB , and mgtC .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	lacZ	regulator	18399940	5	ver/dev	The lacZ promoter fragment was used as positive control for CRP binding , as described elsewhere .	278	The lacZ promoter fragment was used as positive control for CRP binding , as described elsewhere ( first panel ; Cameron and Redfield , 2006 ) .	6	CYAR EXPRESSION IS STRICTLY CRP-DEPENDENT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	dgoA	activator	12438352	8	ver/dev	Similarly , PmrA activated transcription of the dgoA locus by nearly 500-fold .	177	Similarly , PmrA activated transcription of the dgoA locus by nearly 500-fold .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	dgoA	activator	12438352	25	ver/dev	However , no consensus site was apparent in dgoA , suggesting indirect activation by PmrA .	333	However , no consensus site was apparent in dgoA , suggesting indirect activation by PmrA .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	dgoA	activator	15681155	7	att	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	191	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	11	3. RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
PmrA	gene	dgoA	activator	15681155	7	att	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	191	Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .	11	3. RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
CRP	gene	mglA	activator	19843227	42	att	( ii ) Regulation of CRP-cAMP-dependent genes ( e.g. glpF , dctA , mglA ) is restricted to the late exponential phase .	302	( ii ) Regulation of CRP-cAMP-dependent genes ( e.g. glpF , dctA , mglA ) is restricted to the late exponential phase .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	fimA	regulator	27909434	0	att	The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA , which was confirmed by yeast agglutination assay .	15	The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA , which was confirmed by yeast agglutination assay .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimA	regulator	31139165	11	ver/dev	More recent studies revealed that direct binding of Lrp to the fimA promoter is indispensable for repression of T1F expression .	125	More recent studies revealed that direct binding of Lrp to the fimA promoter is indispensable for activation as well as repression of T1F expression ( Baek et al. , 2011 ) .	5	GLOBAL REGULATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	fimA	regulator	31139165	11	ver/dev	More recent studies revealed that direct binding of Lrp to the fimA promoter is indispensable for activation .	125	More recent studies revealed that direct binding of Lrp to the fimA promoter is indispensable for activation as well as repression of T1F expression ( Baek et al. , 2011 ) .	5	GLOBAL REGULATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of H-NS to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	csgDEFG	regulator	25462918	0	ver/dev	The regulation of biofilm production in this bacterium involves the binding of H-NS to csgDEFG operon .	50	The regulation of biofilm production in this bacterium is very complex and involves the binding of several regulatory proteins , such as RpoS , OmpR , H-NS , CpxR , I-HF and MlrA to csgDEFG operon ( Davidson et al. , 2008 ; Gerstel and Römling , 2003 ; Prigent-Combaret et al. , 2001 ; Römling et al. , 1998a , 1998b ) .	4	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	avrA	regulator	19042154	7	ver/dev	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by opening ATG for translation , depending on the above-mentioned critical concentration .	251	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on positions 8 , 12 , and 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame ( AY769769 ) , or by blocking or opening the RBS and ATG for translation ( for review see Gottesman , 2004 ) , depending on the above-mentioned critical concentration .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	7	ver/dev	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by opening the RBS , depending on the above-mentioned critical concentration .	251	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on positions 8 , 12 , and 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame ( AY769769 ) , or by blocking or opening the RBS and ATG for translation ( for review see Gottesman , 2004 ) , depending on the above-mentioned critical concentration .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	7	ver/dev	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by blocking ATG for translation , depending on the above-mentioned critical concentration .	251	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on positions 8 , 12 , and 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame ( AY769769 ) , or by blocking or opening the RBS and ATG for translation ( for review see Gottesman , 2004 ) , depending on the above-mentioned critical concentration .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	7	ver/dev	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by blocking the RBS , depending on the above-mentioned critical concentration .	251	Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on positions 8 , 12 , and 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame ( AY769769 ) , or by blocking or opening the RBS and ATG for translation ( for review see Gottesman , 2004 ) , depending on the above-mentioned critical concentration .	14	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	9	ver/dev	it is suggested here that the CsrA protein can directly regulate the avrA mRNA	254	Thus , it is suggested here that the CsrA protein can directly regulate the avrA mRNA , and this regulation ( activation or inhibition ) depends on a critical or effective relative concentration of CsrA ( in connection with the avrA-mRNA concentration ) .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	12	ver/dev	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA destabilising the avrA mRNA provides a extremely sensitive means to alter virulence gene expression in response to environmental conditions .	261	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA and CsrB either through stabilising or destabilising the avrA mRNA provides a rapid and extremely sensitive means to alter virulence gene expression in response to environmental conditions ( see also Lawhon et al. , 2003 ) .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	12	ver/dev	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA destabilising the avrA mRNA provides a rapid means to alter virulence gene expression in response to environmental conditions .	261	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA and CsrB either through stabilising or destabilising the avrA mRNA provides a rapid and extremely sensitive means to alter virulence gene expression in response to environmental conditions ( see also Lawhon et al. , 2003 ) .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	12	ver/dev	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA stabilising the avrA mRNA provides a extremely sensitive means to alter virulence gene expression in response to environmental conditions .	261	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA and CsrB either through stabilising or destabilising the avrA mRNA provides a rapid and extremely sensitive means to alter virulence gene expression in response to environmental conditions ( see also Lawhon et al. , 2003 ) .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	avrA	regulator	19042154	12	ver/dev	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA stabilising the avrA mRNA provides a rapid means to alter virulence gene expression in response to environmental conditions .	261	It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA and CsrB either through stabilising or destabilising the avrA mRNA provides a rapid and extremely sensitive means to alter virulence gene expression in response to environmental conditions ( see also Lawhon et al. , 2003 ) .	14	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	lacZ	regulator	17908208	14	ver/dev	Interestingly , lacZ fusion was also positively regulated by LeuO .	55	Interestingly , the pRO310 ompS1 -- lacZ fusion was also positively regulated by LeuO , but at higher concentrations of IPTG than previously reported for ompS2 .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	STM1513	regulator	32193977	0	ver/dev	family proteins STM1513 / are regulated by RpoS in E. coli .	438	The KGG family proteins YciG , YmdF , and STM1513 / STM14_1829 are regulated by RpoS in S. Typhimurium and E. coli [ 14,16,39 ] .	28	IN SILICO ANALYSIS OF SEN1538 PROTEIN	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	STM1513	regulator	32193977	0	ver/dev	family proteins STM1513 / are regulated by RpoS in S. Typhimurium .	438	The KGG family proteins YciG , YmdF , and STM1513 / STM14_1829 are regulated by RpoS in S. Typhimurium and E. coli [ 14,16,39 ] .	28	IN SILICO ANALYSIS OF SEN1538 PROTEIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	STM1513	regulator	32193977	0	ver/dev	The KGG proteins STM1513 / are regulated by RpoS in E. coli .	438	The KGG family proteins YciG , YmdF , and STM1513 / STM14_1829 are regulated by RpoS in S. Typhimurium and E. coli [ 14,16,39 ] .	28	IN SILICO ANALYSIS OF SEN1538 PROTEIN	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	STM1513	regulator	32193977	0	ver/dev	The KGG proteins STM1513 / are regulated by RpoS in S. Typhimurium .	438	The KGG family proteins YciG , YmdF , and STM1513 / STM14_1829 are regulated by RpoS in S. Typhimurium and E. coli [ 14,16,39 ] .	28	IN SILICO ANALYSIS OF SEN1538 PROTEIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	16045614	7	ver/dev	RtsA in particular , also activate , independent of the effector gene slrP , encoding the periplasmic disulphide bond isomerase .	44	The three regulators , RtsA in particular , also activate , independent of HilA and InvF , the effector gene slrP ( Ellermeier and Slauch , 2003 ) and dsbA , encoding the periplasmic disulphide bond isomerase required for the function of SPI1 and other TTSSs ( Ellermeier and Slauch , 2004 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	slrP	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by RtsA independently of InvF .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by RtsA independently of both HilA .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	25182488	3	ver/dev	In this context , slrP is induced by overexpression of RtsA independently of the central SPI1 regulator HilA , with RtsA .	38	In this context , slrP is induced by overexpression of HilC , HilD , and RtsA independently of the central SPI1 regulator HilA , with RtsA being the best inducer .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	25182488	3	ver/dev	In this context , slrP is induced by overexpression of RtsA independently of the central SPI1 regulator HilA , with RtsA .	38	In this context , slrP is induced by overexpression of HilC , HilD , and RtsA independently of the central SPI1 regulator HilA , with RtsA being the best inducer .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	25182488	3	ver/dev	In this context , slrP is induced by overexpression of HilD independently of the central SPI1 regulator HilA , with RtsA .	38	In this context , slrP is induced by overexpression of HilC , HilD , and RtsA independently of the central SPI1 regulator HilA , with RtsA being the best inducer .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	25182488	3	ver/dev	In this context , slrP is induced by overexpression of HilC independently of the central SPI1 regulator HilA , with RtsA .	38	In this context , slrP is induced by overexpression of HilC , HilD , and RtsA independently of the central SPI1 regulator HilA , with RtsA being the best inducer .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	slrP	activator	31484980	47	ver/dev	Previous studies revealed that RtsA induce expression of slrP by an undefined way62 ,63 .	220	Previous studies revealed that HilD and RtsA induce expression of slrP by an undefined way62 ,63 .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FruR	gene	acrD	regulator	27879336	0	ver/dev	fruBKA , under the control of FruR , was upregulated in the acrD mutant .	275	The fructose operon ( fruBKA ) , under the control of FruR ( 45 ) , was upregulated in the acrD mutant .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FruR	gene	acrD	regulator	27879336	0	ver/dev	The fructose operon , under the control of FruR , was upregulated in the acrD mutant .	275	The fructose operon ( fruBKA ) , under the control of FruR ( 45 ) , was upregulated in the acrD mutant .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CspE	gene	fliA	regulator	32159509	4	ver/dev	Although the lass III flagellar genes are transcriptionally regulated by the sigma factor fliA -LRB- whose levels were comparable in the two strains -RRB- , there might be an additional role of CspE since , in its absence , the transcript levels of class II flagellar genes are negatively affected .	197	Although the lass III flagellar genes are transcriptionally regulated by the sigma factor fliA ( whose levels were comparable in the two strains ) , there might be an additional role of CspE since , in its absence , the transcript levels of class II flagellar genes are negatively affected .	13	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
FimW	gene	fimA	regulator	11133935	10	ver/dev	These results are consistent with the role of FimW as a negative regulator of fimbrial expression , acting either directly on the fimA promoter to indirectly through the activity of other regulatory molecules .	345	These results are consistent with the role of FimW as a negative regulator of fimbrial expression , acting either directly on the fimA promoter to repress transcription or indirectly through the activity of other regulatory molecules .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimW	gene	fimA	regulator	11133935	10	ver/dev	These results are consistent with the role of FimW as a negative regulator of fimbrial expression , acting either directly on the fimA promoter to repress transcription .	345	These results are consistent with the role of FimW as a negative regulator of fimbrial expression , acting either directly on the fimA promoter to repress transcription or indirectly through the activity of other regulatory molecules .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FimW	gene	fimA	regulator	11133935	13	ver/dev	that the regulatory effect of FimW is not due to the binding of FimW alone at the fimA promoter	360	These results suggest that FimW and FimZ interact in vivo and that the regulatory effect of FimW is not due to the binding of FimW alone at the fimA promoter .	7	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FimW	gene	fimA	regulator	22654583	3	ver/dev	These results demonstrate that the fimZ gene encodes a positive regulator for fimA , while FimW is a repressor for fimA .	363	These results demonstrate that the fimZ gene encodes a positive regulator for fimA , while FimW is a repressor for fimA [ 6 , 7 ] .	5	4. DISCUSSIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FimW	gene	fimA	regulator	31139165	1	ver/dev	three major regulatory proteins , FimW ( each ) control fim operon expression primarily through regulation of the fimA promotor	84	In Salmonella , there are three major regulatory proteins , FimZ , FimY , and FimW ( each expressed under its own promoter ) , that control fim operon expression primarily through regulation of the fimA promotor ( PfimA ; Yeh et al. , 1995 , 2002b ; Tinker and Clegg , 2000 , 2001 ) .	4	DIRECT REGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TyrR	gene	aroP	activator	32111072	4	ver/dev	The primary mechanism of TyrR-mediated gene regulation is repression , nevertheless activation by TyrR was reported for the aroP promoter P3 .	67	The primary mechanism of TyrR-mediated gene regulation is repression , nevertheless activation by TyrR was reported for three genes , namely mtr , tyrP and the aroP promoter P3 [ 23 ] .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from S. bongori , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in -LRB- JW1889 -RRB- with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	nan	1	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from S. bongori , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	nan	1	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from E. coli , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in -LRB- JW1889 -RRB- with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	Escherichia coli	0	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from E. coli , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	Escherichia coli	0	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from S. bongori , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	nan	1	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from E. coli , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	Escherichia coli	0	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from S. bongori , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in JW1316 in minimal-medium with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	nan	1	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from S. bongori , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in defective strain in minimal-medium with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	nan	1	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from E. coli , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in JW1316 in minimal-medium with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	Escherichia coli	0	L2	SPEC	Other	NEG	Other	Level 1
TyrR	gene	aroP	activator	32111072	6	ver/dev	To ascertain whether the aroP P3 promoter from E. coli , can be activated by aromatic-amino-acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in defective strain in minimal-medium with or without phenylalanine .	252	To ascertain whether the aroP P3 promoter from E. coli and S. bongori , can be activated by aromatic amino acids via TyrR binding to the TyrR boxes , expression from the P3 usp-lacZ fusion was investigated in the tyrR + ( JW1889 ) and in the tyrR - defective strain ( JW1316 ) in minimal medium with or without phenylalanine .	14	3.3. POSITIVE REGULATION OF THE USP P3 PROMOTER	Escherichia coli	0	L2	SPEC	Other	NEG	Other	Level 1
FliA	gene	flgM	repressor	1655712	5	ver/dev	a regulatory circuit in which flgM , negatively regulates FliA function in flagellar-mutant backgrounds	278	This would suggest a regulatory circuit in which flgM , transcribed by a FliA-containing RNA polymerase , negatively regulates FliA function in flagellar-mutant backgrounds .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	flgM	repressor	8288531	0	ver/dev	In flagellum-defective strains , the flgM gene product of S. typhimurium negatively regulates flagellar genes by inhibiting the activity of FliA .	7	In flagellum-defective strains , the flgM gene product of S. typhimurium negatively regulates flagellar genes by inhibiting the activity of FliA , the flagellin-specific sigma factor .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
YfeR	gene	yfeH	repressor	21175741	8	ver/dev	Whereas this suggests that YfeR is a repressor of yfeH transcription , it is also apparent that factors other than YfeR modulate YfeH expression .	339	Whereas this suggests that YfeR is a repressor of yfeH transcription , it is also apparent that factors other than YfeR modulate YfeH expression .	18	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MntR	gene	cdtB	repressor	17555437	3	ver/dev	Instead , as MntR has been shown to work as a repressor , MntR may exert its effect by repressing the expression of a repressor of cdtB expression .	274	Instead , as MntR has been shown to work as a repressor , MntR may exert its effect by repressing the expression of a repressor of cdtB expression such as IgeR .	8	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
MntR	gene	cdtB	repressor	17555437	3	ver/dev	Instead , as MntR has been shown to work as a repressor , MntR may exert its effect by repressing the expression of a repressor of cdtB expression .	274	Instead , as MntR has been shown to work as a repressor , MntR may exert its effect by repressing the expression of a repressor of cdtB expression such as IgeR .	8	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
H	gene	hilA	repressor	23515315	28	att	In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145 - and 9.5-fold compared with H-NSWT levels .	258	In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145 - and 9.5-fold compared with H-NSWT levels .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FabR	gene	fabB	repressor	27004424	6	ver/dev	Combining it with a transcriptomics approach reduces its inherent noise This provided the first evidence for the direct repression of fabB expression by FabR in S. Typhimurium .	52	Combining it with a transcriptomics approach allows the discrimination between direct and indirect target genes and reduces its inherent noise [ 33 -- 36 ] This provided the first evidence for the direct repression of fabA , fabB and yqfA expression by FabR in S. Typhimurium , confirming current knowledge generated in E. coli .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FabR	gene	fabB	repressor	27004424	6	ver/dev	its inherent noise This provided the first evidence for the direct repression of fabB expression by FabR in S. Typhimurium _ confirming current knowledge	52	Combining it with a transcriptomics approach allows the discrimination between direct and indirect target genes and reduces its inherent noise [ 33 -- 36 ] This provided the first evidence for the direct repression of fabA , fabB and yqfA expression by FabR in S. Typhimurium , confirming current knowledge generated in E. coli .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
StpA	gene	pagC	repressor	19843227	36	att	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	262	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	relA	repressor	19091955	4	ver/dev	PhoP-dependent genes , was repressed greatly in a relA spoT mutant	38	ppGpp has no influence on the PhoP/PhoQ system ( 22 ) , but transcription of several SlyA - and PhoP-dependent genes , including ugtL and pagC , was repressed greatly in a relA spoT ( ppGpp0 ) mutant ( 23 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Leiostomus xanthurus	0	L3	OTHER	Other	OTHER	Other	Level 2
FNR	TU	frdABCD	activator	21767810	1	att	Low oxygen conditions stabilize the Fe-S cluster , allowing the Fnr-dependent expression of anaerobic metabolic genes including frdABCD .	132	Low oxygen conditions stabilize the Fe-S cluster , allowing the Fnr-dependent expression of anaerobic metabolic genes including frdABCD .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	repressor	25547794	19	ver/dev	The Mlc global regulator has been shown to downregulate an hilE promoter .	210	The Mlc global regulator has been shown to downregulate an hilE promoter ( 27 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Mlc	gene	hilE	repressor	31428589	5	ver/dev	Mlc downregulates hilE expression by binding to the hilE P3 promoter .	160	Mlc downregulates hilE expression by binding to the hilE P3 promoter ( Lim et al. , 2007 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Mlc	gene	hilE	repressor	31428589	5	ver/dev	Mlc downregulates hilE expression by binding to the hilE P3 promoter .	160	Mlc downregulates hilE expression by binding to the hilE P3 promoter ( Lim et al. , 2007 ) .	4	THE REGULATION OF SPI-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgC	regulator	11254626	1	att	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	208	It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .	6	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgC	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseA	regulator	17630976	0	att	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	14	Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM .	2	SUMMARY	synthetic construct	0	L3	OTHER	Analysis	OTHER	New	Level 2
ChbR	gene	chiP	repressor	24450479	20	ver/dev	From the data in Fig. 3 , it is apparent that inactivation of the ChbR repressor completely prevents residual chiP induction by chitobiose in ΔchiX background in E. coli as it does in Salmonella .	99	From the data in Fig. 3 , it is apparent that inactivation of the ChbR repressor completely prevents residual chiP induction by chitobiose in ΔchiX background in E. coli as it does in Salmonella .	5	THE CHIP GENE IS UNDER THE TRANSCRIPTIONAL CONTROL OF THE NAGC REPRESSOR	Escherichia coli;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
ChbR	gene	chiP	repressor	24450479	45	ver/dev	In the presence of chitobiose -LRB- induced -RRB- , ChbR bound to the product of the action of the ChbG enzyme , probably monoacetylated Chb6P sequesters the ChiX sRNA so relieving the translational repression of chiP .	202	In the presence of chitobiose ( induced ) , ChbR bound to its inducing signal ( the product of the action of the ChbG enzyme , probably monoacetylated Chb6P ) activates expression of the chbBCARFG operon and sequesters the ChiX sRNA so relieving the translational repression of chiP .	8	DISCUSSION	nan	1	L2	SPEC	Other	OTHER	New	Level 1
ChbR	gene	chiP	repressor	24450479	45	ver/dev	In the presence of chitobiose -LRB- induced -RRB- , ChbR bound to its inducing signal sequesters the ChiX sRNA so relieving the translational repression of chiP .	202	In the presence of chitobiose ( induced ) , ChbR bound to its inducing signal ( the product of the action of the ChbG enzyme , probably monoacetylated Chb6P ) activates expression of the chbBCARFG operon and sequesters the ChiX sRNA so relieving the translational repression of chiP .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
ChbR	gene	chiP	repressor	24450479	47	ver/dev	Activation of chbBCA expression by ChbR is essential to relieve ChiX repression of chiP .	220	Activation of chbBCA expression by ChbR is essential to relieve ChiX repression of chiP .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	STM1056	activator	17379730	7	att	SlyA-activated ) , STM1056 ( msgA homologue )	441	SlyA-activated ) , STM1056 ( msgA homologue )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	ompA	activator	28874380	0	ver/dev	These data suggest that CRP activates ompA expression during stationary-phase .	108	These data suggest that CRP activates ompF expression in exponential growth and activates ompF and ompA expression during stationary phase but does not directly regulate ompC under these conditions .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
EmrR	gene	emrA	repressor	30992361	8	ver/dev	The RNA-Seq data were first validated by increased RNA levels of the emrA genes in the ΔemrR mutant , since transcription of these genes was shown to be repressed by EmrR previously .	81	The RNA-Seq data were first validated by increased RNA levels of the emrA and emrB genes in the ΔemrR mutant ( 5.7 - and 5.9-fold , respectively ; Table S3 ) , since transcription of these genes was shown to be repressed by EmrR previously ( 9 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
QseB	gene	invF	repressor	28062286	2	ver/dev	Considering the overexpression of qseB in the absence of qseC , the repression of invF transcription in DqseC provides further evidence that QseB can attenuate the invasion of epithelial cells by S. Typhi .	155	Considering the overexpression of qseB in the absence of qseC , the repression of invF transcription in DqseC provides further evidence that QseB can attenuate the invasion of epithelial cells by S. Typhi .	14	3.2. QSEB MAY HAVE DUAL REGULATORY FUNCTIONS TO BIOFILM RELATED GENES IN A QSEC-DEPENDENT WAY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	New	Level 1
CsrA	gene	proP	repressor	30682134	25	ver/dev	CsrA repressed the translation of proP 2.7-fold in S2 Table .	251	CsrA repressed the translation of proP 2.7-fold in mLPM ( S2 Table ) , which encodes a permease that imports L-proline and glycine betaine , which is required for long term survival of Salmonella in low moisture environments [ 90 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	proP	repressor	30682134	25	ver/dev	CsrA repressed the translation of proP 2.7-fold in mLPM .	251	CsrA repressed the translation of proP 2.7-fold in mLPM ( S2 Table ) , which encodes a permease that imports L-proline and glycine betaine , which is required for long term survival of Salmonella in low moisture environments [ 90 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LysR	gene	envZ	regulator	24720747	12	ver/dev	Therefore , the LysR regulator LtrR is implicated in the regulation of envZ .	195	Therefore , the LysR regulator LtrR is implicated in the regulation of envZ .	7	LTRR-DEPENDENT AND -INDEPENDENT OMPR PROMOTERS ARE INVOLVED IN OMPR SYNTHESIS FOR OMPC AND OMPF PRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
InvF	gene	sicA	regulator	28887382	0	ver/dev	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of sicA .	258	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of SPI-1 T3SS genes such as sopB , sicA and sopE ( 35 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sicA	regulator	28887382	0	ver/dev	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of sicA .	258	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of SPI-1 T3SS genes such as sopB , sicA and sopE ( 35 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IHF	gene	hilA	regulator	21680637	46	ver/dev	In vitro binding of IHF to the hilA regulatory region	269	In vitro binding of H-NS and IHF to the hilA regulatory region	9	IN VITRO BINDING OF H-NS AND IHF TO THE HILA REGULATORY REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IHF	gene	hilA	regulator	21680637	50	ver/dev	The effect of ihB mutant alleles on hilA expression in cells growing in LB-medium suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	278	The effect of ihfA or ihB mutant alleles on hilA expression in cells growing in LB medium and entering the stationary phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants , as well as the gel-shift data presented above suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
IHF	gene	hilA	regulator	21680637	50	ver/dev	The effect of ihB mutant alleles on hilA expression in cells entering the stationary-phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	278	The effect of ihfA or ihB mutant alleles on hilA expression in cells growing in LB medium and entering the stationary phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants , as well as the gel-shift data presented above suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
IHF	gene	hilA	regulator	21680637	50	ver/dev	The effect of ihB mutant alleles on hilA expression in cells entering the gel-shift data suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	278	The effect of ihfA or ihB mutant alleles on hilA expression in cells growing in LB medium and entering the stationary phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants , as well as the gel-shift data presented above suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .	10	IHF ALLEVIATES H-NS-MEDIATED REPRESSION OF HILA TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
IHF	gene	hilA	regulator	21680637	64	ver/dev	EMSA experiments suggest that binding of IHF to the hilA regulatory region might abolish the silencing of such a promoter region .	345	EMSA experiments suggest that binding of IHF to the hilA regulatory region might abolish H-NS binding and hence the silencing of such a promoter region .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
IHF	gene	hilA	regulator	21680637	64	ver/dev	EMSA experiments suggest that binding of IHF to the hilA regulatory region might abolish H-NS binding .	345	EMSA experiments suggest that binding of IHF to the hilA regulatory region might abolish H-NS binding and hence the silencing of such a promoter region .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
StpA	gene	katE	repressor	23936152	4	ver/dev	StpA is known to repress expression of the RpoS regulon -LRB- including katE -RRB- during exponential-growth .	350	StpA is known to repress expression of the RpoS regulon ( including katE ) during exponential growth [ 24 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
BaeR	gene	mdtA	activator	22173828	7	ver/dev	These results indicate that Asp 61 residue from BaeR are essential for the activation of the target gene mdtA in S. Typhimurium .	151	These results indicate that His 250 residue from BaeS and Asp 61 residue from BaeR are essential for the function of this two-component system and the activation of the target gene mdtA in S. Typhimurium .	18	DETECTION OF MDTA MRNA AFTER CIPROXOXACIN TREATMENT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	msgA	regulator	10844662	1	att	Downstream of oafA , but within the same horizontal acquisition , is the site of a second SsrB-regulated fusion ( srfE ) , within an msgA ( macrophage survival gene ) 29 homologue ( P 10 ; Fig. 2 ) .	108	Downstream of oafA , but within the same horizontal acquisition , is the site of a second SsrB-regulated fusion ( srfE ) , within an msgA ( macrophage survival gene ) 29 homologue ( P 10 ; Fig. 2 ) .	10	MOLECULAR CHARACTERIZATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	tcfA	regulator	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	marA	activator	28650690	2	ver/dev	Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	marA	activator	28650690	2	ver/dev	Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	marA	activator	28650690	2	ver/dev	Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
AcrR	gene	marA	activator	28650690	2	ver/dev	Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .	34	Ruiz and Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated or inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS and marA expression .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	ygaU	regulator	24271167	2	ver/dev	Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , ygaU are regulated by the alternative sigma factor RpoS .	186	Among other genes with significantly reduced expression in LP strains , many genes ( yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB , yddX , ygaU , yibJ , psiF , yciF , and osmY ) are regulated by the alternative sigma factor RpoS , which is not only required for survival of bacteria under starvation or other cellular stresses but also essential for Salmonella virulence ( 94 -- 96 ) .	4	RESULTS AND DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
DksA	TU	ssrAB	activator	29930310	0	ver/dev	The RNA polymerase-binding protein DksA activates the ssrAB regulon post-transcriptionally , whereas ppGpp relieves the negative regulation .	9	The RNA polymerase-binding protein DksA activates the ssrAB regulon post-transcriptionally , whereas the alarmone guanosine tetraphosphate ( ppGpp ) relieves the negative regulation imposed by the AT-rich ssrA discriminator region .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DksA	TU	ssrAB	activator	29930310	0	ver/dev	The RNA polymerase-binding protein DksA activates the ssrAB regulon post-transcriptionally , whereas the alarmone guanosine tetraphosphate relieves the negative regulation .	9	The RNA polymerase-binding protein DksA activates the ssrAB regulon post-transcriptionally , whereas the alarmone guanosine tetraphosphate ( ppGpp ) relieves the negative regulation imposed by the AT-rich ssrA discriminator region .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DksA	TU	ssrAB	activator	29930310	7	ver/dev	Requirement of DksA for the activation of ssrAB transcription .	79	Requirement of DksA and ( p ) ppGpp for the activation of ssrAB transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	activator	22149171	2	ver/dev	LeuO activates sdiA expression to a lesser extent than does CRP .	9	LeuO activates sdiA expression to a lesser extent than does CRP .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	activator	22149171	25	ver/dev	LeuO is an activator of sdiA	264	LeuO binds the sdiA promoter and is an activator of sdiA	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	sdiA	activator	22149171	58	ver/dev	In this study , we show that LeuO are the minor activators of sdiA , respectively .	377	In this study , we show that CRP and LeuO are the major and minor activators of sdiA , respectively .	21	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
LeuO	gene	sdiA	activator	22149171	58	ver/dev	In this study , we show that LeuO are the major activators of sdiA , respectively .	377	In this study , we show that CRP and LeuO are the major and minor activators of sdiA , respectively .	21	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
LeuO	gene	sdiA	activator	25566242	13	ver/dev	In S. enterica serovar Typhimurium , LeuO was reported to increase sdiA expression in low levels .	102	In S. enterica serovar Typhimurium , LeuO was reported to increase sdiA expression in low levels ( 90 ) ( Figure 1 ) .	5	THE LEUO REGULATOR IN OTHER GRAM-NEGATIVE BACTERIA	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CspE	gene	cspA	repressor	32159509	6	ver/dev	CspE negatively regulates cspA expression during biofilm formation .	238	CspE negatively regulates cspA expression during biofilm formation .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CspE	gene	cspA	repressor	32159509	7	ver/dev	The probable mechanism of transcriptional repression of CspA by CspE involves physical binding of CspE to the cold box region ' proximal part of 5 ′ - UTR of cspA mRNA .	273	The probable mechanism of transcriptional repression of CspA by CspE involves physical binding of CspE to the cold box region which is located in the 5 ' proximal part of 5 ′ - UTR of cspA mRNA .	14	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
NorR	gene	hmp	regulator	22039967	0	ver/dev	These genes are regulated by hmp and NorR -LRB- norV -RRB- ,	114	These genes are regulated by the cytoplasmic NO-responsive transcription factors NsrR ( hmp and hcp ) and NorR ( norV ) ,	8	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to metal resistance and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of exposure to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , cooper .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , zinc .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , Ail/OmpX-like was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
BaeR	gene	STM3031	regulator	30448437	0	ver/dev	These systems contribute to envelope stress response and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of spheroplasting to indole , tannin .7 e9 It also mediates drug resistance by regulating the expression of genes .10 In a previous study , the outer membrane protein STM3031 was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	44	These systems contribute to envelope stress response , metal resistance , and drug resistance of Escherichia coli and Salmonella .6 Among them , the TCS BaeSR responds to a wide range of environmental stresses such as spheroplasting and exposure to indole , tannin , zinc , or cooper .7 e9 It also mediates drug resistance by regulating the expression of genes encoding drug transporters in Sal-monella .10 In a previous study , the outer membrane protein STM3031 ( Ail/OmpX-like ) was determined to be involved in ceftriaxone resistance , and its production in S. Typhimu-rium was found to be regulated by BaeR .11 The finding that deletion of the stm3031 gene results in a > 64-fold reduction in resistance to ceftriaxone indicates the role of STM3031 in ceftriaxone resistance .12	3	INTRODUCTION	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
IlvY	gene	sdiA	activator	22149171	45	ver/dev	IlvY overexpression increases sdiA expression , with the largest effects in stationary-phase -LRB- Fig .	332	IlvY overexpression increases sdiA expression , with the largest effects in stationary phase ( Fig .	18	ILVY, NHAR, AND FUR ARE INDIRECT ACTIVATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	sseA	activator	17630976	33	att	The activity of the sseA promoter displayed a similar induction between 2 and 6 h post infection , but induction levelled off between 6 and 18 h. SsrB-dependent induction peaked at 6 h ( 90-fold ) and remained high at 18 h ( 60-fold ; Fig. 9B ) .	262	The activity of the sseA promoter displayed a similar induction between 2 and 6 h post infection , but induction levelled off between 6 and 18 h. SsrB-dependent induction peaked at 6 h ( 90-fold ) and remained high at 18 h ( 60-fold ; Fig. 9B ) .	8	ACTIVATION OF SPI-2 GENES IN VITRO REQUIRES SSRB AND ACIDIC PH	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : sseA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : sseA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : sseA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseA	activator	26880544	40	ver/dev	When the SsrA kinase is activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : sseA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	sseA	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 co-regulated genes , including : sseA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseA	activator	26880544	40	ver/dev	When the SsrA kinase is present , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 , including : sseA .	319	When the SsrA kinase is present and activated by acid stress , SsrB is phosphorylated and SsrB ~ P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes , including : sifA ( Walthers et al. , 2011 ) , ssaB , ssaM , sseA and ssaG ( Walthers et al. , 2007 ) .	15	SSRB SITS AT A PIVOTAL DECISION POINT THAT DETERMINES SALMONELLA LIFESTYLES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	micF	regulator	28302471	1	ver/dev	T. Suzuki , C. Ueguchi , T. Mizuno , H-NS regulates OmpF expression through micF antisense RNA in Escherichia coli , J. Bacteriol .	418	[ 58 ] T. Suzuki , C. Ueguchi , T. Mizuno , H-NS regulates OmpF expression through micF antisense RNA in Escherichia coli , J. Bacteriol .	37	REFERENCES	Lateolabrax japonicus;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	activator	31501286	39	att	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	283	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	activator	31501286	39	att	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	283	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	activator	31501286	31	ver/dev	Since SoxS showed the strongest effects on posttranscriptional flagellar regulation with induction of flhDC by high ATc concentrations , we wanted to understand the effects of native SoxS concentrations on flhDC regulation .	224	Since SoxS showed the strongest effects on posttranscriptional flagellar regulation with induction of flhDC by low and high ATc concentrations ( Fig. 3 ) , we wanted to understand the effects of native SoxS concentrations on flhDC regulation ( Fig. 4 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SoxS	TU	flhDC	activator	31501286	31	ver/dev	Since SoxS showed the strongest effects on posttranscriptional flagellar regulation with induction of flhDC by low ATc concentrations , we wanted to understand the effects of native SoxS concentrations on flhDC regulation .	224	Since SoxS showed the strongest effects on posttranscriptional flagellar regulation with induction of flhDC by low and high ATc concentrations ( Fig. 3 ) , we wanted to understand the effects of native SoxS concentrations on flhDC regulation ( Fig. 4 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilE	gene	hilE	activator	29378886	26	att	Lim et al. showed that loss of Mlc leads to a 2-fold increase in hilE mRNA levels and a 4-fold HilE-dependent decrease in invasion ( 32 ) .	258	Lim et al. showed that loss of Mlc leads to a 2-fold increase in hilE mRNA levels and a 4-fold HilE-dependent decrease in invasion ( 32 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilE	gene	hilE	activator	29378886	32	ver/dev	However , our data show that PhoPQ can repress the system independently of HilE ; thus , this transcriptional induction of hilE is apparently superfluous .	266	However , our data show that PhoPQ can repress the system independently of HilD and HilE ( reference 6 and unpublished data ) ; thus , this transcriptional induction of hilE is apparently superfluous .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CsgD	gene	STM3388	regulator	16629664	34	ver/dev	STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	389	STM2123 and STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	STM3388	regulator	16629664	38	ver/dev	STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	435	STM2123 and STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools .	14	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
EcnR	TU	flhDC	repressor	24706743	1	ver/dev	The known posttranscriptional inhibitors of flhDC expression included in this study were EcnR .	126	The known transcriptional and posttranscriptional inhibitors of flhDC expression included in this study were EcnR , RscB , LrhA , FliT , DskA , and YdiV .	4	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
EcnR	TU	flhDC	repressor	24706743	1	ver/dev	The known transcriptional inhibitors of flhDC expression included in this study were EcnR .	126	The known transcriptional and posttranscriptional inhibitors of flhDC expression included in this study were EcnR , RscB , LrhA , FliT , DskA , and YdiV .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
H	gene	ssrA	repressor	23515315	28	att	In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145 - and 9.5-fold compared with H-NSWT levels .	258	In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145 - and 9.5-fold compared with H-NSWT levels .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	srfJ	activator	29270156	0	ver/dev	Initially , it was proposed as a putative effector because the gene srfJ is positively regulated by SsrB .	59	Initially , it was proposed as a putative effector because the gene srfJ is positively regulated by SsrB ( Worley et al. , 2000 ) , the main positive regulator of T3SS2 ( Fass and Groisman , 2009 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	srfJ	activator	30531898	2	ver/dev	SsrB has also been identified to induce srfJ .	254	SsrB has also been identified to induce srfJ that is located on the MI degradation island41 ,61,62 .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	pagC	regulator	18270203	2	ver/dev	In vivo , H-NS remained bound to the pagC promoters under inducing conditions that promoted RNA polymerase recruitment and transcription of the pagC genes .	14	In vivo , H-NS remained bound to the ugtL and pagC promoters under inducing conditions that promoted RNA polymerase recruitment and transcription of the ugtL and pagC genes .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	pagC	regulator	18270203	3	ver/dev	pagC genes are normally bound by the H-NS protein	37	Thus , to understand this process , we investigated the expression of the PhoP - and SlyA-dependent ugtL and pagC genes , which are normally bound by the H-NS protein ( 4 , 5 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	pagC	regulator	18270203	51	ver/dev	The H-NS proteins bind to several sites in the pagC promoter .	247	The H-NS and SlyA proteins bind to several sites in the pagC promoter .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	pagC	regulator	18270203	56	ver/dev	the pagC promoter els for the ugtL mRNAs are probably due to the less are bound by the H-NS proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HNS	gene	pagC	regulator	18270203	56	ver/dev	the pagC promoter els for the pagC mRNAs are probably due to the less are bound by the H-NS proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HNS	gene	pagC	regulator	18270203	56	ver/dev	the pagC promoter els for the pagC mRNAs are probably due to the less are bound by the H-NS proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
HNS	gene	pagC	regulator	18270203	74	ver/dev	The apparent simultaneous occupancy of the pagC by the H-NS , SlyA , and PhoP proteins and even RNA polymerase is not unprecedented , since many regions of the E. coli genome can also associate with binding of H-NS to various promoters is not mutually exclusive , at least in-vitro ( Fig .	304	The apparent simultaneous occupancy of the pagC and ugtL promoter regions by the H-NS , SlyA , and PhoP proteins and even RNA polymerase is not unprecedented , since many regions of the E. coli genome bound by H-NS can also associate with RNA polymerase ( 6 , 39 ) , and binding of H-NS and of SlyA to various promoters is not mutually exclusive , at least in vitro ( 40 , 41 ) ( Fig .	4	DISCUSSION	Escherichia coli	0	L2	OTHER	Other	NEG	Other	Level 1
HNS	gene	pagC	regulator	33201432	5	ver/dev	Among these genes , pagC are bound by H-NS proteins in Salmonella .	185	Among these genes , pagC and ugtL are bound by H-NS proteins in Salmonella .	7	POST-TRANSLATIONAL MODIFICATION OF H-NS GENE-SILENCING FACTOR	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	pagC	regulator	34202800	30	ver/dev	In Salmonella , pagC are bound by H-NS proteins .	472	In Salmonella , pagC and ugtL are bound by H-NS proteins .	15	3.6. THE HISTONE-LIKE PROTEIN FAMILY (H-NS)	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	luxS	activator	24018968	4	att	The luxS gene , which encodes a synthase that produces a quorum-sensing signal-molecule termed autoinducer ( AI-2 ) , is necessary for the growth-dependent induction of a subset of SPI1 genes , including invF and InvF-dependent genes , but not hilA [ 9 ] .	139	The luxS gene , which encodes a synthase that produces a quorum-sensing signal molecule termed autoinducer ( AI-2 ) , is necessary for the growth-dependent induction of a subset of SPI1 genes , including invF and InvF-dependent genes , but not hilA [ 9 ] .	14	STATIONARY PHASE UNDER SHAKING CULTURE CONDITIONS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
Fis	gene	topA	regulator	21276095	3	ver/dev	A role for FIS in the regulation of S. enterica topA expression has not been previously detected	41	A role for FIS in the regulation of S. enterica topA expression has not been previously detected ( Kelly et al. , 2004 ) , but FIS does bind and directly regulate the E. coli topA promoter ( Weinstein-Fischer et al. , 2000 ) .	3	INTRODUCTION	Salmonella;Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
Fis	gene	topA	regulator	21276095	3	ver/dev	FIS does directly regulate the E. coli topA promoter	41	A role for FIS in the regulation of S. enterica topA expression has not been previously detected ( Kelly et al. , 2004 ) , but FIS does bind and directly regulate the E. coli topA promoter ( Weinstein-Fischer et al. , 2000 ) .	3	INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	topA	regulator	21276095	8	ver/dev	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of topA might differ between the two species .	179	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of the genes responsible for supercoiling ( gyrA , gyrB and topA ) might differ between the two species .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	topA	regulator	21276095	8	ver/dev	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of topA might differ between the two species .	179	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of the genes responsible for supercoiling ( gyrA , gyrB and topA ) might differ between the two species .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	topA	regulator	21276095	10	ver/dev	FIS control of topA gene expression .	184	FIS control of gyrA , gyrB and topA gene expression .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	topA	regulator	21276095	20	ver/dev	FIS control of topA expression .	249	FIS control of topA expression .	8	DIFFERENTIAL EFFECTS OF OSMOTIC PRESSURE AND AERATION ON TOPA EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	oxyR	regulator	30145252	0	ver/dev	In the oxyR mutant strain , β-galacto-sidase assa confirmed that the viaB operon was positively regulated by OxyR .	15	In the oxyR mutant strain , microarray analysis , quantitative real time PCR and β-galacto-sidase assay confirmed that the viaB operon was positively regulated by OxyR .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OxyR	gene	oxyR	regulator	30145252	0	ver/dev	In the oxyR mutant strain , quantitative real time PCR confirmed that the viaB operon was positively regulated by OxyR .	15	In the oxyR mutant strain , microarray analysis , quantitative real time PCR and β-galacto-sidase assay confirmed that the viaB operon was positively regulated by OxyR .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OxyR	gene	oxyR	regulator	30145252	0	ver/dev	In the oxyR mutant strain , microarray analysis confirmed that the viaB operon was positively regulated by OxyR .	15	In the oxyR mutant strain , microarray analysis , quantitative real time PCR and β-galacto-sidase assay confirmed that the viaB operon was positively regulated by OxyR .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	otsA	activator	23676436	14	att	We also found that the expression of several RpoS-dependent genes , e.g. osmC , otsA and yciF , was significantly increased , which is consistent with our observation of increased level of RpoS in the DclpP mutant .	390	We also found that the expression of several RpoS-dependent genes , e.g. osmC , otsA and yciF , was significantly increased , which is consistent with our observation of increased level of RpoS in the DclpP mutant .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Lrp	gene	traJ	activator	12067346	4	ver/dev	These observations support the model that Lrp acts as a conjugation activator by promoting traJ transcription , whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis .	17	These observations support the model that Lrp acts as a conjugation activator by promoting traJ transcription , whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	traJ	activator	12067346	8	ver/dev	This result suggested that Lrp activates the transcription of traJ .	76	This result suggested that Lrp activates the transcription of traJ .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Lrp	gene	traJ	activator	12067346	9	ver/dev	The concomitant observation that the tra operon remains repressed in TraJ - background is also relevant , as it suggests that Lrp activates the tra operon indirectly by enhancing traJ transcription .	77	The concomitant observation that the tra operon remains repressed in an Lrp + TraJ - background ( Fig. 2 ; data not shown ) is also relevant , as it suggests that Lrp activates the tra operon indirectly by enhancing traJ transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Lrp	gene	traJ	activator	12067346	9	ver/dev	The concomitant observation that the tra operon remains repressed in an Lrp - background is also relevant , as it suggests that Lrp activates the tra operon indirectly by enhancing traJ transcription .	77	The concomitant observation that the tra operon remains repressed in an Lrp + TraJ - background ( Fig. 2 ; data not shown ) is also relevant , as it suggests that Lrp activates the tra operon indirectly by enhancing traJ transcription .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Lrp	gene	traJ	activator	12067346	20	ver/dev	Analysis of b-galactosidase activity in Lrp + and Lrp - backgrounds indicated that Lrp-mediated activation of traJ transcription requires the presence of the Lrp binding site located upstream of traJ .	117	Analysis of b-galactosidase activity in Lrp + and Lrp - backgrounds indicated that Lrp-mediated activation of traJ transcription requires the presence of the Lrp binding site located upstream of traJ ( Fig. 6 ) .	5	DELETION ANALYSIS OF THE TRAJ UAS: EFFECT ON TRAJ EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	TU	csgDEFG	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons involved in bio-film formation , EPS production	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	TU	csgDEFG	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons involved in bio-film formation , transport production	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	TU	csgDEFG	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons involved in bio-film formation , virulence production	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	TU	csgDEFG	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of lpfE genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	TU	csgDEFG	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of fimA genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	TU	csgDEFG	regulator	23548899	0	ver/dev	CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under stressrelated conditions .	42	CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under stressrelated conditions , including low osmolarity and low temperature ( 30 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgDEFG	regulator	23548899	0	ver/dev	CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under low-temperature .	42	CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under stressrelated conditions , including low osmolarity and low temperature ( 30 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	TU	csgDEFG	regulator	23548899	0	ver/dev	CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under low-osmolarity .	42	CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under stressrelated conditions , including low osmolarity and low temperature ( 30 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	sopE	activator	24018968	2	ver/dev	HilA activates sopE SPI1 .	40	HilA activates expression of the prg/org and inv/spa genes , which encode a functional type III secretion system ( T3SS ) apparatus [ 25 , 26 ] , whereas InvF is required to induce transcription of several effector genes encoded both within ( sic/sip genes ) and outside ( sigD and sopE ) SPI1 [ 12 , 13 ] .	3	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	tnpA	activator	28335027	0	ver/dev	As InvF is a transcriptional activator of other effector proteins , tnpA indirectly represses these genes .	11	As InvF is a transcriptional activator of SPI-1 encoded and other effector proteins , tnpA indirectly represses these genes .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	tnpA	activator	28335027	0	ver/dev	As InvF is a transcriptional activator of SPI-1 , tnpA indirectly represses these genes .	11	As InvF is a transcriptional activator of SPI-1 encoded and other effector proteins , tnpA indirectly represses these genes .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	lacZ	repressor	9765212	13	ver/dev	b-Ga-lactosidase assays _ demonstrating inhibition of s28-dependent lacZ expression by the His -- FlgM proteins ( both wild type and mutant ) in-vivo	361	b-Ga-lactosidase assays demonstrating inhibition of s28-dependent lacZ expression by the His -- FlgM proteins ( both wild type and mutant ) in vivo .	12	PURIFICATION OF FLGM AND DERIVATIVES	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CadC	TU	araBAD	regulator	18487329	2	ver/dev	pBAD24-CadC-HA expressed CadC-HA under the control of araBAD promoter	142	To further confirm CadC degradation , we constructed a pBAD24 derivative ( pBAD24-CadC-HA ) that expressed CadC-HA under the control of araBAD promoter , which is strictly regulated by the concentration of extracellular arabinose .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CadC	TU	araBAD	regulator	18487329	2	ver/dev	a pBAD24 derivative expressed CadC-HA under the control of araBAD promoter	142	To further confirm CadC degradation , we constructed a pBAD24 derivative ( pBAD24-CadC-HA ) that expressed CadC-HA under the control of araBAD promoter , which is strictly regulated by the concentration of extracellular arabinose .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CadC	TU	araBAD	regulator	29214489	8	ver/dev	pBAD24-CadC-HA expressed CadC-HA under control of the arabinose-inducible araBAD promoter	99	To assess effects of CadC on the OmpR protein level , we used a pBAD24 derivative ( pBAD24-CadC-HA ) that expressed CadC-HA under control of the arabinose-inducible araBAD promoter ( Guzman et al. , 1995 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CadC	TU	araBAD	regulator	29214489	8	ver/dev	a pBAD24 derivative expressed CadC-HA under control of the arabinose-inducible araBAD promoter	99	To assess effects of CadC on the OmpR protein level , we used a pBAD24 derivative ( pBAD24-CadC-HA ) that expressed CadC-HA under control of the arabinose-inducible araBAD promoter ( Guzman et al. , 1995 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	hilA	activator	17993530	0	ver/dev	three AraC family members can independently activate hilA	9	Expression of the SPI1 T3SS is tightly regulated by the combined action of HilC , HilD , and RtsA , three AraC family members that can independently activate hilA , which encodes the direct regulator of the SPI1 structural genes .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
AraC	gene	hilA	activator	17993530	0	ver/dev	three AraC family members can independently activate hilA	9	Expression of the SPI1 T3SS is tightly regulated by the combined action of HilC , HilD , and RtsA , three AraC family members that can independently activate hilA , which encodes the direct regulator of the SPI1 structural genes .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
AraC	gene	hilA	activator	17993530	0	ver/dev	three AraC family members can independently activate hilA	9	Expression of the SPI1 T3SS is tightly regulated by the combined action of HilC , HilD , and RtsA , three AraC family members that can independently activate hilA , which encodes the direct regulator of the SPI1 structural genes .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RcsB	gene	osmB	regulator	33638994	19	ver/dev	These assays confirmed binding of phosphorylated RcsB to osmB promoters .	398	These assays confirmed binding of phosphorylated RcsB to fepE , osmB and ytfK promoters and to flgA and nlpD Intra-CDS sequences ( Figure 7A and C ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	tatA	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of tatA we performed EMSA with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged Fig 3B .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	tatA	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of tatA we performed EMSA with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	tatA	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of tatA we performed electrophoretic-mobility-shift assays with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged Fig 3B .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	tatA	regulator	30716090	19	ver/dev	In order to demonstrate direct binding of CpxR to the promoter regions of tatA we performed electrophoretic-mobility-shift assays with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein .	322	In order to demonstrate direct binding of CpxR to the promoter regions of eco , pgtE , ssrB and tatA we performed electrophoretic mobility shift assays ( EMSA ) with purified , phosphorylated His6-CpxR ( CpxR ~ P ) tagged protein ( Fig 3B ) .	21	GENOME WIDE SCREEN FOR CPX INTERACTIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	clpP	activator	12213919	0	att	Since the stationary-phase sigma factor , RpoS , is a target of the Clp proteolytic complex , the effect of the clpP deletion in the absence of RpoS was examined ; it was observed that growth of the S. typhimurium clpP mutant is affected in both an RpoS-dependent and an RpoS-independent manner .	14	Since the stationary-phase sigma factor , RpoS , is a target of the Clp proteolytic complex , the effect of the clpP deletion in the absence of RpoS was examined ; it was observed that growth of the S. typhimurium clpP mutant is affected in both an RpoS-dependent and an RpoS-independent manner .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	clpP	activator	12213919	2	ver/dev	a clpP mutation results in increased concentrations of RpoS	113	In both S. typhimurium and E. coli , the ClpXP protease is involved in the regulation of the level of RpoS by degradation and a clpP mutation results in increased concentrations of RpoS ( Schweder et al. , 1996 ; Webb et al. , 1999 ) .	8	CLPP AFFECTS GROWTH OF S. TYPHIMURIUM INDEPENDENTLY OF RPOS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	clpP	activator	25123657	25	ver/dev	As previously reported , the RpoS level was increased both in the clpP mutants at 37 °	218	As previously reported [ 13 ] , the RpoS level was increased both in the clpP and csrA mutants at 37 °C , and further it increased when transferred to 15 °C for 3 h ( Figure 3B ) .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	pstS	regulator	26386064	0	ver/dev	the former _ being regulated by a promoter located upstream of the pstS gene regulated by RpoS	148	Both operons have been shown to be induced under phosphate starvation conditions , with the former being regulated by a promoter located upstream of the pstS gene and the latter regulated by RpoS , PhoB , and CRP ( 16 , 17 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	pstS	regulator	26386064	0	ver/dev	the former _ being regulated by a promoter located upstream of the pstS gene regulated by RpoS	148	Both operons have been shown to be induced under phosphate starvation conditions , with the former being regulated by a promoter located upstream of the pstS gene and the latter regulated by RpoS , PhoB , and CRP ( 16 , 17 ) .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	TU	ilvBN	activator	11591661	14	ver/dev	IHF activates the transcription of ilvBN .	369	IHF activates the transcription of ilvBN and the ilvGp2 promoter ( 41 , 42 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NorR	gene	norV	activator	23651595	11	ver/dev	Furthermore , addition of NO to E. coli cultures leads to upregulation of norV via transcriptional activation by the regulator NorR .	588	Furthermore , addition of NO to E. coli cultures leads to upregulation of norV via transcriptional activation by the regulator NorR ( Flatley et al. , 2005 ; Justino , Vicente , Teixeira , & Saraiva , 2005 ; Mukhopadhyay et al. , 2004 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NorR	gene	norV	activator	23651595	11	ver/dev	Furthermore , addition of NO to E. coli cultures leads to upregulation of norV via transcriptional activation by the regulator NorR .	588	Furthermore , addition of NO to E. coli cultures leads to upregulation of norV via transcriptional activation by the regulator NorR ( Flatley et al. , 2005 ; Justino , Vicente , Teixeira , & Saraiva , 2005 ; Mukhopadhyay et al. , 2004 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NorR	gene	norV	activator	23651595	21	ver/dev	The NorR protein of Escherichia coli activates expression of the Flavorubredoxin gene norV in response to reactive-nitrogen-species .	983	The NorR protein of Escherichia coli activates expression of the Flavorubredoxin gene norV in response to reactive nitrogen species .	60	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
NorR	gene	norV	activator	27583250	5	ver/dev	The NorR protein of Escherichia coli activates expression of the flavorubredoxin gene norV in response to reactive-nitrogen-species .	344	The NorR protein of Escherichia coli activates expression of the flavorubredoxin gene norV in response to reactive nitrogen species .	19	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	hilD	regulator	20008574	18	ver/dev	However , with the potential exception of FliZ , post-transcriptional regulators of hilD seem to affect either HilD protein activity .	295	However , with the potential exception of FliZ ( Kage et al. 2008 ) and CsrA ( Altier et al. 2000 ; Ellermeier and Slauch 2007 ) , post-transcriptional regulators of hilD seem to affect either the HilD protein level ( Takaya et al. 2005 ; Matsui et al. 2008 ) or HilD protein activity ( Baxter et al. 2003 ; Ellermeier and Slauch 2008 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
FliZ	gene	hilD	regulator	20008574	18	ver/dev	However , with the potential exception of FliZ , post-transcriptional regulators of hilD seem to affect either the HilD protein level .	295	However , with the potential exception of FliZ ( Kage et al. 2008 ) and CsrA ( Altier et al. 2000 ; Ellermeier and Slauch 2007 ) , post-transcriptional regulators of hilD seem to affect either the HilD protein level ( Takaya et al. 2005 ; Matsui et al. 2008 ) or HilD protein activity ( Baxter et al. 2003 ; Ellermeier and Slauch 2008 ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
FliZ	gene	hilD	regulator	26386070	3	ver/dev	To study the influence of hilD , we utilized pub - there-lished strain JS1180 - the influence of overexpression of FliZ on hilA-lacZ in remosomal copy of hilD-3 flag was tested .	365	To study the influence of hilD , we utilized pub - protein ( 41 ) through an unknown posttranslational step ; there-lished strain JS1180 , which carries a tetracycline-inducible chro - fore , the influence of overexpression of FliZ on hilA-lacZ in remosomal copy of hilD-3 flag and the hilA-lacZ fusion integrated sponse to temperature was tested .	4	RESULTS	Tetragenococcus koreensis;Iris germanica	0	L3	OTHER	Investigation	OTHER	Other	Level 2
FliZ	gene	hilD	regulator	26386070	3	ver/dev	To study the influence of hilD , we utilized pub - there-lished strain JS1180 - the influence of overexpression of FliZ on hilA-lacZ in remosomal copy of hilD-3 flag was tested .	365	To study the influence of hilD , we utilized pub - protein ( 41 ) through an unknown posttranslational step ; there-lished strain JS1180 , which carries a tetracycline-inducible chro - fore , the influence of overexpression of FliZ on hilA-lacZ in remosomal copy of hilD-3 flag and the hilA-lacZ fusion integrated sponse to temperature was tested .	4	RESULTS	Tetragenococcus koreensis;Iris germanica	0	L3	OTHER	Investigation	OTHER	Other	Level 2
RpoS	gene	slyA	regulator	9284144	5	ver/dev	To ascertain whether slyA expression is regulated by RpoS , an isogenic rpoS S. typhimurium mutant was transformed with the slyA : : the level of b-galactosidase expression was determined .	113	To ascertain whether slyA expression is regulated by the stationary-phase sigma factor sS ( RpoS ) , an isogenic rpoS S. typhimurium mutant was transformed with the slyA : : lacZ plasmid , and the level of b-galactosidase expression was determined .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	slyA	regulator	9284144	5	ver/dev	To ascertain whether slyA expression is regulated by RpoS , an isogenic rpoS S. typhimurium mutant was transformed with the slyA : : lacZ plasmid was determined .	113	To ascertain whether slyA expression is regulated by the stationary-phase sigma factor sS ( RpoS ) , an isogenic rpoS S. typhimurium mutant was transformed with the slyA : : lacZ plasmid , and the level of b-galactosidase expression was determined .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	ssaH	regulator	12675799	5	ver/dev	An ssaH reporter , was regulated by OmpR similarly to previously described results .	228	An ssaH reporter , which was shown previously to require ompR for full activation , was included as a control and was regulated by OmpR similarly to previously described results ( Lee et al. , 2000 ) .	5	IDENTIFICATION OF SPI-2 CO-EXPRESSED GENES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by OmpR through SsrA -- both protein pairs being two-component regulators -- and not by PhoQ .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by OmpR through SsrA -- both protein pairs being two-component regulators -- and not by PhoP .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoQ .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	ssaH	regulator	12874347	2	ver/dev	The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .	288	The ssaH promoter was previously shown to be regulated by OmpR and EnvZ through SsrB and SsrA -- both protein pairs being two-component regulators -- and not by PhoP and PhoQ ( 33 , 59 ) .	6	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
IHF	gene	prpBCDE	regulator	16616438	1	ver/dev	The transcriptional expression of prpBCDE from PprpB is regulated by IHF , cAMP-CRP complex , a transcriptional regulator , .	37	The transcriptional expression of prpBCDE from the prpBCDE promoter ( PprpB ) is regulated by IHF , cAMP-CRP complex , PrpR ( a transcriptional regulator ) , and 2-methycitrate ( 2-MC ) ( Horswill et al. , 2001 ; Lee and Keasling , 2005 ; Lee et al. , 2005 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	prpBCDE	regulator	16616438	1	ver/dev	The transcriptional expression of prpBCDE from PprpB is regulated by IHF , cAMP-CRP complex , PrpR , .	37	The transcriptional expression of prpBCDE from the prpBCDE promoter ( PprpB ) is regulated by IHF , cAMP-CRP complex , PrpR ( a transcriptional regulator ) , and 2-methycitrate ( 2-MC ) ( Horswill et al. , 2001 ; Lee and Keasling , 2005 ; Lee et al. , 2005 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	prpBCDE	regulator	16616438	1	ver/dev	The transcriptional expression of prpBCDE from the prpBCDE promoter is regulated by IHF , cAMP-CRP complex , a transcriptional regulator , .	37	The transcriptional expression of prpBCDE from the prpBCDE promoter ( PprpB ) is regulated by IHF , cAMP-CRP complex , PrpR ( a transcriptional regulator ) , and 2-methycitrate ( 2-MC ) ( Horswill et al. , 2001 ; Lee and Keasling , 2005 ; Lee et al. , 2005 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	prpBCDE	regulator	16616438	1	ver/dev	The transcriptional expression of prpBCDE from the prpBCDE promoter is regulated by IHF , cAMP-CRP complex , PrpR , .	37	The transcriptional expression of prpBCDE from the prpBCDE promoter ( PprpB ) is regulated by IHF , cAMP-CRP complex , PrpR ( a transcriptional regulator ) , and 2-methycitrate ( 2-MC ) ( Horswill et al. , 2001 ; Lee and Keasling , 2005 ; Lee et al. , 2005 ) .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	activator	11755416	5	att	Strikingly , no environmental condition has ever been found that affects HilA-dependent TTSS-1 genes without also affecting hilA expression .	156	Strikingly , no environmental condition has ever been found that affects HilA-dependent TTSS-1 genes without also affecting hilA expression .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilA	gene	hilA	activator	12396235	2	att	It has been assumed that there is a direct correlation between hilA transcription , production of the HilA protein and HilA-activated gene expression .	40	It has been assumed that there is a direct correlation between hilA transcription , production of the HilA protein and HilA-activated gene expression .	4	BACKGROUND	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	activator	12396235	9	att	These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .	106	These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilA	gene	hilA	activator	25688233	0	ver/dev	The HilA protein increases in expression of the hilA gene typically decrease on invasion .	117	The HilA protein is the master regulator of SPI-1 , and increases or decreases in expression of the hilA gene typically have a corresponding increase or decrease on invasion ( Lee et al. , 1992 ) .	16	DIFFERENTIAL EXPRESSION OF THE HILA GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	activator	25688233	0	ver/dev	The HilA protein increases in expression of the hilA gene typically have a corresponding increase .	117	The HilA protein is the master regulator of SPI-1 , and increases or decreases in expression of the hilA gene typically have a corresponding increase or decrease on invasion ( Lee et al. , 1992 ) .	16	DIFFERENTIAL EXPRESSION OF THE HILA GENE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	hilA	activator	26386070	2	att	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	262	These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilA	gene	hilA	activator	30223195	0	ver/dev	The protein HilA is an activator of Salmonella the regulator of hilA is Fur .	260	The protein HilA is an activator of Salmonella Pathogenicity Island 1 ( SPI1 ) and the regulator of hilA is Fur , which is required for virulence in S. Typhimurium and activation of hilA and the hilA-dependent genes invF and sipC ( Troxell et al. , 2011 ) .	26	3.3.5. TRANSPORTER AND REGULATION-RELATED PROTEINS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilA	activator	32021316	1	ver/dev	Environmental conditions activate transcriptional regulatory proteins of HilD so that they can bind to the upstream of master regulatory hilA .155 HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	195	Environmental conditions such as pH and osmolarity activate transcriptional regulatory proteins of HilC and HilD so that they can bind to the upstream of master regulatory hilA .155 HilC and HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Investigation	OTHER	Other	Level 1
HilA	gene	hilA	activator	32021316	1	ver/dev	Environmental conditions activate transcriptional regulatory proteins of HilC so that they can bind to the upstream of master regulatory hilA .155 HilC counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	195	Environmental conditions such as pH and osmolarity activate transcriptional regulatory proteins of HilC and HilD so that they can bind to the upstream of master regulatory hilA .155 HilC and HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Investigation	OTHER	Other	Level 1
HilA	gene	hilA	activator	32021316	1	ver/dev	osmolarity activate transcriptional regulatory proteins of HilD so that they can bind to the upstream of master regulatory hilA .155 HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	195	Environmental conditions such as pH and osmolarity activate transcriptional regulatory proteins of HilC and HilD so that they can bind to the upstream of master regulatory hilA .155 HilC and HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Investigation	OTHER	Other	Level 1
HilA	gene	hilA	activator	32021316	1	ver/dev	osmolarity activate transcriptional regulatory proteins of HilC so that they can bind to the upstream of master regulatory hilA .155 HilC counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	195	Environmental conditions such as pH and osmolarity activate transcriptional regulatory proteins of HilC and HilD so that they can bind to the upstream of master regulatory hilA .155 HilC and HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Investigation	OTHER	Other	Level 1
HilA	gene	hilA	activator	32021316	1	ver/dev	pH activate transcriptional regulatory proteins of HilD so that they can bind to the upstream of master regulatory hilA .155 HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	195	Environmental conditions such as pH and osmolarity activate transcriptional regulatory proteins of HilC and HilD so that they can bind to the upstream of master regulatory hilA .155 HilC and HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Investigation	OTHER	Other	Level 1
HilA	gene	hilA	activator	32021316	1	ver/dev	pH activate transcriptional regulatory proteins of HilC so that they can bind to the upstream of master regulatory hilA .155 HilC counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	195	Environmental conditions such as pH and osmolarity activate transcriptional regulatory proteins of HilC and HilD so that they can bind to the upstream of master regulatory hilA .155 HilC and HilD counteract global repressor H-NS on the hilA promotor .156 Following the activation of HilA , InvF is subsequently activated .157 InvF activates the gene inside and outside of SPI-1 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Investigation	OTHER	Other	Level 1
SlyA	gene	ssrB	activator	19229334	3	ver/dev	The complementation result suggests that many of the regulators may function on SPI-2 through SlyA activation of ssrB .	410	The complementation result suggests that many of the regulators may function on SPI-2 through SlyA activation of ssrB or alternatively via both regulators ( slyA and ssrB ) acting together .	13	SLYA CAN COMPLEMENT OTHER REGULATORS FOR SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	ssrB	activator	19229334	3	ver/dev	SPI-2 through SlyA activation of ssrB _ acting together	410	The complementation result suggests that many of the regulators may function on SPI-2 through SlyA activation of ssrB or alternatively via both regulators ( slyA and ssrB ) acting together .	13	SLYA CAN COMPLEMENT OTHER REGULATORS FOR SPI-2 EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ssrB	activator	21388802	6	ver/dev	SlyA activates ssrB expression .	201	SlyA activates himD , phoP and ssrB expression .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tppB	activator	23782700	2	att	A , - galactosidase activity from lacZ-transcriptional-fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	168	A , - galactosidase activity from lacZ transcriptional fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	tppB	activator	24185747	3	att	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB-medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	87	The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg / mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .	12	STAINING SOLUTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Chryseobacterium gallinarum	0.5	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tppB	activator	31611347	3	att	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ-transcriptional-fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	94	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ transcriptional fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tppB	activator	31611347	4	att	The inhibition action was calculated on the basis of the - galactosidase activity from lacZ-transcriptional-fusions to two different PhoP-activated genes ( virK and pagC ) and one PhoP-unrelated control reporter gene ( tppB ) .	129	The inhibition action was calculated on the basis of the - galactosidase activity from lacZ transcriptional fusions to two different PhoP-activated genes ( virK and pagC ) and one PhoP-unrelated control reporter gene ( tppB ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mig-14	activator	15225317	5	att	Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .	35	Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .	3	2 ND POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mig-14	activator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	mig-14	activator	18350168	2	att	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	294	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	mig-14	activator	21511762	0	att	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	217	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	4	METHODS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mig-14	activator	30685290	0	ver/dev	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal-medium , when treated with antimicrobial peptides , indicating it is controlled by the global regulator PhoP .	296	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal medium containing low magnesium , within macrophages , or when treated with antimicrobial peptides , indicating it is controlled by the global regulator PhoP ( Brodsky et al. , 2002 , 2005 ) .	20	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mig-14	activator	30685290	0	ver/dev	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal-medium , within macrophages , indicating it is controlled by the global regulator PhoP .	296	mig-14 expression can be induced by growing in different unfavorable environments , such as in acidic pH conditions , in minimal medium containing low magnesium , within macrophages , or when treated with antimicrobial peptides , indicating it is controlled by the global regulator PhoP ( Brodsky et al. , 2002 , 2005 ) .	20	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mig-14	activator	30967459	9	att	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	144	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	3	RESULTS	Salmonella;unidentified plasmid;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
Fis	gene	rpoS	activator	17784910	1	ver/dev	An rpoS mutant displayed elevated levels of Fis .	33	An rpoS mutant displayed elevated levels of Fis and had a higher frequency of epithelial cell invasion under these growth conditions .	4	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	rpoS	activator	17784910	26	ver/dev	an rpoS mutant _ displaying elevated levels of Fis expression under these conditions	489	Therefore , we postulated that an rpoS mutant displaying elevated levels of Fis expression under these conditions should be more adept at invasion of epithelial cells .	13	RPOS, FIS AND INVASION OF EPITHELIAL CELLS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	rpoS	activator	18061487	2	ver/dev	Hirsch M , Elliot T. Fis regulates transcriptional induction of rpoS in Salmonella enterica .	323	[ 15 ] Hirsch M , Elliot T. Fis regulates transcriptional induction of rpoS in Salmonella enterica .	26	REFERENCES	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	rpoS	activator	21276095	19	ver/dev	The exponential phase expression of PtopAEc was slightly elevated in the absence of rpoS , perhaps due to stimulation by elevated FIS levels .	241	The exponential phase expression of PtopAEc was slightly elevated in the absence of rpoS , perhaps due to stimulation by elevated FIS levels .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
LeuO	gene	cas1	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas1 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
SirA	gene	sirA	activator	32392214	19	att	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	189	CsrB ( and likely CsrC ) is largely responsible for the BarA - and SirA-dependent activation of RcsB because a plasmid expressing CsrB from a heterologous promoter complemented not only the csrB csrC double mutant but also the sirA and barA single mutants ( S4 Fig ) .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	unidentified plasmid	1	L2	SPEC	Other	OTHER	Other	Level 1
Rho	gene	map	activator	22895254	3	att	To map the presumptive sites of Rho-dependent transcription termination , tandem UAA stop codons were introduced at several positions in the chromosomal chiP gene , and chiQ-lacZ expression was measured in the resulting strains .	131	To map the presumptive sites of Rho-dependent transcription termination , tandem UAA stop codons were introduced at several positions in the chromosomal chiP gene , and chiQ-lacZ expression was measured in the resulting strains .	5	PROFILING THE CHIP POLARITY GRADIENT BY STOP CODON SCANNING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
EmrR	gene	emrR	activator	30992361	31	att	In support of this conclusion , a complementing plasmid which solely contained the emrR coding region ( pemrR-FLAG ) fully recovered EmrR-dependent transcription in the ΔemrR mutant to wild-type levels ( Fig. 2A , D , and E ) .	242	In support of this conclusion , a complementing plasmid which solely contained the emrR coding region ( pemrR-FLAG ) fully recovered EmrR-dependent transcription in the ΔemrR mutant to wild-type levels ( Fig. 2A , D , and E ) .	4	DISCUSSION	unidentified plasmid;Iris germanica	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ssrB	regulator	15491370	20	ver/dev	Our recent observations indicate that SlyA exerts a direct effect by binding at ssrB .	360	Our recent observations indicate that SlyA exerts a direct effect by binding at ssrA and ssrB ( D. Walthers et al. , in preparation ) .	10	SLYA ALSO REGULATES SSRA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ssrB	regulator	33045730	4	ver/dev	Transcription of the horizontally acquired ssrB is regulated by SlyA .	29	Transcription of the horizontally acquired ssrB and spiR genes is regulated by several ancestral regulators , including SlyA ( 20 ) , OmpR ( 6 ) , and PhoP ( 7 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	invF	activator	10844688	5	ver/dev	In the presence of an unknown environmental condition , HilC may activate invF expression .	259	In the presence of an unknown environmental condition , HilC or HilD may activate invF expression , causing induction of invF-dependent genes .	14	MISLEADING CLUES?	unidentified	1	L1	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	10844688	16	ver/dev	Such a situation would be possible if HilC has direct activation of invF .	290	Such a situation would be possible if HilC or HilD has two distinct functions ( derepression of hilA and direct activation of invF ) that are separable by this condition .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilC	gene	invF	activator	10844688	18	ver/dev	If a condition exists in which hilA is repressed while invF expression is induced through HilC , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilC	gene	invF	activator	10844688	19	ver/dev	The direct activation of invF expression by HilC may always accompany derepression of hilA expression such that the two mechanisms act co-operatively rather than independently to induce invF expression .	297	The direct activation of invF expression by HilC or HilD may always accompany derepression of hilA expression such that the two mechanisms act co-operatively rather than independently to induce invF expression .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	activator	10844688	21	ver/dev	certain effectors are produced as a result of direct activation of invF expression by HilC	308	But the situation would be entirely different at sites 3 and 4 , in which hilA and the secretion apparatus are not expressed but InvF and certain effectors are produced as a result of direct activation of invF expression by HilC or HilD .	16	MODELS FOR INVASION GENE REGULATION IN VIVO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	invF	activator	10844688	22	ver/dev	whether direct activation of invF by HilC and/or HilD occurs in wild-type bacteria	326	Various in vitro and in vivo conditions must be tested to determine whether direct activation of invF by HilC and/or HilD occurs in wild-type bacteria and whether this has any relevance in vivo .	16	MODELS FOR INVASION GENE REGULATION IN VIVO	nan	1	L3	SPEC	Other	NEG	New	Level 1
HilC	gene	invF	activator	10844688	22	ver/dev	whether direct activation of invF by HilC and/or HilD occurs in wild-type bacteria	326	Various in vitro and in vivo conditions must be tested to determine whether direct activation of invF by HilC and/or HilD occurs in wild-type bacteria and whether this has any relevance in vivo .	16	MODELS FOR INVASION GENE REGULATION IN VIVO	nan	1	L3	SPEC	Other	NEG	New	Level 1
HilC	gene	invF	activator	12535071	42	att	A HilD- and HilC-dependent invF transcription start site lies far upstream of the HilA-dependent transcription start site	115	A HilD- and HilC-dependent invF transcription start site lies far upstream of the HilA-dependent transcription start site	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	43	att	In order to determine where the HilD - and HilC-dependent promoter of invF is located , we performed primer-extension experiments .	116	In order to determine where the HilD - and HilC-dependent promoter of invF is located , we performed primer extension experiments .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	synthetic construct	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	invF	activator	12535071	53	att	Based on these results , we conclude that invF is transcribed from at least two promoters , a HilA-dependent promoter and a newly identified HilD - and HilC-dependent promoter .	144	Based on these results , we conclude that invF is transcribed from at least two promoters , a HilA-dependent promoter and a newly identified HilD - and HilC-dependent promoter .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	invF	activator	12535071	54	att	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD or HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD - and HilC-dependent +1 of invF .	145	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD or HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD - and HilC-dependent +1 of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
HilC	gene	invF	activator	12535071	55	att	Identification of candidate promoter sequences required for HilD - and HilC-dependent activation of invF	146	Identification of candidate promoter sequences required for HilD - and HilC-dependent activation of invF	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	56	att	To better define the sequences required for HilD - and HilC-dependent activation of invF , we cloned 919 bp from upstream of the invF ORF in front of a lacZ reporter gene in the pRW50 vector ( Lodge et al. , 1992 ) .	147	To better define the sequences required for HilD - and HilC-dependent activation of invF , we cloned 919 bp from upstream of the invF ORF in front of a lacZ reporter gene in the pRW50 vector ( Lodge et al. , 1992 ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	60	att	Our primer-extension studies suggested that HilD-and HilC-dependent transcripts initiate 643 and/or 631 nucleotides upstream of the invF ORF .	169	Our primer extension studies suggested that HilD-and HilC-dependent transcripts initiate 643 and/or 631 nucleotides upstream of the invF ORF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	synthetic construct	0	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	66	att	Instead , there appears to be a single HilD - and HilC-dependent promoter in this region corresponding to the predicted transcription start site located 631 bp upstream of the invF ORF ; 499 bp upstream of the HilA-dependent +1 .	180	Instead , there appears to be a single HilD - and HilC-dependent promoter in this region corresponding to the predicted transcription start site located 631 bp upstream of the invF ORF ; 499 bp upstream of the HilA-dependent +1 .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	activator	12535071	90	att	These gel shift assays indicate that HilD and HilC each bind sequences upstream and downstream of the HilD - and HilC-dependent invF promoter .	261	These gel shift assays indicate that HilD and HilC each bind sequences upstream and downstream of the HilD - and HilC-dependent invF promoter .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	0	ver/dev	HilC directly activate invF expressionS.Akbar , L.M.Schechter , C.P.Lostroh and C.A.Lee	0	Blackwell Science , LtdOxford , UKMMIMolecular Microbiology 0950-382X Blackwell Publishing Ltd , 200347Original ArticleHilD and HilC directly activate invF expressionS.Akbar , L.M.Schechter , C.P.Lostroh and C.A.Lee	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	4	ver/dev	Our studies show that HilC activate transcription of invF from a promoter .	16	Our studies show that HilD and HilC activate transcription of invF from a promoter that is far upstream of its HilA-dependent promoter .	2	ABSTRACT	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	16	ver/dev	We show that HilC can directly activate invF .	63	We show that HilD and HilC can directly bind and activate invF , which leads to the non-co-ordinate expression of a subset of SPI1 genes .	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	24	ver/dev	We propose that HilC can independently activate invF expression .	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	25	ver/dev	In this scheme , activation of invF transcription by HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter .	84	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	invF	activator	12535071	25	ver/dev	In this scheme , activation of invF transcription by HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter .	84	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	invF	activator	12535071	28	ver/dev	In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	28	ver/dev	In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilC , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	28	ver/dev	In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilD , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	34	ver/dev	HilC do not activate invF expression from the HilA-dependent invF promoter	106	HilD and HilC do not activate invF expression from the HilA-dependent invF promoter	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilC	gene	invF	activator	12535071	54	ver/dev	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain HilC-dependent +1 of invF .	145	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD or HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD - and HilC-dependent +1 of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
HilC	gene	invF	activator	12535071	54	ver/dev	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD .	145	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD or HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD - and HilC-dependent +1 of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
HilC	gene	invF	activator	12535071	55	ver/dev	Identification of HilC-dependent activation of invF	146	Identification of candidate promoter sequences required for HilD - and HilC-dependent activation of invF	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	56	ver/dev	To better define HilC-dependent activation of invF , we cloned 919 bp from upstream of the invF ORF in front of a lacZ reporter gene in the pRW50 vector .	147	To better define the sequences required for HilD - and HilC-dependent activation of invF , we cloned 919 bp from upstream of the invF ORF in front of a lacZ reporter gene in the pRW50 vector ( Lodge et al. , 1992 ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	68	ver/dev	It is possible that HilC , activates invF expression from a second promoter .	182	It is possible that HilD , but not HilC , activates invF expression from a second promoter .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilC	gene	invF	activator	12535071	70	ver/dev	In order to address whether additional S. typhimuriumspecific genes are required for HilC to activate invF , we examined both pSA7 reporters in E. coli TOP-10 cells .	185	In order to address whether additional S. typhimuriumspecific genes are required for HilD and HilC to activate invF , we examined both pVV448 and pSA7 reporters in E. coli TOP-10 cells .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Escherichia coli	0	L3	SPEC	Investigation	OTHER	Other	Level 1
HilC	gene	invF	activator	12535071	70	ver/dev	In order to address whether additional S. typhimuriumspecific genes are required for HilC to activate invF , we examined both pVV448 reporters in E. coli TOP-10 cells .	185	In order to address whether additional S. typhimuriumspecific genes are required for HilD and HilC to activate invF , we examined both pVV448 and pSA7 reporters in E. coli TOP-10 cells .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Prairie vole hantavirus;Escherichia coli	0	L3	SPEC	Investigation	OTHER	Other	Level 1
HilC	gene	invF	activator	12535071	71	ver/dev	We found that HilC induce invF expression from pSA7 in E. coli , comparable to that .	186	We found that HilD and HilC induce invF expression from pSA7 in E. coli , comparable to that seen in S. typhimurium ( data not shown ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Escherichia coli	0	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	72	ver/dev	We also found that HilC , activates invF expression from pVV448 , also comparable to that .	187	We also found that HilD , but not HilC , activates invF expression from pVV448 , also comparable to that seen in S. typhimurium ( data not shown ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Prairie vole hantavirus	0	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	73	ver/dev	These results suggest that HilC might directly activate invF expression by binding to sequences upstream of invF .	188	These results suggest that HilD and HilC might directly activate invF expression by binding to sequences upstream of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	73	ver/dev	These results suggest that HilC might directly activate invF expression by binding to sequences upstream of invF .	188	These results suggest that HilD and HilC might directly activate invF expression by binding to sequences upstream of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	76	ver/dev	HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	76	ver/dev	HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	79	ver/dev	HilC directly activate invF expression by binding downstream of a HilD/C-dependent promoter	229	HilD and HilC directly activate invF expression by binding upstream and downstream of a HilD/C-dependent promoter	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	79	ver/dev	HilC directly activate invF expression by binding upstream of a HilD/C-dependent promoter	229	HilD and HilC directly activate invF expression by binding upstream and downstream of a HilD/C-dependent promoter	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	12535071	80	ver/dev	Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .	230	Previous studies have shown that HilD and HilC can indirectly activate invF expression by derepressing hilA ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilC	gene	invF	activator	12535071	83	ver/dev	HilC appear to activate transcription of invF from a HilD/C-dependent start site .	233	HilD and HilC appear to activate transcription of invF from a HilD/C-dependent start site that is 631 nucleotides upstream of the invF ORF .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	activator	12535071	85	ver/dev	Our studies also suggest that the downstream binding site is required for HilC to activate invF .	235	Our studies also suggest that the downstream binding site is required for HilD and HilC to activate invF .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	activator	12535071	101	ver/dev	HilC directly activate invF expression 723 can be secreted independently of SPI1 .	290	HilD and HilC directly activate invF expression 723 can be secreted independently of SPI1 .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	activator	16045614	54	ver/dev	HilC are each capable of partially activating invF	390	Transcription of invF is primarily regulated by HilA , but HilD , HilC and RtsA are each capable of partially activating invF ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Akbar et al. , 2003 ; Ellermeier and Slauch , 2003 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	invF	activator	21168230	5	ver/dev	In addition , HilC directly activate invF in non-HilA dependent manner .	344	In addition , HilD and HilC directly activate invF , sipA and sipC in non-HilA dependent manner ( Akbar et al. , 2003 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	21573071	0	ver/dev	Moreover , HilC can directly activate invF independently of HilA .	8	Moreover , HilC and HilD can directly activate invF independently of HilA [ 11 ] .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	activator	25991823	1	ver/dev	HilC can activate expression of the invF and sicA/sip transcriptional units independently of HilA .	25	HilC and HilD relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) and can activate expression of the invF and sicA/sip transcriptional units independently of HilA ( Rakeman et al. 1999 ; Akbar et al. 2003 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	activator	27404739	1	ver/dev	HilC , activate directly the expression of the invF operon , independently of HilA .	131	Two additional regulators , HilC and HilD , activate directly the expression of hilA and the invF operon , independently of HilA ( Dieye et al. , 2007 ) .	6	SPI-1 RELATED GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	activator	28335027	11	att	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	768	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	activator	28335027	11	att	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	768	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	activator	28335027	12	att	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	770	As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstream of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	activator	28335027	11	ver/dev	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF .	768	An additional role of tnpA may be to prevent leaky expression of invF , particularly HilC-dependent activation of the alternative promoter for invF ( pinvF-2 , Figure 8 ) ( 67,68 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	sopD	regulator	29857034	22	ver/dev	To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in DslyA strains under conditions of oxidative-stress .	341	To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP , and pagC genes in vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT and DslyA strains under conditions of oxidative stress .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	sopD	regulator	29857034	22	ver/dev	To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT strains under conditions of oxidative-stress .	341	To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP , and pagC genes in vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT and DslyA strains under conditions of oxidative stress .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	sopD	regulator	29857034	33	ver/dev	Direct regulation of sopD genes by SlyA in response to ROS .	380	Direct regulation of sopD , sopE2 , hilA , fruK , glpA , kgtP and pagC genes by SlyA in response to ROS .	26	3.5. DIRECT BINDING TO PROMOTER REGIONS OF METABOLISM AND VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	sopD	regulator	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopD were negatively regulated by SlyA , with DslyA expression increased five-times , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	sopD	regulator	29857034	36	ver/dev	Our results showed that at 3 h post-infection only , sopD were negatively regulated by SlyA , with DslyA expression increased two , respectively .	414	Our results showed that at 3 h post-infection only , sopD and sopE2 were negatively regulated by SlyA ( Fig. 5E ) , with DslyA expression increased two - and five-times , respectively .	27	3.6. METABOLISM AND VIRULENCE ARE REGULATED BY SLYA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	hilD	regulator	26300871	10	ver/dev	To determine if CpxR affects the autoregulation of hilD , the expression of the hilDcat fusion was determined in the WT S. Typhimurium strain and its derivatives 1cpxA , 1hilD , and 1hilD 1cpxA mutants .	372	To determine if CpxR affects the autoregulation of hilD , the expression of the hilDcat fusion was determined in the WT S. Typhimurium strain and its derivatives 1cpxA , 1hilD , and 1hilD 1cpxA mutants .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	hilD	regulator	26300871	23	ver/dev	FIGURE 4 CpxR represses the autoregulation of hilD .	422	FIGURE 4 | CpxR represses the autoregulation of hilD and thus negatively affects the expression of hilA .	17	CPXR AFFECTS STABILITY OF HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	hilA	regulator	17208038	13	ver/dev	These results showed that , whereas OmpR-mediated regulation of hilA expression was dampened in a DhilC DrtsA background , regulation was blocked only in strains missing HilD , suggesting that OmpR controls SPI1 expression by regulating hilD expression .	101	These results showed that , whereas OmpR-mediated regulation of hilA expression was dampened in a DhilC DrtsA background , regulation was blocked only in strains missing HilD , suggesting that OmpR controls SPI1 expression by regulating hilD expression [ 19 ] .	7	ENVZ/OMPR	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CadC	gene	ompR	regulator	29214489	12	ver/dev	Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of motility , at least during acid adaptation .	134	Since our data clearly demonstrated CadCmediated repression of ompR gene expression ( Fig. 1 ) , we speculated that CadC may be involved in the control of fla-gellation and motility , at least during acid adaptation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	ompR	regulator	29214489	12	ver/dev	Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of fla-gellation , at least during acid adaptation .	134	Since our data clearly demonstrated CadCmediated repression of ompR gene expression ( Fig. 1 ) , we speculated that CadC may be involved in the control of fla-gellation and motility , at least during acid adaptation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RstA	gene	modA	activator	30763640	30	att	B ) Alignment of the RstA consensus motif identified in other RstA-dependent genes like ybiL ( Ec ) , nohB ( Ec ) , modA ( Ec ) and leuS ( Ec ) genes , with the STM1485 promoter sequences .	169	B ) Alignment of the RstA consensus motif identified in other RstA-dependent genes like ybiL ( Ec ) , nohB ( Ec ) , modA ( Ec ) and leuS ( Ec ) genes , with the STM1485 promoter sequences .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
TviA	gene	tviA	activator	19745516	0	auto	A positive regulator , TviA ( VipR ) , activates its own synthesis by binding upstream of the tviA promoter [ 27 ] and interacts with RcsB to promote optimal transcription of genes involved in Vi antigen synthesis [ 24 , 25 , 28 , 29 ] .	55	A positive regulator , TviA ( VipR ) , activates its own synthesis by binding upstream of the tviA promoter [ 27 ] and interacts with RcsB to promote optimal transcription of genes involved in Vi antigen synthesis [ 24 , 25 , 28 , 29 ] .	9	REGULATION OF VI POLYSACCHARIDE SYNTHESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TviA	gene	tviA	activator	24992093	1	ver/dev	To delineate the relative contribution of the regulator TviA to reducing inflammatory responses in the bovine , we repeated these studies with derivatives of S. Typhimurium strain ATCC 14028 : viaB mutant , TH170 ) or the tviA gene only ( phoN : : tviA mutant , SW474 ) .	93	To delineate the relative contribution of the Vi capsule and the regulator TviA to reducing inflammatory responses in the bovine ligated ileal loop model [ 23 ] , we repeated these studies with derivatives of S. Typhimurium strain ATCC 14028 in which the phoN gene in the chromosome had been replaced with the entire S. Typhi viaB locus ( phoN : : viaB mutant , TH170 ) or the tviA gene only ( phoN : : tviA mutant , SW474 ) .	8	TVIA REDUCES T3SS-1-MEDIATED INFLAMMATION IN THE BOVINE LIGATED ILEAL LOOP MODEL	Bos taurus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Investigation	OTHER	Other	Level 2
TviA	gene	tviA	activator	25644011	1	ver/dev	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi fliC expression simultaneously .	246	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic ( 35 ) and would affect Vi capsular polysaccharide expression and fliC expression simultaneously .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
TviA	gene	tviA	activator	25644011	1	ver/dev	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi fliC expression simultaneously .	246	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic ( 35 ) and would affect Vi capsular polysaccharide expression and fliC expression simultaneously .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
TviA	gene	tviA	activator	25644011	1	ver/dev	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi capsular polysaccharide expression simultaneously .	246	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic ( 35 ) and would affect Vi capsular polysaccharide expression and fliC expression simultaneously .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
TviA	gene	tviA	activator	25644011	1	ver/dev	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi capsular polysaccharide expression simultaneously .	246	We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic ( 35 ) and would affect Vi capsular polysaccharide expression and fliC expression simultaneously .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilA	gene	STM4257	activator	23419780	7	ver/dev	HilA are transcription activators of effectors downregulates the first gene of SPI-4 , STM4257 .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	cueO	regulator	17919284	0	att	Among these , we identified the GolS-target operators from the golTS operon and the golB gene ( Checa et al. , 2007 ) , as well as the CueR-controlled operators from cueO and copA genes ( Kim et al. , 2002 ; Espariz et al. , 2007 ) .	66	Among these , we identified the GolS-target operators from the golTS operon and the golB gene ( Checa et al. , 2007 ) , as well as the CueR-controlled operators from cueO and copA genes ( Kim et al. , 2002 ; Espariz et al. , 2007 ) .	8	THE SALMONELLA-SPECIFIC CBA EFFLUX SYSTEM IS PART OF THE GOL REGULON	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	cueO	regulator	24858080	10	att	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	336	Real-time RT-PCR was used to determine the levels of transcription of the CueR-controlled genes cueO and copA and the ZntR-controlled zntA obtained after 10 min incubation in the presence of 1000 mM CuSO or 250 mM 4 ZnSO in SLB ( Cu-SLB or Zn-SLB , respectively ) or 10 mM 4 CuSO4 or 50 mM ZnSO4 in M9 medium ( Cu-M9 or Zn-M9 , respectively ) .	7	RELATIVE TRANSCRIPTIO	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CueR	gene	cueO	regulator	24858080	3	att	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	264	The pattern of induction/repression of the CueR-controlled cueO and copA genes as well as the ZntR-controlled zntA gene in the conditions tested was verified by real-time reverse transcription-PCR ( qRT-PCR ) ( Fig. 2 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CueR	gene	cueO	regulator	28924031	0	ver/dev	CueR regulates cueO .	67	CueR regulates copA , cueO , and cueP ( 28 -- 30 ) .	3	KEYWORDS COPPER EFFLUX, SALMONELLA, SODC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CueR	gene	cueO	regulator	34125582	5	ver/dev	cueO _ regulated by CueR	249	As expected , the known copper efflux and detoxification genes copA , cueO , and cusCFBA , regulated by CueR and CusR , are upregulated in E. coli during growth in copper-supplemented media .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	bglJ	activator	22804842	17	ver/dev	LeuO is known to activate bglJ in E. coli while RcsB-BglJ heterodimers activate leuO transcription .	336	LeuO is known to activate bglJ in E. coli ( Stratmann et al. , 2008 ) while RcsB-BglJ heterodimers activate leuO transcription ( Stratmann et al. , 2012 ) .	8	GENOME-WIDE PREDICTION AND VALIDATION OF LEUO BINDING SITES	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
NtrC	gene	rtcA	activator	30201777	8	ver/dev	Because rtcA was upregulated by nitrogen-limitation but independently of Fig. 3C , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen-limitation .	115	Because rtcA was upregulated by nitrogen limitation but independently of RtcR ( Fig. 3C ) , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen limitation .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
NtrC	gene	rtcA	activator	30201777	8	ver/dev	Because rtcA was upregulated by nitrogen-limitation but independently of Fig. 3C , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen-limitation .	115	Because rtcA was upregulated by nitrogen limitation but independently of RtcR ( Fig. 3C ) , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen limitation .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
NtrC	gene	rtcA	activator	30201777	8	ver/dev	Because rtcA was upregulated by nitrogen-limitation but independently of RtcR , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen-limitation .	115	Because rtcA was upregulated by nitrogen limitation but independently of RtcR ( Fig. 3C ) , we speculated that NtrC could be required for upregulation of the RNA repair operon during nitrogen limitation .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	rstA	repressor	18790861	18	att	We next examined transcription of the two Fur-repressed genes in the strain that carried deletions of the rstA and fur genes and harbored either the RstA expression plasmid or the plasmid vector ; analysis determined that the mRNA levels of fhuA and fhuF were similar to those in the fur deletion strain regardless of RstA expression ( Fig. 1B ) .	154	We next examined transcription of the two Fur-repressed genes in the strain that carried deletions of the rstA and fur genes and harbored either the RstA expression plasmid or the plasmid vector ; analysis determined that the mRNA levels of fhuA and fhuF were similar to those in the fur deletion strain regardless of RstA expression ( Fig. 1B ) .	4	RESULTS	unidentified plasmid;unidentified plasmid	1	L3	OTHER	Investigation	NEG	Other	Level 1
PhoP	gene	rstA	regulator	18790861	4	att	The rstA gene also seems to be a member of the PhoP regulon in Salmonella because a computational approach discovered the rstA promoter features shared with a group of PhoP-regulated promoters ( 35 , 36 ) .	18	The rstA gene also seems to be a member of the PhoP regulon in Salmonella because a computational approach discovered the rstA promoter features shared with a group of PhoP-regulated promoters ( 35 , 36 ) .	2	MAIN	Salmonella	1	L2	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	rstA	regulator	18790861	3	ver/dev	It has been reported that the PhoP protein , a response regulator of the PhoP/PhoQ two-component system , directly activates transcription of the rstA gene .	17	It has been reported that the PhoP protein , a response regulator of the PhoP/PhoQ two-component system , directly activates transcription of the rstA gene encoding the response regulator RstA in E. coli ( 17 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	rstA	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	fur	regulator	26944792	0	ver/dev	Putative regulation by the global regulators RcsB was evaluated by generating three isogenic S. Typhi deletion mutants of fur .	261	Putative regulation by the global regulators RcsB , Fur and ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of rcsDBC , fur and argR .	8	REGULATION OF TCF EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Other	OTHER	Other	Level 1
RpoS	gene	rpoS	repressor	11814668	1	ver/dev	There was a reprodu-cible decrease of approximately 200 Miller units in the rpoS null strain background suggesting either a small or indirect RpoS-mediated e ¡ ec	148	There was a reprodu-cible decrease of approximately 200 Miller units in the rpoS null strain background suggesting either a small or indirect RpoS-mediated e ¡ ect , but RpoS is not the main stationary-phase regulator of dsbA .	9	3. RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoS	repressor	17227702	0	ver/dev	Measurement of rpoS promoter activity demonstrated repression of rpoS in a ppk background , confirming a role for polyphosphate in RpoS induction .	20	Measurement of rpoS promoter activity using a lacZ transcriptional fusion demonstrated repression of rpoS in a ppk background , confirming a role for polyphosphate in RpoS induction .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + spoT : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	Leiostomus xanthurus	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + spoT : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	Leiostomus xanthurus	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + spoT : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	Leiostomus xanthurus	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + relA : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + relA : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + relA : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2173 strain : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2173 strain : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2173 strain : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2238 : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2238 : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2238 : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : its crp-803 : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : its crp-803 : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : its crp-803 : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2210 derivatives to obtain rpoS : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2210 derivatives to obtain rpoS : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2210 derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : ppGpp0 derivatives to obtain rpoS : : Apr-carry-ing strains DA2260 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : ppGpp0 derivatives to obtain rpoS : : Apr-carry-ing strains DA2246 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	rpoS	repressor	19940937	2	ver/dev	To that purpose , RpoS was inactivated by introducing mutation rpoS : ppGpp0 derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , respectively .	224	To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr ( Fang et al. 1992 ) into the crp + relA + spoT + DA2173 strain ( designated as wild-type in Fig. 4 ) and its crp-803 ( DA2238 ) and ppGpp0 ( DA2210 ) derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , DA2246 , and DA2260 , respectively ( Table 1 ) .	11	EFFECTS OF RPOS DEFICIENCY ON EXPRESSION OF THE OPGG1::MUDJ FUSION AND OPG CONTENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	11162188	2	ver/dev	As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .	112	As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .	6	TRANSCRIPTION OF THE VIRULENCE-ASSOCIATED GENES IN THE FLIZ MUTANT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	11162188	2	ver/dev	As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .	112	As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .	6	TRANSCRIPTION OF THE VIRULENCE-ASSOCIATED GENES IN THE FLIZ MUTANT	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	12453229	4	ver/dev	In addition to these conditions , hilA is repressed by PhoP / PhoQ .	54	In addition to these conditions , hilA is repressed by PhoP / PhoQ ( Bajaj et al. , 1996 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	18350168	3	att	According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .	295	According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	18350168	5	att	Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .	335	Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .	19	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	hilA	repressor	26441883	0	ver/dev	The response regulator PhoP represses hilA , whereas transcription of pag is activated .	72	The response regulator PhoP represses hilA and the prg ( PhoP-repressed genes ) genes ( Pegues et al. , 1995 ; Bajaj et al. , 1996 ) , whereas transcription of PhoP-activated genes ( pag ) required for survival within macrophages is activated ( Miller et al. , 1989 ; Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	26441883	0	ver/dev	The response regulator PhoP represses hilA , whereas transcription of PhoP-activated genes is activated .	72	The response regulator PhoP represses hilA and the prg ( PhoP-repressed genes ) genes ( Pegues et al. , 1995 ; Bajaj et al. , 1996 ) , whereas transcription of PhoP-activated genes ( pag ) required for survival within macrophages is activated ( Miller et al. , 1989 ; Belden and Miller , 1994 ) .	6	SURVIVAL IN THE INTESTINAL LUMEN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	27564394	6	ver/dev	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	2	ver/dev	PhoP negatively regulates direct transcriptional repression of the hilA promoter .	13	PhoP negatively regulates hilA through multiple distinct mechanisms : direct transcriptional repression of the hilA promoter , indirect transcriptional repression of both the hilD and rtsA promoters , and activation of the small RNA ( sRNA ) PinT .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	2	ver/dev	PhoP negatively regulates direct transcriptional repression of the hilA promoter .	13	PhoP negatively regulates hilA through multiple distinct mechanisms : direct transcriptional repression of the hilA promoter , indirect transcriptional repression of both the hilD and rtsA promoters , and activation of the small RNA ( sRNA ) PinT .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	2	ver/dev	PhoP negatively regulates hilA through multiple distinct mechanisms .	13	PhoP negatively regulates hilA through multiple distinct mechanisms : direct transcriptional repression of the hilA promoter , indirect transcriptional repression of both the hilD and rtsA promoters , and activation of the small RNA ( sRNA ) PinT .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	5	ver/dev	We hypothesized that PhoP could repress hilA expression through RtsA , by functioning through another transcriptional regulator within the PhoPQ regulon .	48	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , HilC , and RtsA , by affecting hilA transcription directly or by functioning through another transcriptional regulator within the PhoPQ regulon .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	5	ver/dev	We hypothesized that PhoP could repress hilA expression through RtsA , by affecting hilA transcription directly .	48	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , HilC , and RtsA , by affecting hilA transcription directly or by functioning through another transcriptional regulator within the PhoPQ regulon .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	5	ver/dev	We hypothesized that PhoP could repress hilA expression through HilC , by functioning through another transcriptional regulator within the PhoPQ regulon .	48	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , HilC , and RtsA , by affecting hilA transcription directly or by functioning through another transcriptional regulator within the PhoPQ regulon .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	5	ver/dev	We hypothesized that PhoP could repress hilA expression through HilC , by affecting hilA transcription directly .	48	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , HilC , and RtsA , by affecting hilA transcription directly or by functioning through another transcriptional regulator within the PhoPQ regulon .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	5	ver/dev	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , by functioning through another transcriptional regulator within the PhoPQ regulon .	48	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , HilC , and RtsA , by affecting hilA transcription directly or by functioning through another transcriptional regulator within the PhoPQ regulon .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	5	ver/dev	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , by affecting hilA transcription directly .	48	We hypothesized that PhoP could repress hilA expression through the upstream regulators HilD , HilC , and RtsA , by affecting hilA transcription directly or by functioning through another transcriptional regulator within the PhoPQ regulon .	2	KEYWORDS PHOPQ, SALMONELLA, VIRULENCE REGULATION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	8	ver/dev	PhoP represses hilA	66	Thus , PhoQ activates PhoP , which represses hilA , but how that repression occurs remains unknown .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	10	ver/dev	This demonstrates that PhoP represses expression of hilA independently of any of these PhoP-activated regulatory systems .	78	This demonstrates that PhoP represses expression of hilA independently of any of these PhoP-activated regulatory systems .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	11	ver/dev	FIG 2 PhoP represses hilA expression .	79	FIG 2 PhoP represses hilA expression .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	12	ver/dev	PhoP represses hilA expression by repressing rtsA transcription .	87	PhoP represses hilA expression by repressing hilD and rtsA transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	12	ver/dev	PhoP represses hilA expression by repressing hilD transcription .	87	PhoP represses hilA expression by repressing hilD and rtsA transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating rtsA , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating hilC , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating hilD , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	19	ver/dev	Together , these data suggest that PhoP represses hilA expression , at least partially by rtsA transcription .	105	Together , these data suggest that PhoP represses hilA expression , at least partially by controlling hilD transcription and rtsA transcription .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	19	ver/dev	Together , these data suggest that PhoP represses hilA expression , at least partially by controlling hilD transcription .	105	Together , these data suggest that PhoP represses hilA expression , at least partially by controlling hilD transcription and rtsA transcription .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	21	ver/dev	PhoP also represses hilA independently of rtsA transcription .	112	PhoP also represses hilA independently of hilD and rtsA transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	21	ver/dev	PhoP also represses hilA independently of hilD transcription .	112	PhoP also represses hilA independently of hilD and rtsA transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	24	ver/dev	This allowed us to identify repression of hilA by PhoP independently of the hilD transcriptional effect .	122	This allowed us to identify repression of hilA by PhoP independently of the hilD transcriptional effect .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	25	ver/dev	Thus , PhoP represses hilA expression through some additional mechanism .	124	Thus , PhoP represses hilA expression through some additional mechanism .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	27	ver/dev	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from the tetRA promoter were deleted .	129	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from the tetRA promoter and spi1 , rtsA , pinT , and fliZ were deleted .	3	RESULTS	Triportheus paranensis	0	L1	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31182495	27	ver/dev	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from fliZ were deleted .	129	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from the tetRA promoter and spi1 , rtsA , pinT , and fliZ were deleted .	3	RESULTS	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31182495	27	ver/dev	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from pinT were deleted .	129	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from the tetRA promoter and spi1 , rtsA , pinT , and fliZ were deleted .	3	RESULTS	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31182495	27	ver/dev	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from rtsA were deleted .	129	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from the tetRA promoter and spi1 , rtsA , pinT , and fliZ were deleted .	3	RESULTS	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31182495	27	ver/dev	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from spi1 were deleted .	129	To test if FliZ was responsible for this residual repression , we asked if PhoP could still repress hilA when hilD was expressed from the tetRA promoter and spi1 , rtsA , pinT , and fliZ were deleted .	3	RESULTS	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31182495	28	ver/dev	Deletion of fliZ led to decreased hilA expression as expected ; however , PhoP repressed hilA to similar levels in the presence or absence of Fig. 5B .	130	Deletion of fliZ led to decreased hilA expression as expected ; however , PhoP repressed hilA to similar levels in the presence or absence of fliZ ( Fig. 5B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	28	ver/dev	Deletion of fliZ led to decreased hilA expression as expected ; however , PhoP repressed hilA to similar levels in the presence or absence of fliZ .	130	Deletion of fliZ led to decreased hilA expression as expected ; however , PhoP repressed hilA to similar levels in the presence or absence of fliZ ( Fig. 5B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	30	ver/dev	FIG 5 PhoP additionally represses hilA independently of pinT .	147	FIG 5 PhoP additionally represses hilA independently of hilD , rtsA , and pinT .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	30	ver/dev	FIG 5 PhoP additionally represses hilA independently of rtsA .	147	FIG 5 PhoP additionally represses hilA independently of hilD , rtsA , and pinT .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	30	ver/dev	FIG 5 PhoP additionally represses hilA independently of hilD .	147	FIG 5 PhoP additionally represses hilA independently of hilD , rtsA , and pinT .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	35	ver/dev	We hypothesized that PhoP represses transcription through direct binding to the hilA promoter .	164	We hypothesized that PhoP represses transcription through direct binding to the hilA promoter , which we tested through an electrophoretic mobility shift assay .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	44	ver/dev	PhoP represses hilA expression primarily by blocking binding of HilD/HilC / RtsA .	206	PhoP represses hilA expression primarily by blocking binding of HilD/HilC / RtsA .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	31182495	47	ver/dev	The data suggest that PhoP could repress hilA transcription by blocking binding of HilD/HilC/RtsA .	213	The data described above suggest that PhoP could repress hilA transcription by blocking binding of HilD/HilC/RtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilA	repressor	31182495	57	ver/dev	PhoP was known to repress hilA	254	PhoP was known to repress hilA , but the mechanism of repression was unknown .	4	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
PhoP	gene	hilA	repressor	31182495	58	ver/dev	However , we show clearly that while loss of HilE increases hilA expression in both phoQ24 backgrounds , PhoP represses hilA expression independently of HilE .	256	However , we show clearly that while loss of HilE increases hilA expression in both wild-type and phoQ24 backgrounds , PhoP represses hilA expression independently of HilE .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
PhoP	gene	hilA	repressor	31182495	59	ver/dev	In this work , we have demonstrated that PhoP represses direct transcriptional repression at the hilA promoter .	258	In this work , we have demonstrated that PhoP represses hilA expression by four main mechanisms : hilD transcription , rtsA transcription , via the sRNA pinT , and direct transcriptional repression at the hilA promoter .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	59	ver/dev	In this work , we have demonstrated that PhoP represses direct transcriptional repression at the hilA promoter .	258	In this work , we have demonstrated that PhoP represses hilA expression by four main mechanisms : hilD transcription , rtsA transcription , via the sRNA pinT , and direct transcriptional repression at the hilA promoter .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	59	ver/dev	In this work , we have demonstrated that PhoP represses hilA expression by four main mechanisms .	258	In this work , we have demonstrated that PhoP represses hilA expression by four main mechanisms : hilD transcription , rtsA transcription , via the sRNA pinT , and direct transcriptional repression at the hilA promoter .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31182495	68	ver/dev	PhoP repression of hilA correlates with in-vivo data .	282	PhoP repression of hilA correlates with in vivo data .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31262841	4	ver/dev	We have shown that the PhoP represses hilA transcription by blocking activation of the promoter , providing mechanistic insight into how the SPI1 system is shut off after invasion .	54	We have shown that the PhoP represses hilA transcription by blocking activation of the promoter and also indirectly affects hilD and rtsA transcription , providing mechanistic insight into how the SPI1 system is shut off after invasion ( 60 ) .	3	KEYWORDS PHOPQ, SPI1, SALMONELLA, SRNA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilA	repressor	31262841	11	ver/dev	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both hilA ( and hilD ) .	169	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both hilA and rtsA ( and hilD ) ( 60 ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31484980	49	ver/dev	Following this idea , it has been shown that activated PhoP represses expression of hilA ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in dynamic regulatory network governing expression of Salmonella invasion genes .	231	Following this idea , it has been shown that activated PhoP represses expression of hilD , hilA and rtsA , and thus the SP-1 invasion genes67 ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in the complex and dynamic regulatory network governing expression of Salmonella invasion genes .	3	RESULTS	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	31484980	49	ver/dev	Following this idea , it has been shown that activated PhoP represses expression of hilA ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in the complex governing expression of Salmonella invasion genes .	231	Following this idea , it has been shown that activated PhoP represses expression of hilD , hilA and rtsA , and thus the SP-1 invasion genes67 ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in the complex and dynamic regulatory network governing expression of Salmonella invasion genes .	3	RESULTS	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilA	repressor	34202800	13	ver/dev	PhoP negatively regulates hilA via direct repression of hilA transcription .	328	PhoP negatively regulates hilA via direct repression of hilA transcription , indirect repression of both hilD and rtsA expression , and activation of small RNA ( sRNA ) PinT .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	34202800	13	ver/dev	PhoP negatively regulates hilA via direct repression of hilA transcription .	328	PhoP negatively regulates hilA via direct repression of hilA transcription , indirect repression of both hilD and rtsA expression , and activation of small RNA ( sRNA ) PinT .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilA	repressor	34202800	13	ver/dev	PhoP negatively regulates hilA via direct repression of hilA transcription .	328	PhoP negatively regulates hilA via direct repression of hilA transcription , indirect repression of both hilD and rtsA expression , and activation of small RNA ( sRNA ) PinT .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
sigma-28	gene	sapA	regulator	18407759	0	ver/dev	Synthesis of vitamin-B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin -LRB- enterochelin -RRB- and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F -LRB- sigma-28 -RRB- factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR -LRB- or CreC -RRB- PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB -LRB- OmpR family -RRB- aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold-shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine-sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor -LRB- Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	222	Synthesis of vitamin B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin ( enterochelin ) and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F ( sigma 28 ) factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR ( or CreC ) PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB ( OmpR family ) aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor ( Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	18	RESULTS AND DISCUSSION	Salmonella;Salmonella;Enterobacteria phage Ox2;Salmonella	0.5	L2	OTHER	Other	OTHER	Other	Level 1
sigma-28	gene	sapA	regulator	18407759	0	ver/dev	Synthesis of vitamin-B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin -LRB- enterochelin -RRB- and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F -LRB- sigma-28 -RRB- factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR -LRB- or CreC -RRB- PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB -LRB- OmpR family -RRB- aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold-shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine-sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor -LRB- Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	222	Synthesis of vitamin B12 adenosyl cobalamide precursor Outer membrane porin , receptor for ferric enterobactin ( enterochelin ) and colicins B and D Nicotinamidase = pyrazinamidase Transcriptional regulator of cai and fix operon Glutamate = aspartate transporter Sigma F ( sigma 28 ) factor of RNA polymerase ABC-type transport systems Putative acyl-coA dehydrogenase Copper homeostasis protein Surface presentation of antigens Fur regulated salmonella iron transporter Putative chemotaxis signal transduction protein Regulator of flagellar biosynthesis , Hook-filament junction protein 1 Fur regulated salmonella iron transporter Related to carnitine metabolism protein Putative ornithine carbamoyltransferase Dcu family anaerobic dicarboxylate transport protein Secretion system effector Homolog of sapA Response regulator in two-component regulatory system with PhoR ( or CreC ) PhoB-dependent ATP-binding pho regulon component Secretion system effector Putative thiol-alkyl hydroperoxide reductase Putative outer membrane protein Secretion system chaparone Secretion system effector Response regulator in two-component regulatory system with RstB ( OmpR family ) aga operon transcriptional repressor Putative hemolysin Outer membrane protease , receptor for phage OX2 Putative HlyD family secretion protein Putative cytoplasmic protein MFS superfamily nitrate extrusion protein Secretion system apparatus protein Secretion system apparatus protein PhoPQ-activated gene Putative PTS permease Homology with cold shock proteins Cytochrome o ubiquinol oxidase subunit III Gifsy-2 prophage putative type III secreted protein Secretion system regulator : transcriptonal activator Putative component in type IV pilin biogenesis Secretion system apparatus protein Secretion system apparatus protein Secretion system regulator : Sensor component PhoPQ-activated protein Salmonella translocated effector Secretion system effector Peptide methionine sulfoxide reductase PhoPQ-activated protein Putative transcriptional regulator in curly assembly = transport , 2nd curli operon Gifsy-2 prophage superoxide dismutase precursor ( Cu-Zn Putative outer membrane receptor Outer membrane protein E Putative outer membrane protein Reduced macrophage survival protein Similar to virK in Shigella PhoP regulated	18	RESULTS AND DISCUSSION	Salmonella;Salmonella;Enterobacteria phage Ox2;Salmonella	0.5	L2	OTHER	Other	OTHER	Other	Level 1
CspE	gene	cspE	regulator	30992363	8	ver/dev	YciF regulation is imparted through the function of Phe-30 residue in CspE during bile-salts stress To better understand the regulation of YciF by CspE , we utilized the cspE complementation system along with previously known data about CSP functional mutants .	171	YciF regulation is imparted through the function of Phe-30 residue in CspE during bile salts stress To better understand the regulation of YciF by CspE , we utilized the cspE complementation system ( pcspE ) along with previously known data about CSP functional mutants .	5	CSPE INCREASES THE STABILITY OF YCIF MRNA	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CspE	gene	cspE	regulator	32159509	1	ver/dev	To confirm the importance of CspE-dependent biofilm formation , a cspE complementation approach was utilized ( pcspE -- cspE was expressed in the pRS424 plasmid under the control of its native promoter ) .	148	To confirm the importance of CspE-dependent biofilm formation , a cspE complementation approach was utilized ( pcspE -- cspE was expressed in the pRS424 plasmid under the control of its native promoter ) .	13	RESULTS	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CspE	gene	cspE	regulator	32159509	5	ver/dev	To understand whether the CspE mediated biofilm regulatory pathway overlapped with the regulation of swarming motility , the cspE complementation was used .	217	To understand whether the CspE mediated biofilm regulatory pathway overlapped with the regulation of swarming motility , the cspE complementation ( pcspE ) and cspA over-expression system ( pcspA ) was used .	13	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CsrA	gene	fucR	activator	30682134	43	ver/dev	In LB , CsrA activated the translation of genes for fucR metabolism -LRB- S2 Table -RRB- .	297	In LB , CsrA activated the translation of genes for fucose ( fucR ) , 1,2-propanediol ( pocR ) , and threonine/serine ( tdcA ) metabolism ( S2 Table ) .	14	CSRA REGULATES METABOLISM IMPORTANT FOR ESTABLISHING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	pagP	activator	19843227	18	att	Our data show that ugtL is StpA-dependent , as are other genes involved in LPS modification including pagC and pagP .	107	Our data show that ugtL is StpA-dependent , as are other genes involved in LPS modification including pagC and pagP .	8	STPA REPRESSES GENES REQUIRED FOR CELL ENVELOPE MODIFICATION AND RESISTANCE TO CATIONIC PEPTIDES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	spaO	regulator	28575106	5	att	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	167	Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .	8	THE GENE LOIA IS THE VIRULENCE DETERMINANT IN SPI-14	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , DNA repair endonuclease IV .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , nfo .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , fpr .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , ferrodoxin oxidoreductase .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , NADPH .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , an efflux pump .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , acrAB .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , antisense RNA to the porin OmpF mRNA .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , micF .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , glucose-6-phosphate dehydrogenase .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , zwf .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , heat resistant fumarase C .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	sodA	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , fumC .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , glucose-6-phosphate dehydrogenase .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , zwf .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , antisense RNA to the porin OmpF mRNA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , micF .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , DNA repair endonuclease IV .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , nfo .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , fpr .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , ferrodoxin oxidoreductase .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , NADPH .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , efflux pump .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , acrAB .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , aconitase .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , acnA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , heat-resistant fumarase .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , fumC .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , nitroreductase A .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	12886427	0	ver/dev	SoxS protein , activates sodA , nfsA .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	sodA	activator	21193816	1	ver/dev	the oxidative induction of sodA expression is dependent on SoxS	175	The sodA gene is a member of the SoxSR regulon , and the oxidative induction of sodA expression is dependent on SoxS [ 16 ] .	13	GENES REQUIRES SOXS PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hfq	repressor	23676436	27	ver/dev	CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site .	496	CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine -- Dalgarno sequence .	10	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hfq	repressor	30682134	48	ver/dev	CsrA in E. coli represses hfq expression	367	CsrA in E. coli represses hfq and pnp expression [ 121,122 ] , but we did not find effects on the expression of these genes in Salmonella ( S2 Table ) .	15	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopB	regulator	10844688	9	ver/dev	For example , sopB seem to be regulated directly by InvF through modulation of invF expression .	273	For example , sopE and sopB seem to be regulated directly by InvF and indirectly by HilA through modulation of invF expression ( Darwin and Miller , 1999b ; Eichelberg and GalaÂn , 1999 ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L2	SPEC	Other	OTHER	New	Level 1
InvF	gene	sopB	regulator	12791144	11	ver/dev	sopB is known to be controlled by the SPI-1 regulator InvF	232	Among these was sopB , which is known to be controlled by the SPI-1 regulator InvF ( Eichelberg and Galán , 1999 ) , and so probably comes under CsrA control indirectly .	10	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
InvF	gene	sopB	regulator	24947562	0	ver/dev	However , it is important to mention that sopB , is cooperatively regulated by lowered levels of InvF were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control .	232	However , it is important to mention that sopB , is cooperatively regulated by InvF and HilA [ 30 ] and lowered levels of all SPI-1-encoded transcriptional regulators ( HilA , HilC , HilD , and InvF ) were found in Salmonella dam mutants , hereby confirming that the entire SPI-1 is under Dam-dependent control [ 24 ] .	19	4. DISCUSSION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sopB	regulator	28887382	0	ver/dev	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of sopB .	258	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of SPI-1 T3SS genes such as sopB , sicA and sopE ( 35 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopB	regulator	28887382	0	ver/dev	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of sopB .	258	Notably , they found positive regulation of sopF by InvF , a transcriptional regulator of SPI-1 T3SS genes such as sopB , sicA and sopE ( 35 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopB	regulator	31428589	0	ver/dev	sopB are regulated cooperatively by InvF .	125	sopA , sopB , and sopE are regulated cooperatively by HilA and InvF ( Thijs et al. , 2007 ) .	3	THE ROLE OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopB	regulator	33119619	5	att	Furthermore , in agreement with previous results on other InvF-regulated genes , we found that the expression of sopB requires the InvF/SicA complex .	28	Furthermore , in agreement with previous results on other InvF-regulated genes , we found that the expression of sopB requires the InvF/SicA complex .	7	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sopB	regulator	33119619	8	ver/dev	Additionally , we show that InvF binds in-vitro to the promoter region of sopB independently of SicA .	73	Additionally , we show that InvF binds in vitro to the promoter region of sopB independently of SicA .	11	HERE WE SHOW THAT, IN CONTRAST TO HILD AND OTHER SALMONELLA TRANSCRIPTIONAL REGULATORS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sopB	regulator	33119619	17	ver/dev	Altogether , these results support that InvF binds in-vitro to the regulatory region of sopB independently of SicA .	226	Altogether , these results support that InvF binds in vitro to the regulatory region of sopB independently of SicA .	22	SICA IS NOT REQUIRED FOR INVF BINDING TO THE SOPB PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
InvF	gene	sopB	regulator	33119619	19	ver/dev	In this work , by analyzing the regulation of the sopB gene by InvF , we further define the mechanism .	268	In this work , by analyzing the regulation of the sopB gene by InvF , we further define the mechanism by which InvF induces expression of target genes .	24	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Sigma32	gene	degP	activator	15895724	0	ver/dev	For example , the activation of transcription of rpoE , leads to the activation of transcription at degP , s32 genes .	424	For example , the activation of transcription of rpoE , which encodes sE , leads to the activation of transcription at promoters for fkpA , degP , rpoH ( s32 genes ) , and rpoE itself ( 25 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	regulator	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating hilD , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilD	regulator	31182495	22	ver/dev	To determine if regulation of hilD is the primary mechanism of repression by PhoP , we tested PhoP-mediated repression in a hilD deletion background .	113	To determine if regulation of hilD is the primary mechanism of repression by PhoP , we tested PhoP-mediated repression in a hilD deletion background .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilD	regulator	31182495	43	ver/dev	This suggests that repression of the hilD promoter is not through direct binding by PhoP , though we can not rule out weak interaction with the promoter .	205	This suggests that repression of the hilD promoter is not through direct binding by PhoP , though we can not rule out weak interaction with the promoter .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	hilD	regulator	31182495	62	ver/dev	this PhoP effect is one of the few examples of regulation of hilD transcription	262	Though HilD acts as the primary integration point for signals that activate or repress the SPI1 T3SS , most signals appear to function through HilD protein or via hilD translation ( 9 , 10 , 44 , 72 -- 76 ) , and this PhoP effect is one of the few examples of regulation of hilD transcription .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilD	regulator	31182495	65	ver/dev	More work will be required to determine how PhoP controls hilD transcription .	269	More work will be required to determine how PhoP controls hilD and rtsA transcription .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	marA	repressor	32468234	8	ver/dev	the marA gene in turn led to the hyperproduction of MarA along with repression of expression of OmpF	133	The alteration included deletion of the entire marR gene that resulted in derepression of the marA gene which in turn led to the hyperproduction of MarA and AcrAB along with repression of expression of OmpF ( Balleste-Delpierre et al. 2016 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katN	activator	23651595	1	ver/dev	Activated OxyR induces katN , dps ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katN	activator	23651595	1	ver/dev	Activated OxyR induces katN , dps lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katN	activator	23651595	1	ver/dev	Activated OxyR induces katN , DNA-protection ahpCF .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	katN	activator	23651595	1	ver/dev	Activated OxyR induces katN , DNA-protection lipids .	152	Activated OxyR induces transcription of more than 20 genes in the OxyR regulon that function for instance in the following : H2O2 breakdown ( katG , katE and katN ) , DNA protection ( dps ) , disulfide bond formation ( gorA , grxA ) , iron -- sulfur cluster repair ( sufA ) and reduction of oxidized lipids ( ahpCF ) ( Calhoun & Kwon , 2011 ; Hebrard , Viala , Meresse , Barras , & Aussel , 2009 ; McLean , Bowman , & Poole , 2010 ; Paget & Buttner , 2003 ; Spector & Kenyon , 2012 ) .	10	1.2.3. OXIDATIVE STRESS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hha	activator	16045614	14	att	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	68	Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .	4	INTRODUCTION	unidentified	1	L3	OTHER	Other	OTHER	Other	Level 2
LsrR	gene	fliC	repressor	27920756	1	ver/dev	Inactivation of LsrR by the presence of phosphorylated AI-2 allows SPI-1 and fliC , fliD gene transcription .	84	Inactivation of LsrR by the presence of phosphorylated AI-2 allows SPI-1 ( invF , sicA , sopB , sopE ) and flagella ( fliC , fliD ) gene transcription ( Choi et al. , 2012 ) .	5	SALMONELLA TYPHIMURIUM AUTOINDUCERS AND THEIR ROLE IN VIRULENCE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	STM4242	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CysB	gene	cysJ	regulator	20600858	3	att	Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9-minimal-medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative-stress .	181	Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9 minimal medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative stress .	16	3.4. CYSTEINE BIOSYNTHESIS IS CRITICAL DURING PERIODS OF OXIDATIVE STRESS	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	phoP	activator	18270203	11	att	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	161	Transcription of the Horizontally Acquired pagC and ugtL Genes Is PhoP - and SlyA-dependent -- We examined the mRNA levels of the PhoP-activated pagC , ugtL , mgtA , pagP , rstA , and slyB genes following bacterial growth under inducing ( 10 M ) and repressing ( 10 mM ) Mg2 concentrations in isogenic wildtype , phoP , and slyA Salmonella strains .	3	RESULTS	Salmonella	1	L3	OTHER	Investigation	OTHER	Other	Level 2
SlyA	gene	phoP	activator	19091955	11	ver/dev	our previous study in which SlyA enhanced PhoP binding to the promoter of phoP , lacZ expression	71	Similar to our previous study in which SlyA enhanced PhoP binding to the promoter of phoP ( 29 ) , lacZ expression controlled by up-52 is about twice that controlled by up-1 in wild-type cells , indicating that SlyA also facilitates PhoP binding to the pagC promoter ( Fig. 1C ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	phoP	activator	19091955	23	ver/dev	Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by SlyA because the mRNA level of transcripts is reduced significantly in the phoP mutants grown in low-Mg2 conditions -LRB- Fig .	147	Our results from primer extension demonstrate that transcriptions of the identified loci are activated by PhoP and SlyA because the mRNA level of transcripts is reduced significantly in the phoP and slyA mutants grown in low-Mg2 conditions ( Fig .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	synthetic construct	0	L2	OTHER	Analysis	OTHER	Other	Level 1
SlyA	gene	phoP	activator	21388802	6	ver/dev	SlyA activates phoP expression .	201	SlyA activates himD , phoP and ssrB expression .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	phoP	activator	29857034	18	ver/dev	SlyA can also activate phoP genes	318	SlyA can also activate phoP and other genes controlled by the PhoPQ TCS , and we revealed different loci regulated by SlyA , including pmrA and rstA , which both belong to a TCS that is involved in resistance to antimicrobial peptides and stress , respectively [ 13 ] .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L2	OTHER	Other	OTHER	New	Level 1
DksA	gene	relA	activator	20851888	4	ver/dev	The contribution of DksA to the antioxidant defenses of Sal-monella appears to be independent of the stringent-response alarmone ppGpp because a relA spoT mutant was significantly less susceptible to H2O2 than the isogenic dksA-deficient strain .	167	The contribution of DksA to the antioxidant defenses of Sal-monella appears to be independent of the stringent response alarmone ppGpp because a relA spoT ( ppGpp ° ) mutant was significantly ( p 0.05 ) less susceptible to H2O2 than the isogenic dksA-deficient strain .	4	RESULTS	Salmonella;Salmonella;Leiostomus xanthurus	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	osmY	activator	21563813	1	att	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	204	A previous microarray study showed that IHF had an auxiliary and direct role in the activation of some RpoS-dependent genes ( Figure 5A ) , such as osmY , dps , and treA .39 Interestingly , we found that both subunits of IHF protein ( IHFR and IHFβ ) as well as many IHF/RpoS coregulated proteins ( OsmY , Dps , TreA , WrbA , OsmC , and OsmE )	6	’ RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	osmY	activator	22275872	0	att	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	125	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	9	ADAPTATION OF S. ENTERICA TO LETHAL CONCENTRATIONS OF SODIUM DEOXYCHOLATE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmY	activator	22275872	12	att	This hypothesis was tested by analyzing expression of osmY , an RpoS-dependent gene , and cspD , a stress response gene that does not belong to the RpoS regulon [ 32,33 ] , in individual Salmonella cells grown in the presence and in the absence of a sublethal concentration of DOC .	514	This hypothesis was tested by analyzing expression of osmY , an RpoS-dependent gene , and cspD , a stress response gene that does not belong to the RpoS regulon [ 32,33 ] , in individual Salmonella cells grown in the presence and in the absence of a sublethal concentration of DOC .	12	DISCUSSION	Salmonella	1	L2	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	osmY	activator	22275872	2	att	Activation of the RpoS-dependent general stress response in the presence of sublethal concentrations of DOC was further analyzed by monitoring expression of RpoS-dependent genes other than dps and osmY .	150	Activation of the RpoS-dependent general stress response in the presence of sublethal concentrations of DOC was further analyzed by monitoring expression of RpoS-dependent genes other than dps and osmY .	10	VALIDATION OF MICROARRAY ANALYSIS USING LAC FUSIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmY	activator	22275872	7	att	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	326	Redundancy may also explain why mutants lacking individual RpoS-dependent genes ( osmY , dps , xthA , katE , and ots ) are not bile-sensitive .	10	VALIDATION OF MICROARRAY ANALYSIS USING LAC FUSIONS	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	osmY	activator	22275872	0	ver/dev	The RpoS-dependent genes osmY were found to be strongly upregulated by DOC in exponential cultures .	125	The RpoS-dependent genes osmY , dps , uspB , and ecnB [ 30 ] were found to be strongly upregulated by DOC in exponential cultures .	9	ADAPTATION OF S. ENTERICA TO LETHAL CONCENTRATIONS OF SODIUM DEOXYCHOLATE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmY	activator	22356617	0	att	The expression patterns of rpoS and the two well-known RpoS-dependent genes , osmY and yciF , were assessed by qRT-PCR , which showed a similar immobilization-specific induction ( Fig. 6A and data not shown ) .	286	The expression patterns of rpoS and the two well-known RpoS-dependent genes , osmY and yciF , were assessed by qRT-PCR , which showed a similar immobilization-specific induction ( Fig. 6A and data not shown ) .	8	LINKING THE METABOLOMIC AND TRANSCRIPTOMIC DATA SHOWS A SHIFT FROM AEROBIC TO ANAEROBIC METABOLISM	unidentified	1	L3	OTHER	Fact	NEG	Other	Level 1
RpoS	gene	osmY	activator	33593945	2	att	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary-phase ) .	135	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary phase ) .	3	KEYWORDS DCTA, ESCHERICHIA COLI, IRAP, RPOS, SALMONELLA, DICARBOXYLATES, GENE REGULATION, METABOLISM, SUCCINATE, VIRULENCE REGULATION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	osmY	activator	8045891	26	att	Recently , reports on E. coli have also implicated Lrp and integration host factor in the RpoS-dependent stationary-phase induction of osmY ( 20 ) .	253	Recently , reports on E. coli have also implicated Lrp and integration host factor in the RpoS-dependent stationary-phase induction of osmY ( 20 ) .	5	DISCUSSION	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	osmY	activator	8045891	26	ver/dev	Recently , reports on E. coli have also implicated integration host factor in the RpoS-dependent stationary-phase induction of osmY .	253	Recently , reports on E. coli have also implicated Lrp and integration host factor in the RpoS-dependent stationary-phase induction of osmY ( 20 ) .	5	DISCUSSION	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	osmY	activator	8045891	26	ver/dev	Recently , reports on E. coli have also implicated Lrp host factor in the RpoS-dependent stationary-phase induction of osmY .	253	Recently , reports on E. coli have also implicated Lrp and integration host factor in the RpoS-dependent stationary-phase induction of osmY ( 20 ) .	5	DISCUSSION	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	lpxO	activator	17693506	6	att	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid-A modifications explain most of the alterations in the passive permeability of the OM bilayer .	208	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid A modifications explain most of the alterations in the passive permeability of the OM bilayer .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	lpxO	activator	18350168	4	att	The suppressive effects of spermine NONOate on PhoP-dependent gene transcription appear to be directly related to the production of RNS because the polyamine base spermine did not suppress the acid-induced expression of the PhoP-activated loci lpxO , pqaA , and pcgE ( fig. 6B -- D ) .	301	The suppressive effects of spermine NONOate on PhoP-dependent gene transcription appear to be directly related to the production of RNS because the polyamine base spermine did not suppress the acid-induced expression of the PhoP-activated loci lpxO , pqaA , and pcgE ( fig. 6B -- D ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	lpxO	activator	18350168	6	att	The acid-inducible expression of the PhoP-activated loci lpxO , pqaA and pcgE were monitored in the presence or absence of 250 mM spermine , 250 mM spermine NONOate or 500 mM NaNO2 ( B -- D ) .	343	The acid-inducible expression of the PhoP-activated loci lpxO , pqaA and pcgE were monitored in the presence or absence of 250 mM spermine , 250 mM spermine NONOate or 500 mM NaNO2 ( B -- D ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	repressor	11591661	12	ver/dev	Furthermore , this indicates that a relA-dependent source of ppGpp can compensate for any leucine-mediated inactivation of Lrp , either through elevated lrp expression or through other ppGpp-dependent mechanisms .	359	Furthermore , this indicates that a relA-dependent source of ppGpp can compensate for any leucine-mediated inactivation of Lrp , either through elevated lrp expression or through other ppGpp-dependent mechanisms ( see below ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Lrp	gene	lrp	repressor	12067346	27	ver/dev	In contrast , the presence of both lrp mutations in the donor strain restored the repression of pSLT transfer to a level similar to that of an Lrp .	150	In contrast , the presence of both dam and lrp mutations in the donor strain restored the repression of pSLT transfer to a level similar to that of an Lrp - mutant ( Table 1 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	lrp	repressor	18599829	1	ver/dev	Lrp -- DNA interaction in this region was fully consistent with the observed repression of lrp transcription by this protein .	16	Lrp -- DNA interaction in this region was fully consistent with the observed repression of lrp transcription by this protein .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	repressor	18599829	6	ver/dev	that Lrp repressed the transcription of the lrp gene	128	These data showed that Lrp repressed the transcription of the lrp gene and that this negative effect was partially alleviated by the presence of leucine .	6	NEGATIVE AUTOREGULATION OF LRP TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Lrp	gene	lrp	repressor	18599829	20	ver/dev	This pattern of protein -- DNA interaction is consistent with repression of the lrp promoter by Lrp promoter occlusion .	261	This pattern of protein -- DNA interaction is consistent with repression of the lrp promoter by Lrp promoter occlusion .	8	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
Lrp	gene	lrp	repressor	19074398	20	ver/dev	lrp expression , is repressed , leading to low levels of Lrp	305	In the presence of arabinose , lacI expression is induced and lrp expression , which is transcribed from the Ptrc promoter in lrp-1281 , is repressed , leading to low levels of Lrp ( Fig. 5B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	repressor	19074398	34	ver/dev	Lrp represses the expression of an lrp deletion mutant displays hypervirulence .	492	Lrp represses the expression of key virulence factors and an lrp deletion mutant displays hypervirulence ( Table 4 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	lrp	repressor	32284321	5	ver/dev	lrp mutant strains _ supporting the notion that ltrR1 is repressed by both Lrp at its coding region	148	However , the transcriptional expression of pKK8/ltrR1 -35 616 , pKK8/ltrR1 -35 678 , pKK8/ltrR1 -35 836 , and pKK8/ltrR1 -35 887 increased to 432 , 264 , 529 , and 432 CAT units in the hns lrp double mutant compared with the values observed for the wild type ( 167 , 105 , 27 , and 35 CAT units , respectively ) or for the individual hns ( 199 , 107 , 224 , and 272 CAT units , respectively ) and lrp ( 219 , 51 , 40 , and 21 CAT units , respectively ) mutant strains ( Fig. 4B ) , supporting the notion that ltrR1 is repressed by both H-NS and Lrp at its coding region .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	lrp	repressor	32284321	5	ver/dev	lrp mutant strains _ supporting the notion that ltrR1 is repressed by both Lrp at its coding region	148	However , the transcriptional expression of pKK8/ltrR1 -35 616 , pKK8/ltrR1 -35 678 , pKK8/ltrR1 -35 836 , and pKK8/ltrR1 -35 887 increased to 432 , 264 , 529 , and 432 CAT units in the hns lrp double mutant compared with the values observed for the wild type ( 167 , 105 , 27 , and 35 CAT units , respectively ) or for the individual hns ( 199 , 107 , 224 , and 272 CAT units , respectively ) and lrp ( 219 , 51 , 40 , and 21 CAT units , respectively ) mutant strains ( Fig. 4B ) , supporting the notion that ltrR1 is repressed by both H-NS and Lrp at its coding region .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	lrp	repressor	32284321	5	ver/dev	lrp mutant strains _ supporting the notion that ltrR1 is repressed by both Lrp at its coding region	148	However , the transcriptional expression of pKK8/ltrR1 -35 616 , pKK8/ltrR1 -35 678 , pKK8/ltrR1 -35 836 , and pKK8/ltrR1 -35 887 increased to 432 , 264 , 529 , and 432 CAT units in the hns lrp double mutant compared with the values observed for the wild type ( 167 , 105 , 27 , and 35 CAT units , respectively ) or for the individual hns ( 199 , 107 , 224 , and 272 CAT units , respectively ) and lrp ( 219 , 51 , 40 , and 21 CAT units , respectively ) mutant strains ( Fig. 4B ) , supporting the notion that ltrR1 is repressed by both H-NS and Lrp at its coding region .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hilC	activator	32571967	12	ver/dev	H-NS contributes to silencing of hilC	223	Rcs could , for example , be functioning through H-NS , which contributes to silencing of hilD , hilC , rtsA , and hilA ( 33 , 78 -- 80 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	himD	repressor	21388802	2	ver/dev	CsrA represses himD .	151	CsrA activates spvR and rpoE expression and represses himD .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	hilA	activator	17993530	17	att	As expected from the results described above , deletion of hilC or rtsA decreased but did not abrogate Fur-dependent induction of hilA .	197	As expected from the results described above , deletion of hilC or rtsA decreased but did not abrogate Fur-dependent induction of hilA .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
Fur	gene	hilA	activator	17993530	17	ver/dev	As expected from the results , deletion of rtsA did not abrogate Fur-dependent induction of hilA .	197	As expected from the results described above , deletion of hilC or rtsA decreased but did not abrogate Fur-dependent induction of hilA .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
Fur	gene	hilA	activator	17993530	17	ver/dev	As expected from the results , deletion of hilC did not abrogate Fur-dependent induction of hilA .	197	As expected from the results described above , deletion of hilC or rtsA decreased but did not abrogate Fur-dependent induction of hilA .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
InvF	gene	sptP	activator	21168230	1	att	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	208	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sptP	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sptP and located outside -LRB- sopE -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sptP	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sptP and located outside -LRB- sopD -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sptP	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sptP and located outside -LRB- sopB -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	rcsB	regulator	30510144	3	ver/dev	We also determined that SlyA is able to bind to these rcsB promoters .	13	We also determined that SlyA is able to recognize and bind to these predicted sites to modulate the activity of both rcsB promoters .	1	ABSTRACT	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SlyA	gene	rcsB	regulator	30510144	21	ver/dev	These results indicate that both rcsB could be controlled by the SlyA virulence transcriptional factor .	90	These results indicate that both transcript rcsDB and rcsB could be controlled by the SlyA virulence transcriptional factor .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	rcsB	regulator	30510144	26	ver/dev	SlyA protein binds to rcsB promoters in-vitro .	104	SlyA protein binds to rcsB promoters in vitro .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	rcsB	regulator	30510144	29	ver/dev	We hypothesized that SlyA repression of rcsB transcription affects the motility behavior of Salmonella , since both regulators also participate in the regulation of flagellar gene expression .	123	We hypothesized that SlyA repression of rcsB transcription affects the motility behavior of Salmonella , since both regulators also participate in the regulation of flagellar gene expression ( 6 , 28 -- 30 ) .	4	RESULTS	Salmonella	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilA	gene	sigD	activator	24018968	2	ver/dev	HilA activates sigD SPI1 .	40	HilA activates expression of the prg/org and inv/spa genes , which encode a functional type III secretion system ( T3SS ) apparatus [ 25 , 26 ] , whereas InvF is required to induce transcription of several effector genes encoded both within ( sic/sip genes ) and outside ( sigD and sopE ) SPI1 [ 12 , 13 ] .	3	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
TyrR	gene	tyrP	activator	32111072	4	ver/dev	The primary mechanism of TyrR-mediated gene regulation is repression , nevertheless activation by TyrR was reported for tyrP .	67	The primary mechanism of TyrR-mediated gene regulation is repression , nevertheless activation by TyrR was reported for three genes , namely mtr , tyrP and the aroP promoter P3 [ 23 ] .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	STM2595	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	yciF	activator	15145463	2	att	yciF was initially identified by a screen for RpoSregulated genes and a putative RpoS-dependent promoter has been located upstream of yciG [ 39 ] .	210	yciF was initially identified by a screen for RpoSregulated genes and a putative RpoS-dependent promoter has been located upstream of yciG [ 39 ] .	12	3.2. BILE ACTIVATES YCIF INDEPENDENTLY OF RPOS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	yciF	activator	22356617	0	att	The expression patterns of rpoS and the two well-known RpoS-dependent genes , osmY and yciF , were assessed by qRT-PCR , which showed a similar immobilization-specific induction ( Fig. 6A and data not shown ) .	286	The expression patterns of rpoS and the two well-known RpoS-dependent genes , osmY and yciF , were assessed by qRT-PCR , which showed a similar immobilization-specific induction ( Fig. 6A and data not shown ) .	8	LINKING THE METABOLOMIC AND TRANSCRIPTOMIC DATA SHOWS A SHIFT FROM AEROBIC TO ANAEROBIC METABOLISM	unidentified	1	L3	OTHER	Fact	NEG	Other	Level 1
RpoS	gene	yciF	activator	23676436	14	att	We also found that the expression of several RpoS-dependent genes , e.g. osmC , otsA and yciF , was significantly increased , which is consistent with our observation of increased level of RpoS in the DclpP mutant .	390	We also found that the expression of several RpoS-dependent genes , e.g. osmC , otsA and yciF , was significantly increased , which is consistent with our observation of increased level of RpoS in the DclpP mutant .	8	PHENOTYPIC EFFECTS OF RPOS AND CSRA DELETION DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
LeuO	gene	cse2	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas3 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas2 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas1 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas6e mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
LeuO	gene	cse2	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
OxyR	gene	hemA	activator	12081946	5	ver/dev	Induction of heme synthesis during oxidative-stress seems reasonable because OxyR also induces the synthesis of hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative-stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .	373	Induction of heme synthesis during oxidative stress seems reasonable because OxyR also induces the synthesis of a major heme-requir-ing enzyme , hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .	8	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	hemA	activator	12081946	5	ver/dev	Induction of heme synthesis during oxidative-stress seems reasonable because OxyR also induces the synthesis of hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative-stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .	373	Induction of heme synthesis during oxidative stress seems reasonable because OxyR also induces the synthesis of a major heme-requir-ing enzyme , hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .	8	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OxyR	gene	hemA	activator	12081946	5	ver/dev	Induction of heme synthesis during oxidative-stress seems reasonable because OxyR also induces the synthesis of a major heme-requir-ing enzyme Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative-stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .	373	Induction of heme synthesis during oxidative stress seems reasonable because OxyR also induces the synthesis of a major heme-requir-ing enzyme , hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .	8	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LysR	gene	uhpT	regulator	15781495	1	ver/dev	Putative transcriptional regulator , LysR family Sensory histidine kinase of NarP Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of LysR family	294	Putative transcriptional regulator , LysR family Sensory histidine kinase of a two-component regulatory system ( NarP ) Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of a multi-component regulatory system ( TorS ) Transcriptional regulator , LysR family	14	PLASMIDS AND ANTIMICROBIAL RESISTANCE	nan	1	L2	SPEC	Other	OTHER	New	Level 1
LysR	gene	uhpT	regulator	15781495	1	ver/dev	Putative transcriptional regulator , LysR family Sensory histidine kinase of NarP Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of a multi-component regulatory system ( TorS ) Transcriptional regulator	294	Putative transcriptional regulator , LysR family Sensory histidine kinase of a two-component regulatory system ( NarP ) Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of a multi-component regulatory system ( TorS ) Transcriptional regulator , LysR family	14	PLASMIDS AND ANTIMICROBIAL RESISTANCE	nan	1	L2	SPEC	Other	OTHER	New	Level 1
LysR	gene	uhpT	regulator	15781495	1	ver/dev	Putative transcriptional regulator , LysR family Sensory histidine kinase of a two-component regulatory system Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of LysR family	294	Putative transcriptional regulator , LysR family Sensory histidine kinase of a two-component regulatory system ( NarP ) Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of a multi-component regulatory system ( TorS ) Transcriptional regulator , LysR family	14	PLASMIDS AND ANTIMICROBIAL RESISTANCE	nan	1	L2	SPEC	Other	OTHER	New	Level 1
LysR	gene	uhpT	regulator	15781495	1	ver/dev	Putative transcriptional regulator , LysR family Sensory histidine kinase of a two-component regulatory system Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of a multi-component regulatory system ( TorS ) Transcriptional regulator	294	Putative transcriptional regulator , LysR family Sensory histidine kinase of a two-component regulatory system ( NarP ) Putative transcriptional regulator , LysR family Membrane protein , regulator of uhpT expression Periplasmic sensor of a multi-component regulatory system ( TorS ) Transcriptional regulator , LysR family	14	PLASMIDS AND ANTIMICROBIAL RESISTANCE	nan	1	L2	SPEC	Other	OTHER	New	Level 1
LeuO	gene	dsbI	activator	22343301	4	att	The transcriptional-fusions assT 688/dsbL 105 and assT 688/dsbI 107 , containing the assT LeuO-dependent promoter , as well as the upstream regions of dsbL and dsbI , respectively , also showed null transcriptional activity in the wild-type strain with the plasmid vector ( data not shown ) .	124	The transcriptional fusions assT 688/dsbL 105 and assT 688/dsbI 107 , containing the assT LeuO-dependent promoter , as well as the upstream regions of dsbL and dsbI , respectively , also showed null transcriptional activity in the wild-type strain with the plasmid vector ( data not shown ) .	4	RESULTS	unidentified plasmid;unidentified	1	L3	OTHER	Analysis	NEG	New	Level 1
LeuO	gene	dsbI	activator	22343301	7	att	These data indicate that assT , dsbL , and dsbI are functionally organized as a LeuO-dependent operon in the rich MA medium .	130	These data indicate that assT , dsbL , and dsbI are functionally organized as a LeuO-dependent operon in the rich MA medium .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	regulator	10692170	1	ver/dev	hilA expression is regulated by Salmonella invasion regulator ; however , it is not known how SirA is it known how sirA expression is itself regulated .	61	hilA expression is regulated by SirA ( Salmonella invasion regulator ) , a protein which is conserved in several of the Enterobacteriaceae ( Johnston et al. , 1996 ) ; however , it is not known how SirA modulates hilA expression nor is it known how sirA expression is itself regulated .	4	MAIN	Salmonella	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilA	regulator	10692170	1	ver/dev	hilA expression is regulated by Salmonella invasion regulator ; however , it is not known how SirA modulates hilA expression .	61	hilA expression is regulated by SirA ( Salmonella invasion regulator ) , a protein which is conserved in several of the Enterobacteriaceae ( Johnston et al. , 1996 ) ; however , it is not known how SirA modulates hilA expression nor is it known how sirA expression is itself regulated .	4	MAIN	Salmonella	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilA	regulator	10692170	1	ver/dev	hilA expression is regulated by SirA ; however , it is not known how SirA is it known how sirA expression is itself regulated .	61	hilA expression is regulated by SirA ( Salmonella invasion regulator ) , a protein which is conserved in several of the Enterobacteriaceae ( Johnston et al. , 1996 ) ; however , it is not known how SirA modulates hilA expression nor is it known how sirA expression is itself regulated .	4	MAIN	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilA	regulator	10692170	1	ver/dev	hilA expression is regulated by SirA ; however , it is not known how SirA modulates hilA expression .	61	hilA expression is regulated by SirA ( Salmonella invasion regulator ) , a protein which is conserved in several of the Enterobacteriaceae ( Johnston et al. , 1996 ) ; however , it is not known how SirA modulates hilA expression nor is it known how sirA expression is itself regulated .	4	MAIN	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilA	regulator	10692170	1	ver/dev	hilA expression is regulated by a protein ; however , it is not known how SirA is it known how sirA expression is itself regulated .	61	hilA expression is regulated by SirA ( Salmonella invasion regulator ) , a protein which is conserved in several of the Enterobacteriaceae ( Johnston et al. , 1996 ) ; however , it is not known how SirA modulates hilA expression nor is it known how sirA expression is itself regulated .	4	MAIN	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilA	regulator	10692170	1	ver/dev	hilA expression is regulated by a protein ; however , it is not known how SirA modulates hilA expression .	61	hilA expression is regulated by SirA ( Salmonella invasion regulator ) , a protein which is conserved in several of the Enterobacteriaceae ( Johnston et al. , 1996 ) ; however , it is not known how SirA modulates hilA expression nor is it known how sirA expression is itself regulated .	4	MAIN	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
SirA	gene	hilA	regulator	12453229	5	ver/dev	Genes in SPI-5 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .	62	Genes in SPI-4 and SPI-5 are controlled by HilA , a transcriptional regulator encoded within SPI-1 , and by SirA , a regulator of hilA ( Ahmer et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilA	regulator	12453229	5	ver/dev	Genes in SPI-5 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .	62	Genes in SPI-4 and SPI-5 are controlled by HilA , a transcriptional regulator encoded within SPI-1 , and by SirA , a regulator of hilA ( Ahmer et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilA	regulator	12453229	5	ver/dev	Genes in SPI-4 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .	62	Genes in SPI-4 and SPI-5 are controlled by HilA , a transcriptional regulator encoded within SPI-1 , and by SirA , a regulator of hilA ( Ahmer et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilA	regulator	12453229	5	ver/dev	Genes in SPI-4 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .	62	Genes in SPI-4 and SPI-5 are controlled by HilA , a transcriptional regulator encoded within SPI-1 , and by SirA , a regulator of hilA ( Ahmer et al. , 1999 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilA	regulator	12453229	8	ver/dev	BarA / SirA are positive regulators of hilA transcription .	73	BarA / SirA are positive regulators of hilA transcription .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilA	regulator	12453229	9	ver/dev	SirA regulates hilA	77	SirA regulates hilA and is	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	regulator	16045614	8	ver/dev	Although it has been proposed that SirA directly controls expression of both hilA , it was also determined that HilC was not required for SirA to control hilA expression .	54	Although it has been proposed that SirA directly controls expression of both hilA and hilC ( Teplitski et al. , 2003 ) , it was also determined that HilC was not required for SirA to control hilA expression ( Lucas and Lee , 2001 ) .	4	INTRODUCTION	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
SirA	gene	hilA	regulator	16045614	42	ver/dev	Thus SirA controls expression of hilA .	242	Thus SirA controls expression of the three hilA regulators and hilA .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilA	regulator	16045614	42	ver/dev	Thus SirA controls expression of the three hilA regulators .	242	Thus SirA controls expression of the three hilA regulators and hilA .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilA	regulator	16045614	44	ver/dev	Previous attempts have been made to determine how SirA controls expression of hilA .	245	Previous attempts have been made to determine how SirA controls expression of hilA ( Lucas and Lee , 2001 ; Teplitski et al. , 2003 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	regulator	16045614	79	ver/dev	This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both hilA .	550	This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both the hilC and hilA , but not the hilD , promoters ( Teplitski et al. , 2003 ) .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	regulator	16949866	9	ver/dev	Once phosphorylated , SirA directly binds the hilA promoters .	60	Once phosphorylated , SirA directly binds the hilA and hilC promoters and contributes to Salmonella enteropathogenesis in a bovine model ( Ahmer et al. , 1999a ; Teplitski et al. , 2003 ) .	5	CORRESPONDING AUTHOR. TEL.: +1 352 392 1951X254; FAX: +1 352 392 3902.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	regulator	16949866	30	ver/dev	SirA controls these genes by directly binding the hilA .	455	SirA controls these genes by directly binding and activating the hilA and hilC regulatory genes that are encoded within the horizontal acquisition , SPI1 ( Teplitski et al. , 2003 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	regulator	17074910	19	ver/dev	However , this may seem unexpected , as SirA can directly bind the hilA , so SirA would be expected to activate these genes independently of csrC .	510	However , this may seem unexpected , as SirA can directly bind the hilA , hilC and fimA promoters , so SirA would be expected to activate these genes independently of csrB and csrC .	10	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	regulator	17074910	19	ver/dev	However , this may seem unexpected , as SirA can directly bind the hilA , so SirA would be expected to activate these genes independently of csrB .	510	However , this may seem unexpected , as SirA can directly bind the hilA , hilC and fimA promoters , so SirA would be expected to activate these genes independently of csrB and csrC .	10	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	regulator	17208038	20	ver/dev	Conversely , previously published gel-shift data suggested that SirA is able to bind to the promoters of hilA .	121	Conversely , previously published gel-shift data [ 44 ] suggested that SirA is able to bind to the promoters of hilC and hilA , but not to that of hilD .	8	BARA/SIRA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	regulator	17208038	22	ver/dev	Whereas SirA might bind to the hilA promoters during in-vitro gel-shift experiments , genetic data shows that SirA is incapable of directly activating these promoters ; SirA binding to DNA in-vitro does not represent activation .	123	Whereas SirA might bind to the hilA and hilC promoters during in vitro gel-shift experiments , genetic data shows that SirA is incapable of directly activating these promoters ; SirA binding to DNA in vitro does not represent activation .	8	BARA/SIRA	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
SirA	gene	hilA	regulator	19537165	7	ver/dev	Scenario-3: Regulation of the network by SirA via hilA in combination with regulation through HilD	253	Scenario-3: Regulation of the network by SirA via hilC and hilA in combination with regulation through HilD	16	SCENARIO-3: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA IN COMBINATION WITH REGULATION THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	regulator	24929817	0	ver/dev	SirA , directly regulates the hilA genes at the top of the invasion cascade .	165	SirA , a global regulator necessary for enteropathogenesis , directly regulates the hilA and hilC genes at the top of the invasion cascade ( Prouty and gunn 2000 ; Teplitski et al. 2006 ) .	9	SURVIVAL AND PROPHAGE INDUCTION OF LYSOGENIC S. TYPHIMURIUM EXPOSED TO GASTROINTESTINAL JUICES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilE	regulator	34048498	5	ver/dev	To determine whether CsrA regulates hilE directly , EMSAs were performed using purified the 5 ' - end-labelled leader RNA of hilE .	122	To determine whether CsrA regulates hilE directly , quantitative electrophoretic mobility shift assays ( EMSAs ) were performed using purified CsrA and the 5 ' - end-labelled leader RNA of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilE	regulator	34048498	5	ver/dev	To determine whether CsrA regulates hilE directly , EMSAs were performed using purified CsrA 5 ' - end-labelled leader RNA of hilE .	122	To determine whether CsrA regulates hilE directly , quantitative electrophoretic mobility shift assays ( EMSAs ) were performed using purified CsrA and the 5 ' - end-labelled leader RNA of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilE	regulator	34048498	5	ver/dev	To determine whether CsrA regulates hilE directly , quantitative electrophoretic-mobility-shift assays were performed using purified the 5 ' - end-labelled leader RNA of hilE .	122	To determine whether CsrA regulates hilE directly , quantitative electrophoretic mobility shift assays ( EMSAs ) were performed using purified CsrA and the 5 ' - end-labelled leader RNA of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilE	regulator	34048498	5	ver/dev	To determine whether CsrA regulates hilE directly , quantitative electrophoretic-mobility-shift assays were performed using purified CsrA 5 ' - end-labelled leader RNA of hilE .	122	To determine whether CsrA regulates hilE directly , quantitative electrophoretic mobility shift assays ( EMSAs ) were performed using purified CsrA and the 5 ' - end-labelled leader RNA of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	hilE	regulator	34048498	7	ver/dev	These data support that CsrA binds two sites on the hilE transcript .	125	These data support that CsrA binds two sites on the hilE transcript .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	hilE	regulator	34048498	9	ver/dev	In agreement with these results , data from a previous global analysis by CLIP-seq showed that CsrA binds in-vivo to a sequence located near the translation start codon of the hilE mRNA .	129	In agreement with these results , data from a previous global analysis by CLIP-seq showed that CsrA binds in vivo to a sequence located near the translation start codon of the hilE mRNA [ 49 ] .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	hilE	regulator	34048498	10	ver/dev	Thus , we conclude that CsrA binds specifically to the hilE leader transcript .	130	Thus , we conclude that CsrA binds specifically to the hilE leader transcript .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsrA	gene	hilE	regulator	34048498	12	ver/dev	CsrA controls the expression of hilE	134	To define the complete regulatory cascade involving CsrA that controls the expression of hilE , the expression of HilE-FLAG and that of the lacZ-hilE fusion was monitored in the WT S. Typhi-murium strain and its ΔsirA , ΔcsrB , ΔcsrC and ΔcsrB ΔcsrC derivative mutants , grown in SPI-1-inducing conditions .	8	SIRA/BARA INDUCES THE EXPRESSION OF HILE THROUGH CSRB/C	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ydhJ	repressor	29857034	15	ver/dev	For genes , we found two genes , ydhJ are negatively regulated by SlyA .	312	For genes involved in multidrug resistance , we found two genes , ydhJ and ydhI ( STM14_1740 ; STM14_1741 ) , which are transcribe divergent to slyA and are negatively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sicA	activator	10692170	5	att	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	92	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	sicA	activator	10692170	5	att	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	92	In addition , sicA , like sigD , has an InvF-dependent promoter ( PsicA ) immediately upstream of it ; but , unlike sigD , sicA can also be expressed from a promoter upstream of PsicA ( presumably the promoter upstream of invF ) ( Darwin and Miller , 1999b ) .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
InvF	gene	sicA	activator	10692170	6	att	Because sicA has an InvF-dependent promoter , we wanted to determine whether , in addition to cis-polar effects , the spaS mutations could affect sicAsipBCDA expression in trans .	93	Because sicA has an InvF-dependent promoter , we wanted to determine whether , in addition to cis-polar effects , the spaS mutations could affect sicAsipBCDA expression in trans .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sicA	activator	10692170	9	att	Because sicA was required for its own expression as well as for the expression of other InvF-dependent genes , it was possible that SicA was this cofactor .	208	Because sicA was required for its own expression as well as for the expression of other InvF-dependent genes , it was possible that SicA was this cofactor .	8	INVF AND SICA ARE SUFFICIENT TO ACTIVATE TRANSCRIPTION OF SICA- AND SIGD±LACZYA IN E:COLI CC118LPIR.	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
InvF	gene	sicA	activator	10692170	8	ver/dev	AraC requires arabinose for the expression of AraC-activated promoters , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sicA .	207	AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA .	8	INVF AND SICA ARE SUFFICIENT TO ACTIVATE TRANSCRIPTION OF SICA- AND SIGD±LACZYA IN E:COLI CC118LPIR.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
InvF	gene	sicA	activator	11755416	8	ver/dev	InvF activates a promoter upstream of sicA , causing additional expression of sicAsipBCDA .	164	InvF activates a promoter upstream of sicA , causing additional expression of sicAsipBCDA [ 49 , 55 ] .	6	4. SPI1-ENCODED TRANSCRIPTION FACTORS AND THE REGULATION OF TTSS-1	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sicA	activator	27601571	26	ver/dev	Our RNA - explaining how SPI-4 gene expression is coordinated with that of seq data show strong upregulation of sicA by InvF ( see SPI-1 .	239	Our RNA - explaining how SPI-4 gene expression is coordinated with that of seq data show strong upregulation of sopB and sicA by InvF ( see SPI-1 .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sicA	activator	28335027	8	ver/dev	As the sicA promoter has the longest relaxation time for SPI-1 , induction of sic/sip by InvF represents a key commitment step to the associated burden of producing effector proteins .	760	As the sicA promoter has the longest relaxation time for SPI-1 encoded genes ( 64 ) , induction of sic/sip by InvF represents a key commitment step to virulence and the associated burden of producing effector proteins .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sicA	activator	28335027	8	ver/dev	As the sicA promoter has the longest relaxation time for SPI-1 , induction of sic/sip by InvF represents a key commitment step to virulence .	760	As the sicA promoter has the longest relaxation time for SPI-1 encoded genes ( 64 ) , induction of sic/sip by InvF represents a key commitment step to virulence and the associated burden of producing effector proteins .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsA	gene	yrfF	repressor	12757942	3	ver/dev	Since the lethality was not relieved by mutations by inactivation of RcsA , it can be concluded that cps genes do not participate in yrfF lethality .	213	Since the lethality caused by yrfF loss was not relieved by mutations interfering with colanic acid synthesis nor by inactivation of RcsA , a short-lived protein required to optimize RcsB-positive regulation of cps genes [ 14 ] , it can be concluded that cps genes do not participate in yrfF lethality .	13	4. DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
Fur	gene	fes	regulator	18554972	0	att	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	215	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	15	3.1. TRANSPOSON MUTAGENESIS IDENTIFIES IRON RESPONSE GENES INVOLVED IN NOREPINEPHRINE-ENHANCED GROWTH OF SALMONELLA TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfeR	gene	yfeH	regulator	21175741	4	ver/dev	The location of yfeH divergently transcribed makes yfeH a likely candidate to be regulated by YfeR .	306	The location of yfeH adjacent to yfeR and divergently transcribed makes yfeH a likely candidate to be regulated by YfeR .	17	REGULATION OF YFEH EXPRESSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
YfeR	gene	yfeH	regulator	21175741	4	ver/dev	The location of yfeH adjacent to yfeR makes yfeH a likely candidate to be regulated by YfeR .	306	The location of yfeH adjacent to yfeR and divergently transcribed makes yfeH a likely candidate to be regulated by YfeR .	17	REGULATION OF YFEH EXPRESSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
FliA	TU	flhDC	regulator	17074910	22	ver/dev	Transcriptional regulation of flhDC by sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	555	Transcriptional regulation of flhDC by QseBC and sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	23	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	TU	flhDC	regulator	17074910	22	ver/dev	Transcriptional regulation of flhDC by QseBC ( FliA ) in enterohaemorrhagic Escherichia coli .	555	Transcriptional regulation of flhDC by QseBC and sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	23	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	TU	flhDC	regulator	21166907	0	ver/dev	Clarke , M.B. , and Sperandio , V. Transcriptional regulation of flhDC by FliA in enterohaemorrhagic Escherichia coli .	508	Clarke , M.B. , and Sperandio , V. ( 2005 ) Transcriptional regulation of flhDC by QseBC and sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	TU	flhDC	regulator	26442936	8	ver/dev	Transcriptional regulation of flhDC by QseBC ( FliA ) in enterohaemorrhagic Esche-richia coli .	844	Transcriptional regulation of flhDC by QseBC and sigma 28 ( FliA ) in enterohaemorrhagic Esche-richia coli .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	TU	flhDC	regulator	26443762	6	ver/dev	Transcriptional regulation of flhDC by QseBC ( FliA ) in enterohaemorrhagic Escherichia coli .	626	Transcriptional regulation of flhDC by QseBC and sigma 28 ( FliA ) in enterohaemorrhagic Escherichia coli .	27	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	TU	flhDC	regulator	29473025	4	ver/dev	Transcriptional regulation of flhDC by sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	578	Transcriptional regulation of flhDC by QseBC and sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	19	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	TU	flhDC	regulator	29473025	4	ver/dev	Transcriptional regulation of flhDC by QseBC ( FliA ) in enterohaemorrhagic Escherichia coli .	578	Transcriptional regulation of flhDC by QseBC and sigma ( FliA ) in enterohaemorrhagic Escherichia coli .	19	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipB	regulator	33617591	6	att	Using sipB : : lacZY , a representative HilD-regulated gene , as a reporter , we examined SPI-1 gene expression in cultures grown with 20 μM c2-HDA .	96	Using sipB : : lacZY , a representative HilD-regulated gene , as a reporter , we examined SPI-1 gene expression in cultures grown with 20 μM c2-HDA .	10	SPECIFIC AMINO ACID RESIDUES OF HILD ARE ESSENTIAL FOR REPRESSION BY C2-HDA	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PmrA	gene	pmrD	regulator	15569938	11	ver/dev	When system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter .	169	When the Salmonella PmrA PmrB system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter and represses pmrD transcription ( 30 ) ( Fig. 1 A ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	regulator	15569938	11	ver/dev	When the Salmonella PmrA PmrB is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter .	169	When the Salmonella PmrA PmrB system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter and represses pmrD transcription ( 30 ) ( Fig. 1 A ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrD	regulator	15703297	9	ver/dev	the pmrD promoter harbors binding sites for both PmrA proteins	115	We have previously identified a multicomponent loop in Sal-monella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA , and activated PmrA represses transcription from the pmrD promoter , which harbors binding sites for both the PhoP and PmrA proteins ( 18 ) ( Fig. 1D ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DksA	TU	ssrAB	regulator	29930310	22	ver/dev	However , in contrast to ppGpp , our data suggest that DksA does not regulate ssrAB transcription .	191	However , in contrast to ( p ) ppGpp , our data suggest that DksA does not regulate ssrAB transcription .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
RpoS	gene	yghA	repressor	30524381	0	ver/dev	rpoS , _ relieving RpoS repression of yghA	66	In S. Typhimurium , OmpR represses the alternative stationary phase sigma factor , rpoS , relieving RpoS repression of yghA .	4	NTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	yghA	repressor	30524381	0	ver/dev	the alternative stationary-phase sigma factor , _ relieving RpoS repression of yghA	66	In S. Typhimurium , OmpR represses the alternative stationary phase sigma factor , rpoS , relieving RpoS repression of yghA .	4	NTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
GatR	gene	gatY	regulator	27956522	8	ver/dev	The promoters of gatY are negatively regulated by GatR .	102	The promoters of gatZ , gatY , and gatR are negatively regulated by GatR .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	katN	regulator	20713450	4	ver/dev	The results reveal differential regulation of katN locus by H-NS in these two closely related bacteria .	40	The results reveal differential regulation of the yciGFE ( katN ) locus by YncC and H-NS ( the Histone-like Nucleoid Structuring protein , 14 -- 16 ) in these two closely related bacteria .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CysB	gene	cysE	activator	18957594	0	ver/dev	Evidence suggests that cysE may be activated by CysB .	57	Evidence presented in this study suggests that cysE may be activated by CysB .	3	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CysB	gene	cysE	activator	20600858	4	ver/dev	This swarm-cell-specific induction of cysE is independent of CysB .	228	This swarm-cell-specific induction of cysE is independent of CysB ( data not shown ) .	19	3.7. SUPPLEMENTING SWIM CULTURES WITH NAS INDUCES THE SWARM ANTIBIOTIC RESISTANCE PHENOTYPE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysE	activator	20600858	6	ver/dev	We reasoned that if cysE upregulation is driving induction of the CysB regulon by increasing NAS levels , adding NAS to swim cells should be able to induce the anti-biotic resistance phenotype in non-swarming cells .	230	We reasoned that if cysE upregulation is driving induction of the CysB regulon by increasing NAS levels , adding NAS to swim cells should be able to induce the anti-biotic resistance phenotype in non-swarming cells .	19	3.7. SUPPLEMENTING SWIM CULTURES WITH NAS INDUCES THE SWARM ANTIBIOTIC RESISTANCE PHENOTYPE	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
BaeR	gene	mdtABC	regulator	33751923	13	ver/dev	BaeR binds to the promoter region of mdtABC .	473	BaeR binds to the promoter region of arcD and mdtABC and regulates their transcription in response to indole , copper , and zinc ( Nishino et al. 2007 ) .	13	BAESR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	flgB	regulator	29061704	2	ver/dev	However , no significant differences were observed in flgB mRNA levels between isolates , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected .	48	However , no significant differences were observed in fliN and flgB mRNA levels between the two classes of isolates , suggesting that class 3 genes ( controlled by FliA sigma factor ) , but not class 2 genes , were affected .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
FliA	gene	flgB	regulator	29061704	2	ver/dev	However , no significant differences were observed in flgB mRNA levels between the two classes , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected .	48	However , no significant differences were observed in fliN and flgB mRNA levels between the two classes of isolates , suggesting that class 3 genes ( controlled by FliA sigma factor ) , but not class 2 genes , were affected .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
StpA	gene	ugtL	regulator	19843227	36	ver/dev	Two StpA-repressed PhoP-dependent genes _ bound by ugtL	262	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	sdhA	activator	33593945	2	att	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary-phase ) .	135	An analysis of dctA ( encoding the primary dicarboxylate transporter ) and sdhA ( encoding succinate dehydrogenase for succinate metabolism ) gene expression in the Salmonella Gene Expression Compendium ( SalCom ) database ( 43 , 44 ) showed that they generally anticorrelated with the expression of RpoS-activated genes like osmY and correlated with growth phases where RpoS is inactive ( e.g. , dctA was downregulated in response to osmotic shock and in late stationary phase ) .	3	KEYWORDS DCTA, ESCHERICHIA COLI, IRAP, RPOS, SALMONELLA, DICARBOXYLATES, GENE REGULATION, METABOLISM, SUCCINATE, VIRULENCE REGULATION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	ilvBN	activator	11591661	0	ver/dev	The ilvBN genes are also under catabolite control , requiring CRP for activation of expression .	47	The ilvBN genes are also under catabolite control , requiring cyclic AMP ( cAMP ) - cAMP receptor protein ( CRP ) for activation of expression ( 18 , 53 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	TU	ilvBN	activator	11591661	0	ver/dev	The ilvBN genes are also under catabolite control , requiring cAMP-receptor-protein for activation of expression .	47	The ilvBN genes are also under catabolite control , requiring cyclic AMP ( cAMP ) - cAMP receptor protein ( CRP ) for activation of expression ( 18 , 53 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	cspE	regulator	30992363	27	ver/dev	Jawali , N. Cyclic-AMP-receptor-protein regulates cspE , in Esche-richia coli .	561	Uppal , S. , Maurya , S. R. , Hire , R. S. , and Jawali , N. ( 2011 ) Cyclic AMP receptor protein regulates cspE , an early cold-inducible gene , in Esche-richia coli .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	tufB	regulator	26934594	7	ver/dev	These results indicate that the autoregulation of tufB gene expression is independent from transcriptional initiation of its regulation by Fis .	262	These results indicate that the autoregulation of tufB gene expression is uncoupled from tRNA production and show that it is a secondary regulatory mechanism specific for EF-TuB , and independent from transcriptional initiation of the operon and its regulation by Fis .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	tufB	regulator	26934594	7	ver/dev	These results indicate that the autoregulation of tufB gene expression is independent from transcriptional initiation of its regulation by Fis .	262	These results indicate that the autoregulation of tufB gene expression is uncoupled from tRNA production and show that it is a secondary regulatory mechanism specific for EF-TuB , and independent from transcriptional initiation of the operon and its regulation by Fis .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	tufB	regulator	26934594	7	ver/dev	These results indicate that the autoregulation of tufB gene expression is independent from transcriptional initiation of the operon by Fis .	262	These results indicate that the autoregulation of tufB gene expression is uncoupled from tRNA production and show that it is a secondary regulatory mechanism specific for EF-TuB , and independent from transcriptional initiation of the operon and its regulation by Fis .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	tufB	regulator	26934594	9	ver/dev	Fis-binding sites upstream of the promoter ( Van Delft independent regulation of the tufB gene in Salmonella ,	270	Fis-binding sites upstream of the promoter ( Van Delft independent regulation of the tufB gene in Salmonella ,	13	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	cadC	repressor	22804842	29	ver/dev	LeuO has also been shown to repress the acid stress regulator cadC in E. coli	416	Transcriptional activation by LeuO is well documented but LeuO has also been shown to repress the acid stress regulator cadC , the small RNA dsrA and the fimAICDFGH operon in E. coli ( Shi and Bennett , 1995 ; Repoila and Gottesman , 2001 ; Shimada et al. , 2011 ) .	8	GENOME-WIDE PREDICTION AND VALIDATION OF LEUO BINDING SITES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	acnA	regulator	23637460	3	att	P1 is an RpoS-regulated gearbox promoter located 407 bp upstream of the acnA start codon and is responsible for stationary-phase induction of acnA expression .	223	P1 is an RpoS-regulated gearbox promoter located 407 bp upstream of the acnA start codon and is responsible for stationary phase induction of acnA expression .	7	EXPRESSION OF S. TYPHIMURIUM ACNA IS REGULATED BY CRP, FNR, FUR AND SOXR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	orgA	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of orgA remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	orgA	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of orgA remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	orgA	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of orgA remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	hilA	regulator	14633100	1	att	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	49	Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .	4	M A T E R I A LS A N D M E T H O D S	Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	hilA	regulator	14633100	3	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	190	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	hilA	regulator	14633100	4	att	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	426	16S , 16S rDNA ; hilA , a Salmonella pathogenicity island I virulence gene ; stn , Salmonella enterotoxin gene ; invA , invasion gene ; iroB , Fur-regulated gene ; hist , histidine transport operon ; sipB/C , the junction between sipB and sipC virulence genes ; repseq , a Salmonella-specific repetitive DNA fragment ; multi , multiplex targeting invA gene and spvC gene of the virulence plasmid .	6	HISTIDINE TRANSPORT OPERON ACT GGC GTT ATC CCT TTC TCT GGT G 6 ATG TTG TCC TGC CCC TGG TAA GAG A	Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	iraP	activator	20545866	51	ver/dev	In E. coli , CsgD also regulates genes indirectly as it enhances the expression of the alternative sigma factor RpoS through transcription activation of iraP .	316	In E. coli , CsgD also regulates genes indirectly as it enhances the expression of the alternative sigma factor RpoS through transcription activation of iraP encoding a RpoS stablilization factor ( Gualdi et al. , 2007 ) .	9	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	iraP	activator	20545866	51	ver/dev	transcription activation of iraP _ encoding a RpoS stablilization factor	316	In E. coli , CsgD also regulates genes indirectly as it enhances the expression of the alternative sigma factor RpoS through transcription activation of iraP encoding a RpoS stablilization factor ( Gualdi et al. , 2007 ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	iraP	activator	24885225	56	ver/dev	RpoS stabilization where PhoPQ participates by serving as a transcriptional activator of the iraP gene in S. Typhimurium	214	One component of induction is RpoS stabilization , where PhoPQ participates by serving as a transcriptional activator of the iraP ( yaiB ) gene in S. Typhimurium .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	iraP	activator	30325297	0	ver/dev	The formation of filamentous cells was associated with the upregulation of iraP , while non-filamentous cells consequently contained RpoS .	273	The formation of filamentous cells was associated with the upregulation ( ) of fabH and pflAB and the down regulation ( ) of iraP , while non-filamentous cells had iraP upregulated and consequently contained RpoS ( + ) .	23	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	cas1	activator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas1 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	STM1330	regulator	27564394	11	ver/dev	Furthermore , STM1330 are regulated by PhoP .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	STM2903	repressor	26359211	0	att	A similar phenomenon was observed for 14 Fis-repressed genes in the early exponential phase , with only one ( STM2903 ) that was also negatively regulated in the mid-exponential-phase [ 27 ] .	128	A similar phenomenon was observed for 14 Fis-repressed genes in the early exponential phase , with only one ( STM2903 ) that was also negatively regulated in the mid-exponential phase [ 27 ] .	12	COMPARISON OF THE FIS EFFECT BETWEEN EARLY- AND MID-EXPONENTIAL PHASES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	STM1257	activator	15681155	31	ver/dev	In addition , the lack of consensus PmrA-binding sites in the promoters of STM1257 suggested that these genes may be indirectly activated by PmrA .	339	In addition , the lack of consensus PmrA-binding sites in the promoters of STM1257 , STM3968 , STM4568 and STM0459 suggested that these genes may be indirectly activated by PmrA .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Sigma28	gene	flgI	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgI by introduction of a null mutation in J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgI	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgI by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgI	repressor	9765570	4	ver/dev	Like all genes , mutations in any of flgI genes result in FlgM-dependent inhibition of s28 activity .	90	Like all genes involved in HBB assembly , mutations in any of the flgA , flgH , and flgI genes result in FlgM-dependent inhibition of s28 activity ( 8 ) .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	10844688	5	ver/dev	In the presence of an unknown environmental condition , HilD may activate invF expression .	259	In the presence of an unknown environmental condition , HilC or HilD may activate invF expression , causing induction of invF-dependent genes .	14	MISLEADING CLUES?	unidentified	1	L1	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	invF	activator	10844688	16	ver/dev	Such a situation would be possible if HilD has direct activation of invF .	290	Such a situation would be possible if HilC or HilD has two distinct functions ( derepression of hilA and direct activation of invF ) that are separable by this condition .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilD	gene	invF	activator	10844688	18	ver/dev	If a condition exists in which hilA is repressed while invF expression is induced through HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	292	If a condition exists in which hilA is repressed while invF expression is induced through HilC or HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	invF	activator	10844688	19	ver/dev	The direct activation of invF expression by HilD may always accompany derepression of hilA expression such that the two mechanisms act co-operatively rather than independently to induce invF expression .	297	The direct activation of invF expression by HilC or HilD may always accompany derepression of hilA expression such that the two mechanisms act co-operatively rather than independently to induce invF expression .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	invF	activator	10844688	21	ver/dev	certain effectors are produced as a result of direct activation of invF expression by HilD	308	But the situation would be entirely different at sites 3 and 4 , in which hilA and the secretion apparatus are not expressed but InvF and certain effectors are produced as a result of direct activation of invF expression by HilC or HilD .	16	MODELS FOR INVASION GENE REGULATION IN VIVO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	invF	activator	11755416	34	ver/dev	We have evidence that HilD modestly activates invF expression independently of its effects on hilA , even in WT S. typhimurium .	561	We have evidence that HilD modestly activates invF expression independently of its effects on hilA , even in WT S. typhimurium grown under inducing conditions in vitro ( figure 1B , orange arrow ) .	16	REFERENCES	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	57	att	Determination of the HilD-dependent transcription start site of invF by primer-extension .	154	Determination of the HilD-dependent transcription start site of invF by primer extension .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	synthetic construct	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	4	ver/dev	Our studies show that HilD activate transcription of invF from a promoter .	16	Our studies show that HilD and HilC activate transcription of invF from a promoter that is far upstream of its HilA-dependent promoter .	2	ABSTRACT	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	16	ver/dev	We show that HilD can directly activate invF .	63	We show that HilD and HilC can directly bind and activate invF , which leads to the non-co-ordinate expression of a subset of SPI1 genes .	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of orgA remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgK remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	21	ver/dev	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgH remains unaffected .	79	Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , sipA and sipC , whereas expression of prgH , prgK and orgA remains unaffected .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	24	ver/dev	We propose that HilD can independently activate invF expression .	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	25	ver/dev	In this scheme , activation of invF transcription by HilD leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter .	84	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	invF	activator	12535071	25	ver/dev	In this scheme , activation of invF transcription by HilD leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter .	84	In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	invF	activator	12535071	28	ver/dev	In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	28	ver/dev	In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilC , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	28	ver/dev	In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilD , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	34	ver/dev	HilD do not activate invF expression from the HilA-dependent invF promoter	106	HilD and HilC do not activate invF expression from the HilA-dependent invF promoter	6	HILD AND HILC DO NOT ACTIVATE INVF EXPRESSION FROM THE HILA-DEPENDENT INVF PROMOTER	nan	1	L3	OTHER	Other	NEG	New	Level 1
HilD	gene	invF	activator	12535071	54	ver/dev	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain HilC-dependent +1 of invF .	145	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD or HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD - and HilC-dependent +1 of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
HilD	gene	invF	activator	12535071	54	ver/dev	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD .	145	These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD or HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD - and HilC-dependent +1 of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
HilD	gene	invF	activator	12535071	68	ver/dev	It is possible that HilD , activates invF expression from a second promoter .	182	It is possible that HilD , but not HilC , activates invF expression from a second promoter .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HilD	gene	invF	activator	12535071	70	ver/dev	In order to address whether additional S. typhimuriumspecific genes are required for HilD to activate invF , we examined both pSA7 reporters in E. coli TOP-10 cells .	185	In order to address whether additional S. typhimuriumspecific genes are required for HilD and HilC to activate invF , we examined both pVV448 and pSA7 reporters in E. coli TOP-10 cells .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Escherichia coli	0	L3	SPEC	Investigation	OTHER	Other	Level 1
HilD	gene	invF	activator	12535071	70	ver/dev	In order to address whether additional S. typhimuriumspecific genes are required for HilD to activate invF , we examined both pVV448 reporters in E. coli TOP-10 cells .	185	In order to address whether additional S. typhimuriumspecific genes are required for HilD and HilC to activate invF , we examined both pVV448 and pSA7 reporters in E. coli TOP-10 cells .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Prairie vole hantavirus;Escherichia coli	0	L3	SPEC	Investigation	OTHER	Other	Level 1
HilD	gene	invF	activator	12535071	71	ver/dev	We found that HilD induce invF expression from pSA7 in E. coli , comparable to that .	186	We found that HilD and HilC induce invF expression from pSA7 in E. coli , comparable to that seen in S. typhimurium ( data not shown ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Escherichia coli	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	72	ver/dev	We also found that HilD , activates invF expression from pVV448 , also comparable to that .	187	We also found that HilD , but not HilC , activates invF expression from pVV448 , also comparable to that seen in S. typhimurium ( data not shown ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	Prairie vole hantavirus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	73	ver/dev	These results suggest that HilD might directly activate invF expression by binding to sequences upstream of invF .	188	These results suggest that HilD and HilC might directly activate invF expression by binding to sequences upstream of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	73	ver/dev	These results suggest that HilD might directly activate invF expression by binding to sequences upstream of invF .	188	These results suggest that HilD and HilC might directly activate invF expression by binding to sequences upstream of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	76	ver/dev	HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	76	ver/dev	HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	79	ver/dev	HilD directly activate invF expression by binding downstream of a HilD/C-dependent promoter	229	HilD and HilC directly activate invF expression by binding upstream and downstream of a HilD/C-dependent promoter	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	79	ver/dev	HilD directly activate invF expression by binding upstream of a HilD/C-dependent promoter	229	HilD and HilC directly activate invF expression by binding upstream and downstream of a HilD/C-dependent promoter	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	12535071	80	ver/dev	Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .	230	Previous studies have shown that HilD and HilC can indirectly activate invF expression by derepressing hilA ( Schechter et al. , 1999 ; Schechter and Lee , 2001 ; Olekhnovich and Kadner , 2002 ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	invF	activator	12535071	83	ver/dev	HilD appear to activate transcription of invF from a HilD/C-dependent start site .	233	HilD and HilC appear to activate transcription of invF from a HilD/C-dependent start site that is 631 nucleotides upstream of the invF ORF .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	invF	activator	12535071	85	ver/dev	Our studies also suggest that the downstream binding site is required for HilD to activate invF .	235	Our studies also suggest that the downstream binding site is required for HilD and HilC to activate invF .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	invF	activator	12535071	101	ver/dev	HilD directly activate invF expression 723 can be secreted independently of SPI1 .	290	HilD and HilC directly activate invF expression 723 can be secreted independently of SPI1 .	10	MODELS FOR THE BIOLOGICAL ROLE OF HILA-INDEPENDENT AND HILD/C-DEPENDENT ACTIVATION OF INVF	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	16045614	54	ver/dev	HilD are each capable of partially activating invF	390	Transcription of invF is primarily regulated by HilA , but HilD , HilC and RtsA are each capable of partially activating invF ( Eichelberg et al. , 1999 ; Rakeman et al. , 1999 ; Akbar et al. , 2003 ; Ellermeier and Slauch , 2003 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	invF	activator	21168230	5	ver/dev	In addition , HilD directly activate invF in non-HilA dependent manner .	344	In addition , HilD and HilC directly activate invF , sipA and sipC in non-HilA dependent manner ( Akbar et al. , 2003 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	21573071	0	ver/dev	Moreover , HilD can directly activate invF independently of HilA .	8	Moreover , HilC and HilD can directly activate invF independently of HilA [ 11 ] .	1	ABSTRACT	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	25991823	1	ver/dev	HilD can activate expression of the invF and sicA/sip transcriptional units independently of HilA .	25	HilC and HilD relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha ( Olekhnovich and Kadner 2006 ) and can activate expression of the invF and sicA/sip transcriptional units independently of HilA ( Rakeman et al. 1999 ; Akbar et al. 2003 ) .	3	COPYRIGHT © 2015 BY THE GENETICS SOCIETY OF AMERICA DOI: 10.1534/GENETICS.115.178103	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	27404739	1	ver/dev	HilD , activate directly the expression of the invF operon , independently of HilA .	131	Two additional regulators , HilC and HilD , activate directly the expression of hilA and the invF operon , independently of HilA ( Dieye et al. , 2007 ) .	6	SPI-1 RELATED GENES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	activator	27886269	5	ver/dev	invF is positively regulated by HilD through HilA	65	As a control , the expression of a cat transcriptional fusion of invF , which is positively regulated by HilD through HilA , was also assessed .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	invF	activator	28329249	1	ver/dev	Moreover , HilD can activate invF expression in a	26	Moreover , HilD can activate invF expression in a	3	MAIN	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	invF	activator	29378886	34	att	However , deletion of invS did not affect transcription of HilD-dependent invF , as would be expected if the phenotype were mediated through HilE .	271	However , deletion of invS did not affect transcription of HilD-dependent invF , as would be expected if the phenotype were mediated through HilE .	5	DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
HilD	gene	invF	activator	31484980	40	ver/dev	As a negative control , an invF-cat transcriptional-fusion was also assessed ; HilD induces expression of invF through HilA27 ,60,61 .	187	As a negative control , an invF-cat transcriptional fusion was also assessed ; HilD induces expression of invF through HilA27 ,60,61 .	3	RESULTS	Felis catus	0	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgK	activator	9765570	1	att	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	71	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	flgK	activator	9765570	3	att	The class 3 structural genes are of two types ; the flgK , flgL , and fliD genes are transcribed from both a class 2 promoter and a s28-dependent class	78	The class 3 structural genes are of two types ; the flgK , flgL , and fliD genes are transcribed from both a class 2 promoter and a s28-dependent class	6	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CadC	gene	lysP	activator	23066934	11	ver/dev	These results suggest that the lysine signal represses lysP expression , thereby eliminating the negative regulation of CadC activation by LysP .	212	These results suggest that the lysine signal represses lysP expression , thereby eliminating the negative regulation of CadC activation by LysP .	16	S. TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	invF	regulator	11123690	15	ver/dev	These results indicate that Fis is also involved in the regulation of invF expression in a HilA-independent manner .	135	These results indicate that Fis is also involved in the regulation of invF expression in a HilA-independent manner .	8	MOUSE VIRULENCE OF A S. TYPHIMURIUM FIS MUTANT IS DIMINISHED	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	stpA	repressor	19843227	1	ver/dev	In fact , inactivation of stpA only has phenotypic effects in the absence of hns , indicating that the deletion of stpA is fully compensated by H-NS in E. coli .	39	In fact , inactivation of stpA only has phenotypic effects in the absence of hns , indicating that the deletion of stpA is fully compensated by H-NS in E. coli .	5	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	stpA	repressor	19843227	3	ver/dev	One mechanism is mediated by the negative cross-regulation that both proteins exert on each other ; H-NS represses stpA transcription more strongly than StpA controls hns .	42	One mechanism that maintains the imbalance in levels of the two proteins is mediated by the negative cross-regulation that both proteins exert on each other ; H-NS represses stpA transcription more strongly than StpA controls hns ( Zhang et al. , 1996 ) .	5	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilC	gene	invH	activator	12535071	47	att	The sizes of the different extension products indicate that the HilD - and HilC-dependent transcripts initiate within the divergently transcribed invH ORF ( Fig. 5A -- C ) .	126	The sizes of the different extension products indicate that the HilD - and HilC-dependent transcripts initiate within the divergently transcribed invH ORF ( Fig. 5A -- C ) .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MarA	TU	flhDC	regulator	31501286	18	ver/dev	For this reason , we hypothesized that MarA may bind to flhDC as well .	193	For this reason , we hypothesized that MarA , SoxS , and RamA may bind to flhDC as well .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	TU	flhDC	regulator	31501286	22	ver/dev	Based on these findings , we conclude that MarA bind to the flhDC promoter , while RamA do not , under the conditions .	203	Based on these findings , we conclude that MarA and Rob bind to the flhDC promoter , while SoxS and RamA do not , under the conditions tested .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
MarA	TU	flhDC	regulator	31501286	22	ver/dev	Based on these findings , we conclude that MarA bind to the flhDC promoter , while SoxS do not , under the conditions .	203	Based on these findings , we conclude that MarA and Rob bind to the flhDC promoter , while SoxS and RamA do not , under the conditions tested .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
MarA	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test MarA , we replaced class I in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test MarA , we replaced the native flhDC promoter in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	acs	regulator	26199328	1	ver/dev	Finally , we show that Crp , regulates acs expression in S. enterica .	62	Finally , we show that Crp , a global regulator of carbon metabolism , regulates pat and acs expression in S. enterica .	0	Unknown	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	acs	regulator	26199328	2	ver/dev	In E. coli , Crp controls the expression of acs .	249	In E. coli , Crp controls the expression of acs ( 30 ) .	4	2	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	15126450	4	ver/dev	Thus , the OmpR regulators positively regulate ompS2 .	15	Thus , the OmpR and LeuO regulators positively regulate ompS2 .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompS2	activator	16428792	7	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	196	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	17908208	65	att	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter ( Fernández-Mora et al. , 2004 ) , the induction of ompS1 can occur independent of OmpR .	257	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter ( Fernández-Mora et al. , 2004 ) , the induction of ompS1 can occur independent of OmpR .	13	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
OmpR	gene	ompS2	activator	17908208	81	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	451	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	24	ACKNOWLEDGEMENTS	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	18156266	50	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	449	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	17	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	19447191	19	ver/dev	Calva E. OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	197	Fernandez-Mora M , Puente JL , Calva E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	21398529	11	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	456	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	22149171	67	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	562	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	35	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	22343301	39	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	408	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	29	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	22804842	32	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	647	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	26	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	24354910	59	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	414	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	36	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	24659766	23	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	412	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	20	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	24720747	23	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	495	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	31	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	28337196	0	ver/dev	Calva E. OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	277	Fernandez-Mora M , Puente JL , Calva E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	8	FUNDING	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	activator	33854491	18	ver/dev	OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	377	OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .	25	THIS WORK WAS SUPPORTED BY GRANTS FROM THE DIRECCIÓN GENERAL AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB.2021.657404/ DE ASUNTOS DEL PERSONAL ACADÉMICO, DGAPA/UNAM (IN203618 FULL#SUPPLEMENTARY-MATERIAL	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	rpoS	regulator	19843227	41	ver/dev	The negative effect of StpA on s38 levels at MEP does not occur during LEP as StpA-dependent control of s38 stability is probably compensated at the rpoS mRNA level .	300	The negative effect of StpA on s38 levels at MEP does not occur during LEP as StpA-dependent control of s38 stability is probably compensated at the rpoS mRNA level .	15	DISCUSSION	nan	1	L2	SPEC	Other	NEG	Other	Level 1
YfhA	gene	rcsB	regulator	24079299	2	ver/dev	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of and its homolog FlrC in the upstream regions and ORFs of rcsB , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	120	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA ( and its homolog FlrC ) in the upstream regions and ORFs of rcsB and sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfhA	gene	rcsB	regulator	24079299	2	ver/dev	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA in the upstream regions and ORFs of rcsB , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	120	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA ( and its homolog FlrC ) in the upstream regions and ORFs of rcsB and sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfhA	gene	rcsB	regulator	24079299	5	ver/dev	In the present study , rcsB were also predicted to have binding sites of YfhA within their ORFs .	125	In the present study , rcsB and sciS were also predicted to have binding sites of YfhA ( and its homolog FlrC ) within their ORFs ( Additional file 4 ) .	5	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YfhA	gene	rcsB	regulator	24079299	6	ver/dev	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA-P mediated regulation of rcsB .	126	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA ( YfhA-P ) mediated regulation of sciS and rcsB .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfhA	gene	rcsB	regulator	24079299	6	ver/dev	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA mediated regulation of rcsB .	126	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA ( YfhA-P ) mediated regulation of sciS and rcsB .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxS	gene	soxS	activator	31501286	39	att	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	283	Since elevated soxS expression resulted in reduced flhDC translation , we looked to better understand the mechanism underlying SoxS-dependent posttranscriptional regulation of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	soxS	activator	34125582	6	ver/dev	While soxS is induced by copper-stress in S. enterica , none of the genes from the SoxS regulon were identified as copper-responsive genes .	257	While soxS is induced by copper stress in S. enterica , none of the genes from the SoxS regulon were identified as copper-responsive genes .	8	COPPER RESPONSE AND DEFENSE MECHANISMS	Salmonella;Salmonella;unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	sseB	repressor	26300871	18	ver/dev	Taken together , these results show that CpxR represses the autoregulation of sseB located in SPI-2 .	390	Taken together , these results show that CpxR represses the autoregulation of HilD , which in turn affects the expression of hilA and thus the SPI-1 genes , as well as of other virulence genes regulated by HilD , such as ssrB and sseB located in SPI-2 .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	ycfR	regulator	33024855	13	att	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative-stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino-acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	696	As detected by q-RT-PCR , gene expression of the NsrR-regulated gene ygbA , the oxidative stress gene soxR , stress response/host adaptation genes ycfR , marA and yjbE and the amino acid biosynthesis genes trpD and trpE were significantly higher than the control ( p < 0.05 ) .	15	3.6. CARBOHYDRATE, LIPID AND INORGANIC ION METABOLISM AND EFFLUX TRANSPORTERS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
NsrR	TU	yeaR-yoaG	regulator	23651595	18	att	These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .	625	These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	sipB	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YgaE	gene	ompC	repressor	24592164	1	ver/dev	Here we report that YgaE is a repressor of ompC in S. Typhi ; it can be partially explained why the expression of ompC is not up-regulated under hyperosmotic-stress .	213	Here we report that YgaE is a repressor of ompC in S. Typhi ; it can be partially explained why the expression of ompC is not up-regulated under hyperosmotic stress .	8	3.2. YGAE REPRESSES THE EXPRESSION OF OMPF/OMPC AT THE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
YgaE	gene	ompC	repressor	24592164	5	ver/dev	The repression of YgaE to ompC means less pathways for antibiotics .	227	The repression of YgaE to ompC and ompF means less pathways for nutrition and antibiotics .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YgaE	gene	ompC	repressor	24592164	5	ver/dev	The repression of YgaE to ompC means less pathways for nutrition .	227	The repression of YgaE to ompC and ompF means less pathways for nutrition and antibiotics .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YgaE	gene	ompC	repressor	24592164	7	ver/dev	One explanation for these phenomena is the repression of YgaE to ompC occurs only in the very early stage of hyperosmotic-stress as an emergency approach to protect the bacteria .	233	One explanation for these phenomena is the repression of YgaE to ompC and ompF occurs only in the very early stage of hyperosmotic stress as an emergency approach to protect the bacteria .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YgaE	gene	ompC	repressor	24592164	8	ver/dev	As time goes by , other mechanisms are involved in the process of handling the hyperosmotic-stress , the repression of YgaE to ompC relieves .	234	As time goes by , other mechanisms are involved in the process of handling the hyperosmotic stress , the repression of YgaE to ompC and ompF relieves .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YgaE	gene	ompC	repressor	24592164	9	ver/dev	the expressions of ompC were obviously repressed by YgaE at the early stage	249	Oppositely , the expressions of ompC and ompF were obviously repressed by YgaE at the early stage and no apparent regulation of OmpC and OmpF by YgaE was observed in the 2-DE results at the late stage of hyperosmotic stress .	10	3.4. YGAE REPRESSES THE EXPRESSION OF OMPA AT THE LATE STAGE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	fur	activator	1624426	1	att	Second , six Fur-dependent , iron-repressed proteins were underexpressed , not overexpressed , in the fur mutant .	230	Second , six Fur-dependent , iron-repressed proteins were underexpressed , not overexpressed , in the fur mutant .	5	SALONLLTOFDUMRUTNTS.OA FIGUE 2NLSSPORORVOI-EETUIAAESYEVI-SI LFU ORANY OF THETHEHRFUR MUTANT STR23(CAINS TAESTED.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	fur	activator	17302823	0	att	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	182	Thus , the S. Typhimu-rium bfr and ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .	11	C	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	ompS2	regulator	12753201	1	ver/dev	Emerging evidence indicates that OmpR regulates ompS2 in S. typhi .	29	Emerging evidence indicates that OmpR regulates many additional genes outside the porin repertoire ( Oshima et al. , 2002 ) , including regulation of the flagellar operon flhDC ( Shin and Park , 1995 ) , curli fimbrial expression ( Vidal et al. , 1998 ) and cryptic porins ompS1 and ompS2 in S. typhi ( Fernandez-Mora et al. , 1995 ; Oropeza et al. , 1999 ) .	3	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
OmpR	gene	ompS2	regulator	15126450	0	ver/dev	OmpR Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin	3	OmpR and LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompS2	regulator	15126450	4	ver/dev	Thus , the OmpR regulators positively regulate ompS2 .	15	Thus , the OmpR and LeuO regulators positively regulate ompS2 .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ompS2	regulator	15126450	19	ver/dev	The experiments described above indicated that both the OmpR regulators were involved in the positive regulation of ompS2 expression .	242	The experiments described above indicated that both the LeuO and the OmpR regulators were involved in the positive regulation of ompS2 expression .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	purB	activator	33045730	64	att	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	283	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	metE	regulator	31479952	5	ver/dev	Accordingly , metE was down regulated by FNR .	190	Accordingly , metE + gene expression was down regulated by FNR .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssaH	activator	11918812	0	att	As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	116	As a first application of the two-colour flow cytometric technique , the in vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .	6	IN VITRO CHARACTERIZATION OF TRANSCRIPTIONAL FUSIONS TO VIRULENCE GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Lrp	gene	spvABCD	regulator	19447191	2	ver/dev	Lrp binds to sequences upstream of the spvABCD operon	82	Integration host factor ( IHF ) binds to DNA sequences upstream of the spvR regulatory region , and the leucine-responsive regulatory protein ( Lrp ) binds to sequences upstream of the spvABCD operon and regulate spv expression ( Marshall et al. , 1999 ) .	5	4.1. SPVR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	virK	regulator	12675799	2	ver/dev	These results indicate that both virK are regulated by PhoP .	196	These results indicate that both virK and somA are regulated by PhoP .	5	IDENTIFICATION OF SPI-2 CO-EXPRESSED GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	virK	regulator	15225317	28	att	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	338	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	virK	regulator	15703297	5	att	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	105	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	virK	regulator	24185747	7	att	Inhibition on the expression was also obtained when the action of linoleic and linolenic fatty-acids were assayed using well-known PhoP-regulated genes other than virK , indicating that the effect was global on the PhoP -- PhoQ controlled regulon ( Viarengo et al. , 2013 ) .	134	Inhibition on the expression was also obtained when the action of linoleic and linolenic fatty acids were assayed using well-known PhoP-regulated genes other than virK , indicating that the effect was global on the PhoP -- PhoQ controlled regulon ( Viarengo et al. , 2013 ) .	13	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	virK	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	virK	regulator	33751923	25	ver/dev	Transcription of virK is positively regulated by PhoP	746	Transcription of virK is positively regulated by PhoP and its inhibition in this bioassay would indicate inhibition of the PhoPQ regulatory system .	32	TWO-COMPONENT SYSTEMS AS POTENTIAL TARGETS FOR NOVEL THERAPEUTICS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	ssrB	regulator	29930310	9	ver/dev	These findings indicate that DksA does not appear to regulate ssrB gene transcription .	83	These findings indicate that DksA does not appear to regulate ssrA or ssrB gene transcription .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
DksA	gene	ssrB	regulator	29930310	23	ver/dev	Our biochemical analyses indicate that the amount of SsrB protein , not ssrB mRNA , is highly reduced in ΔdksA Salmonella , suggesting that DksA regulates ssrB expression post-transcriptionally .	192	Our biochemical analyses indicate that the amount of SsrB protein , not ssrB mRNA , is highly reduced in ΔdksA Salmonella , suggesting that DksA regulates ssrB expression post-transcriptionally .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	ssrB	regulator	29930310	24	ver/dev	Transcriptional control of a small RNA could mediate the DksA-dependent post-transcriptional activation of ssrB .	193	Transcriptional control of a small RNA could mediate the DksA-dependent post-transcriptional activation of ssrB .	4	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CytR	gene	tsx	repressor	16489221	0	ver/dev	Repression by CytR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CytR	gene	tsx	repressor	16489221	0	ver/dev	Repression by CytR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	ssrB	activator	31838175	3	ver/dev	These observations suggested that SoxS induced the expression of SPI-2 genes through ssrB .	154	These observations suggested that SoxS induced the expression of SPI-2 genes through ssrA and ssrB .	17	3.1. RNA-SEQ DATA ANALYSIS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
OxyR	gene	fur	regulator	11932449	5	ver/dev	OxyR regulation of fur .	538	OxyR and SoxRS regulation of fur .	16	KOLB, A., BUSBY, S., BUC, H., GARGRES, S. & ADHYA, S. (1993).	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	fur	regulator	12081946	7	ver/dev	OxyR regulation of fur .	665	OxyR and SoxRS regulation of fur .	30	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	fur	regulator	18790861	60	ver/dev	OxyR regulation of fur .	526	OxyR and SoxRS regulation of fur .	21	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	fur	regulator	23651595	23	ver/dev	OxyR regulation of fur .	1488	OxyR and SoxRS regulation of fur .	102	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	fur	regulator	33838479	8	ver/dev	OxyR regulation of fur .	674	OxyR and SoxRS regulation of fur .	54	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	fliA	regulator	17725646	2	ver/dev	FlhDC acts as a positive regulator for class fliA .	185	FlhDC acts as a positive regulator for class II promoter-transcribed genes , such as fliA and flgM .	7	THE TVIA-DEPENDENT DECREASE IN IL-8 EXPRESSION IS INDEPENDENT OF THE INVASION-ASSOCIATED TYPE III SECRETION SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MntR	TU	sitABCD	regulator	17555437	1	ver/dev	In the presence of Mn , MntR represses the expression of sitABCD , through direct binding of specific sites within the promoter regions of these genes .	270	In the presence of Mn ( 2 + ) , MntR represses the expression of mntH and sitABCD , through direct binding of specific sites within the promoter regions of these genes .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	17555437	5	ver/dev	Slauch , J.M. Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	431	Ikeda , J.S. , Janakiraman , A. , Kehres , D.G. , Maguire , M.E. , and Slauch , J.M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	28	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	17555437	5	ver/dev	Ikeda , J.S. , Janakiraman , A. , Kehres , D.G. , Maguire , M.E. , Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	431	Ikeda , J.S. , Janakiraman , A. , Kehres , D.G. , Maguire , M.E. , and Slauch , J.M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	28	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	17993530	58	ver/dev	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	565	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	17	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	19049822	0	ver/dev	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	343	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	17	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	20008066	21	ver/dev	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	630	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	17	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	21722794	5	ver/dev	Both mntH and sitABCD are under the control of MntR	560	Both mntH and sitABCD are under the control of MntR and Fur , and hence are regulated in response to both iron and manganese , and also possibly involving some overlap with respect to the metal specificities of the sensors ( Kehres et al. , 2002b ; Ikeda et al. , 2005 ) .	18	4.1.1. MNTH AND SITABCD (ALIAS MNTABCD)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MntR	TU	sitABCD	regulator	21722794	15	ver/dev	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	1186	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	58	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	Slauch , J. M. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	M. E. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	Maguire Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	D. G. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	Kehres Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	A. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	Janakiraman Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	J. S. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	24596096	15	ver/dev	Ikeda Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .	517	Ikeda , J. S. , Janakiraman , A. , Kehres , D. G. , Maguire , M. E. , and Slauch , J. M. ( 2005 ) Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR and Fur .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	TU	sitABCD	regulator	28553268	12	ver/dev	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .	1675	Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur .	34	ACKNOWLEDGMENTS	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	cpxR	repressor	26300871	25	ver/dev	the expression of the SPI-1 genes when S. Typhimurium is grown in the presence of cpxR _ indicating that the absence of CpxA leads to the repression of the SPI-1 genes through CpxR	441	In this study , we show that deletion of cpxA negatively affects the expression of the SPI-1 genes when S. Typhimurium is grown in LB medium , but only in the presence of cpxR , indicating that the absence of CpxA leads to the repression of the SPI-1 genes through CpxR .	18	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	cpxR	repressor	33751923	16	ver/dev	I-1 ge only in the presence of cpxR , indicating that the absence of CpxA leads to the repression of the SPI-1 genes through CpxR .	525	This study showed that a cpxA mutation leads to almost complete loss of hilA expression at low pH. The mechanism behind the regulation of SPI-1 genes by CpxRA was shown by De La Cruz et al. ( 2015 ) , where they dem-onstrated that deletion of cpxA negatively affects the expression of the SPI-1 genes only in the presence of cpxR , indicating that the absence of CpxA leads to the repression of the SPI-1 genes through CpxR .	17	CPXRA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	ppiA	activator	24858080	7	ver/dev	Our microarray data revealed the activation of at least five CpxR-controlled genes ( including ppiA ) .	289	Our microarray data revealed the activation of at least five CpxR-controlled genes ( including ppiA ) when Salmonella was grown in the presence of CuSO4 in both SLB and M9 , as well as in the presence of ZnSO4 in SLB ( Fig. 1 , Table S3 ) .	6	A CONSORTIUM OF GLOBAL AND SPECIFIC REGULATORY PATHWAYS IS INDUCED IN RESPONSE TO COPPER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
YfhA	gene	sciS	regulator	24079299	2	ver/dev	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of and its homolog FlrC in the upstream regions and ORFs of sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	120	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA ( and its homolog FlrC ) in the upstream regions and ORFs of rcsB and sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfhA	gene	sciS	regulator	24079299	2	ver/dev	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA in the upstream regions and ORFs of sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	120	Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA ( and its homolog FlrC ) in the upstream regions and ORFs of rcsB and sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfhA	gene	sciS	regulator	24079299	5	ver/dev	In the present study , sciS were also predicted to have binding sites of YfhA within their ORFs .	125	In the present study , rcsB and sciS were also predicted to have binding sites of YfhA ( and its homolog FlrC ) within their ORFs ( Additional file 4 ) .	5	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
YfhA	gene	sciS	regulator	24079299	6	ver/dev	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA-P mediated regulation of sciS .	126	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA ( YfhA-P ) mediated regulation of sciS and rcsB .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YfhA	gene	sciS	regulator	24079299	6	ver/dev	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA mediated regulation of sciS .	126	Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA ( YfhA-P ) mediated regulation of sciS and rcsB .	5	RESULTS AND DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	flgA	regulator	33638994	19	ver/dev	These assays confirmed binding of phosphorylated RcsB to flgA Intra-CDS sequences .	398	These assays confirmed binding of phosphorylated RcsB to fepE , osmB and ytfK promoters and to flgA and nlpD Intra-CDS sequences ( Figure 7A and C ) .	26	VALIDATION OF RCSB BOXES IDENTIFIED IN THE GENOME-WIDE ANAL- YSIS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
FabR	gene	ompA	regulator	27004424	7	ver/dev	Moreover , next to UFA biosynthesis , a number of other genes , known to be involved in biofilm formation -LRB- in -RRB- directly regulated by e.g. ribosomal genes , ompA , ompC , ompX , osmB , osmC , sseI , could possibly contribute to the effect of FabR on biofilm formation .	55	Moreover , next to UFA biosynthesis , a number of other genes , known to be involved in biofilm formation , identified to be ( in ) directly regulated by FabR ( e.g. ribosomal genes , ompA , ompC , ompX , osmB , osmC , sseI ) , could possibly contribute to the effect of FabR on biofilm formation .	5	BACKGROUND	nan	1	L1	SPEC	Fact	OTHER	New	Level 1
CRP	gene	pgtP	activator	33563986	1	ver/dev	pgtP transcription levels _ implying that CRP positively regulates pgtP expression	189	crp mutation significantly decreased vrpA and pgtP transcription levels ( Fig. 5g ) , implying that CRP positively regulates vrpA and pgtP expression .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	pgtP	activator	33563986	3	ver/dev	that cAMP-CRP activates pgtP expression through VrpA , facilitating 3GP uptake	203	Collectively , these data indicate that during STM infection of macrophages , the bacterial cAMP-CRP content increases owing to decreased glucose levels in macrophages , and that cAMP-CRP activates pgtP expression through VrpA , facilitating 3GP uptake .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	flhC	activator	16430704	6	ver/dev	The FlhD levels were determined by immunoblotting analysis at various times after flhC transcription was induced by 50 µM IPTG .	171	The FlhD and FlhC levels were determined by immunoblotting analysis at various times after flhD and flhC transcription was induced by 50 µM IPTG .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxR	gene	soxS	activator	11120941	0	ver/dev	In the soxRS system , SoxR protein is activated by nitrosylation to trigger transcription of the soxS gene .	18	In the soxRS system , SoxR protein is activated by oxidation ( 18 ) or nitrosylation ( 11 ) to trigger transcription of the soxS gene .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	11120941	0	ver/dev	In the soxRS system , SoxR protein is activated by oxidation to trigger transcription of the soxS gene .	18	In the soxRS system , SoxR protein is activated by oxidation ( 18 ) or nitrosylation ( 11 ) to trigger transcription of the soxS gene .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	15516576	3	ver/dev	these strains _ perceiving high levels of oxidative-stress in the absence of PQ and/or a role for these gene products in the reduction of the cluster in SoxR ( reduction of the SoxR Fe-S clusters is required to cease activation of soxS )	328	The constitutive level of fpr expression in the gshA , apbC , apbE , and rseC mutants was consistent with these strains perceiving high levels of oxidative stress in the absence of PQ and/or a role for these gene products in the reduction of the cluster in SoxR ( reduction of the SoxR Fe-S clusters is required to cease activation of soxS ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	15516576	3	ver/dev	these strains _ perceiving high levels of oxidative-stress in the absence of PQ and/or a role for these gene products in the reduction of the cluster in SoxR ( reduction of the SoxR Fe-S clusters is required to cease activation of soxS )	328	The constitutive level of fpr expression in the gshA , apbC , apbE , and rseC mutants was consistent with these strains perceiving high levels of oxidative stress in the absence of PQ and/or a role for these gene products in the reduction of the cluster in SoxR ( reduction of the SoxR Fe-S clusters is required to cease activation of soxS ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	15895724	1	ver/dev	When it is converted to an active form , SoxR , enhances transcription of soxS .	429	When it is converted to an active form , SoxR , which increased specifically in the recovering cells in this study , enhances transcription of soxS and increases the level of SoxR protein , a positive regulator stimulating transcription of superoxide anion -- responsive genes such as zwf , which encodes glucose-6-phos-phate dehydrogenase .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	16842216	4	ver/dev	Expression of soxS is activated by superoxide-generating agents via the conversion of its local transcriptional activator SoxR into SoxR * .	348	Expression of soxS is activated by superoxide-generating agents via the conversion of its local transcriptional activator SoxR into an active form ( SoxR * ) .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	16842216	4	ver/dev	Expression of soxS is activated by superoxide-generating agents via the conversion of its local transcriptional activator SoxR into an active form .	348	Expression of soxS is activated by superoxide-generating agents via the conversion of its local transcriptional activator SoxR into an active form ( SoxR * ) .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	25805724	0	ver/dev	SoxR is an activator of soxS .	339	SoxR is an activator of soxS , which in turn can upregulate the expression of efflux pumps .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	25805724	1	ver/dev	SoxR is an activator of soxS .	393	SoxR is an activator of soxS , which in turn can upregulate the expression of efflux pumps .	6	LB 1.00 1.093 (0.093)	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	gene	soxS	activator	31838175	0	ver/dev	the activated SoxR induces the expression of the soxS gene	35	Subsequently , the activated SoxR induces the expression of the soxS gene , and SoxS can , in turn , induce the expression of genes that help to prevent or repair the damage caused by oxidants .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxR	gene	soxS	activator	32468234	4	ver/dev	SoxR activates soxS expression , usually in response to oxidative-stress .	123	SoxR activates soxS expression , usually in response to oxidative stress .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxR	gene	soxS	activator	32468234	14	ver/dev	SoxR is a well-studied transcriptional activator of the MerR family in Salmonellae and , as described before , activates soxS expression in response to oxidative-stress .	170	SoxR is a well-studied transcriptional activator of the MerR family in Salmonellae and , as described before , activates soxS expression in response to oxidative stress .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxR	gene	soxS	activator	32468234	14	ver/dev	SoxR is a well-studied transcriptional activator of the MerR family in Salmonellae and , as described before , activates soxS expression in response to oxidative-stress .	170	SoxR is a well-studied transcriptional activator of the MerR family in Salmonellae and , as described before , activates soxS expression in response to oxidative stress .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SoxR	gene	soxS	activator	33838479	0	ver/dev	SoxR transcriptionally activates the soxS gene	203	The oxidation of SoxR results in a conformational change producing oxidized SoxR ( SoxRox ) , which transcriptionally activates the soxS gene ( Wu and Weiss , 1991 ) .	22	4.3. OXIDATIVE STRESS RESPONSE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	marA	activator	15155237	5	ver/dev	This result demonstrates that in E. coli RamA can mediate an MDR phenotype independently of a functionally intact marA , likely by direct activation of MarA-controlled genes .	78	This result demonstrates that in E. coli RamA can mediate an MDR phenotype independently of a functionally intact marA , likely by direct activation of MarA-controlled genes .	3	MAIN	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	marA	activator	20237076	7	ver/dev	These results , together with the results of the induction of marA by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	marA	activator	20237076	7	ver/dev	These results , together with the results of the induction of marA by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	marA	activator	20237076	7	ver/dev	These results , together with the results of the induction of marA by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .	330	These results , together with the results of the induction of marA , micF and acrAB by salicylate in broth at 378C , and the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate , which in turn activates the expression of the AcrAB efflux pumps , leading to a reduction in ciprofloxacin accumulation .	23	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	marA	activator	21829527	3	ver/dev	Sequencing showed upregulation of MarA was not due to a mutation in the marA promoter or within marR .	99	Sequencing showed upregulation of MarA was not due to a mutation in the marA promoter or within marR .	15	TR 1% 32 8 2 0.12 0.06	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SlyA	gene	siiB	regulator	24021902	5	ver/dev	an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein _ regulated by SlyA c srcA STM2138 SPI-2 effector chaperone	127	pipB2 STM2780 Type III secretion system effector protein , regulated by SlyA siiA STM4257 SPI-4 genes that encode an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein , regulated by SlyA c srcA STM2138 SPI-2 effector chaperone required for systemic infection in c mice sseK2 STM2137 Type III secretion system effector protein c sseL STM2287 Type III secretion system effector protein , functions as a c deubiquitinase in vivo , regulated by SlyA steB STM1629 Type III secretion system effector protein c steC STM1698 Type III secretion system effector protein c STM2239 SPI-12-encoded genes regulated by SsrB , enhance fitness in c vivo , STM2239 encodes a transcriptional regulator STM2340 STM3117 SPI-13-encoded genes with suggested function in c biosynthesis of the cell wall peptidoglycan layer STM3118 c STM3119	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	hmpA	regulator	21833325	0	ver/dev	Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- S -RSB- cluster is reversibly inactivated by NO .	258	Expression of hmpA is under the control of the redox active repressor NsrR ( Bang et al. , 2006 ) , whose [ Fe -- S ] cluster is reversibly inactivated by NO .	12	INDUCIBLE DETOXIFICATION OF RNS ENZYMATIC DETOXIFICATION OF NO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	hmpA	regulator	21833325	0	ver/dev	Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- Fe is reversibly inactivated by NO .	258	Expression of hmpA is under the control of the redox active repressor NsrR ( Bang et al. , 2006 ) , whose [ Fe -- S ] cluster is reversibly inactivated by NO .	12	INDUCIBLE DETOXIFICATION OF RNS ENZYMATIC DETOXIFICATION OF NO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	hmpA	regulator	25107963	2	ver/dev	genes _ involved in nitrosative-stress protection under the control of NsrR ( hmpA , , ygbA , hcp , yeaR-yoaG )	193	Comparably to the genes involved in the shock response , genes involved in nitrosative-stress protection under the control of NsrR ( hmpA , STM14_2185 , ygbA , hcp , yeaR-yoaG ) displayed increased transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	hmpA	regulator	32231649	3	att	Transcription of the NsrR-regulated hmpA and yoaG genes in Salmonella on fruit was also higher when ROS was not attenuated , suggesting that higher levels of ROS may be related to NO levels .	400	Transcription of the NsrR-regulated hmpA and yoaG genes in Salmonella on fruit was also higher when ROS was not attenuated , suggesting that higher levels of ROS may be related to NO levels .	18	MODULATING TOMATO SURFACE NO LEVELS SIGNIFICANTLY AFFECTED SEN COLONIZATION	Salmonella	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	prgK	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
TviA	gene	tviB	regulator	10899868	0	ver/dev	The TviA protein interacts in conjunction with the RcsB regulator protein at the promoter upstream of tviA to control the transcription of tviB -LRB- encoding an enzyme similar to GDP-mannose dehydrogenase , .	203	The TviA protein interacts in conjunction with the RcsB regulator protein at the promoter upstream of tviA to control the transcription of tviB ( encoding an enzyme similar to GDP-mannose dehydrogenase involved tality among mice immunized with CVD 909 ( 3 of 8 [ 38 % ] ) was significantly lower ( P 5 0.0065 ) , yielding a protection rate of 62 % ( Table 4 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhD	gene	STM1344	regulator	25437188	45	ver/dev	STM1344 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .	552	STM1344 ( YdiV ) and Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis [ 168,174 ] .	12	RELATIONSHIP BETWEEN REGULATION OF BIOFILM FORMATION & MOTILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FliZ	gene	bamB	repressor	32571967	8	ver/dev	Because repression of SPI1 expression is partially independent of FliZ , we tested if the bamB effect also functions through rtsA transcription .	145	Because repression of SPI1 expression caused by loss of bamB is partially independent of FliZ ( Fig. 3B ) and because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD , hilC , or rtsA transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	bamB	repressor	32571967	8	ver/dev	Because repression of SPI1 expression is partially independent of FliZ , we tested if the bamB effect also functions through hilC .	145	Because repression of SPI1 expression caused by loss of bamB is partially independent of FliZ ( Fig. 3B ) and because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD , hilC , or rtsA transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	gene	bamB	repressor	32571967	8	ver/dev	Because repression of SPI1 expression is partially independent of FliZ , we tested if the bamB effect also functions through hilD .	145	Because repression of SPI1 expression caused by loss of bamB is partially independent of FliZ ( Fig. 3B ) and because Lin et al. suggested that part of the dsbA effect is HilD dependent , we tested if the bamB effect also functions through hilD , hilC , or rtsA transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	sifA	activator	21059643	4	ver/dev	Thus , SsrB regulates transcription of sifA by both direct activation of H-NS repression .	70	Thus , SsrB regulates transcription of sifA , sifB , and sseJ by both direct activation and relief of H-NS repression .	4	SILENCING BY DISPLACING H-NS BOUND IN POLYMERIZATION AND DIRECTLY ACTIVATES TRANSCRIPTION*□	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	mgtBC	activator	12492857	0	att	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	mgtBC	activator	18407759	3	att	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgtBC	activator	18407759	3	ver/dev	These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- mgtBC .	305	These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .	21	PHOP=PHOQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	STM2603	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssrB	repressor	23690578	1	ver/dev	We establish that the PmrA protein represses transcription of ssrB .	8	We establish that the PmrA protein binds to the promoter and represses transcription of ssrB , a virulence regulatory gene required for expression of the Spi/Ssa type three-secretion system inside macrophages .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	ssrB	repressor	23690578	3	ver/dev	the ssrB promoter abolished repression by the PmrA protein	10	A mutation in the ssrB promoter that abolished repression by the PmrA protein rendered Salmonella as hypervirulent as the pmrA null mutant .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ssrB	repressor	23690578	5	ver/dev	We establish that the PmrA protein down-regulates expression of spi/ssa genes by repressing transcription from the ssrB promoter .	32	We establish that the PmrA protein down-regulates expression of spi/ssa genes by repressing transcription from the ssrB promoter .	3	SALMONELLA PATHOGENICITY ISLAND 2 | CYTOTOXICITY	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	ssrB	repressor	23690578	6	ver/dev	The hypervirulence of the pmrA null mutant can be recapitulated by rendering the ssrB promoter resistant to repression by PmrA .	33	The hypervirulence of the pmrA null mutant can be recapitulated by rendering the ssrB promoter resistant to repression by PmrA .	3	SALMONELLA PATHOGENICITY ISLAND 2 | CYTOTOXICITY	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	17	ver/dev	The PmrA protein appears to repress ssrB directly because : First , the purified PmrA protein protected the − 45 to − 16 region from ATG of of the ssrB gene in-vitro -LRB- Fig .	84	The PmrA protein appears to repress ssrB directly because : First , the purified PmrA protein protected the − 45 to − 16 region from ATG of the ssrB gene in vitro ( Fig. 4B ) , which contains the predicted PmrA binding site in the ssrB promoter ( Fig. 4A ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the OmpR proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in ompR pmrA mutants -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the OmpR proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in ompR -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the OmpR proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in phoP pmrA -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the OmpR proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in phoP -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in ompR pmrA mutants -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	New	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in ompR -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in phoP pmrA -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	27	ver/dev	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP proteins from activating ssrB transcription because there were similarly low levels of ssaG expression in phoP -LRB- Fig .	99	Finally , PmrA 's role as a repressor of ssrB transcription is not simply to prevent the PhoP and OmpR proteins from activating ssrB transcription ( 21 , 36 ) because there were similarly low levels of ssaG expression in phoP , phoP pmrA , ompR , and ompR pmrA mutants ( Fig .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	28	ver/dev	Taken together , the results indicate that PmrA 's effects on ssaG expression result from direct repression of ssrB transcription .	101	Taken together , the results presented in this section indicate that PmrA 's effects on ssaG expression result from direct repression of ssrB transcription .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	ssrB	repressor	23690578	33	ver/dev	To examine the physiological consequences of PmrA repression of ssrB transcription , we examined the kinetics of SPI-2 -- promoted macro-phage death .	126	To examine the physiological consequences of PmrA repression of ssrB transcription , we examined the kinetics of SPI-2 -- promoted macro-phage death , which is critical for Salmonella virulence ( 37 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PmrA	gene	ssrB	repressor	23690578	34	ver/dev	PmrA Reduces Salmonella Virulence by Repressing ssrB Transcription .	132	PmrA Reduces Salmonella Virulence by Repressing ssrB Transcription .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	ssrB	repressor	23690578	35	ver/dev	The results presented above suggested that the hypervirulence phenotype of the pmrA null mutant might be due to PmrA repression of ssrB transcription .	133	The results presented above suggested that the hypervirulence phenotype of the pmrA null mutant might be due to PmrA repression of ssrB transcription .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	36	ver/dev	the ssrB promoter mutant is refractory to repression by the PmrA protein	134	If this notion were the case , one would expect : First , that the ssrB promoter mutant that is refractory to repression by the PmrA protein would display the same hypervirulence phenotype as the pmrA null mutant .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	ssrB	repressor	23690578	38	ver/dev	The antivirulence function of PmrA can be ascribed to its role as transcriptional repressor of the regulatory gene ssrB .	153	The antivirulence function of PmrA can be ascribed to its role as transcriptional repressor of the regulatory gene ssrB , which is essential for expression of genes required for proliferation inside macrophages and systemic infection in mice ( 23 , 41 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PmrA	gene	ssrB	repressor	23690578	40	ver/dev	These results suggest that PmrA repression of ssrB might enable Salmonella to favor dissemination to neighboring cells .	159	These results suggest that PmrA repression of ssrB might enable Salmonella to control bacterial proliferation within a cell and to favor dissemination to neighboring cells .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	ssrB	repressor	23690578	40	ver/dev	These results suggest that PmrA repression of ssrB might enable Salmonella to control bacterial proliferation within a cell .	159	These results suggest that PmrA repression of ssrB might enable Salmonella to control bacterial proliferation within a cell and to favor dissemination to neighboring cells .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L2	SPEC	Analysis	OTHER	New	Level 1
PmrA	gene	ssrB	repressor	23690578	49	ver/dev	Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .	182	Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	ssrB	repressor	24643535	19	ver/dev	Interestingly , the PmrA protein repressed SPI-2 expression in a manner similar to the Fur regulator ; PmrA was shown to repress ssrB transcription .	290	Interestingly , the PmrA protein repressed SPI-2 expression in a manner similar to the Fur regulator ; PmrA was shown to bind to a region overlapping with the SsrB-binding site on the ssrB promoter ( Fig. 4A ) and repress ssrB transcription ( 21 ) .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	sseL	regulator	21625519	13	ver/dev	Subsequently , we were interested in assessing the relative contribution of SsrB to the integrated regulation of sseL .	69	Subsequently , we were interested in assessing the relative contribution of PhoP and SsrB to the integrated regulation of sseL .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	STM3595	activator	31333620	5	ver/dev	Similarly , transcription of STM3595 -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS in .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	STM3595	activator	31333620	5	ver/dev	Similarly , transcription of STM3595 -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS high Mg2 + .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	STM3595	activator	31333620	5	ver/dev	Similarly , transcription of STM3595 -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS low + .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	STM3595	activator	31333620	5	ver/dev	Similarly , transcription of STM3595 -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS Figures 2B , data not shown .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	gene	STM3595	activator	31333620	5	ver/dev	Similarly , transcription of STM3595 -LRB- a gene -RRB- was also upregulated by T13 phosphorylation of H-NS Figures 2B , C not shown .	265	Similarly , transcription of other PhoP/PhoQ-activated genes ( Miller et al. , 1989 ; Soncini et al. , 1996 ) including pagC and STM3595 ( a gene predicted to encode a phosphatase ) was also upregulated by T13 phosphorylation of H-NS in both low and high Mg2 + ( Figures 2B , C , and data not shown ) .	17	T13 PHOSPHORYLATION OF H-NS PARTIALLY RELEASES REPRESSION OF THE	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	hns	activator	17908208	25	ver/dev	those _ observed in the hns single mutant upon induction of LeuO	80	In the hns ompR double mutant , the levels of expression were half of those observed in the hns single mutant upon induction of LeuO ( Fig. 2A ) .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	12453229	15	ver/dev	Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	557	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	12453229	15	ver/dev	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	557	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	12791144	5	ver/dev	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , chemotaxis/aerotaxis are co-ordinately regulated by flhDC	87	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , flagellar biosynthesis and chemotaxis/aerotaxis are co-ordinately regulated by flhDC	6	REGULATION OF INVASION GENES BY CSRA	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	TU	flhDC	regulator	12791144	5	ver/dev	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , chemotaxis/aerotaxis are co-ordinately regulated by flhDC	87	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , flagellar biosynthesis and chemotaxis/aerotaxis are co-ordinately regulated by flhDC	6	REGULATION OF INVASION GENES BY CSRA	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	TU	flhDC	regulator	12791144	5	ver/dev	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , flagellar biosynthesis are co-ordinately regulated by flhDC	87	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , flagellar biosynthesis and chemotaxis/aerotaxis are co-ordinately regulated by flhDC	6	REGULATION OF INVASION GENES BY CSRA	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	TU	flhDC	regulator	12791144	5	ver/dev	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , flagellar biosynthesis are co-ordinately regulated by flhDC	87	Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella and E. coli , flagellar biosynthesis and chemotaxis/aerotaxis are co-ordinately regulated by flhDC	6	REGULATION OF INVASION GENES BY CSRA	Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	TU	flhDC	regulator	12791144	14	ver/dev	flhDC _ known in E. coli to be controlled by CsrA	280	One potential example of an undetected regulator is flhDC , known in E. coli to be controlled by CsrA , but showing little change in expression in the S. typhimurium csrA mutant .	10	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
CsrA	TU	flhDC	regulator	16952964	5	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	421	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	12	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	17074910	13	ver/dev	Of these , CsrA is known to directly regulate the flhDC mRNA in E. coli .	409	Of these , CsrA is known to directly bind and regulate the flhDC mRNA in E. coli ( Romeo , 1998 ; Wei et al. , 2001 ) .	8	FLAGELLAR REGULATORS CONTRIBUTE TO S. TYPHIMURIUM BIOFILM FORMATION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
CsrA	TU	flhDC	regulator	17074910	13	ver/dev	Of these , CsrA is known to directly bind the flhDC mRNA in E. coli .	409	Of these , CsrA is known to directly bind and regulate the flhDC mRNA in E. coli ( Romeo , 1998 ; Wei et al. , 2001 ) .	8	FLAGELLAR REGULATORS CONTRIBUTE TO S. TYPHIMURIUM BIOFILM FORMATION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
CsrA	TU	flhDC	regulator	17074910	24	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	735	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	75	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	19042154	14	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	487	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	43	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	19376870	36	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	687	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	31	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	21166907	1	ver/dev	Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	625	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	38	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	21166907	1	ver/dev	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	625	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	38	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	23443158	16	ver/dev	Wei , B.L. ; Brun-Zinkernagel , A.M. ; Simecka , J.W. ; Pruss , B.M. ; Babitzke , P. ; Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	455	Wei , B.L. ; Brun-Zinkernagel , A.M. ; Simecka , J.W. ; Pruss , B.M. ; Babitzke , P. ; Romeo , T. Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	9	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	24706743	5	ver/dev	CsrA is a positive regulator of flhDC mRNA stability	147	As a control , we included CsrA , which is a positive regulator of flhDC mRNA stability ( 34 ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsrA	TU	flhDC	regulator	24706743	14	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	525	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	7	8	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	25972986	6	ver/dev	J Mol Biol 355:798 -- 808 Epub 2005 Nov 2022 Wei BL , Brun-Zinkernagel AM , Simecka JW , Pruss BM , Babitzke P , Romeo T Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	569	J Mol Biol 355:798 -- 808 Epub 2005 Nov 2022 Wei BL , Brun-Zinkernagel AM , Simecka JW , Pruss BM , Babitzke P , Romeo T ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	27	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	26293911	7	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	334	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	28	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	P. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	Babitzke , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	B.M. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	Pruss , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	J.W. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	Simecka , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	A.M. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	Brun-Zinkernagel , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	B.L. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	28973452	80	ver/dev	Wei , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	446	Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. and Romeo , T. ( 2001 ) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	29247060	1	ver/dev	This is in line with the fact that the flhDC operon is controlled by CsrA in soft rot .	193	This is in line with the fact that the flhDC operon is controlled by CsrA ( 48 , 53 ) and our finding that csrB and csrC increase S. Typhimurium 14028 growth in soft rot .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	TU	flhDC	regulator	29473025	5	ver/dev	Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	845	Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli .	19	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	regulator	31501286	7	ver/dev	Apart from sRNA , flhDC mRNA stability is also regulated by direct binding of the carbon storage regulator CsrA .	117	Apart from sRNA , flhDC mRNA stability is also regulated by direct binding of the carbon storage regulator CsrA ( 33 , 34 ) .	3	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsrA	TU	flhDC	regulator	31501286	7	ver/dev	Apart from sRNA , flhDC mRNA stability is also regulated by direct binding of the carbon storage regulator CsrA .	117	Apart from sRNA , flhDC mRNA stability is also regulated by direct binding of the carbon storage regulator CsrA ( 33 , 34 ) .	3	MAIN	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsrA	TU	flhDC	regulator	34098734	0	ver/dev	the RNA binding protein CsrA exert posttranscriptional control of flhDC .	39	Small RNAs and the RNA binding protein CsrA exert posttranscriptional control of flhDC ( 17 , 18 ) .	3	KEYWORDS SALMONELLA, FLAGELLAR GENE REGULATION, GASTROINTESTINAL INFECTION, HOST- PATHOGEN INTERACTIONS, TRANSCRIPTIONAL REGULATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rstA	repressor	18248433	1	ver/dev	those _ required for repression of rstA , other PhoP-activated genes	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rstA	repressor	18248433	1	ver/dev	those _ required for repression of rstA , other PhoP-activated genes	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	yshA	regulator	21148209	4	ver/dev	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of yshA transcriptional unit , showing that yshA operon belongs to the CRP regulon in Salmonella .	31	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of the yihU -- yshA transcriptional unit , showing that the yihU -- yshA operon belongs to the CRP regulon in Salmonella .	3	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yshA	regulator	21148209	4	ver/dev	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of yshA transcriptional unit , showing that the yihU belongs to the CRP regulon in Salmonella .	31	It is positively regulated by the global transcriptional factor CRP , which , in the presence of cAMP , interacts directly with the regulatory region of the yihU -- yshA transcriptional unit , showing that the yihU -- yshA operon belongs to the CRP regulon in Salmonella .	3	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yshA	regulator	21148209	7	ver/dev	the results suggested that yshA transcriptional unit is regulated by the global regulatory protein CRP	161	In order to identify global regulatory proteins involved in the genetic expression of the yihU -- yshA operon , bioinformatics analyses of the 59 region of yihU were performed , and the results suggested that the yihU -- yshA transcriptional unit is regulated by the global regulatory protein CRP .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	yshA	regulator	21148209	10	ver/dev	In order to determine whether the CRP protein directly regulates yshA , EMSAs were performed with the entire yihU regulatory region .	175	In order to determine whether the CRP protein directly regulates the genetic expression of yihU -- yshA , EMSAs were performed with purified CRP and with the entire yihU regulatory region .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	yshA	regulator	21148209	10	ver/dev	In order to determine whether the CRP protein directly regulates yshA , EMSAs were performed with purified CRP .	175	In order to determine whether the CRP protein directly regulates the genetic expression of yihU -- yshA , EMSAs were performed with purified CRP and with the entire yihU regulatory region .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	lon	repressor	32209674	0	ver/dev	The marked decrease in H-NS amounts appears to result from H-NS degradation because H-NS amounts did not decrease in a lon mutant .	22	The marked decrease in H-NS amounts appears to result from H-NS degradation because H-NS amounts did not decrease in a lon mutant ( Fig. 1A ) , which lacks a cytoplasmic protease ( 27 , 28 ) required for Salmonella virulence ( 29 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
HNS	gene	lon	repressor	32209674	4	ver/dev	For unknown reasons , H-NS basal amounts were slightly lower in the lon mutants than in the wild-type strain in some of the biological replicates .	55	For unknown reasons , H-NS basal amounts were slightly lower in the phoP and lon mutants than in the wild-type strain in some of the biological replicates ( Fig. 1A , − 0.5 h ; see Mendeley : doi : 10.17632 / m4vt7hwrgc .1 ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	hlyE	regulator	17259627	39	ver/dev	For example , E. coli hlyE -LRB- also known as sheA -RRB- , is regulated positively by SlyA .	365	For example , E. coli hlyE ( also known as clyA and sheA ) , which encodes a novel pore-forming toxin , is regulated positively by the global transcriptional factors FNR ( fumarate and nitrate reduction ) and CRP ( cAMP receptor protein ) and by SlyA , and negatively by the nucleoid-structuring protein H-NS ( Wyborn et al. , 2004 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
SlyA	gene	hlyE	regulator	17259627	39	ver/dev	For example , E. coli hlyE -LRB- also known as clyA -RRB- , is regulated positively by SlyA .	365	For example , E. coli hlyE ( also known as clyA and sheA ) , which encodes a novel pore-forming toxin , is regulated positively by the global transcriptional factors FNR ( fumarate and nitrate reduction ) and CRP ( cAMP receptor protein ) and by SlyA , and negatively by the nucleoid-structuring protein H-NS ( Wyborn et al. , 2004 ) .	12	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
SlyA	gene	hlyE	regulator	19763423	2	ver/dev	SlyA nucleoprotein complexes control hlyE expre	407	SlyA and H-NS nucleoprotein complexes control hlyE expre	12	REPUBLIC OF KOREA.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	regulator	23790417	0	ver/dev	It was reported that hlyE could be activated by SlyA , an important regulator of virulence genes in Salmonella .	23	It was reported that hlyE could be activated by the Salmonella transcription factor SlyA ( Oscarsson et al. 2002 ; von Rhein et al. 2009 ) , an important regulator of virulence genes in Salmonella ( Ellison and Miller , 2006 ) .	3	ABSTRACT	Salmonella	1	L1	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	slyA	regulator	27886269	36	ver/dev	slyA is positively regulated by HilD	203	Interestingly , between these genes are SL1265 and SL4248 , located in the S. Typhimurium genomic islands carrying lpxR ( SL1263 ) and SL4247 , respectively , as well as slyA that is positively regulated by HilD ( our unpublished results ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slyA	regulator	27886269	36	ver/dev	slyA is positively regulated by HilD	203	Interestingly , between these genes are SL1265 and SL4248 , located in the S. Typhimurium genomic islands carrying lpxR ( SL1263 ) and SL4247 , respectively , as well as slyA that is positively regulated by HilD ( our unpublished results ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YfeR	gene	yfeR	regulator	21175741	5	att	To further search for additional YfeR-regulated genes we performed a transcriptomic analysis in LB at low-osmolarity , which are the conditions rendering higher yfeR expression levels .	313	To further search for additional YfeR-regulated genes we performed a transcriptomic analysis in LB at low osmolarity , which are the conditions rendering higher yfeR expression levels .	17	REGULATION OF YFEH EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YfeR	gene	yfeR	regulator	21175741	3	ver/dev	Determination of binding of YfeR protein to the yfeR-yfeH intergenic region	244	Determination of transcription start points of yfeR and yfeH genes and binding of YfeR protein to the yfeR-yfeH intergenic region	16	REGULATION OF YFER EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	hup	repressor	21212121	9	ver/dev	in Salmonella , RpoS protein expression was also reduced by the inactivation of both hup genes	344	We found that in Salmonella , RpoS protein expression was also reduced by the inactivation of both hup genes and the earlier data for E. coli C600 ( Balandina et al. , 2001 ) were confirmed here ( see Supplementary Fig .	11	HU AND THE RPOS REGULON	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hilD	repressor	31182495	2	ver/dev	PhoP negatively regulates indirect transcriptional repression of both the hilD .	13	PhoP negatively regulates hilA through multiple distinct mechanisms : direct transcriptional repression of the hilA promoter , indirect transcriptional repression of both the hilD and rtsA promoters , and activation of the small RNA ( sRNA ) PinT .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	repressor	31182495	2	ver/dev	PhoP negatively regulates indirect transcriptional repression of both the hilD .	13	PhoP negatively regulates hilA through multiple distinct mechanisms : direct transcriptional repression of the hilA promoter , indirect transcriptional repression of both the hilD and rtsA promoters , and activation of the small RNA ( sRNA ) PinT .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	repressor	31182495	12	ver/dev	PhoP represses hilA expression by repressing hilD transcription .	87	PhoP represses hilA expression by repressing hilD and rtsA transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	repressor	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating rtsA , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilD	repressor	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating hilC , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilD	repressor	31182495	15	ver/dev	To test if PhoP might repress hilA by regulating hilD , we tested for repression of hilD - , hilC -	90	To test if PhoP might repress hilA by regulating hilD , hilC , or rtsA , we tested for repression of hilD - , hilC - , and rtsA-lacZ transcriptional fusions in wild-type and phoQ24 backgrounds .	3	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	hilD	repressor	31182495	18	ver/dev	Most importantly , repression was still observed in the phoQ24 background , suggesting that PhoP represses expression of the hilD promoter independently of RtsA .	104	Most importantly , repression was still observed in the phoQ24 background , suggesting that PhoP represses expression of the hilD promoter independently of HilD , HilC , or RtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31182495	18	ver/dev	Most importantly , repression was still observed in the phoQ24 background , suggesting that PhoP represses expression of the hilD promoter independently of HilC .	104	Most importantly , repression was still observed in the phoQ24 background , suggesting that PhoP represses expression of the hilD promoter independently of HilD , HilC , or RtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31182495	18	ver/dev	Most importantly , repression was still observed in the phoQ24 background , suggesting that PhoP represses expression of the hilD promoter independently of HilD .	104	Most importantly , repression was still observed in the phoQ24 background , suggesting that PhoP represses expression of the hilD promoter independently of HilD , HilC , or RtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31182495	22	ver/dev	To determine if regulation of hilD is the primary mechanism of repression by PhoP , we tested PhoP-mediated repression in a hilD deletion background .	113	To determine if regulation of hilD is the primary mechanism of repression by PhoP , we tested PhoP-mediated repression in a hilD deletion background .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilD	repressor	31182495	29	ver/dev	FIG 4 PhoP represses hilD transcription .	132	FIG 4 PhoP represses hilD and rtsA transcription .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	repressor	31182495	41	ver/dev	PhoP repression of hilD expression occurs via an unknown mechanism .	199	PhoP repression of hilD expression occurs via an unknown mechanism .	3	RESULTS	unidentified	1	L3	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31182495	43	ver/dev	This suggests that repression of the hilD promoter is not through direct binding by PhoP , though we can not rule out weak interaction with the promoter .	205	This suggests that repression of the hilD promoter is not through direct binding by PhoP , though we can not rule out weak interaction with the promoter .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	hilD	repressor	31182495	59	ver/dev	In this work , we have demonstrated that PhoP represses hilD transcription , rtsA transcription , via the sRNA pinT .	258	In this work , we have demonstrated that PhoP represses hilA expression by four main mechanisms : hilD transcription , rtsA transcription , via the sRNA pinT , and direct transcriptional repression at the hilA promoter .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hilD	repressor	31182495	60	ver/dev	Our data suggest that PhoP transcriptionally represses hilD .	259	Our data suggest that PhoP transcriptionally represses hilD .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	hilD	repressor	31182495	61	ver/dev	a low-affinity PhoP binding site could explain this repression of hilD ( see Fig	260	Although we suspect that this effect is indirect , we can not rule out a low-affinity PhoP binding site that could explain this repression of hilD ( see Fig .	4	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31262841	11	ver/dev	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both rtsA ( and hilD ) .	169	As expected , constitutive activation of PhoP in the phoQ24 background led to significant repression of both hilA and rtsA ( and hilD ) ( 60 ) .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31484980	49	ver/dev	Following this idea , it has been shown that activated PhoP represses expression of hilD ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in dynamic regulatory network governing expression of Salmonella invasion genes .	231	Following this idea , it has been shown that activated PhoP represses expression of hilD , hilA and rtsA , and thus the SP-1 invasion genes67 ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in the complex and dynamic regulatory network governing expression of Salmonella invasion genes .	3	RESULTS	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	31484980	49	ver/dev	Following this idea , it has been shown that activated PhoP represses expression of hilD ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in the complex governing expression of Salmonella invasion genes .	231	Following this idea , it has been shown that activated PhoP represses expression of hilD , hilA and rtsA , and thus the SP-1 invasion genes67 ; therefore , the HilD-SprB-UgtL-PhoP / PhoQ pathway could work as an additional negative feedback control in the complex and dynamic regulatory network governing expression of Salmonella invasion genes .	3	RESULTS	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	hilD	repressor	34202800	13	ver/dev	PhoP negatively regulates indirect repression of both hilD .	328	PhoP negatively regulates hilA via direct repression of hilA transcription , indirect repression of both hilD and rtsA expression , and activation of small RNA ( sRNA ) PinT .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hilD	repressor	34202800	13	ver/dev	PhoP negatively regulates indirect repression of both hilD .	328	PhoP negatively regulates hilA via direct repression of hilA transcription , indirect repression of both hilD and rtsA expression , and activation of small RNA ( sRNA ) PinT .	9	3.3.1. THE PHOP-PHOQ SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliD	activator	9765570	1	att	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	71	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	fliD	activator	9765570	3	att	The class 3 structural genes are of two types ; the flgK , flgL , and fliD genes are transcribed from both a class 2 promoter and a s28-dependent class	78	The class 3 structural genes are of two types ; the flgK , flgL , and fliD genes are transcribed from both a class 2 promoter and a s28-dependent class	6	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilC	regulator	20008574	2	ver/dev	For instance , expression of hilC in the absence of HilA was not tested because hilC is not regulated by hilA .	148	For instance , expression of hilC in the absence of HilA was not tested because hilC is not regulated by hilA ( Rakeman et al. 1999 ; Lostroh et al. 2000 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	yshA	activator	21148209	14	att	In order to determine the CRP-dependent sequences involved in the transcriptional activation of yihU , we constructed transcriptional-fusions encompassing different lengths of the yihU -- yshA promoter region ( Fig. 5a ) .	180	In order to determine the CRP-dependent sequences involved in the transcriptional activation of yihU , we constructed transcriptional fusions encompassing different lengths of the yihU -- yshA promoter region ( Fig. 5a ) .	9	TWO CRP BOXES MEDIATE YIHU TRANSCRIPTIONAL ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	yshA	activator	21148209	23	ver/dev	Hence , we expected that if CRP complex positively regulated yshA operon , its activity should decrease in medium supplemented-with-glucose as the carbon source .	241	Hence , we expected that if the cAMP -- CRP complex positively regulated the yihU -- yshA operon , its activity should decrease in medium supplemented with glucose as the carbon source .	11	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
OmpR	gene	ompB	regulator	23316043	2	ver/dev	Primary characterization of the protein products of the Escherichia coli ompB locus : regulation of synthesis of the OmpR proteins .	342	Primary characterization of the protein products of the Escherichia coli ompB locus : structure and regulation of synthesis of the OmpR and EnvZ proteins .	26	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hcp	regulator	21487806	2	ver/dev	A previous comprehensive study on the regulation of V. cholerae revealed that hcp is regulated by the global regulator CRP .	181	A previous comprehensive study on the regulation of V. cholerae revealed that hcp is regulated by the alternative sigma factor r54 , the global regulator CRP , and the HapR transcription factor [ 23 ] .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hcp	regulator	21487806	2	ver/dev	A previous comprehensive study on the regulation of V. cholerae revealed that hcp is regulated by the global regulator CRP .	181	A previous comprehensive study on the regulation of V. cholerae revealed that hcp is regulated by the alternative sigma factor r54 , the global regulator CRP , and the HapR transcription factor [ 23 ] .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	ompC	activator	30682134	28	ver/dev	CsrA activated UTR of ompC .	255	CsrA activated expression of both ompF and ompC , which encode outer membrane porins ( S2 Table ) , and Holmqvist et al. identified a CLIP-seq peak in the 5 ' - UTR of ompC [ 52 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IscR	gene	invF	regulator	27704705	21	ver/dev	the PinvF probe in EMSA _ supporting the notion that expression of invF is indirectly regulated by IscR	170	Noticeably , IscR was not found to shift the PinvF probe in EMSA , supporting the notion that expression of invF is indirectly regulated by IscR ( Figure S3 ) .	10	2.3 | ISCR BINDS ON THE PROMOTER OF HILD	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	4	ver/dev	Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	4	ver/dev	Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	4	ver/dev	Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	4	ver/dev	Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	4	ver/dev	Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	4	ver/dev	Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .	157	Two of these loci , pmrC and yijP ( STM4118 , hereafter called cptA ) , have been previously shown to be regulated by PmrA ( 15 , 31 , 34 ) , while the role of PmrA-PmrB in the regulation of STM0834 and STM3635 was unknown .	4	RESULTS	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	STM3635	regulator	15866924	6	ver/dev	This analysis demonstrated that neither STM3635 was regulated by PmrA .	159	This analysis demonstrated that neither STM0834 nor STM3635 was regulated by PmrA ( data not shown ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
AraC	gene	lacZ	activator	24272778	21	att	To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .	251	To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured - galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	flgL	activator	9765570	1	att	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	71	Class 3 genes include s28-dependent promoters and encode proteins required late in flagellar assembly , including the flgK , flgL , and fliD genes , and the filament genes fliC and fliB .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	flgL	activator	9765570	3	att	The class 3 structural genes are of two types ; the flgK , flgL , and fliD genes are transcribed from both a class 2 promoter and a s28-dependent class	78	The class 3 structural genes are of two types ; the flgK , flgL , and fliD genes are transcribed from both a class 2 promoter and a s28-dependent class	6	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	TU	flhDC	activator	31501286	24	att	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FliA	gene	eptA	activator	33257526	36	att	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	269	pKD46 Para-lRed recombinase ( Repts Apr ) pBA428 rck transcriptional luciferase fusion pGB135 Empty lucCDABE ( luciferase ) reporter plasmid pJRP33 pGB135 translational luciferase fusion , STM1300 upstream region pJRP34 pGB135 translational luciferase fusion , STM1300 upstream region , putative FliA site mutated pJRP37 pGB135 translational luciferase fusion , sdiA upstream region pJRP38 pGB135 translational luciferase fusion , sdiA upstream region , putative FliA site mutated pJRP39 pGB135 translational luciferase fusion , ycgO upstream region pJRP40 pGB135 translational luciferase fusion , ycgO upstream region , putative FliA site mutated pJRP43 pGB135 translational luciferase fusion , ybeM upstream region pJRP44 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP45 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA site 1 mutated pJRP46 pGB135 translational luciferase fusion , ybeM upstream region , putative FliA sites 1 and 2 mutated pAMD-BA-lacZ Empty lacZ reporter plasmid pJRP54 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of igaA pJRP56 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within STM2275 pJRP58 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within tdcB pJRP60 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within gudT pJRP62 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM0581 pJRP64 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within ygaC pJRP66 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within eptA pJRP68 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter within kbl pJRP70 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of STM4242 pJRP72 pAMD-BA-lacZ transcriptional lacZ fusion , putative FliA-dependent promoter upstream of ompR pBAD24 Empty plasmid with PBAD promoter for arabinose-inducible expression pJRP81 pBAD24-fliA aUnless indicated otherwise , all plasmids were constructed for this work .	5	ACKNOWLEDGMENTS	unidentified plasmid;unidentified plasmid;unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sigD	regulator	27886269	14	ver/dev	Additionally , sigD , a gene not directly regulated by HilD , was included in the binding reactions as an internal negative control .	114	Additionally , a DNA fragment containing the intergenic region upstream of ppk , a gene not regulated by HilD , or sigD , a gene not directly regulated by HilD , was included in the binding reactions as an internal negative control .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	cspD	activator	22275872	12	att	This hypothesis was tested by analyzing expression of osmY , an RpoS-dependent gene , and cspD , a stress response gene that does not belong to the RpoS regulon [ 32,33 ] , in individual Salmonella cells grown in the presence and in the absence of a sublethal concentration of DOC .	514	This hypothesis was tested by analyzing expression of osmY , an RpoS-dependent gene , and cspD , a stress response gene that does not belong to the RpoS regulon [ 32,33 ] , in individual Salmonella cells grown in the presence and in the absence of a sublethal concentration of DOC .	12	DISCUSSION	Salmonella	1	L2	OTHER	Analysis	NEG	Other	Level 1
BglJ	gene	leuO	activator	24659766	4	ver/dev	More recently , it was shown that leuO expression in E. coli can be activated by the BglJ regulators .	18	More recently , it was shown that leuO expression in E. coli can be activated by the RcsB and BglJ regulators ( 26 ) .	2	MAIN	Escherichia coli	0	L2	OTHER	Analysis	OTHER	Other	Level 1
BglJ	gene	leuO	activator	25566242	14	ver/dev	Also , LeuO expression was detected in a phosphate-restricted media ; and recently it was shown that the expression of the leuO gene can be activated by the BglJ regulators	115	Also , LeuO expression was detected in a phosphate-restricted media ( 98 ) ; and recently it was shown that the expression of the leuO gene can be activated by the RcsB and BglJ regulators ( 58 , 101 )	6	LEUO EXPRESSION CONDITIONS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Fis	gene	gyrA	regulator	12898222	1	ver/dev	In electro-phoretic mobility-shift assays , Fis was found to bind to both the gyrA of S. enterica , despite the strong divergence from the E. coli sequence on the part of the former .	9	In electro-phoretic mobility shift assays , Fis was found to bind to both the gyrA and gyrB promoters of S. enterica , despite the strong divergence from the E. coli sequence on the part of the former .	1	ABSTRACT	Salmonella;Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrA	regulator	12898222	28	ver/dev	The retention of Fis-mediated repression of gyrA in S. enterica despite the radically different nucleotide sequence found immediately upstream of the Pribnow box is indicative of the physiological importance for the cell of regulation of gyrase expression by Fis .	217	The retention of Fis-mediated repression of gyrA in S. enterica despite the radically different nucleotide sequence found immediately upstream of the Pribnow box is indicative of the physiological importance for the cell of regulation of gyrase expression by Fis .	18	DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrA	regulator	16999831	13	ver/dev	Fis also binds to and represses the promoters of the gyrA genes in both E. coli and S. Typhimurium , resulting in reduced levels of DNA supercoiling .	142	Fis also binds to and represses the promoters of the gyrA and gyrB genes in both E. coli ( Schneider et al. , 1999 ) and S. Typhimurium ( Keane and Dorman , 2003 ) , resulting in reduced levels of DNA supercoiling .	12	FIS LEVELS INFLUENCE DNA SUPERCOILING AND THE SSRA PROMOTER	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	gyrA	regulator	21276095	2	ver/dev	In E. coli , FIS binds the gyrA promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrA .	40	In E. coli , FIS binds the gyrA and gyrB promoters to repress their expression ( Schneider et al. , 1999 ) ; similarly , FIS has been found to repress S. enterica gyrA and gyrB ( Keane and Dorman , 2003 ) .	3	INTRODUCTION	Escherichia coli;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	gyrA	regulator	21276095	8	ver/dev	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrA might differ between the two species .	179	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of the genes responsible for supercoiling ( gyrA , gyrB and topA ) might differ between the two species .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	gyrA	regulator	21276095	8	ver/dev	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrA might differ between the two species .	179	Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of the genes responsible for supercoiling ( gyrA , gyrB and topA ) might differ between the two species .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Fis	gene	gyrA	regulator	21276095	10	ver/dev	FIS control of gyrA .	184	FIS control of gyrA , gyrB and topA gene expression .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	0	att	The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by Fe3 + via the PmrA -- PmrB two-component system and by low Mg2 + in a process that requires the PhoP -- PhoQ two-component system , the PhoP-activated PmrD protein and the PmrA -- PmrB system .	7	The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by Fe3 + via the PmrA -- PmrB two-component system and by low Mg2 + in a process that requires the PhoP -- PhoQ two-component system , the PhoP-activated PmrD protein and the PmrA -- PmrB system .	2	ABSTRACT	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugd	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	activator	12519186	21	att	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	62	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB medium was determined for strains harbouring lac transcriptional fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugd	activator	12519186	21	att	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	62	b-Galactosidase activity ( Miller units ) expressed by strains grown in LB medium was determined for strains harbouring lac transcriptional fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugd	activator	12519186	28	att	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	93	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	32	att	The ugd promoter was induced inside mammalian cells in a PhoP-dependent fashion because no expression was observed in a phoP mutant ( Fig. 6 ) .	103	The ugd promoter was induced inside mammalian cells in a PhoP-dependent fashion because no expression was observed in a phoP mutant ( Fig. 6 ) .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- the RcsA protein .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- RcsB systems .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- YojN .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- PmrA .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- PhoQ .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- RcsC .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	16	ver/dev	Different pathways of activation of the ugd genes mediated by the PhoP -- PmrB .	54	Different pathways of activation of the ugd and cps genes promoted by various signals and mediated by the PhoP -- PhoQ , PmrA -- PmrB and RcsC -- YojN -- RcsB systems and the RcsA protein .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	12519186	37	ver/dev	Role of the PhoP binding sites for activation of ugd transcription promoted by different signals .	110	Role of the PhoP , PmrA and RcsB binding sites for activation of ugd transcription promoted by different signals .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	15703297	22	att	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo ( Fig. 1 A ) and in-vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	activator	15703297	22	att	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo ( Fig. 1 A ) and in-vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella;Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	ugd	activator	15703297	22	ver/dev	the PhoP-dependent conditions activate ugd expression in Salmonella	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	15703297	22	ver/dev	the PhoP-dependent conditions activate ugd expression in Salmonella	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	15703297	22	ver/dev	the PhoP-dependent conditions activate ugd expression in Salmonella	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	15703297	22	ver/dev	the PhoP-dependent conditions activate ugd expression in Salmonella	167	Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in vivo ( Fig. 1 A ) and in vitro ( 33 ) , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription ( 33 ) , and Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions that activate ugd expression in Salmonella ( C. Mouslim and E.A.G. , unpublished results ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugd	activator	20593264	2	att	For example , despite the absence of the pmrD gene , Yersinia pestis ( Y. pestis ) can mediate PhoP-dependent modification of lipid-A with Ara4N through transcription of the pbgP and ugd genes ( Winfield et al. , 2005 ) .	226	For example , despite the absence of the pmrD gene , Yersinia pestis ( Y. pestis ) can mediate PhoP-dependent modification of lipid A with Ara4N through transcription of the pbgP and ugd genes ( Winfield et al. , 2005 ) .	12	5.3 ADDITIONAL BACTERIA CAPABLE OF MODIFYING LPS	Yersinia pestis	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	sipC	repressor	27185788	4	ver/dev	To confirm the involvement of HilD in bile-mediated repression of SPI-1 , we assessed chromosomal sipC : .	182	To confirm the involvement of HilD in bile-mediated repression of SPI-1 , we assessed chromosomal sipC : : lacZY expression in a hilD mutant ( Fig. 3B ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SoxS	TU	ssrAB	regulator	31838175	4	ver/dev	To examine whether SoxS could directly regulate SPI-2 expression via ssrAB , we performed EMSAs .	206	To examine whether SoxS could directly regulate SPI-2 expression via ssrAB , we performed EMSAs .	20	4. DISCUSSION	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HNS	gene	ompS1	regulator	17908208	8	ver/dev	We report here that the silencing proteins H-NS are the main negative regulators of ompS1 expression in Salmonella .	48	We report here that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	3	B	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	17908208	8	ver/dev	We report here that the silencing proteins H-NS are the main positive regulators of ompS1 expression in Salmonella .	48	We report here that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	3	B	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	17908208	41	ver/dev	DNase footprinting was performed to determine the binding of H-NS to the ompS1 regulatory region in the vicinity of OmpR-binding box IV ( -70 to -200 bp upstream	143	DNase footprinting was performed to determine the binding of H-NS to the ompS1 regulatory region in the vicinity of OmpR-binding box IV ( -70 to -200 bp upstream	9	B	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	17908208	76	ver/dev	Moreover , previous genetic data show that the removal of upstream regions from -310 to -88 gradually caused the derepression of ompS1 expression which , together with Fig. 4D , suggest that H-NS binds at the two nucleation sites .	301	Moreover , previous genetic data show that the removal of upstream regions from -310 to -88 gradually caused the derepression of ompS1 expression ( Fig. 5C , Oropeza et al. , 1999 ; Flores-Valdez et al. , 2003 ) which , together with the H-NS DNase footprinting data ( Fig. 4D ) , suggest that H-NS binds at the two nucleation sites proposed and polymerizes throughout the entire 5 ′ upstream region , a type of interaction that has been proposed for H-NS ( Dorman , 2007 ) .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	ompS1	regulator	17908208	76	ver/dev	Moreover , previous genetic data show that the removal of upstream regions from -310 to -88 gradually caused the derepression of ompS1 expression which , together with the H-NS DNase footprinting data , suggest that H-NS binds at the two nucleation sites .	301	Moreover , previous genetic data show that the removal of upstream regions from -310 to -88 gradually caused the derepression of ompS1 expression ( Fig. 5C , Oropeza et al. , 1999 ; Flores-Valdez et al. , 2003 ) which , together with the H-NS DNase footprinting data ( Fig. 4D ) , suggest that H-NS binds at the two nucleation sites proposed and polymerizes throughout the entire 5 ′ upstream region , a type of interaction that has been proposed for H-NS ( Dorman , 2007 ) .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes StpA in ompS1 739 rather causes a displacement of H-NS , hence preventing its binding at its polymerization .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes StpA in ompS1 739 rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes StpA in ompS1 739 does not block the progress of H-NS , hence preventing its binding at its polymerization .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes StpA in ompS1 739 does not block the progress of H-NS , hence preventing its binding at the nucleation sites .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes H-NS in ompS1 739 rather causes a displacement of H-NS , hence preventing its binding at its polymerization .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes H-NS in ompS1 739 rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes H-NS in ompS1 739 does not block the progress of H-NS , hence preventing its binding at its polymerization .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
HNS	gene	ompS1	regulator	17908208	78	ver/dev	LeuO antagonizes H-NS in ompS1 739 does not block the progress of H-NS , hence preventing its binding at the nucleation sites .	307	LeuO antagonizes H-NS and StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites and its polymerization , and causing a change in DNA structure as shown by the formation of a DNase hypersensitive site ( Figs 6B and C and 4F ) .	13	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	New	Level 1
HNS	gene	ompS1	regulator	18156266	41	ver/dev	H-NS are involved in regulation of ompS1 .	349	LeuO and H-NS are involved in regulation of leuO and ompS1 ( 2 , 5 ) , in addition to bgl , cadC , dsrA , and rovA ( 27 , 45 , 50 , 55 ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	19406898	1	ver/dev	Another key element in the transcriptional regulation of ompS1 is the global regulatory protein H-NS , a nucleoid protein of 137 amino-acids .	24	Another key element in the transcriptional regulation of ompS1 is the global regulatory protein H-NS , a nucleoid protein of 137 amino acids ( 15 kDa ) that negatively regulates its expression ( FloresValdez et al. , 2003 ; De la Cruz et al. , 2007 ) .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	19406898	3	ver/dev	a static curvature plays an important role in the binding of H-NS , the silencer proteins of ompS1	37	Here we present a topological analysis of the ompS1 59 upstream regulatory region and the identification of a static curvature that plays an important role in the binding of H-NS and StpA , the silencer proteins of ompS1 .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	regulator	19406898	4	ver/dev	H-NS regulate ompS1 expression	66	This region was of interest for further research in this work , because it is located in the vicinity of the binding sites of two main transcription factors , LeuO and H-NS , which regulate ompS1 expression ( De la Cruz et al. , 2007 ) .	9	DIMINISHED AND RESTORED OMPS1 DNA CURVATURE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	regulator	19406898	17	ver/dev	a model where the derepression is due to the lowering of the affinity of these two silencing proteins by the change in DNA curvature of the ompS1 regulatory region that the effect of the introduced mutations is indeed on the alteration of the binding of H-NS to its nucleation site	169	These data are in accord with a model where the derepression observed with the pRO310-mt fusion ( Fig. 2 ) is due to the lowering of the affinity of these two silencing proteins by the change in DNA curvature of the ompS1 regulatory region , and with the notion that the effect of the introduced mutations is indeed on the DNA curvature and not on the alteration of the binding of H-NS to its nucleation site .	11	EFFECT OF CURVATURE ON H-NS, STPA AND LEUO BINDING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	19406898	20	ver/dev	Effect of DNA curvature on the binding of H-NS to ompS1 .	184	Effect of DNA curvature on the binding of H-NS , StpA and LeuO to ompS1 .	12	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ompS1	regulator	19447191	4	ver/dev	Moreover it has been reported that the silencing proteins H-NS are the main negative regulators of ompS1 expression in Salmonella .	96	Moreover it has been reported that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	6	4.2. LEUO	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ompS1	regulator	19447191	4	ver/dev	Moreover it has been reported that the silencing proteins H-NS are the main positive regulators of ompS1 expression in Salmonella .	96	Moreover it has been reported that LeuO and the silencing proteins H-NS and StpA are the main positive and negative regulators of ompS1 expression in Salmonella .	6	4.2. LEUO	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MetR	gene	metA	activator	21768276	2	ver/dev	The MetR protein acts as an activator for the transcription of metA .	727	The MetR protein acts as an activator for the transcription of metE , metA , metF , and metH ( 93 ) .	8	TRANSCRIPTION STM3773 PUTATIVE TRANSCRIPTIONAL REGULATOR	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
ClpX	gene	fliC	regulator	29369799	3	ver/dev	L.A. Cummings , W.D. Wilkerson , T. Bergsbaken , B.T. Cookson , In vivo , fliC expression by Salmonella enterica serovar Typhimurium is eterogeneous , regulated by ClpX , Mol .	431	[ 73 ] L.A. Cummings , W.D. Wilkerson , T. Bergsbaken , B.T. Cookson , In vivo , fliC expression by Salmonella enterica serovar Typhimurium is heterogeneous , regulated by ClpX , and anatomically restricted , Mol .	41	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	invF	regulator	10899868	1	ver/dev	Under conditions of low-osmolarity , the transcription of invF is negatively controlled by the RcsB regulator , acting in concert with the TviA protein .	322	Under conditions of low osmolarity , the transcription of iagA , invF , and sipB ( encoding proteins involved in cell invasion ) is negatively controlled by the RcsB regulator , acting in concert with the TviA protein , which is encoded by tviA within the viaB locus .	6	CVD 908-HTRA 9/10 A (90) 10 CVD 909B 3/8 B (38) 62 PBS 10/10 C (100) 0	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	invF	regulator	19901065	1	ver/dev	The transcription of invF is negatively controlled by the RcsB regulator .	29	The transcription of the iagA , invF , and sipB genes is negatively controlled by the RcsB regulator ( 2 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	invF	regulator	25028458	29	att	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	322	Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	hlyE	repressor	19763423	1	ver/dev	SlyA , antagonizes H-NS-medi-ated repression of hlyE transcription in E. coli .	15	SlyA , which is an important regulator of genes required for virulence in Sal-monella ( Ellison and Miller , 2006 ) , antagonizes H-NS-medi-ated repression of hlyE transcription in E. coli ( Wyborn et al. , 2004 ; Lithgow et al. , 2007 ) .	0	Unknown	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	STM1485	regulator	30763640	2	ver/dev	Accordingly , we investigated if RcsB is able to control STM1485 expression when the bacterium is exposed to low pH.	51	Accordingly , we investigated if RcsB is able to control STM1485 expression when the bacterium is exposed to low pH.	3	MAIN	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493	0.5	L2	OTHER	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	regulator	30763640	22	ver/dev	These results allowed us to confirm that the RcsB regulator binds to the specific sequence into the STM1485 promoter region , forming a DNA-RcsB complex to exert a direct repressor effect .	155	These results allowed us to confirm that the RcsB regulator binds to the specific sequence into the STM1485 promoter region , forming a DNA-RcsB complex to exert a direct repressor effect .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	STM1485	regulator	30763640	51	ver/dev	Since the RcsCDB system is considering that this condition induces the asr gene expression in E. coli , we asked ourselves whether in Salmonella the STM1485 gene could be controlled by RcsB activation .	250	Since the RcsCDB system is activated at moderate acidity ( pH 5 ) and considering that this condition induces the asr gene expression in E. coli , we asked ourselves whether in Salmonella the STM1485 gene could be controlled by RcsB activation .	16	4. DISCUSSION	Escherichia coli;Salmonella	0.5	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	regulator	30763640	51	ver/dev	Since the RcsCDB system is activated at moderate acidity , we asked ourselves whether in Salmonella the STM1485 gene could be controlled by RcsB activation .	250	Since the RcsCDB system is activated at moderate acidity ( pH 5 ) and considering that this condition induces the asr gene expression in E. coli , we asked ourselves whether in Salmonella the STM1485 gene could be controlled by RcsB activation .	16	4. DISCUSSION	Salmonella	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	regulator	30763640	53	ver/dev	In spite of this , our results suggest that STM1485 genes are controlled in the same way by the RcsB regulator .	275	In spite of this , our results suggest that asr and STM1485 genes are controlled in the same way by the RcsB regulator .	16	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	STM1485	regulator	30763640	63	ver/dev	Based on those from other authors , we propose that in acid environments the RcsB compete to regulate the STM1485 expression in an opposite manner .	292	Based on our results and those from other authors , we propose that in acid environments the RcsB and RstA transcriptional factors compete to regulate the STM1485 expression in an opposite manner .	16	4. DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	STM1485	regulator	30763640	63	ver/dev	Based on our results , we propose that in acid environments the RcsB compete to regulate the STM1485 expression in an opposite manner .	292	Based on our results and those from other authors , we propose that in acid environments the RcsB and RstA transcriptional factors compete to regulate the STM1485 expression in an opposite manner .	16	4. DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
FNR	gene	ansB	regulator	18559530	0	ver/dev	In E. coli , ansB is positively coregulated by Fnr .	145	In E. coli , ansB is positively coregulated by Fnr and by CRP ( cyclic AMP receptor protein ) , a carbon source utilization regulator ( 24 ) .	6	RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RstA	gene	narZ	regulator	31563538	9	ver/dev	RstA also controls narZ transcription	205	3.4. RstA also controls narZ transcription	13	3.4. RSTA ALSO CONTROLS NARZ TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	cysB	repressor	30682134	22	ver/dev	CsrA also repressed expression of cysB .	240	CsrA also repressed expression of cysB , which encodes a LysR-family transcriptional regulator of cysteine biosynthesis that in E. coli is critical for expression of adiA and participates in the acid shock response [ 82,83 ] .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IHF	gene	spvR	repressor	11553591	6	ver/dev	the positive regulator IHF could indicate that loss of RpoS , but not of IHF , ensures a significant repression of the spvR gene in the intracellular environment of fibroblasts	354	No overgrowing mutant was selected with a defect in the positive regulator IHF , which could indicate that loss of RpoS , but not of IHF , ensures a significant repression of the spvR gene in the intracellular environment of fibroblasts .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
PhoP	gene	amgR	regulator	26231375	4	ver/dev	PhoP also binds to the promoter region of the amgR with lower affinity and transcribes the AmgR antisense RNA , resulting in an RNase E-dependent degradation of the mgtC portion of the mgtCBR messages .	60	PhoP also binds to the promoter region of the amgR with lower affinity and transcribes the AmgR antisense RNA , resulting in an RNase E-dependent degradation of the mgtC portion of the mgtCBR messages .	6	REGULATION AT THE LEVEL OF TRANSCRIPTION ELONGATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	6	ver/dev	At the same time , PhoP also binds to the amgR promoter located in the intergenic region between the mgtB genes .	74	At the same time , PhoP also binds to the amgR promoter located in the intergenic region between the mgtC and mgtB genes and transcribes AmgR RNA towards the mgtC coding region ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	6	ver/dev	At the same time , PhoP also binds to the amgR promoter located in the intergenic region between the mgtC genes .	74	At the same time , PhoP also binds to the amgR promoter located in the intergenic region between the mgtC and mgtB genes and transcribes AmgR RNA towards the mgtC coding region ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	7	ver/dev	PhoP binds to the amgR with different affinities , the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition .	76	PhoP binds to both promoters for the mgtCBR operon and the amgR with different affinities , the former higher and the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition such as low Mg2 + media ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	7	ver/dev	PhoP binds to the amgR with different affinities , the former higher , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition .	76	PhoP binds to both promoters for the mgtCBR operon and the amgR with different affinities , the former higher and the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition such as low Mg2 + media ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	7	ver/dev	PhoP binds to the amgR with different affinities , the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in media .	76	PhoP binds to both promoters for the mgtCBR operon and the amgR with different affinities , the former higher and the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition such as low Mg2 + media ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	7	ver/dev	PhoP binds to the amgR with different affinities , the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in low Mg2 .	76	PhoP binds to both promoters for the mgtCBR operon and the amgR with different affinities , the former higher and the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition such as low Mg2 + media ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	7	ver/dev	PhoP binds to the amgR with different affinities , the former higher , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in media .	76	PhoP binds to both promoters for the mgtCBR operon and the amgR with different affinities , the former higher and the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition such as low Mg2 + media ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	regulator	26231375	7	ver/dev	PhoP binds to the amgR with different affinities , the former higher , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in low Mg2 .	76	PhoP binds to both promoters for the mgtCBR operon and the amgR with different affinities , the former higher and the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition such as low Mg2 + media ( Lee and Groisman , 2010 ) .	8	REGULATION AT THE LEVEL OF MRNA STABILITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrB	activator	31182500	0	ver/dev	PhoP is known to repress the expression of SPI-1 genes , while activating the expression of pmrB , inside macrophages .	177	PhoP is a response regulator and is known to repress the expression of SPI-1 genes ( 48 ) , while activating the expression of pag genes , including mgtCB , pmrB , and SPI-2 genes , inside macrophages .	4	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	csgD	activator	16313619	0	ver/dev	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	40	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	activator	16313619	0	ver/dev	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	40	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	activator	22336758	15	ver/dev	Consequently , we conclude that besides upregulation of RpoS , other Hfq-dependent factor are required to restore csgD morphotype expression in the hfq mutant of UMR1 .	130	Consequently , we conclude that besides upregulation of RpoS , other Hfq-dependent factor ( s ) are required to restore csgD and rdar morphotype expression in the hfq mutant of UMR1 .	2	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	csgD	activator	22336758	21	ver/dev	To further distinguish between the contribution of RpoS to csgD morphotype expression , we compared the phenotype of an arcZ mutant with an rpoS mutant in the MAE52 strain background .	229	To further distinguish between the contribution of RpoS and ArcZ to csgD and rdar morphotype expression , we compared the phenotype of an arcZ mutant with an rpoS mutant in the MAE52 strain background .	2	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	csgD	activator	25437188	29	att	In addition , the RpoS-dependent sRNA SdsR identified as a positive regulator of rdar phenotype development controls csgD expression most likely via a transcriptional regulator ( Figure 2 ) [ 104 ] .	327	In addition , the RpoS-dependent sRNA SdsR identified as a positive regulator of rdar phenotype development controls csgD expression most likely via a transcriptional regulator ( Figure 2 ) [ 104 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	csgD	activator	25437188	11	ver/dev	This finding also suggests that bistable expression of csgD is regulated via RpoS and/or upregulation of promoter activity .	198	This finding also suggests that bistable expression of csgD is regulated via RpoS and/or upregulation of promoter activity [ 64 ] .	8	REGULATION OF CSGD TRANSCRIPTION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	csgD	activator	25437188	31	ver/dev	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by RtsA .	339	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs ( see above ) , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator , RtsA [ 86,87,123 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	activator	25437188	31	ver/dev	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator .	339	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs ( see above ) , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator , RtsA [ 86,87,123 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	activator	25437188	31	ver/dev	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator .	339	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs ( see above ) , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator , RtsA [ 86,87,123 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	activator	25437188	31	ver/dev	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator .	339	Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs ( see above ) , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator , RtsA [ 86,87,123 ] .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	csgD	activator	32604994	25	att	Activation at temperatures below 30 ◦ C is known to represent RpoS-dependent transcription of csgD .	448	Activation at temperatures below 30 ◦ C is known to represent RpoS-dependent transcription of csgD .	14	4. DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	csgD	activator	33251260	10	ver/dev	These data indicated that S11923-3 RpoS enhanced the expression activity of csgD promoter	298	These data indicated that S11923-3 RpoS enhanced the expression activity of csgD promoter , and loss of the RpoS resulted in reduced expression activity of csgD promoter .	17	RESIDUE L193P CONTRIBUTED TO THE RPOS EXPRESSION DURING BACTERIAL BIOFILM	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	csgD	activator	33251260	16	ver/dev	Overall , the results of RpoS activities indicated that S11923-3 RpoS had stronger effects on biofilm formation in S. Pullorum by activating csgD promotor .	358	Overall , the results of RpoS activities indicated that S11923-3 RpoS ( 193P ) had stronger effects on biofilm formation in S. Pullorum by enhancing the afinity to RNAP and activating csgD promotor .	18	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	csgD	activator	33251260	18	ver/dev	RpoS can enhance binding activity to expression activity of csgD gene promoter ,	365	In conclusion , we found a new potential amino acid site ( residue 193P ) in RpoS that can enhance the RpoS expression level , binding activity to RNAP and expression activity of csgD gene promoter , resulting in enhanced biofilm formation in S. Pullorum .	18	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RpoS	gene	csgD	activator	33251260	18	ver/dev	RpoS can enhance binding activity to RNAP activity of csgD gene promoter ,	365	In conclusion , we found a new potential amino acid site ( residue 193P ) in RpoS that can enhance the RpoS expression level , binding activity to RNAP and expression activity of csgD gene promoter , resulting in enhanced biofilm formation in S. Pullorum .	18	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RpoS	gene	csgD	activator	33251260	18	ver/dev	RpoS can enhance binding activity to expression activity of csgD gene promoter ,	365	In conclusion , we found a new potential amino acid site ( residue 193P ) in RpoS that can enhance the RpoS expression level , binding activity to RNAP and expression activity of csgD gene promoter , resulting in enhanced biofilm formation in S. Pullorum .	18	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RpoS	gene	csgD	activator	33251260	18	ver/dev	RpoS can enhance binding activity to RNAP activity of csgD gene promoter ,	365	In conclusion , we found a new potential amino acid site ( residue 193P ) in RpoS that can enhance the RpoS expression level , binding activity to RNAP and expression activity of csgD gene promoter , resulting in enhanced biofilm formation in S. Pullorum .	18	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CysB	gene	cysP	regulator	20600858	3	att	Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9-minimal-medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative-stress .	181	Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9 minimal medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative stress .	16	3.4. CYSTEINE BIOSYNTHESIS IS CRITICAL DURING PERIODS OF OXIDATIVE STRESS	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysP	regulator	24659766	26	ver/dev	Stoichiometry of binding of CysB to cysP promoter regions of Salmonella typhimurium .	559	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	44	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysP	regulator	27530757	4	ver/dev	Stoichiometry of binding of CysB to cysP promoter regions of Salmonella typhimurium .	315	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	18	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysP	regulator	30538683	11	ver/dev	Stoichiometry of binding of CysB to cysP promoter regions of Salmonella typhimurium .	444	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	26	FUNDING	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	osmC	activator	33751923	21	ver/dev	When phosphorylated , RcsB binds RcsA to activate expression of osmC .	645	When phosphorylated , RcsB binds RcsA to activate expression of several genes , such as osmB , osmC , bdm , ftsZ , rprA , wza , and rcsA .	25	RCSBCD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CreB	gene	talA	regulator	25136333	1	ver/dev	It has been demonstrated that CreB can control the expression of talA .	1090	It has been demonstrated that CreB can control the expression of talA , an enzyme associated with the shuttling of glyceraldehyde-3-phophate away from glycolysis to the non-oxidative PPP ( Avison et al. , 2001 ) .	14	MODIFICATIONS IN GENERAL CELL METABOLISM COMPARING ST24WT AND ST24CHX	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	phoP	activator	18792679	20	att	PhoQlPhoP 's sole role in the PmrD-mediated pathway is to promote PmrD expression because transcription of the pmrD gene from a heterologous promoter renders production of PmrA-activated mRNAs phoP - and phoQ-independent .42 Moreover , the PhoP-regulated PmrD protein functions at a posttranslationallevel because expression ofPmrA-activared genes was still phoP - andpmrD-dependent when thepmrA andpmrBgenes were expressed using a heterologous promoter and ribosome-binding site .	234	PhoQlPhoP 's sole role in the PmrD-mediated pathway is to promote PmrD expression because transcription of the pmrD gene from a heterologous promoter renders production of PmrA-activated mRNAs phoP - and phoQ-independent .42 Moreover , the PhoP-regulated PmrD protein functions at a posttranslationallevel because expression ofPmrA-activared genes was still phoP - andpmrD-dependent when thepmrA andpmrBgenes were expressed using a heterologous promoter and ribosome-binding site .	9	PHOP AS A CO-ACTIVATOR PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	cse1	repressor	28270274	0	ver/dev	Previously , we have determined that the cse1 promoter is repressed by the global regulators H-NS and LRP whereas LeuO participates in its positive regulation ; also , it can be expressed independently of LeuO in N-MM .	96	Previously , we have determined that the cse1 promoter is repressed by the global regulators H-NS and LRP whereas LeuO participates in its positive regulation ; also , it can be expressed independently of LeuO in N-MM [ 22 ] .	15	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
DksA	gene	hmp	activator	22311927	11	ver/dev	Our investigations indicate that DksA does not appear to contribute to hmp transcription	237	Our investigations indicate that DksA does not appear to contribute to hmp transcription , and dksA-deficient and hmp-deficient Salmonella strains display distinct hypersusceptibilities to NO .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
Fis	gene	dps	repressor	32900812	6	ver/dev	Fis represses dps transcription by RNA polymerase .	71	Fis represses dps transcription by RNA polymerase containing the RpoD sigma factor , but not RpoS ( 58 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	flhDC	repressor	31501286	25	ver/dev	This approach allowed detection of possible posttranscriptional effects on flhDC expression , since reductions in flagellar expression and motility could not occur through transcriptional repression of the native flhDC promoter when SoxS was ectopically expressed .	207	This approach allowed detection of possible posttranscriptional effects on flhDC expression , since reductions in flagellar expression and motility could not occur through transcriptional repression of the native flhDC promoter when MarA , SoxS , Rob , or RamA was ectopically expressed .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	flhDC	repressor	31501286	33	ver/dev	To test whether translation of flhDC mRNA was inhibited by SoxS expression , we generated a 3 FLAG epitope-tagged version of FlhC-3 FLAG .	228	To test whether translation of flhDC mRNA was inhibited by SoxS expression , we generated a 3 FLAG epitope-tagged version of FlhC ( FlhC-3 FLAG ) expressed by the tetracycline-inducible flhDC construct , similar to the work of Saini and coworkers ( 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	Iris germanica;Iris germanica	0	L3	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	flhDC	repressor	31501286	33	ver/dev	To test whether translation of flhDC mRNA was inhibited by SoxS expression , we generated a 3 FLAG epitope-tagged version of FlhC .	228	To test whether translation of flhDC mRNA was inhibited by SoxS expression , we generated a 3 FLAG epitope-tagged version of FlhC ( FlhC-3 FLAG ) expressed by the tetracycline-inducible flhDC construct , similar to the work of Saini and coworkers ( 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	Iris germanica	0	L3	SPEC	Other	OTHER	Other	Level 1
SoxS	TU	flhDC	repressor	31501286	36	ver/dev	FIG 3 Production of SoxS _ resulting in posttranscriptional repression of flhDC	269	FIG 3 Production of MarA , SoxS , Rob , and RamA resulting in posttranscriptional repression of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	flhDC	repressor	31501286	38	ver/dev	Posttranscriptional repression of flhDC expression by SoxS is hfq independent .	282	Posttranscriptional repression of flhDC expression by SoxS is hfq independent .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	repressor	31501286	40	ver/dev	an Hfq-dependent sRNA _ mediating repression of flhDC when SoxS was expressed	284	Specifically , we explored the possibility of an Hfq-dependent sRNA mediating repression of flhDC when SoxS was expressed ( Fig. 5 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	TU	flhDC	repressor	31501286	42	ver/dev	FIG 4 Moderate constitutive levels of SoxS _ resulting in posttranscriptional repression of flhDC	304	FIG 4 Moderate constitutive levels of SoxS resulting in posttranscriptional repression of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	TU	flhDC	repressor	31501286	43	ver/dev	Consistent with SoxS _ inhibiting flhDC expression	315	Consistent with SoxS inhibiting flhDC expression , the soxRCon mutant showed reduced motility , compared to the wild-type strain ( Fig. 5B ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	SPEC	Other	OTHER	New	Level 1
SoxS	TU	flhDC	repressor	31501286	47	ver/dev	SoxS , however , primarily controls flhDC expression through a posttranscriptional pathway , resulting in decreased translation of flhDC .	448	SoxS , however , primarily controls flhDC expression through a posttranscriptional pathway , resulting in decreased translation of flhDC .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	dsbA	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilD independently of InvF .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	dsbA	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilD independently of both HilA .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	rpoS	regulator	11814668	2	ver/dev	overall expression was a ¡ ected to the same extent as seen in the rpoS mutant leading to the conclusion that SlyA is also not a main regulator of dsb	150	When activity of the dsbA : : lacZ transcriptional fusion was assayed in a slyA null mutant , induction of dsbA expression at the onset of stationary phase was still observed , and overall expression was a ¡ ected to the same extent as seen in the rpoS mutant ( Fig. 3 ) leading to the conclusion that SlyA is also not a main regulator of dsbA .	9	3. RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	rpoS	regulator	9284144	10	att	Recent studies with Salmonella rpoS expression suggest that conditions encountered within host cells may partially resemble stationary-phase ( 20 ) ; however , the patterns of SlyA-regulated proteins were significantly different in stationary-phase and during infection of macrophages .	177	Recent studies with Salmonella rpoS expression suggest that conditions encountered within host cells may partially resemble stationary phase ( 20 ) ; however , the patterns of SlyA-regulated proteins were significantly different in stationary phase and during infection of macrophages .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	flgH	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgH by introduction of a null mutation in J. Bacteriol .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgH	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgH by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgH	repressor	9765570	4	ver/dev	Like all genes , mutations in any of flgH result in FlgM-dependent inhibition of s28 activity .	90	Like all genes involved in HBB assembly , mutations in any of the flgA , flgH , and flgI genes result in FlgM-dependent inhibition of s28 activity ( 8 ) .	6	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	repressor	19835951	1	ver/dev	On the other hand , the transcriptional regulator Crp , previously described as an activator of hlyE transcription in Escherichia coli , is involved in transcriptional repression of hlyE in S. Typhi .	12	On the other hand , the transcriptional regulator Crp , previously described as an activator of hlyE transcription in Escherichia coli , is involved in transcriptional repression of hlyE in S. Typhi .	2	ABSTRACT	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	repressor	19835951	8	ver/dev	The Crp regulator is involved in transcriptional repression of S. Typhi hlyE	162	3.2. The Crp regulator is involved in transcriptional repression of S. Typhi hlyE	16	3.2. THE CRP REGULATOR IS INVOLVED IN TRANSCRIPTIONAL REPRESSION OF S. TYPHI HLYE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hlyE	repressor	19835951	10	ver/dev	increased b-galactosidase activity in comparison with the parental strain _ suggesting that Crp is involved in downregulation of hlyE transcription in S. Typhi	170	In Fig. 5A , we observed that the crp mutant exhibited increased b-galactosidase activity in comparison with the parental strain , suggesting that Crp is involved in downregulation of hlyE transcription in S. Typhi .	16	3.2. THE CRP REGULATOR IS INVOLVED IN TRANSCRIPTIONAL REPRESSION OF S. TYPHI HLYE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	hlyE	repressor	19835951	12	ver/dev	All these results together suggest that Crp is involved in downregulation of hlyE in S. Typhi .	183	All these results together suggest that Crp is involved in downregulation of hlyE in S. Typhi .	16	3.2. THE CRP REGULATOR IS INVOLVED IN TRANSCRIPTIONAL REPRESSION OF S. TYPHI HLYE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	hlyE	repressor	19835951	13	ver/dev	Moreover , the addition of glucose to the growth medium results in decreasing the hlyE mRNA , suggesting that there is another factor related to catabolite-repression , different from Crp , involved in downregulation of hlyE	184	Moreover , the addition of glucose to the growth medium results in decreasing the hlyE mRNA , suggesting that there is another factor related to catabolite repression , different from Crp , involved in downregulation of hlyE	16	3.2. THE CRP REGULATOR IS INVOLVED IN TRANSCRIPTIONAL REPRESSION OF S. TYPHI HLYE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	hlyE	repressor	19835951	20	ver/dev	In addition , we found that Crp is involved in downregulation of hlyE in S. Typhi .	230	In addition , we found that Crp is involved in downregulation of hlyE in S. Typhi .	17	4. DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hlyE	repressor	24885225	11	ver/dev	Nevertheless , addition of glucose to the growth medium results in a decrease of hlyE mRNA in S. Typhi Δcrp mutant , suggesting that there is another factor related to catabolite-repression , different from CRP , involved in down-regulation of hlyE in S. Typhi .	49	Nevertheless , addition of glucose to the growth medium results in a decrease of hlyE mRNA in S. Typhi Δcrp mutant , suggesting that there is another factor related to catabolite repression , different from CRP , involved in down-regulation of hlyE in S. Typhi [ 14 ] .	3	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	hlyE	repressor	24885225	19	ver/dev	Nevertheless , genetic experiments showed that CRP participates in the negative regulation of hlyE in S. Typhi since crp deletion led to increased β-galactosidase activit .	61	Nevertheless , genetic experiments showed that CRP participates in the negative regulation of hlyE in S. Typhi since crp deletion led to increased β-galactosidase activity associated to the ΔhlyE : : lacZ strain [ 14 ] .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hlyE	repressor	24885225	24	ver/dev	Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .	103	CRP and Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay using purified CRP activated with cAMP and the DNA corresponding to the taiA -- hlyE promoter region .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	hlyE	repressor	24885225	24	ver/dev	CRP participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .	103	CRP and Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay using purified CRP activated with cAMP and the DNA corresponding to the taiA -- hlyE promoter region .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	hlyE	repressor	24885225	24	ver/dev	CRP participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .	103	CRP and Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay using purified CRP activated with cAMP and the DNA corresponding to the taiA -- hlyE promoter region .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	hlyE	repressor	24885225	29	ver/dev	Thus , CRP might repress hlyE expression by repressing rpoS in S. Typhi .	109	Thus , CRP might repress hlyE expression by repressing rpoS in S. Typhi .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
PhoP	TU	phoPQ	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	TU	phoPQ	activator	14742517	0	att	Mutations in the phoPQ operon affect the expression of two sets of genes , the PhoP-activated genes ( pag ) and	22	Mutations in the phoPQ operon affect the expression of two sets of genes , the PhoP-activated genes ( pag ) and	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	phoPQ	activator	17158330	5	att	Despite synthesizing the PhoP protein constitutively , there was no occupancy of PhoP-activated promoters ( Fig. 3C ) or transcription of PhoP-activated genes ( Fig. 3D ) in the strain with the -- 35 sequence in the phoPQ promoter growing under repressing conditions .	23	Despite synthesizing the PhoP protein constitutively , there was no occupancy of PhoP-activated promoters ( Fig. 3C ) or transcription of PhoP-activated genes ( Fig. 3D ) in the strain with the -- 35 sequence in the phoPQ promoter growing under repressing conditions .	4	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	TU	phoPQ	activator	17158330	2	ver/dev	a regulated promoter is activated by the PhoP protein transcription in one with the wild-type phoPQ promoter -LSB- is , harboring the PhoP box is responsible for transcriptional autoregulation	19	The PhoP and PhoQ proteins are encoded in a bi-cistronic operon that is transcribed from two promoters : a constitutive promoter that provides the basal levels of these proteins required for sensing and responding to changes in environmental conditions , and a regulated promoter that is activated by the PhoP protein transcription in two isogenic strains : one with the wild-type phoPQ promoter [ that is , harboring the PhoP box that is responsible for transcriptional autoregulation ( 13 ) ] and one in which the PhoP box was replaced by a consensus -- 35 sequence ( Fig. 3A ) .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	TU	phoPQ	activator	17158330	2	ver/dev	a regulated promoter is activated by the PhoP protein transcription in one with the wild-type phoPQ promoter -LSB- is , harboring the PhoP box is responsible for transcriptional autoregulation	19	The PhoP and PhoQ proteins are encoded in a bi-cistronic operon that is transcribed from two promoters : a constitutive promoter that provides the basal levels of these proteins required for sensing and responding to changes in environmental conditions , and a regulated promoter that is activated by the PhoP protein transcription in two isogenic strains : one with the wild-type phoPQ promoter [ that is , harboring the PhoP box that is responsible for transcriptional autoregulation ( 13 ) ] and one in which the PhoP box was replaced by a consensus -- 35 sequence ( Fig. 3A ) .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	TU	phoPQ	activator	17158330	4	ver/dev	the steady-state levels _ achieved by the strain with the wild-type phoPQ promoter after induction of the PhoP/PhoQ system	21	In contrast , the strain with the -- 35 sequence in the phoPQ promoter produced the PhoP protein constitutively ( Fig. 3B ) at levels that were similar to the steady-state levels achieved by the strain with the wild-type phoPQ promoter after induction of the PhoP/PhoQ system ( Fig. 3B ) .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	phoPQ	activator	17158330	4	ver/dev	the steady-state levels _ achieved by the strain with the wild-type phoPQ promoter after induction of the PhoP/PhoQ system	21	In contrast , the strain with the -- 35 sequence in the phoPQ promoter produced the PhoP protein constitutively ( Fig. 3B ) at levels that were similar to the steady-state levels achieved by the strain with the wild-type phoPQ promoter after induction of the PhoP/PhoQ system ( Fig. 3B ) .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	TU	phoPQ	activator	23782700	4	att	The Transcriptional Activity of phoPQ Is Down-regulated by the Action of C18 :2 -- Taking into account that phoPQ expression is subjected to autoregulation as part of the PhoP/PhoQ regulon ( 40 ) , the concerted down-regulation in the expression of PhoP-activated genes allowed us to predict that the transcriptional activity of phoP would be turned off when bacteria are grown in the presence of LCUFAs .	203	The Transcriptional Activity of phoPQ Is Down-regulated by the Action of C18 :2 -- Taking into account that phoPQ expression is subjected to autoregulation as part of the PhoP/PhoQ regulon ( 40 ) , the concerted down-regulation in the expression of PhoP-activated genes allowed us to predict that the transcriptional activity of phoP would be turned off when bacteria are grown in the presence of LCUFAs .	3	EXPERIMENTAL PROCEDURES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	TU	phoPQ	activator	23782700	7	att	We demonstrated that free LCUFAs specifically repress the PhoP/PhoQ system because they down-regulated the expression of both the phoPQ operon and PhoP-activated genes at the transcriptional level , whereas these compounds exerted no effect on genes controlled by other signal transduction mechanisms .	287	We demonstrated that free LCUFAs specifically repress the PhoP/PhoQ system because they down-regulated the expression of both the phoPQ operon and PhoP-activated genes at the transcriptional level , whereas these compounds exerted no effect on genes controlled by other signal transduction mechanisms .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	TU	phoPQ	activator	32834002	1	att	We have previously noted that phoPQ null mutants have lower expression of macAB when grown in InSPI2 medium [ 50 ] , while others have seen that S. Typhi production of MacA protein under low magnesium conditions is PhoP-dependent [ 83 ] .	309	We have previously noted that phoPQ null mutants have lower expression of macAB when grown in InSPI2 medium [ 50 ] , while others have seen that S. Typhi production of MacA protein under low magnesium conditions is PhoP-dependent [ 83 ] .	15	WE THUS DO NOT EXCLUDE A DIRECT ROLE FOR MACAB IN OXIDATIVE STRESS RESISTANCE IN SALMONELLA	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	repressor	15661008	28	ver/dev	HilE negatively regulates hilA transcription .	381	HilE interacts with HilD and negatively regulates hilA transcription ( Baxter et al. , 2003 ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	15765064	32	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimu-rium invasive phenotype .	217	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimu-rium invasive phenotype .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	15790293	16	ver/dev	HilE negatively regulates hilA transcription and expression of Salmonella enterica serovar Typhimurium invasive phenotype .	404	HilE interacts with HilD and negatively regulates hilA transcription and expression of Salmonella enterica serovar Typhimurium invasive phenotype .	30	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	16045614	12	ver/dev	HilD _ suggesting that HilE represses expression of hilA by inhib-iting the activity of HilD	63	Using two-hybrid analysis it was determined that HilE interacts with HilD suggesting that HilE represses expression of hilA by inhib-iting the activity of HilD ( Baxter et al. , 2003 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilE	gene	hilA	repressor	16495536	7	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	458	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	12	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	16585772	8	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	232	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	5	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	16949866	44	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	571	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	27	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	17993530	8	ver/dev	HilE has been shown via two-hybrid studies to interact with HilD , suggesting that HilE represses hilA by directly preventing HilD function .	43	HilE has been shown via two-hybrid studies to interact with HilD , suggesting that HilE represses hilA by directly preventing HilD function ( 7 ) .	2	MAIN	hybrid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include HilD , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include CsrB , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include FadD , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include EnvZ/OmpR , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include FliZ , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include BarA/SirA , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include Fis , HU , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	18563621	0	ver/dev	Positive regulators include some nucleoid binding proteins , while HilE are negatively regulating hilA transcription .	18	Positive regulators include BarA/SirA , FliZ , EnvZ/OmpR , FadD , CsrB , HilD and some nucleoid binding proteins ( Fis , HU ) , while Pag , HilE , Ams and the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription ( Altier et al. 2000a , b Fahlen et al. 2000 ; Lucas et al. 2000 ; Wilson et al. 2001 ; Schechter et al. 2003 ; Baxter et al. 2003 ) .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	19074398	46	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	584	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	20008574	20	ver/dev	2003 HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	341	Baxter , M. A. , T. F. Fahlen , R. L. Wilson and B. D. Jones , 2003 HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	8	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	21680637	71	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	379	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	21	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	24018968	16	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	267	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	19	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	25182488	31	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	673	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	4	8	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	25547794	18	ver/dev	We have shown by two-hybrid analysis that HilE interacts with HilD to repress hilA transcription .	207	We have shown by two-hybrid analysis that HilE interacts with HilD to repress hilA transcription ( 39 ) .	5	DISCUSSION	hybrid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	repressor	25547794	38	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	506	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	33	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	26300871	44	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	913	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	25	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	26441883	39	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	597	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	18	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	27185788	21	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	430	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	18	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	27564394	21	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	1222	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	30	ACKNOWLEDGMENTS	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	27601571	55	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	782	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	37	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	27886215	5	ver/dev	Baxter , M. A. , Fahlen , T. F. , Wilson , R. L. & Jones , B. D. HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	388	Baxter , M. A. , Fahlen , T. F. , Wilson , R. L. & Jones , B. D. HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	13	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	28575106	18	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	706	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	33	1	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	31182495	9	ver/dev	Expression increased in both phoQ24 mutant background , demonstrating that HilE decreases hilA expression independently of PhoP .	70	Expression increased in both a wild-type phoQ and phoQ24 mutant background , demonstrating that HilE decreases hilA expression independently of PhoP ( Fig. 3 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilE	gene	hilA	repressor	31182495	9	ver/dev	Expression increased in both a wild-type phoQ , demonstrating that HilE decreases hilA expression independently of PhoP .	70	Expression increased in both a wild-type phoQ and phoQ24 mutant background , demonstrating that HilE decreases hilA expression independently of PhoP ( Fig. 3 ) .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilE	gene	hilA	repressor	31428589	16	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	282	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	6	AUTHOR CONTRIBUTIONS	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	31991172	2	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	398	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	38	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilE	gene	hilA	repressor	33593291	17	ver/dev	HilE is a known repressor of hilA expression	123	However , HilE is a known repressor of hilA expression , and there is no evidence to suggest that it is capable of activating hilA expression based on current models .	6	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilE	gene	hilA	repressor	33593291	20	ver/dev	These results demonstrate that the Rcs system is necessary for repression of hilA expression in the absence of HilE .	149	These results demonstrate that the Rcs system is necessary for repression of hilA expression in the absence of HilE .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	repressor	33751923	28	ver/dev	HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	911	HilE interacts with HilD and negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .	49	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	tcfA	repressor	28922626	5	ver/dev	Similar results have been previously demonstrated for fimA in S. Typhimu-rium .34 Transcriptional repression of other genes have been shown to occur by the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator .	245	Similar results have been previously demonstrated for the major type 1 fimbrial subunit gene , fimA in S. Typhimu-rium .34 Transcriptional repression of other genes including the papBA operon by Lrp have been shown to occur by cooperative interactions between Lrp and the nucleoidbinding proteins H-NS .48 The regulation of tcfA by an ancestral regulator such as Lrp , demonstrates the assimilation of the horizontally acquired tcf cluster into the core regulatory setup of Salmonella and emphasize the regulatory linkage between ancestral metabolic pathways and acquired virulence traits in Salmonella .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	sbmC	regulator	21102598	2	ver/dev	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is LexA .	92	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS and LexA mediated .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	sbmC	regulator	21102598	2	ver/dev	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS .	92	Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS and LexA mediated .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	sbmC	regulator	21102598	3	ver/dev	The Escherichia coli SOS gene sbmC is regulated by H-NS during stationary growth phase .	412	The Escherichia coli SOS gene sbmC is regulated by H-NS and RpoS during the SOS induction and stationary growth phase .	13	ACKNOWLEDGEMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	sbmC	regulator	21102598	3	ver/dev	The Escherichia coli SOS gene sbmC is regulated by H-NS during the SOS-induction .	412	The Escherichia coli SOS gene sbmC is regulated by H-NS and RpoS during the SOS induction and stationary growth phase .	13	ACKNOWLEDGEMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	arcA	activator	11238977	0	att	When , finally , the RpoS-controlled stationary-phase of growth is reached , arcA is suppressed in an RpoS-dependent fashion .	17	When , finally , the RpoS-controlled stationary phase of growth is reached , arcA is suppressed in an RpoS-dependent fashion .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mig-14	repressor	15225317	5	ver/dev	Candidate genes for this activity include mig-14 because inactivation of these PhoP-activated genes results in strains .	35	Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .	3	2 ND POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	ycgR	regulator	28553268	8	att	The FlhDC-regulated ycgR and yhjH genes ( Ko and Park , 2000 ) were also strongly repressed ( 0.08 - and 0.18-fold at 45 min respectively ; Table 8 ) .	585	The FlhDC-regulated ycgR and yhjH genes ( Ko and Park , 2000 ) were also strongly repressed ( 0.08 - and 0.18-fold at 45 min respectively ; Table 8 ) .	22	CELL DAMAGE/STRESS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsB	gene	galF	regulator	27601571	43	ver/dev	a galF transcript is regulated by RtsB	379	The 5 = UTR of a galF transcript that is regulated by RtsB is indicated by a blue bracket .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	TU	PSLT024	regulator	18336553	0	att	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	107	The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .	11	VIRULENCE OPERONS, GENES AND LOCI	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	feoB	regulator	25313398	0	ver/dev	However , given that the Fnr regulators can efficiently control feoB mRNA levels in response to different levels of iron , the reason remains unknown .	28	However , given that the Fur and Fnr regulators can efficiently control feoB mRNA levels in response to different levels of oxygen and iron , the reason why Salmonella also controls FeoB levels using the FeoC protein remains unknown .	2	MAIN	unidentified	1	L2	OTHER	Fact	OTHER	New	Level 1
FNR	gene	feoB	regulator	25313398	0	ver/dev	However , given that the Fnr regulators can efficiently control feoB mRNA levels in response to different levels of oxygen , the reason remains unknown .	28	However , given that the Fur and Fnr regulators can efficiently control feoB mRNA levels in response to different levels of oxygen and iron , the reason why Salmonella also controls FeoB levels using the FeoC protein remains unknown .	2	MAIN	unidentified	1	L2	OTHER	Fact	OTHER	New	Level 1
SdiA	gene	srgE	regulator	15130116	2	ver/dev	the only chromosomal gene _ regulated by SdiA , srgE , except that it appears to be a single gene the predicted product contains a putative coiled-coil domain	150	Nothing is known about the only chromosomal gene regulated by SdiA , srgE , except that it appears to be a single gene horizontal acquisition and the predicted product contains a putative coiled-coil domain ( Smith and Ahmer , 2003 ) .	5	THE SALMONELLA SDIA SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgE	regulator	15130116	2	ver/dev	the only chromosomal gene _ regulated by SdiA , srgE , except that it appears to be a single gene horizontal acquisition contains a putative coiled-coil domain	150	Nothing is known about the only chromosomal gene regulated by SdiA , srgE , except that it appears to be a single gene horizontal acquisition and the predicted product contains a putative coiled-coil domain ( Smith and Ahmer , 2003 ) .	5	THE SALMONELLA SDIA SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgE	regulator	22660944	0	att	srgE ( SdiA-regulated gene E ) is a chromosomal gene regulated by SdiA that also appears to be found on the virulence plasmid pSLT [ 13 ] .	43	srgE ( SdiA-regulated gene E ) is a chromosomal gene regulated by SdiA that also appears to be found on the virulence plasmid pSLT [ 13 ] .	2	MAIN	unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgE	regulator	25080967	43	att	Habyarimana , F. , Sabag-Daigle , A. , and Ahmer , B.M.M. ( 2014 ) The SdiA-regulated gene srgE encodes a type III secreted effector .	489	Habyarimana , F. , Sabag-Daigle , A. , and Ahmer , B.M.M. ( 2014 ) The SdiA-regulated gene srgE encodes a type III secreted effector .	31	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	regulator	25080967	4	ver/dev	Besides the putative ` rck operon ' , SdiA regulates the transcription of srgE .	62	Besides the putative ` rck operon ' , SdiA regulates the transcription of srgE ( STM1554 ) , an apparently horizontally acquired gene encoding a type III secreted effector whose function remains unknown ( Habyarimana et al. , 2014 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Other	OTHER	New	Level 1
SdiA	gene	srgE	regulator	25080967	35	ver/dev	The other gene _ regulated by SdiA in S. Typhimurium , srgE ,	306	The other gene regulated by SdiA in S. Typhimurium , srgE , is absent in the S. Enteritidis genomes available in the nucleotide databases .	13	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	regulator	25966179	2	ver/dev	Another gene potentially regulated by SdiA is srgE .	175	Another gene potentially regulated by SdiA is srgE , which was acquired by horizontal transfer and has an unknown function ( Sabag-Daigle et al. , 2012 ) .	11	QUORUM SENSING IN SALMONELLA ENTERITIDIS PT4 578	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SdiA	gene	srgE	regulator	25972862	7	att	The SdiA-regulated gene srgE encodes a type III secreted effector .	601	The SdiA-regulated gene srgE encodes a type III secreted effector .	38	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	regulator	26442936	1	att	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that carries seven genes and the srgE gene ( 30 , 50 ) .	105	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that carries seven genes and the srgE gene ( 30 , 50 ) .	8	AI-1 SIGNALING IN SALMONELLA	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	regulator	26442936	2	att	The second SdiA-regulated locus is located in the chromosome and consists of the gene srgE that is predicted to encode a protein containing a coiled-coil domain ( 50 , 61 ) .	112	The second SdiA-regulated locus is located in the chromosome and consists of the gene srgE that is predicted to encode a protein containing a coiled-coil domain ( 50 , 61 ) .	8	AI-1 SIGNALING IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	regulator	26443762	1	att	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 19 , 35 ) .	93	Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 19 , 35 ) .	8	AI-1 SIGNALING IN SALMONELLA	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	regulator	26443762	2	att	The second SdiA-regulated locus is encoded in the chromosome and consists of the gene srgE that is predicted to encode a protein containing a coiled-coil domain ( 35 , 46 ) .	107	The second SdiA-regulated locus is encoded in the chromosome and consists of the gene srgE that is predicted to encode a protein containing a coiled-coil domain ( 35 , 46 ) .	8	AI-1 SIGNALING IN SALMONELLA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SdiA	gene	srgE	regulator	26497459	5	att	The SdiA-regulated gene srgE encodes a type III secreted effector .	691	The SdiA-regulated gene srgE encodes a type III secreted effector .	50	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	regulator	33133465	4	att	The SdiA-regulated gene srgE encodes a type III secreted effector .	193	The SdiA-regulated gene srgE encodes a type III secreted effector .	13	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SdiA	gene	srgE	regulator	33133465	2	ver/dev	srgE is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence-factors ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes	147	Typhimurium including pefI/srgC operon , srgE and sirA genes is under the control of SdiA QS system ,7 thus reductions in sdiA gene expression can affect the expression of these QS-controlled virulence factors which in turn will decrease the flagella formation ( motility ) , fimbria formation , bacterial invasion , biofilm production , virulence-associated type III secretion systems and the phenotypes derived from genes located on the pathogenic islands 1 and 4.18,28-31	8	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
LeuO	gene	cas5	regulator	33854491	0	ver/dev	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 mutants .	12	Furthermore , the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin , in individual S. Typhi cse2 , cas5 , cas6e , cas1 , cas2 , and cas3 mutants .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Other	NEG	Other	Level 1
MarA	gene	ramA	regulator	32514543	1	ver/dev	by ramA in S. Typhimurium .40,41 MarA are positive regulators of the AcrAB	99	In E. coli and S. Typhimurium , the AcrAB -- TolC efflux system and OmpF are regulated by the marA/soxS/robA regulon , and , in add-ition , by ramA in S. Typhimurium , which is absent from E. coli .40,41 MarA and Rob are positive regulators of the AcrAB -- TolC efflux system , and MarA , in addition , is a negative regulator of the outer 40 membrane porin , OmpF .	14	REGULATOR GENES INVOLVED IN CIPROFLOXACIN SUSCEPTIBILITY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	ramA	regulator	32514543	1	ver/dev	by ramA in S. Typhimurium .40,41 MarA are positive regulators of the AcrAB	99	In E. coli and S. Typhimurium , the AcrAB -- TolC efflux system and OmpF are regulated by the marA/soxS/robA regulon , and , in add-ition , by ramA in S. Typhimurium , which is absent from E. coli .40,41 MarA and Rob are positive regulators of the AcrAB -- TolC efflux system , and MarA , in addition , is a negative regulator of the outer 40 membrane porin , OmpF .	14	REGULATOR GENES INVOLVED IN CIPROFLOXACIN SUSCEPTIBILITY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	ramA	regulator	32514543	1	ver/dev	by ramA in S. Typhimurium .40,41 MarA are positive regulators of the AcrAB	99	In E. coli and S. Typhimurium , the AcrAB -- TolC efflux system and OmpF are regulated by the marA/soxS/robA regulon , and , in add-ition , by ramA in S. Typhimurium , which is absent from E. coli .40,41 MarA and Rob are positive regulators of the AcrAB -- TolC efflux system , and MarA , in addition , is a negative regulator of the outer 40 membrane porin , OmpF .	14	REGULATOR GENES INVOLVED IN CIPROFLOXACIN SUSCEPTIBILITY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	ramA	regulator	32514543	1	ver/dev	by ramA in S. Typhimurium .40,41 MarA are positive regulators of the AcrAB	99	In E. coli and S. Typhimurium , the AcrAB -- TolC efflux system and OmpF are regulated by the marA/soxS/robA regulon , and , in add-ition , by ramA in S. Typhimurium , which is absent from E. coli .40,41 MarA and Rob are positive regulators of the AcrAB -- TolC efflux system , and MarA , in addition , is a negative regulator of the outer 40 membrane porin , OmpF .	14	REGULATOR GENES INVOLVED IN CIPROFLOXACIN SUSCEPTIBILITY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FimW	gene	fimA	activator	11133935	9	ver/dev	In addition , fimA expression from a fimA-lacZ reporter was increased in the absence of a functional FimW , in both a serovar Typhimurium background .	344	In addition , fimA expression from a fimA-lacZ reporter was increased in the absence of a functional FimW , in both an E. coli and a serovar Typhimurium background .	7	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
FimW	gene	fimA	activator	11133935	9	ver/dev	In addition , fimA expression from a fimA-lacZ reporter was increased in the absence of a functional FimW , in both an E. coli Typhimurium background .	344	In addition , fimA expression from a fimA-lacZ reporter was increased in the absence of a functional FimW , in both an E. coli and a serovar Typhimurium background .	7	DISCUSSION	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	lexA	repressor	12399494	1	att	The tum homologue of Fels-2 was responsible for lexA lethality and had a LexA-repressed promoter .	11	The tum homologue of Fels-2 was responsible for lexA lethality and had a LexA-repressed promoter .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	lexA	repressor	19525399	0	ver/dev	Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a lexA mutant with a concomitant 50-fold reduction in deletion rate .	17	Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a lexA ( def ) mutant with a concomitant 50-fold reduction in deletion rate .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	lexA	repressor	26784887	0	auto	After its autohydrolysis , the LexA repressor is no longer able to repress either its own expression or that of the genes it controls ( including recA , which is also part of the SOS network ) , thereby inducing the SOS response [ 37 ] .	47	After its autohydrolysis , the LexA repressor is no longer able to repress either its own expression or that of the genes it controls ( including recA , which is also part of the SOS network ) , thereby inducing the SOS response [ 37 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SlyA	gene	pagC	repressor	18270203	59	ver/dev	H-NS binding site in the pagC promoter is dispensable for H-NS repression by SlyA .	266	An overlapping SlyA and H-NS binding site in the pagC promoter is dispensable for H-NS repression but necessary for derepression by SlyA .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	pagC	repressor	18270203	61	ver/dev	A Site Is Dispensable for H-NS-mediated Repression by the SlyA Protein -- If competition were the sole basis for relieving H-NS-promoted repression , elimination of a binding site should result in SlyA-independent pagC transcription .	274	A Site Bound by the SlyA and H-NS Proteins in the pagC Promoter Is Dispensable for H-NS-mediated Repression but Necessary for Derepression by the SlyA Protein -- If competition were the sole basis for relieving H-NS-promoted repression , elimination of a binding site shared by H-NS and SlyA should result in SlyA-independent pagC transcription .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
SlyA	gene	pagC	repressor	29857034	13	ver/dev	Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates Fig. 3G .	299	Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression ( Fig. 3G ) .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	pagC	repressor	29857034	13	ver/dev	Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression .	299	Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression ( Fig. 3G ) .	24	3.3. SLYA-DEPENDENT GENES DIFFERENTIALLY EXPRESSED AFTER NAOCL TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NarL	gene	narL	regulator	17906148	4	ver/dev	Nitrate repression was abolished in the narL strain , indicating that NarL mediates the nitrate regulation of hya .	275	Nitrate repression was abolished in the narL strain ( Table 5 ) , indicating that NarL mediates the nitrate regulation of hya .	8	REGULATION OF HYA BY NITRATE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	srfJ	regulator	29270156	0	ver/dev	Initially , it was proposed as a putative effector because the gene srfJ is positively regulated by SsrB .	59	Initially , it was proposed as a putative effector because the gene srfJ is positively regulated by SsrB ( Worley et al. , 2000 ) , the main positive regulator of T3SS2 ( Fass and Groisman , 2009 ) .	4	INTRODUCTION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	srfJ	regulator	29270156	1	ver/dev	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by the repressor of the myo-inositol utilization genes in S. Typhimurium .	60	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR ( Cordero-Alba et al. , 2012 ) , the repressor of the myo-inositol ( MI ) utilization genes in S. Typhimurium ( Kröger and Fuchs , 2009 ) .	4	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfJ	regulator	29270156	1	ver/dev	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by the repressor of the myo-inositol utilization genes in S. Typhimurium .	60	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR ( Cordero-Alba et al. , 2012 ) , the repressor of the myo-inositol ( MI ) utilization genes in S. Typhimurium ( Kröger and Fuchs , 2009 ) .	4	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfJ	regulator	29270156	1	ver/dev	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR .	60	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR ( Cordero-Alba et al. , 2012 ) , the repressor of the myo-inositol ( MI ) utilization genes in S. Typhimurium ( Kröger and Fuchs , 2009 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfJ	regulator	29270156	1	ver/dev	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR .	60	Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR ( Cordero-Alba et al. , 2012 ) , the repressor of the myo-inositol ( MI ) utilization genes in S. Typhimurium ( Kröger and Fuchs , 2009 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfJ	regulator	29270156	3	ver/dev	Interestingly , a transcriptional lux fusion with 2357 bp upstream of srfJ is regulated by SsrB , recapitulating the regulation patterns .	285	Interestingly , a transcriptional lux fusion with 2357 bp upstream of srfJ containing both promoters and the intervening genes ( PiolE -- PsrfJ ) is regulated by IolR , PhoP , SsrB , and Rcs , recapitulating the regulation patterns observed with the isolated promoters ( Figures 2B , D ) .	25	DIFFERENTIAL REGULATION OF PIOLE AND PSRFJ	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	17908208	9	ver/dev	LeuO positively regulated the ompS1 expression by derepressing both promoters and antagonizing the negative effect of StpA , displacing them from the 5 ′ regulatory region .	49	LeuO positively regulated the ompS1 expression by derepressing both promoters and antagonizing the negative effect of H-NS and StpA , displacing them from the 5 ′ regulatory region .	3	B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	17908208	9	ver/dev	LeuO positively regulated the ompS1 expression by derepressing both promoters and antagonizing the negative effect of H-NS , displacing them from the 5 ′ regulatory region .	49	LeuO positively regulated the ompS1 expression by derepressing both promoters and antagonizing the negative effect of H-NS and StpA , displacing them from the 5 ′ regulatory region .	3	B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	17908208	11	ver/dev	LeuO positively regulated ompS1 expression in Salmonella enterica	52	LeuO positively regulated ompS1 expression in Salmonella enterica	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	17908208	14	ver/dev	Interestingly , the pRO310 ompS1 was also positively regulated by LeuO .	55	Interestingly , the pRO310 ompS1 -- lacZ fusion was also positively regulated by LeuO , but at higher concentrations of IPTG than previously reported for ompS2 .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	17908208	17	ver/dev	OmpS2 can be observed when LeuO is induced at 50 mM IPTG in the ompS1 mutant .	63	OmpS2 can be observed when LeuO is induced at 50 mM IPTG in the ompS1 mutant .	5	LEUO POSITIVELY REGULATED OMPS1 EXPRESSION IN SALMONELLA ENTERICA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
LeuO	gene	ompS1	activator	17908208	26	ver/dev	LeuO positively regulates both ompS1 promoters .	85	LeuO positively regulates both ompS1 promoters .	6	LEUO DEREPRESSED BOTH OMPS1 PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	17908208	48	ver/dev	The highest level of ompS1 expression was attained either upon induction of LeuO in the wild type or else in an hns stpA background .	198	The highest level of ompS1 expression was attained either upon induction of LeuO in the wild type or else in an hns stpA background ( Figs 1 -- 3 ) .	12	LEUO ACTED AS A DEREPRESSOR, DISPLACING H-NS FROM THE OMPS1 REGULATORY REGION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
LeuO	gene	ompS1	activator	17908208	65	ver/dev	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter , the induction of ompS1 can occur independent of OmpR .	257	Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter ( Fernández-Mora et al. , 2004 ) , the induction of ompS1 can occur independent of OmpR .	13	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS1	activator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	18156266	36	att	The results showed that two LeuO protected sites were found in the LeuO-dependent genes reported in this work , and a DNase I hypersensitivity region was observed when increasing amounts of LeuO were used , suggesting that there was a DNA conformational change upon binding of LeuO ( Fig. 3 ) , which is consistent with our previous observations for the ompS2 and ompS1 genes ( 5 , 12 ) .	336	The results showed that two LeuO protected sites were found in the LeuO-dependent genes reported in this work , and a DNase I hypersensitivity region was observed when increasing amounts of LeuO were used , suggesting that there was a DNA conformational change upon binding of LeuO ( Fig. 3 ) , which is consistent with our previous observations for the ompS2 and ompS1 genes ( 5 , 12 ) .	6	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	ompS1	activator	18156266	32	ver/dev	the transcriptional results showed that LeuO positively induced ompS1 at different points of the growth curve	329	Interestingly , the transcriptional results showed that LeuO positively induced STY3070 , assT , and ompS1 at different points of the growth curve , and the highest activity was observed in stationary phase ( Fig. 2a to c ) .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	19406898	2	ver/dev	an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	19406898	2	ver/dev	StpA , was found to repress ompS1 in an hns background ; and LeuO , positively regulates ompS1 expression by antagonizing H-NS and	26	StpA , an H-NS paralogue , was found to repress ompS1 in an hns background ; and LeuO , a LysR-type regulator , positively regulates ompS1 expression by antagonizing H-NS and	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	19406898	10	ver/dev	The maximum level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG from pFMTrcleuO-50 .	111	The maximum level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG from pFMTrcleuO-50 , the same as that attained in a double hns stpA background ( De la Cruz et al. , 2007 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	19406898	10	ver/dev	The maximum level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG from the same as that stpA background .	111	The maximum level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG from pFMTrcleuO-50 , the same as that attained in a double hns stpA background ( De la Cruz et al. , 2007 ) .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	19447191	5	ver/dev	LeuO positively regulates the ompS1 expression by derepressing both the promoters .	97	LeuO positively regulates the ompS1 expression by derepressing both the promoters and antagonizing the negative effect of H-NS and StpA .	6	4.2. LEUO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	19447191	5	ver/dev	LeuO positively regulates the ompS1 expression by antagonizing the negative effect of StpA .	97	LeuO positively regulates the ompS1 expression by derepressing both the promoters and antagonizing the negative effect of H-NS and StpA .	6	4.2. LEUO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	19447191	5	ver/dev	LeuO positively regulates the ompS1 expression by antagonizing the negative effect of H-NS .	97	LeuO positively regulates the ompS1 expression by derepressing both the promoters and antagonizing the negative effect of H-NS and StpA .	6	4.2. LEUO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	ompS1	activator	21398529	9	ver/dev	Previously , we demonstrated that a TATgTcATAT region located at positions 125 to 134 with respect to the transcriptional start site was necessary for the LeuO induction of the ompS1 gene .	319	Previously , we demonstrated that a TATgTcATAT region located at positions 125 to 134 with respect to the transcriptional start site was necessary for the LeuO induction of the ompS1 gene ( 16 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	ompS1	activator	22804842	9	ver/dev	LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 , consistent with LeuO .	147	LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 ( De la Cruz et al. , 2007 ) , consistent with LeuO having a higher affinity for the regulatory region of ompS2 .	6	EXTENSION OF THE LEUO REGULON	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
LeuO	gene	ompS1	activator	22804842	9	ver/dev	LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 , consistent with LeuO .	147	LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 ( De la Cruz et al. , 2007 ) , consistent with LeuO having a higher affinity for the regulatory region of ompS2 .	6	EXTENSION OF THE LEUO REGULON	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
LeuO	gene	ompS1	activator	24659766	1	ver/dev	In Salmonella enterica serovar Typhi , LeuO activates the expression of ompS1 .	11	In Salmonella enterica serovar Typhi , LeuO activates the expression of ompS1 and ompS2 ( 12 , 13 ) .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	soxS	activator	20237076	8	ver/dev	paraquat .34 Since Salmonella is faced with oxidative-stress in the macrophages , it is not surprising that intracellular bacteria levels of soxS mRNA are 3.7-fold higher compared with those in extracellular bacteria .31,32 Bile salts were shown to induce the expression of AcrAB by activation of RamA ; 35 however , it is possible that RamA contributes to the induction of AcrAB in macrophages by the detection of other signals in the host .	355	H2O2 and paraquat .34 Since Salmonella is faced with oxidative stress in the macrophages , it is not surprising that intracellular bacteria levels of soxS mRNA are 3.7-fold higher compared with those in extracellular bacteria .31,32 Bile salts were shown to induce the expression of AcrAB by activation of RamA ; 35 however , it is possible that RamA contributes to the induction of AcrAB in macrophages by the detection of other signals in the host .	23	DISCUSSION	Salmonella	1	L1	SPEC	Analysis	NEG	Other	Level 1
RamA	gene	soxS	activator	20237076	8	ver/dev	paraquat .34 Since Salmonella is faced with oxidative-stress in the macrophages , it is not surprising that intracellular bacteria levels of soxS mRNA are 3.7-fold higher compared with those in extracellular bacteria .31,32 Bile salts were shown to induce the expression of AcrAB by activation of RamA ; 35 however , it is possible that RamA contributes to the induction of AcrAB in macrophages by the detection of other signals in the host .	355	H2O2 and paraquat .34 Since Salmonella is faced with oxidative stress in the macrophages , it is not surprising that intracellular bacteria levels of soxS mRNA are 3.7-fold higher compared with those in extracellular bacteria .31,32 Bile salts were shown to induce the expression of AcrAB by activation of RamA ; 35 however , it is possible that RamA contributes to the induction of AcrAB in macrophages by the detection of other signals in the host .	23	DISCUSSION	Salmonella	1	L1	SPEC	Analysis	NEG	Other	Level 1
SlyA	gene	STM1330	regulator	27564394	11	ver/dev	Furthermore , STM1330 are regulated by SlyA .	335	Furthermore , STM2585 and STM1330 are regulated by SlyA and PhoP [ 44 ] , the master regulators of the SsrB regulon .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	amgR	activator	31866990	1	ver/dev	In conditions , PhoP activates the amgR promoter located in mgtB intergenic region .	58	In low Mg2 + conditions , PhoP binds to and activates the amgR promoter located in the mgtC -- mgtB intergenic region ( Lee and Groisman , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	activator	31866990	1	ver/dev	In conditions , PhoP activates the amgR promoter located in the mgtC .	58	In low Mg2 + conditions , PhoP binds to and activates the amgR promoter located in the mgtC -- mgtB intergenic region ( Lee and Groisman , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	activator	31866990	1	ver/dev	In low Mg2 , PhoP activates the amgR promoter located in mgtB intergenic region .	58	In low Mg2 + conditions , PhoP binds to and activates the amgR promoter located in the mgtC -- mgtB intergenic region ( Lee and Groisman , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	amgR	activator	31866990	1	ver/dev	In low Mg2 , PhoP activates the amgR promoter located in the mgtC .	58	In low Mg2 + conditions , PhoP binds to and activates the amgR promoter located in the mgtC -- mgtB intergenic region ( Lee and Groisman , 2010 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YdcI	gene	ydcI	repressor	30038032	7	ver/dev	Notably , we observed significantly higher transcript levels of these genes in the ydcI cells compared with the WT , indicating their transcriptional repression by YdcI .	317	Notably , we observed significantly higher transcript levels of these genes in the ydcI cells compared with the WT , indicating their transcriptional repression by YdcI .	7	REPRESSION OF THE ETHANOLAMINE UTILIZATION OPERON BY ARCA—	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
AcrR	gene	acrB	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	acrB	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , MarA , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	acrB	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , SoxS , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
AcrR	gene	acrB	regulator	26679248	0	ver/dev	AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , RamA , have been associated with increased acrB .	28	AcrR is the local repressor encoded upstream of the acrAB genes and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , RamA , SoxS and MarA , have been associated with increased acrB and tolC expression levels .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	cadB	regulator	25875623	8	ver/dev	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadB .	248	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC and cadB .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	cadB	regulator	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in SCV of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadB	regulator	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in the Salmonellacontaining vacuole of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadB	regulator	29214489	15	ver/dev	Activated OmpR then represses the cadC/BA operon by directly binding to both cadB promo-ters , leading to cytoplasmic acidification .	163	Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC and cadB promo-ters , leading to cytoplasmic acidification and reduced flagellation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	lexA	regulator	10852882	0	ver/dev	the concentration of ssDNA returns to normal levels , cleavage of LexA is terminated -LRB- the lexA gene is itself regulated by LexA -RRB-	32	Once recombination and repair have ceased , the concentration of ssDNA returns to normal levels , cleavage of LexA is terminated ( the lexA gene is itself regulated by LexA ) , and homeostatic levels of LexA are reached .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	lexA	regulator	10852882	0	ver/dev	the concentration of ssDNA returns to normal levels , cleavage of LexA is terminated -LRB- the lexA gene is itself regulated by LexA -RRB-	32	Once recombination and repair have ceased , the concentration of ssDNA returns to normal levels , cleavage of LexA is terminated ( the lexA gene is itself regulated by LexA ) , and homeostatic levels of LexA are reached .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	lexA	regulator	16713610	3	att	Among kanamycin-resistant tranductants , the presence of the lexA ( Ind ) mutation was confirmed through β-galactosidase assay after introduction of the pGE108 plasmid ( Table 2 ) which contains a LexA-regulated cea ∷ lacZ fusion ( Salles et al. , 1987 ) .	197	Among kanamycin-resistant tranductants , the presence of the lexA ( Ind ) mutation was confirmed through β-galactosidase assay after introduction of the pGE108 plasmid ( Table 2 ) which contains a LexA-regulated cea ∷ lacZ fusion ( Salles et al. , 1987 ) .	7	CONSTRUCTION OF S. ENTERICA MUTANTS	unidentified plasmid	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LexA	gene	lexA	regulator	19525399	5	att	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	175	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	3	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	lexA	regulator	20421601	1	att	The increase in mutation rates in the lexA ( def ) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho .	9	The increase in mutation rates in the lexA ( def ) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	lexA	regulator	20421601	6	att	To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .	121	To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .	4	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
NtrC	gene	glnA	regulator	10074092	0	ver/dev	Studies with the glnA promoter of S. typhimurium have shown that NtrC bound at the enhancer , located between 2140 , interacts di-54 rectly with s holoenzyme by means of DNA loop formation .	177	Studies with the glnA promoter of S. typhimurium have shown that NtrC bound at the enhancer , located between 2108 and 2140 , interacts di-54 rectly with s holoenzyme by means of DNA loop formation ( 25 , 30 ) .	4	0	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
NtrC	gene	glnA	regulator	10074092	0	ver/dev	Studies with the glnA promoter of S. typhimurium have shown that NtrC bound at the enhancer , located between 2108 , interacts di-54 rectly with s holoenzyme by means of DNA loop formation .	177	Studies with the glnA promoter of S. typhimurium have shown that NtrC bound at the enhancer , located between 2108 and 2140 , interacts di-54 rectly with s holoenzyme by means of DNA loop formation ( 25 , 30 ) .	4	0	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	sipB	activator	21168230	1	att	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	208	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipB	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipB and located outside -LRB- sopE -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipB	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipB and located outside -LRB- sopD -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipB	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipB and located outside -LRB- sopB -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipB	activator	21320585	0	ver/dev	InvF induces the expression of sipB -LSB- 14e16 -RSB- .	42	InvF is required for the efficient invasion of Salmonella into host epithelial cells , and induces the expression of other genes involved in invasion , such as sipB , sipC , and sopE [ 14e16 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrA	regulator	19206470	13	ver/dev	PhoP has been previously shown to regulate translation of the gene ssrA	296	PhoP has been previously shown to regulate translation of the gene ssrA , but the mechanism is not known .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ssrA	regulator	26880544	1	ver/dev	Under low osmolality , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrA	regulator	26880544	1	ver/dev	Under acidic pH , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .	51	Under acidic pH and low osmolality , the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR ~ P and PhoP ~ P to their promoters ( Feng et al. , 2003 ; Bijlsma and Groisman , 2005 ; Walthers and Kenney unpublished ) whose levels are in turn regulated by the respective sensor kinases , EnvZ and PhoQ .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ssrA	regulator	29270156	4	ver/dev	Since PhoP regulates expression of ssrA , it also regulates expression of genes in the SsrB regulon .	437	Since PhoP regulates expression of ssrA and ssrB ( Bijlsma and Groisman , 2005 ) , it also regulates expression of genes in the SsrB regulon .	32	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ssrA	regulator	29930310	4	ver/dev	PhoP competes with histone-like proteins for binding to the ssrA promoter , counter-silencing the repressive activity of these nucleoid-structuring proteins19 ,20 .	21	PhoP competes with histone-like proteins for binding to the ssrA promoter , counter-silencing the repressive activity of these nucleoid-structuring proteins19 ,20 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PocR	gene	pocR	activator	1312999	4	ver/dev	It is surprising that either glycerol can serve as effectors of PocR for induction of the cob operons , yet only propanediol is able to induce pocR transcription .	560	It is surprising that either propanediol or glycerol can serve as effectors of PocR for induction of the pdu and cob operons , yet only propanediol is able to induce pocR transcription .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PocR	gene	pocR	activator	1312999	4	ver/dev	It is surprising that either glycerol can serve as effectors of PocR for induction of the pdu operons , yet only propanediol is able to induce pocR transcription .	560	It is surprising that either propanediol or glycerol can serve as effectors of PocR for induction of the pdu and cob operons , yet only propanediol is able to induce pocR transcription .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PocR	gene	pocR	activator	1312999	4	ver/dev	It is surprising that either propanediol can serve as effectors of PocR for induction of the cob operons , yet only propanediol is able to induce pocR transcription .	560	It is surprising that either propanediol or glycerol can serve as effectors of PocR for induction of the pdu and cob operons , yet only propanediol is able to induce pocR transcription .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PocR	gene	pocR	activator	1312999	4	ver/dev	It is surprising that either propanediol can serve as effectors of PocR for induction of the pdu operons , yet only propanediol is able to induce pocR transcription .	560	It is surprising that either propanediol or glycerol can serve as effectors of PocR for induction of the pdu and cob operons , yet only propanediol is able to induce pocR transcription .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PocR	gene	pocR	activator	8636018	0	ver/dev	In this manner , we were able to isolate clones of pocR in which expression of pocR was not increased by transcription from Plac on the plasmid , since high-level expression of pocR by Plac led to constitutive -LRB- 1,2-PDL-indepen-dent -RRB- PocR activity in-vivo .	69	In this manner , we were able to isolate clones of pocR in which expression of pocR was not increased by transcription from Plac on the plasmid , since high-level expression of pocR by Plac led to constitutive ( 1,2-PDL-indepen-dent ) PocR activity in vivo .	3	MATERIALS AND METHODS	unidentified plasmid	1	L2	OTHER	Other	NEG	Other	Level 1
CsgD	gene	STM1344	activator	19376870	27	ver/dev	STM1344 positively regulated the expression of its major regulator CsgD .	328	STM1344 positively regulated the expression of the multicellular rdar morphotype behavior and its major regulator CsgD and suppressed motility .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	STM1344	activator	19376870	33	ver/dev	The effect of STM1344 on c-di-GMP concentrations as determined in this study is , however , in agreement with the effect of STM1344 on the motility phenotypes , e.g. , the expression of STM1344 leads to the upregulation of CsgD .	362	The effect of STM1344 on c-di-GMP concentrations as determined in this study is , however , in agreement with the effect of STM1344 on the multicellular and motility phenotypes , e.g. , the expression of STM1344 leads to higher c-di-GMP levels , the upregulation of CsgD ( as CsgD expression is activated by c-di-GMP [ 16 ] ) , and the inhibition of motility ( as motility is inhibited by c-di-GMP [ 38 ] ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	STM1344	activator	19376870	33	ver/dev	The effect of STM1344 on c-di-GMP concentrations as determined in this study is , however , in agreement with the effect of STM1344 on the multicellular phenotypes , e.g. , the expression of STM1344 leads to the upregulation of CsgD .	362	The effect of STM1344 on c-di-GMP concentrations as determined in this study is , however , in agreement with the effect of STM1344 on the multicellular and motility phenotypes , e.g. , the expression of STM1344 leads to higher c-di-GMP levels , the upregulation of CsgD ( as CsgD expression is activated by c-di-GMP [ 16 ] ) , and the inhibition of motility ( as motility is inhibited by c-di-GMP [ 38 ] ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagO	activator	32522778	0	att	Cluster II encodes 3 putative membrane proteins , including pagO , a PhoP-activated gene ( 23 ) .	209	Cluster II encodes 3 putative membrane proteins , including pagO , a PhoP-activated gene ( 23 ) .	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HNS	gene	ssrA	repressor	29930310	18	ver/dev	The conversion of the discriminator from GTTTTTA to GTCCCTA may have also affected the repression of ssrA locus via the nucleoid proteins H-NS and YdgT .	163	The conversion of the discriminator from GTTTTTA to GTCCCTA may have also affected the repression of ssrA locus via the nucleoid proteins H-NS and YdgT .	4	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	stpA	activator	19843227	32	att	The bar chart shows the effect of stpA deletion on the expression of genes that are designated as CRP-dependent in the closely related bacterium E. coli .	193	The bar chart shows the effect of stpA deletion on the expression of genes that are designated as CRP-dependent in the closely related bacterium E. coli .	13	STPA MODULATES S38 STABILITY	Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-2074;bacterium;bacterium IFAM-3215;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-1493;Escherichia coli	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
LexA	gene	yafD	activator	30760616	1	att	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	148	The endonuclease/exonuclease/phosphatase family member yafD and cas1 , cas2 , and yigN encoding a putative recombinase with LexA-dependent expression were all upregulated in egg white .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
TyrR	gene	mtr	activator	32111072	4	ver/dev	The primary mechanism of TyrR-mediated gene regulation is repression , nevertheless activation by TyrR was reported for namely mtr .	67	The primary mechanism of TyrR-mediated gene regulation is repression , nevertheless activation by TyrR was reported for three genes , namely mtr , tyrP and the aroP promoter P3 [ 23 ] .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MltE	gene	csgD	regulator	25437188	37	ver/dev	the mechanism _ resulting in regulation of csgD expression by MltE	378	Although the mechanism resulting in regulation of csgD expression and rdar morphotype development by MltE and MltC is not known , regulation of csgD expression is dependent on the enzymatic activity of the LTs .	10	REGULATION OF THE RDAR MORPHOTYPE BY SMALL NONCODING RNAS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	hns	activator	17908208	5	ver/dev	Analysis of hns expression has indicated that the two gene products are capable of both cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .	38	Analysis of stpA and hns expression has indicated that the two gene products are capable of both negative autogenous control and cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	17908208	5	ver/dev	Analysis of hns expression has indicated that the two gene products are capable of both negative autogenous control ; that is , StpA levels are significantly increased in an hns mutant background .	38	Analysis of stpA and hns expression has indicated that the two gene products are capable of both negative autogenous control and cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .	2	MAIN	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
StpA	gene	hns	activator	17908208	5	ver/dev	Analysis of stpA expression has indicated that the two gene products are capable of both cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .	38	Analysis of stpA and hns expression has indicated that the two gene products are capable of both negative autogenous control and cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	17908208	5	ver/dev	Analysis of stpA expression has indicated that the two gene products are capable of both negative autogenous control ; that is , StpA levels are significantly increased in an hns mutant background .	38	Analysis of stpA and hns expression has indicated that the two gene products are capable of both negative autogenous control and cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .	2	MAIN	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
StpA	gene	hns	activator	17908208	33	ver/dev	However , as the expression of lacZ pRO310 fusion was still partially repressed in mutant , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .	98	However , as the expression of the ompS1 -- lacZ pRO310 fusion was still partially repressed in a Salmonella hns mutant ( Flores-Valdez et al. , 2003 ; Fig. 2A ) , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background ( Sondén and Uhlin , 1996 ; Zhang et al. , 1996 ; Sonnenfield et al. , 2001 ) .	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	17908208	33	ver/dev	However , as the expression of lacZ pRO310 fusion was still partially repressed in a Salmonella hns , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .	98	However , as the expression of the ompS1 -- lacZ pRO310 fusion was still partially repressed in a Salmonella hns mutant ( Flores-Valdez et al. , 2003 ; Fig. 2A ) , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background ( Sondén and Uhlin , 1996 ; Zhang et al. , 1996 ; Sonnenfield et al. , 2001 ) .	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	17908208	33	ver/dev	However , as the expression of the ompS1 was still partially repressed in mutant , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .	98	However , as the expression of the ompS1 -- lacZ pRO310 fusion was still partially repressed in a Salmonella hns mutant ( Flores-Valdez et al. , 2003 ; Fig. 2A ) , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background ( Sondén and Uhlin , 1996 ; Zhang et al. , 1996 ; Sonnenfield et al. , 2001 ) .	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	17908208	33	ver/dev	However , as the expression of the ompS1 was still partially repressed in a Salmonella hns , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .	98	However , as the expression of the ompS1 -- lacZ pRO310 fusion was still partially repressed in a Salmonella hns mutant ( Flores-Valdez et al. , 2003 ; Fig. 2A ) , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background ( Sondén and Uhlin , 1996 ; Zhang et al. , 1996 ; Sonnenfield et al. , 2001 ) .	7	STPA REPRESSED OMPS1 EXPRESSION IN A MUTANT HNS BACKGROUND	Salmonella	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	19843227	13	att	It has been reported that StpA can negatively regulate expression of a reporter gene under the control of the hns promoter in E. coli ( Zhang et al. , 1996 ) ; although this could only be observed in the absence of hns , this raised the possibility that StpA-dependent gene expression could simply reflect changes in the level of H-NS .	77	It has been reported that StpA can negatively regulate expression of a reporter gene under the control of the hns promoter in E. coli ( Zhang et al. , 1996 ) ; although this could only be observed in the absence of hns , this raised the possibility that StpA-dependent gene expression could simply reflect changes in the level of H-NS .	7	IDENTIFICATION OF THE STPA REGULON	Escherichia coli	0	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	activator	19843227	16	att	This indicates that under the conditions tested , StpA does not regulate gene expression by modulation of H-NS levels , and is consistent with the transcriptomic data , which do not show significant StpA-dependent changes in hns gene expression in S. Typhimurium JH3003 at any time point .	80	This indicates that under the conditions tested , StpA does not regulate gene expression by modulation of H-NS levels , and is consistent with the transcriptomic data , which do not show significant StpA-dependent changes in hns gene expression in S. Typhimurium JH3003 at any time point .	7	IDENTIFICATION OF THE STPA REGULON	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
StpA	gene	hns	activator	31661351	12	att	Our results can not be attributed to a reduced expression of H-NS in the stpA mutant as no significant StpA-dependent changes in hns expression was observed at any S. Typhimurium growth time point [ 29 ] in accordance with other transcriptomic studies in Shigella flexneri or E. coli [ 48,50 ] .	297	Our results can not be attributed to a reduced expression of H-NS in the stpA mutant as no significant StpA-dependent changes in hns expression was observed at any S. Typhimurium growth time point [ 29 ] in accordance with other transcriptomic studies in Shigella flexneri or E. coli [ 48,50 ] .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella flexneri;Escherichia coli	0.5	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	TU	phoPQ	regulator	14563863	17	att	A set of PhoP-regulated loci , including the phoPQ operon , can be found in other enterobacteria such as E. coli , while other pag genes are Salmonella specific ( 31 ) .	160	A set of PhoP-regulated loci , including the phoPQ operon , can be found in other enterobacteria such as E. coli , while other pag genes are Salmonella specific ( 31 ) .	5	DISCUSSION	Escherichia coli;Salmonella;Salmonella	0.5	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	TU	phoPQ	regulator	19783623	0	ver/dev	multiple genomes found that the only targets directly regulated by PhoP in all species were the phoPQ operon itself	292	This finding is somewhat reminiscent of a recent study of the PhoP regulon across multiple genomes , which found that the only targets directly regulated by PhoP in all species were the phoPQ operon itself and its negative regulator slyB ( 36 ) .	5	AVG 20.1 3.4 6.6 3.6 5.7 13.1 3.1 2.9	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	relA	activator	8045891	19	att	Thus , the ppGpp-dependent induction of RpoS , and consequently RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	191	Thus , the ppGpp-dependent induction of RpoS , and consequently RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .	5	DISCUSSION	Leiostomus xanthurus	0	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	sirA	activator	32392214	33	att	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	sirA	activator	32392214	33	ver/dev	This is because a csrB csrC mutant strain behaved the same way as sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5B ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	sirA	activator	32392214	33	ver/dev	This is because a csrB csrC mutant strain behaved the same way as sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RhaS	gene	rhaT	activator	24391637	0	ver/dev	RhaS activates the rhaT genes via binding to another inverted repeat of two sites .	39	RhaS activates the rhaBAD and rhaT genes via binding to another inverted repeat of two sites whose sequence differs from the RhaR consensus binding site .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilD	regulator	21573071	12	ver/dev	Specifically , Fur is able to indirectly through H-NS ( in hilD ) , all the main regulators of SPI1 .	344	Specifically , Fur is able to control , either directly ( in the case of HilD ) or indirectly through H-NS ( in hilA , hilD , hilC , and rtsA ) , all the main regulators of SPI1 .	17	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	hilD	regulator	21573071	13	ver/dev	H-NS control of the hilD promoters is also shown .	358	H-NS control of the hilD , hilC , rtsA and hilA promoters is also shown [ 21,22,31 ] .	19	ACKNOWLEDGMENTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hilD	regulator	31182495	63	ver/dev	H-NS binds the hilD promoter .	263	H-NS binds the hilD promoter repressing transcriptional activity ( 12 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sipB	repressor	33617591	8	ver/dev	No significant repression of sipB was observed in these mutants , compared to almost 11-fold reduction in the strain with a wild type HilD .	99	No significant repression of sipB was observed in these mutants , compared to almost 11-fold reduction in the strain with a wild type HilD .	10	SPECIFIC AMINO ACID RESIDUES OF HILD ARE ESSENTIAL FOR REPRESSION BY C2-HDA	nan	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	slyB	repressor	18248433	1	ver/dev	those _ required for repression of slyB , other PhoP-activated genes	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	slyB	repressor	18248433	1	ver/dev	those _ required for repression of slyB , other PhoP-activated genes	173	Mg - repression of mgtA9226 : : MudJ and 21 mgtC9232 : : MudJ was achieved at much lower concentrations than those required for repression of slyB , rstA , or orgB , other PhoP-activated genes ( Fig. 1b ) ( Lejona et al. , 2003 ; Minagawa et al. , 2003 ; Aguirre et al. , 2006 ) .	10	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoE	activator	21388802	5	ver/dev	RpoS activates rpoE expression -LRB- see Bang et al .	196	RpoS activates rpoE expression ( see Bang et al .	7	RELATING ENVIRONMENTALLY REGULATED GENE EXPRESSION TO THE INFECTION SITUATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	rpoE	activator	23960105	0	ver/dev	This tolerance appeared to be reflected in the upregulation of rpoE of the RpoS regulon .	59	This tolerance appeared to be reflected in the upregulation of stress genes ( rpoS , rpoH , and rpoE of the RpoS regulon ) that confers resistance to stationary cells exposed to a range of environmental stresses including in addition to heat , acids , osmotic shock , and starvation ( Loewen and Hengge-Aronis , 1994 ; Sirsat et al. , 2011a ) .	5	OF SALMONELLA AND SUBLETHAL HEAT EXPOSURE	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	rpoE	activator	30084765	2	att	Taking into account our results demonstrating that the double mutant rpoE rpoS is more sensitive to UVA than the single mutants rpoE and rpoS , the protective effect of rpoE against UVA radiation could be classified into two categories : RpoS-dependent and RpoS-independent .	355	Taking into account our results demonstrating that the double mutant rpoE rpoS is more sensitive to UVA than the single mutants rpoE and rpoS , the protective effect of rpoE against UVA radiation could be classified into two categories : RpoS-dependent and RpoS-independent .	16	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	csrB	activator	32392214	33	att	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	353	This is because a csrB csrC mutant strain behaved the same way as barA and sirA single mutant strains regarding activation of the RcsB-dependent rprA-gfp fusion ( Fig 5A and Fig 5B ) .	18	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	csrB	activator	32392214	18	ver/dev	That BarA activation of RcsB may be mediated by CsrC in Salmonella is also supported by the phenotype of a csrB mutant Yersinia pseudotuberculosis .	186	That BarA activation of RcsB may be mediated by CsrB and CsrC in Salmonella is also supported by the phenotype of a csrB mutant Yersinia pseudotuberculosis grown on solid media , which produced 8-fold less RcsB protein than the wild-type strain [ 33 ] .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	Salmonella;Yersinia pseudotuberculosis	0.5	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	csrB	activator	32392214	18	ver/dev	That BarA activation of RcsB may be mediated by CsrB in Salmonella is also supported by the phenotype of a csrB mutant Yersinia pseudotuberculosis .	186	That BarA activation of RcsB may be mediated by CsrB and CsrC in Salmonella is also supported by the phenotype of a csrB mutant Yersinia pseudotuberculosis grown on solid media , which produced 8-fold less RcsB protein than the wild-type strain [ 33 ] .	12	BARA ACTIVATES RCSB IN A TIME-DEPENDENT MANNER	Salmonella;Yersinia pseudotuberculosis	0.5	L1	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	entB	regulator	17720790	0	att	Growth in the presence of cobalt resulted in derepression of the Fur-regulated gene entB , a phenotype that could be reversed by the addition of iron , cysteine , or glutathione to the growth medium or by anoxic growth .	311	Growth in the presence of cobalt resulted in derepression of the Fur-regulated gene entB , a phenotype that could be reversed by the addition of iron , cysteine , or glutathione to the growth medium or by anoxic growth .	5	DISCUSSION	nan	1	L1	OTHER	Other	NEG	Other	Level 1
Fur	gene	entB	regulator	18835989	0	att	Mutant strains are sensitive to hydrogen-peroxide and superoxide , deregulate the expression of the Fur-regulated gene entB , and fail to grow on succinate medium .	8	Mutant strains are sensitive to hydrogen peroxide and superoxide , deregulate the expression of the Fur-regulated gene entB , and fail to grow on succinate medium .	1	ABSTRACT	nan	1	L3	OTHER	Other	NEG	New	Level 1
Fur	gene	entB	regulator	18835989	3	att	The status of labile iron can be monitored via expression of the Fur-regulated gene entB .	119	The status of labile iron can be monitored via expression of the Fur-regulated gene entB .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
Fur	gene	entB	regulator	21952637	0	att	Regardless of the explanation , these results appear at odds with previous studies , which established that cells exposed to Co contain less iron and reported up-regulation of Fur-controlled entB and fhuF also directly destabilize particularly labile Fe -- S clusters such as those present on Fe -- S scaffolds .	135	Regardless of the explanation , these results appear at odds with previous studies , which established that cells exposed to Co contain less iron and reported up-regulation of Fur-controlled entB and fhuF also directly destabilize particularly labile Fe -- S clusters such as those present on Fe -- S scaffolds .	11	1. TRANSCRIPTOMIC ANALYSIS OF E. COLI RESPONSE TO CO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilC	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilC by RtsA .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilC	regulator	17675384	18	ver/dev	In agreement with genetic data , we show that the purified RtsA protein , like HilD , binds to the hilC , hilD , rtsA .	302	In agreement with genetic data , we show that the purified RtsA protein , like HilC and HilD , binds to the hilC , hilD , rtsA , and hilA promoters .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilC	regulator	17675384	18	ver/dev	In agreement with genetic data , we show that the purified RtsA protein , like HilC , binds to the hilC , hilD , rtsA .	302	In agreement with genetic data , we show that the purified RtsA protein , like HilC and HilD , binds to the hilC , hilD , rtsA , and hilA promoters .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilC	regulator	22479568	0	ver/dev	RtsA can activate expression of hilC of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HU	gene	rpoS	regulator	21212121	21	ver/dev	HU regulates rpoS translation .	390	The Escherichia coli histone-like protein HU regulates rpoS translation .	18	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrC	regulator	14563863	10	att	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	125	To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .	4	RESULTS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrC	regulator	14563863	16	ver/dev	PhoP binds to the promoter regions of pmrC genes .	155	PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL , and pmrC genes but not to the promoter region of phoN , pagC , or mgtC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	lon	activator	15661008	26	ver/dev	In the present study , the expression from lac fusion was retained after disruption in Fig. 2A in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	lon	activator	15661008	26	ver/dev	In the present study , the expression from the hilA was retained after disruption in Fig. 2A in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	lon	activator	15661008	26	ver/dev	In the present study , the expression from lac fusion was retained after disruption in hilD in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	lon	activator	15661008	26	ver/dev	In the present study , the expression from lac fusion was retained after disruption in hilC in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	lon	activator	15661008	26	ver/dev	In the present study , the expression from the hilA was retained after disruption in hilD in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	lon	activator	15661008	26	ver/dev	In the present study , the expression from the hilA was retained after disruption in hilC in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	flgM	repressor	9765570	8	ver/dev	A reduction in flgM mRNA translation would relieve inhibition of s28 .	567	A reduction in flgM mRNA translation and subsequent FlgM protein levels in the cell would relieve inhibition of s28 and allow class 3 flagellar gene expression .	11	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
SsrB	gene	mcpC	repressor	27564394	9	ver/dev	mcpC , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI4-encoded genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	mcpC	repressor	27564394	9	ver/dev	mcpC , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-associated genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	mcpC	repressor	27564394	9	ver/dev	mcpC , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-encoded genes , and repressed by SsrB .	294	Two of the 8 genes , mcpA ( STM3138 ) and mcpC ( STM3216 ) , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins [ 40 ] and display similar expression patterns to the SPI1-encoded , SPI1-associated and SPI4-encoded genes which are directly or indirectly activated by HilD , and repressed by SsrB , but are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .	7	CONTROL OF SPI1 AND SPI2 EXPRESSION BY TRANSCRIPTIONAL REGULATORY SYSTEMS UNDER INFECTION-RELEVANT IN VITRO CONDITIONS	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
EutR	gene	eutR	activator	26565973	2	att	Moreover , neither vitamin-B12 or ethanolamine alone activated eutR expression in tissue culture medium , indicating that the intramacrophage environment is conducive to EutR-dependent signaling .	132	Moreover , neither vitamin B12 or ethanolamine alone activated eutR expression in tissue culture medium , indicating that the intramacrophage environment is conducive to EutR-dependent signaling .	8	ETHANOLAMINE INFLUENCES SPI-2 EXPRESSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
AraC	gene	ygeA	activator	24272778	46	ver/dev	ygeA are positively regulated by AraC due to partial read-through of Rho-independent terminators .	423	ygeA and polB are positively regulated by AraC and arabinose due to partial read-through of Rho-independent terminators ( Fig. 2 , 4 , and 5 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sipC	activator	10844688	10	att	For example , sipC has two promoters : a HilA-dependent promoter upstream of spaS and an InvF-dependent promoter downstream of spaS ( Darwin and Miller , 1999b ) .	275	For example , sipC has two promoters : a HilA-dependent promoter upstream of spaS and an InvF-dependent promoter downstream of spaS ( Darwin and Miller , 1999b ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	12535071	24	ver/dev	InvF production indirectly increases transcription of the sipC genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	12535071	24	ver/dev	InvF production directly increases transcription of the sipC genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	12535071	24	ver/dev	InvF production indirectly increases transcription of the sipC genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	12535071	24	ver/dev	InvF production directly increases transcription of the sipC genes	83	We propose that HilD and HilC can independently activate invF expression and InvF production , which directly and indirectly increases transcription of the sipA and sipC genes .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	21168230	1	att	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	208	Naringenin exposure down-regulated InvF-dependent genes of the sip operon sipA , sipB , and sipC and sptP ( Table 3 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipC and located outside -LRB- sopE -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipC and located outside -LRB- sopD -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	21168230	0	ver/dev	InvF positively regulates effector proteins within sipC and located outside -LRB- sopB -RRB- with the help of chaperone SicA .	207	InvF positively regulates effector proteins within SPI1 ( sipA , sipB , sipC and sptP ) and located outside ( sopB , sopD and sopE ) ( Darwin and Miller , 2000 , 2001 ) with the help of chaperone SicA ( Klein et al. , 2000 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
InvF	gene	sipC	activator	21320585	0	ver/dev	InvF induces the expression of sipC -LSB- 14e16 -RSB- .	42	InvF is required for the efficient invasion of Salmonella into host epithelial cells , and induces the expression of other genes involved in invasion , such as sipB , sipC , and sopE [ 14e16 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	11123690	30	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	370	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	32	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	11123690	30	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .	370	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	32	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	17908208	86	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	519	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	24	ACKNOWLEDGEMENTS	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	17908208	86	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .	519	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	24	ACKNOWLEDGEMENTS	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	24354910	64	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	507	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF and repression by H-NS .	46	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	24354910	64	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF by H-NS .	507	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF and repression by H-NS .	46	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	25566242	22	ver/dev	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	455	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	54	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	regulator	25566242	22	ver/dev	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .	455	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	54	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
UvrY	gene	uvrY	regulator	16949866	35	ver/dev	In E. coli , it was questioned whether csrC was directly regulated by UvrY because the amount of LacZ was only two-fold higher whe using S-30 extracts of wild-type E. coli compared to extracts from a uvrY mutant .	485	In E. coli , it was questioned whether csrC was directly regulated by UvrY because the amount of LacZ produced in a transcription -- translation reaction with csrC-lacZ was only two-fold higher whe using S-30 extracts of wild-type E. coli compared to extracts from a uvrY mutant ( Weilbacher et al. , 2003 ) .	19	DISCUSSION	Escherichia coli;Escherichia coli	0	L3	SPEC	Other	OTHER	Other	Level 1
NtrC	gene	argT	regulator	12125817	5	ver/dev	Although argT is controlled by nitrogen status through a sN-dependent promoter , there are no nearby binding sites for the general nitrogen control protein NtrC .	220	Although argT is controlled by nitrogen status through a sN-dependent promoter , there are no nearby binding sites for the general nitrogen control protein NtrC ( Schmitz et al. , 1988 ; Wu et al. , 1999 ) .	9	STM0652 AND STM2361	nan	1	L3	OTHER	Other	NEG	Other	Level 1
NtrC	gene	argT	regulator	12581721	5	ver/dev	Although argT is controlled by nitrogen status through a sN-dependent promoter , there are no nearby binding sites for the general nitrogen control protein NtrC .	220	Although argT is controlled by nitrogen status through a sN-dependent promoter , there are no nearby binding sites for the general nitrogen control protein NtrC ( Schmitz et al. , 1988 ; Wu et al. , 1999 ) .	9	STM0652 AND STM2361	nan	1	L3	OTHER	Other	NEG	Other	Level 1
FabR	gene	fabA	repressor	27004424	6	ver/dev	Combining it with a transcriptomics approach reduces its inherent noise This provided the first evidence for the direct repression of fabA expression by FabR in S. Typhimurium .	52	Combining it with a transcriptomics approach allows the discrimination between direct and indirect target genes and reduces its inherent noise [ 33 -- 36 ] This provided the first evidence for the direct repression of fabA , fabB and yqfA expression by FabR in S. Typhimurium , confirming current knowledge generated in E. coli .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FabR	gene	fabA	repressor	27004424	6	ver/dev	its inherent noise This provided the first evidence for the direct repression of fabA expression by FabR in S. Typhimurium _ confirming current knowledge	52	Combining it with a transcriptomics approach allows the discrimination between direct and indirect target genes and reduces its inherent noise [ 33 -- 36 ] This provided the first evidence for the direct repression of fabA , fabB and yqfA expression by FabR in S. Typhimurium , confirming current knowledge generated in E. coli .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	pipD	activator	23782700	2	att	A , - galactosidase activity from lacZ-transcriptional-fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	168	A , - galactosidase activity from lacZ transcriptional fusions to seven different PhoP-activated genes ( virK , mgtA , pagK , pipD , pcgM , pcgF , and pcgL ) and two PhoP-unrelated control reporters ( tppB and golT ) .	3	EXPERIMENTAL PROCEDURES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pipD	activator	31611347	3	att	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ-transcriptional-fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	94	( B ) Inhibition action was calculated on the basis of the - galactosidase activity of lacZ transcriptional fusions to six different PhoP-activated reporter genes ( virK , pagC , pagK , pcgM , pcgF , and pipD ) and two PhoP-unrelated control reporter genes ( tppB and cpxP ) .	3	KEYWORDS PHOP/PHOQ TWO-COMPONENT SYSTEM, SALMONELLA, ANTIVIRULENCE, DRUG DISCOVERY, QUINAZOLINES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoB	gene	fimZ	activator	25547794	25	ver/dev	These results demonstrate that the activation of the PhoB response regulator leads to increased fimZ expression , in the absence of functional FimZ , although the presence of FimZ further increases fimZ expression due to autoactivation .	243	These results demonstrate that the activation of the PhoB response regulator leads to increased fimZ expression , in the absence of functional FimZ , although the presence of FimZ further increases fimZ expression due to autoactivation .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
H	gene	proV	repressor	23515315	28	att	In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145 - and 9.5-fold compared with H-NSWT levels .	258	In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145 - and 9.5-fold compared with H-NSWT levels .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	hilA	repressor	25991823	7	ver/dev	Lack of AraC suppressed hilA repression by 0.2 % L-arabinose .	214	Lack of AraC suppressed hilA repression by 0.2 % L-arabinose ( Figure 4A , third column ) .	13	SPI-1 REPRESSION BY L-ARABINOSE IS INDEPENDENT OF ARAC	nan	1	L3	OTHER	Other	OTHER	New	Level 2
AraC	gene	hilA	repressor	25991823	10	ver/dev	When araE was expressed constitutively , lack of AraC no longer suppressed hilA repression by L-arabinose .	239	When araE was expressed constitutively , lack of AraC no longer suppressed hilA repression by L-arabinose ( Figure 4B ) .	13	SPI-1 REPRESSION BY L-ARABINOSE IS INDEPENDENT OF ARAC	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	hns	regulator	15256548	28	ver/dev	Antagonistic involvement of FIS proteins in the transcriptional control of hns expression .	937	Antagonistic involvement of FIS and H-NS proteins in the transcriptional control of hns expression .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	acrEF	repressor	19230852	3	ver/dev	We also found that H-NS represses acrEF .	185	We also found that H-NS represses the drug efflux genes , acrEF , mdtEF , and emrKY [ 64 ] .	7	4. REGULATORY NETWORK OF DRUG EFFLUX PUMPS IN E. COLI	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	acrEF	repressor	21081542	2	ver/dev	A recent study has shown that acrEF is repressed by H-NS ,36 whereas acrAB is not repressed .	190	A recent study has shown that acrEF is repressed by the histone-like nucleoid structuring protein ( H-NS ) ,36 whereas acrAB is not repressed and is constitutively expressed in S. enterica .25 AcrAB therefore makes a principal contribution to resistance to tigecycline and other glycylcyclines .	12	CONCLUSIONS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	TU	acrEF	repressor	23040276	5	ver/dev	K. Nishino , M. Hayashi-Nishino , A. Yamaguchi , H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multi-drug efflux genes acrEF , Antimicrob .	478	[ 34 ] K. Nishino , M. Hayashi-Nishino , A. Yamaguchi , H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multi-drug efflux genes acrEF , Antimicrob .	26	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	acrEF	repressor	32468234	17	ver/dev	https://doi.org/10.1128/JB.01045-07 Nishino K , Hayashi-Nishino M , Yamaguchi A H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multidrug efflfflux genes acrEF .	310	https://doi.org/10.1128/JB.01045-07 Nishino K , Hayashi-Nishino M , Yamaguchi A ( 2009 ) H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multidrug efflfflux genes acrEF .	20	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	sopD2	repressor	30682134	6	ver/dev	Consistent with these findings , we found that CsrA repressed the RNA abundance and translation of sopD2 at its native locus in S2 Table	197	Consistent with these findings , we found that CsrA repressed the RNA abundance and translation of sopD2 at its native locus in mLPM and LB ( S2 Table ) , and we confirmed the effect on sopD2 mRNA abundance with qRT-PCR ( Fig 5A ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	sopD2	repressor	30682134	6	ver/dev	Consistent with these findings , we found that CsrA repressed the RNA abundance and translation of sopD2 at its native locus in LB	197	Consistent with these findings , we found that CsrA repressed the RNA abundance and translation of sopD2 at its native locus in mLPM and LB ( S2 Table ) , and we confirmed the effect on sopD2 mRNA abundance with qRT-PCR ( Fig 5A ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	sopD2	repressor	30682134	6	ver/dev	Consistent with these findings , we found that CsrA repressed the RNA abundance and translation of sopD2 at its native locus in mLPM	197	Consistent with these findings , we found that CsrA repressed the RNA abundance and translation of sopD2 at its native locus in mLPM and LB ( S2 Table ) , and we confirmed the effect on sopD2 mRNA abundance with qRT-PCR ( Fig 5A ) .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	hslJ	regulator	18957594	13	att	Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resistance phenotype .	453	Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resistance phenotype .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	hslJ	regulator	19447191	22	att	Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resistance phenotype .	223	Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resistance phenotype .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	hslJ	regulator	27530757	5	att	Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resist-ance phenotype .	448	Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resist-ance phenotype .	29	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FliA	gene	flgM	regulator	8288531	4	att	Thus , the attenuated phenotype of aflgM mutant may be a consequence of overexpression of a FliA-regulated gene whose expression is normally modulated in a flgM ' background .	434	Thus , the attenuated phenotype of aflgM mutant may be a consequence of overexpression of a FliA-regulated gene whose expression is normally modulated in a flgM ' background .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FliA	gene	flgM	regulator	8631681	1	att	In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	6	In this investigation , we observed that ( i ) the in vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	OTHER	Other	OTHER	Other	Level 1
FliA	gene	flgM	regulator	8631681	1	att	In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	6	In this investigation , we observed that ( i ) the in vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .	1	ABSTRACT	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	OTHER	Other	OTHER	Other	Level 1
AraC	gene	ygeA	regulator	24272778	37	att	Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .	377	Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
AraC	gene	ygeA	regulator	24272778	39	att	We also identified AraC-regulated genes that are transcribed due to read-through of inefficient Rho-independent terminators ( ygeA and polB ) .	384	We also identified AraC-regulated genes that are transcribed due to read-through of inefficient Rho-independent terminators ( ygeA and polB ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
AraC	gene	ygeA	regulator	24272778	46	ver/dev	ygeA are positively regulated by AraC due to partial read-through of Rho-independent terminators .	423	ygeA and polB are positively regulated by AraC and arabinose due to partial read-through of Rho-independent terminators ( Fig. 2 , 4 , and 5 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	spvA	activator	11101680	1	ver/dev	the expression of luxCDABE results from the activation of the spvA promoter by RpoS	105	Expression of the SpvR protein requires an active RpoS protein ( Guiney et al. , 1995 ) and the expression of luxCDABE results from the activation of the spvA promoter by SpvR and RpoS .	4	METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	spvA	activator	23936152	8	ver/dev	the RpoS regulon _ suggesting that the increased spvA expression is mediated through another mechanism than increased levels of RpoS	368	However , neither the phoQ nor the stpA mutation increased expression of the RpoS regulon suggesting that the increased spvA expression is mediated through another mechanism than increased levels of RpoS .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	spvA	activator	23936152	8	ver/dev	the RpoS regulon _ suggesting that the increased spvA expression is mediated through another mechanism than increased levels of RpoS	368	However , neither the phoQ nor the stpA mutation increased expression of the RpoS regulon suggesting that the increased spvA expression is mediated through another mechanism than increased levels of RpoS .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	tag	activator	15910283	2	att	We first examined the effect of the C-terminal His tag on PhoQ activity in-vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ-transcriptional-fusion [ 15 ] .	133	We first examined the effect of the C-terminal His tag on PhoQ activity in vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ transcriptional fusion [ 15 ] .	14	RESULTS INFLUENCE OF THE C-TERMINAL HIS TAG ON PHOQ ACTIVITY	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
SirA	gene	hilA	activator	11244064	1	ver/dev	SirA , positively regulates another regulatory gene , hilA .	56	SirA , which is encoded outside of SPI1 , positively regulates another regulatory gene , hilA , that is encoded within SPI1 ( 2 , 32 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	activator	11244064	17	ver/dev	A second formal possibility is that SirA activates expression of hilA .	309	A second formal possibility is that SirA activates expression of a regulatory gene within SPI1 , such as hilA , the product of which represses the flagellar regulon .	7	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	activator	11370771	0	ver/dev	For example , the response regulator SirA has been shown to activate hilA transcription in the presence of suitable environmental signals , providing us with tools for both an on - -LRB- S i r M i l A -RRB- .	203	For example , the response regulator SirA has been shown to activate hilA transcription in the presence of suitable environmental signals ( 79 , SO ) , providing us with tools for both an on - ( S i r M i l A ) and off-switch ( PhoPmediated prg response ) for invasion .	6	REGULATING AN INFECTION: FINE-TUNING THE EXPRESSION OF VIRULENCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	activator	11370771	0	ver/dev	For example , the response regulator SirA has been shown to activate hilA transcription in PhoPmediated prg response for invasion .	203	For example , the response regulator SirA has been shown to activate hilA transcription in the presence of suitable environmental signals ( 79 , SO ) , providing us with tools for both an on - ( S i r M i l A ) and off-switch ( PhoPmediated prg response ) for invasion .	6	REGULATING AN INFECTION: FINE-TUNING THE EXPRESSION OF VIRULENCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	activator	11370771	0	ver/dev	For example , the response regulator SirA has been shown to activate hilA transcription in off-switch for invasion .	203	For example , the response regulator SirA has been shown to activate hilA transcription in the presence of suitable environmental signals ( 79 , SO ) , providing us with tools for both an on - ( S i r M i l A ) and off-switch ( PhoPmediated prg response ) for invasion .	6	REGULATING AN INFECTION: FINE-TUNING THE EXPRESSION OF VIRULENCE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	activator	15130116	8	ver/dev	In Salmonella , SirA also directly activates the horizontally acquired regulatory genes hilA .	221	In Salmonella , SirA also directly activates the horizontally acquired regulatory genes hilA and hilC , the products of which control the majority of genes within Salmonella pathogenicity island 1 ( SPI1 ) ( Johnston et al. , 1996 ; Ahmer et al. , 1999 ; Altier et al. , 2000 ; Teplitski et al. , 2003 ) .	5	THE SALMONELLA SDIA SYSTEM	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	activator	16045614	51	ver/dev	SirA induction of hilA requires HilD Previous evidence suggested that SirA required the entire SPI1 TTSS	299	SirA induction of hilA and invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA and thus the entire SPI1 TTSS	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	activator	16045614	51	ver/dev	SirA induction of hilA requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA	299	SirA induction of hilA and invF requires HilD Previous evidence suggested that SirA required the HilC / HilD/RtsA binding sites in the hilA promoter to induce expression of hilA and thus the entire SPI1 TTSS	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	activator	16045614	56	ver/dev	Therefore , our model predicts that SirA induces expression of hilA -LRB- and invF -RRB- via HilD .	392	Therefore , our model predicts that SirA induces expression of hilA ( and invF ) via HilD ( Fig. 1 ) .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilA	activator	16045614	57	ver/dev	We determined if SirA was still capable of inducing expression of hilA -- and invF -- lac fusions .	393	We introduced deletions of rtsA , hilC , or hilD and determined if SirA produced from a plasmid was still capable of inducing expression of hilA -- and invF -- lac fusions .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	activator	16045614	60	ver/dev	This suggests that SirA induction of hilA expression requires the presence of HilD .	396	This suggests that SirA induction of hilA expression requires the presence of HilD .	7	THE SIRA/BARA TWO-COMPONENT REGULATORY SYSTEM FUNCTIONS THROUGH HILD	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	hilA	activator	16045614	78	ver/dev	In support of our model , we demonstrate that SirA induction of hilA requires the presence of HilD .	549	In support of our model , we demonstrate that SirA induction of hilC , rtsA , hilA and invF requires the presence of HilD .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	hilA	activator	16045614	80	ver/dev	However , the data in Fig. 5 show that SirA , even overproduced , can activate neither hilA in the absence of HilD .	551	However , the data in Fig. 5 show that SirA , even overproduced , can activate neither hilC nor hilA in the absence of HilD .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
SirA	gene	hilA	activator	16905537	5	ver/dev	Despite an up to 2-fold activation of hilA expression in the wild type strain , the overexpression of SirA did not compensate for reduced hilA expression in the relA spoT strain , suggesting that SirA levels were not limiting ( supplemental Fig .	166	Despite an up to 2-fold activation of hilA expression in the wild type strain , the overexpression of SirA did not compensate for reduced hilA expression in the relA spoT strain , suggesting that SirA levels were not limiting ( supplemental Fig .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus	0	L2	SPEC	Analysis	NEG	Other	Level 1
SirA	gene	hilA	activator	16949866	0	ver/dev	SirA does this by directly activating the hilA .	11	SirA does this by directly activating the hilA and hilC regulatory genes encoded within SPI1 .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	hilA	activator	16949866	30	ver/dev	SirA controls these genes by directly activating the hilA .	455	SirA controls these genes by directly binding and activating the hilA and hilC regulatory genes that are encoded within the horizontal acquisition , SPI1 ( Teplitski et al. , 2003 ) .	19	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	activator	17074910	0	ver/dev	In S. typhimurium , SirA activates the virulence gene regulators hilA and hilC .	9	In S. typhimurium , SirA activates the csrB and csrC carbon storage regulatory RNAs and the virulence gene regulators hilA and hilC .	0	Unknown	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	activator	17208038	15	ver/dev	Deletions of rtsA do not affect the induction of hilA by SirA .	107	Deletions of hilC and rtsA alter the total level of hilA expression , but do not affect the induction of hilA by SirA .	8	BARA/SIRA	nan	1	L3	OTHER	Other	NEG	New	Level 1
SirA	gene	hilA	activator	17208038	15	ver/dev	Deletions of hilC do not affect the induction of hilA by SirA .	107	Deletions of hilC and rtsA alter the total level of hilA expression , but do not affect the induction of hilA by SirA .	8	BARA/SIRA	nan	1	L3	OTHER	Other	NEG	New	Level 1
SirA	gene	hilA	activator	17208038	21	ver/dev	On the basis of these data , the authors concluded that SirA activates the system by direct action on hilA .	122	On the basis of these data , the authors concluded that SirA activates the system by direct action on hilC and hilA [ 44 ] .	8	BARA/SIRA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	activator	19537165	5	ver/dev	SirA has been shown to activate the promoters of hilA .	58	SirA has been shown to activate the promoters of hilA and hilC [ Teplitski et al. , 2003 ] .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	hilA	activator	24500522	1	ver/dev	SirA , positively regulates the expression of hilA .	170	The global response regulator , SirA , positively regulates the expression of hilA , hilC , and hilD encoded within SPI-1 and SPI-2 ( Teplitski et al. 2006 ; Martínez et al. 2011 ) .	19	VIABILITY AND MOTILITY OF S. TYPHIMURIUM EXPOSED TO THE SIMULATED INTESTINAL CONDITIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	hilA	activator	27565525	2	ver/dev	SirA , positively regulates the transcription of hilA .	365	SirA , when activated , positively regulates the transcription of hilA and hilC , that serves as an initial effector of bacterial invasion pathway ( Johnston et al. , 1996 ; Teplitski et al. , 2006 ) ; therefore the induction of sirA in Salmonella leads to bacterial association and biofilm formation ( Salazar et al. , 2013 ) .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	regulator	28704543	9	ver/dev	These results show that SsrB specifically binds to the regulatory regions of hilD .	133	These results show that SsrB specifically binds to the regulatory regions of hilD and hilA .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	regulator	28704543	15	ver/dev	EMSAs were performed to confirm that SsrB directly regulates the promoter of hilD .	154	EMSAs were performed to confirm that SsrB directly regulates the promoter of hilD .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	16	ver/dev	The hilD DNA fragments contained in hilD-cat-37 +6 , indicating that SsrB binds to the promoter located between position -37 to +6 relative to the transcriptional start site of hilD .	155	The hilD DNA fragments contained in hilD-cat-108 +88 , hilD-cat-48 +88 and hilD-cat-37 +6 , shifted in the presence of increasing concentrations of 6H-SsrBc ( Fig 5D , 5E and 5F ) , indicating that SsrB binds to the promoter located between position -37 to +6 relative to the transcriptional start site of hilD , which is consistent with our bioinformatics analysis revealing two putative SsrB-binding sites on this region ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	regulator	28704543	16	ver/dev	The hilD DNA fragments contained in hilD-cat-48 +88 +6 , indicating that SsrB binds to the promoter located between position -37 to +6 relative to the transcriptional start site of hilD .	155	The hilD DNA fragments contained in hilD-cat-108 +88 , hilD-cat-48 +88 and hilD-cat-37 +6 , shifted in the presence of increasing concentrations of 6H-SsrBc ( Fig 5D , 5E and 5F ) , indicating that SsrB binds to the promoter located between position -37 to +6 relative to the transcriptional start site of hilD , which is consistent with our bioinformatics analysis revealing two putative SsrB-binding sites on this region ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	regulator	28704543	16	ver/dev	The hilD DNA fragments contained in hilD-cat-108 +88 +6 , indicating that SsrB binds to the promoter located between position -37 to +6 relative to the transcriptional start site of hilD .	155	The hilD DNA fragments contained in hilD-cat-108 +88 , hilD-cat-48 +88 and hilD-cat-37 +6 , shifted in the presence of increasing concentrations of 6H-SsrBc ( Fig 5D , 5E and 5F ) , indicating that SsrB binds to the promoter located between position -37 to +6 relative to the transcriptional start site of hilD , which is consistent with our bioinformatics analysis revealing two putative SsrB-binding sites on this region ( Fig 4B ) .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus	0	L2	SPEC	Analysis	OTHER	New	Level 1
SsrB	gene	hilD	regulator	28704543	17	ver/dev	These results show that SsrB binds to the promoter of hilD .	156	These results show that SsrB binds to the promoter of hilD and thus would repress its transcription .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hilD	regulator	28704543	25	ver/dev	EMSAs were performed to analyze whether SsrB binds to the hilD DNA fragments in the hilD-cat-108 +88 , hilD-cat-48 +88 and hilD-cat-37 +6 fusions .	193	EMSAs were performed to analyze whether SsrB binds to the hilD DNA fragments in the hilD-cat-108 +88 ( D ) , hilD-cat-48 +88 ( E ) and hilD-cat-37 +6 ( F ) fusions .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus;Felis catus	0	L3	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , hilA promoter sequences contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are S4 Fig ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine negative regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	39	ver/dev	Notably , the hilD contained in the hilD-cat-37 +6 -LRB- directly repressed by SsrB -RRB- and hilA-cat-35 +6 -LRB- not repressed by SsrB -RRB- fusions , respectively , are 65 % identical ; thus , only 15 different positions between these sequences determine binding regulation of SsrB on the hilD promoter .	236	Notably , the hilD and hilA promoter sequences contained in the hilD-cat-37 +6 ( directly repressed by SsrB ) and hilA-cat-35 +6 ( not repressed by SsrB ) fusions , respectively , are 65 % identical ( S4 Fig ) ; thus , only 15 different positions between these sequences determine binding and thus negative regulation of SsrB on the hilD promoter , but not on the hilA promoter .	8	SSRB DIRECTLY REPRESSES HILD AND HILA	Felis catus;Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hilD	regulator	28704543	47	ver/dev	The direct binding of SsrB to the promoter of hilD may be preventing RNA polymerase from binding to this region .	294	The direct binding of SsrB to the promoter of hilD may be preventing RNA polymerase from binding to this region .	10	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SsrB	gene	hilD	regulator	32021316	7	ver/dev	SsrB directly binds to the regulatory region of hilD , it has been observed that the intestinal butyrate can inhibit the expression of hilD , encoding the T3SS-1 gene regulator .165 Salmonella utilizes butyrate and , in turn , provides fitness advantages during pathogen growth .	203	SsrB directly binds to the regulatory region of hilA and hilD and suppress it .164 Recently , it has been observed that the intestinal butyrate derived from clos-tridia can inhibit the expression of hilD , encoding the T3SS-1 gene regulator .165 Salmonella utilizes butyrate using β-oxidation and , in turn , provides fitness advantages during pathogen growth .	15	HOW TO ACTIVATE PATHOGENIC GENES	Salmonella	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CpxR	gene	yoaE	regulator	31915212	0	ver/dev	yoaE Gene _ Regulated by CpxR in the Survival of Enteritidis in A	2	Role of yoaE Gene Regulated by CpxR in the Survival of Enteritidis in A	0	Unknown	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	yoaE	regulator	31915212	1	ver/dev	In this study , the role of the gene yoaE , in the survival of its transcriptional regulation by CpxR were investigated .	9	In this study , the role of the gene yoaE , encoding an inner membrane protein , in the survival of Salmonella Enteritidis in egg white , and its transcriptional regulation by CpxR were investigated .	1	ABSTRACT	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
CpxR	gene	yoaE	regulator	31915212	3	ver/dev	CpxR could directly bind to the yoaE promoter region	14	In vitro , results from DNase I footprinting and electrophoretic mobility shift assays further demonstrated that CpxR could directly bind to the yoaE promoter region , and a spe-cific CpxR binding sequence was identified .	1	ABSTRACT	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	yoaE	regulator	31915212	5	ver/dev	This study revealed the importance of yoaE , on the survival of its transcriptional regulation by CpxR .	19	This study revealed the importance of yoaE , a gene with unknown function , on the survival of S. Enteritidis in egg white , as well as its transcriptional regulation by CpxR .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CpxR	gene	yoaE	regulator	31915212	6	ver/dev	Role of yoaE gene regulated by CpxR in the survival of Salmonella enterica serovar Enteritidis in antibacterial egg white .	27	Role of yoaE gene regulated by CpxR in the survival of Salmonella enterica serovar Enteritidis in antibacterial egg white .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	yoaE	regulator	31915212	7	ver/dev	upstream of the yoaE gene _ indicating that this gene was likely to be regulated by CpxR in egg	46	Analysis of the yoaE promoter region revealed conserved CpxR binding sites upstream of the yoaE gene , indicating that this gene was likely to be regulated by CpxR in egg white .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	yoaE	regulator	31915212	11	ver/dev	In order to determine whether CpxR regulates yoaE in egg white in-vivo , we compared the yoaE gene expression level between the WT .	81	In order to determine whether CpxR regulates yoaE in egg white in vivo , we compared the yoaE gene expression level between the WT and the cpxR deletion mutant ( cpxR ) using RT-qPCR assays ( Fig. 3 ) .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	yoaE	regulator	31915212	11	ver/dev	In order to determine whether CpxR regulates yoaE in egg white in-vivo , we compared cpxR .	81	In order to determine whether CpxR regulates yoaE in egg white in vivo , we compared the yoaE gene expression level between the WT and the cpxR deletion mutant ( cpxR ) using RT-qPCR assays ( Fig. 3 ) .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	yoaE	regulator	31915212	11	ver/dev	In order to determine whether CpxR regulates yoaE in egg white in-vivo , we compared the cpxR deletion mutant .	81	In order to determine whether CpxR regulates yoaE in egg white in vivo , we compared the yoaE gene expression level between the WT and the cpxR deletion mutant ( cpxR ) using RT-qPCR assays ( Fig. 3 ) .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	yoaE	regulator	33133053	1	ver/dev	Role of yoaE gene regulated by CpxR in the survival of Salmonella enterica Serovar Enteritidis in antibacterial egg white .	737	Role of yoaE gene regulated by CpxR in the survival of Salmonella enterica Serovar Enteritidis in antibacterial egg white .	60	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
FimZ	TU	flhDC	activator	26441883	18	ver/dev	FimZ is an activator of type was shown to represses flhDC .	366	FimZ is an activator of type 1 fimbriae and was shown to represses flhDC , as well as Spi-1 genes , which indicates that cross-talk between the flagellar , fimbriae and Spi-1 regulatory systems is of importance during the transition from a motile , planktonic lifestyle to intestinal colonization and persistence ( Saini et al. , 2010 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FimZ	TU	flhDC	activator	26441883	18	ver/dev	FimZ is an activator of type 1 fimbriae flhDC .	366	FimZ is an activator of type 1 fimbriae and was shown to represses flhDC , as well as Spi-1 genes , which indicates that cross-talk between the flagellar , fimbriae and Spi-1 regulatory systems is of importance during the transition from a motile , planktonic lifestyle to intestinal colonization and persistence ( Saini et al. , 2010 ) .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	cho	regulator	19525399	5	att	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	175	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	3	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	topA	activator	16999831	14	ver/dev	Fis also stimulates transcription of E. coli topA , when the bacteria experience oxidative-stress , something , although the severity of the oxidative-stress is unclear from an examination of the responses of classic oxidative-stress response genes .	143	Fis also stimulates transcription of E. coli topA , the gene coding for topoisomerase I , when the bacteria experience oxidative stress ( Weinstein-Fischer et al. , 2000 ) , something that may be experienced by S. Typhimurium when growing in macrophage ( Babior , 2000 ; Nathan and Shiloh , 2000 ) , although the severity of the oxidative stress is unclear from an examination of the responses of classic oxidative stress response genes ( Eriksson et al. , 2003 ; Faucher et al. , 2006 ) .	12	FIS LEVELS INFLUENCE DNA SUPERCOILING AND THE SSRA PROMOTER	Escherichia coli	0	L3	SPEC	Other	OTHER	Other	Level 1
Fis	gene	topA	activator	21276095	4	ver/dev	Transcription of E. coli topA is driven by the interplay of at least four transcription start sites , allowing FIS to be both an activator of E. coli topA expression .	42	Transcription of E. coli topA is driven by the interplay of at least four transcription start sites , allowing FIS to be both an activator and a repressor of E. coli topA expression ( WeinsteinFischer and Altuvia , 2007 ) .	3	INTRODUCTION	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over TopA levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over TopA levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	6	ver/dev	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB levels by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA are induced by DNA relaxation whereas topA in induced by increased negative supercoiling .	44	Thus , global supercoiling homeostasis is maintained in part by FIS 's central control over GyrAB and TopA levels , and also in part by the repressive effect of each enzyme 's activity on its antagonist 's promoter : gyrA and gyrB are induced by DNA relaxation whereas topA in induced by increased negative supercoiling ( Tse-Dinh , 1985 ; Menzel and Gellert , 1987 ; Peter et al. , 2004 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	9	ver/dev	E. coli topA was upregulated in the absence of FIS in both exponential-growth and stationary-phase , whereas S. enterica topA expression was elevated in stationary-phase relative to wild-type cells .	182	E. coli topA was upregulated in the absence of FIS in both exponential growth and stationary phase , whereas S. enterica topA expression was unaffected in Dfis cells during exponential growth but was elevated in stationary phase relative to wild-type cells .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	Escherichia coli;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	9	ver/dev	E. coli topA was upregulated in the absence of FIS in both exponential-growth and stationary-phase , whereas S. enterica topA expression was unaffected in Dfis cells during exponential-growth .	182	E. coli topA was upregulated in the absence of FIS in both exponential growth and stationary phase , whereas S. enterica topA expression was unaffected in Dfis cells during exponential growth but was elevated in stationary phase relative to wild-type cells .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	Escherichia coli;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
Fis	gene	topA	activator	21276095	14	ver/dev	Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare 4A -RRB- .	219	Although topA promoter function has routinely been studied using plasmid-based systems ( Tse-Dinh , 1985 ; Tse-Dinh and Beran , 1988 ; Lesley et al. , 1990 ; Marshall et al. , 2000 ; Weinstein-Fischer and Altuvia , 2007 ) , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS ( compare Figs 3A and 4A ) .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	unidentified plasmid;Escherichia coli;unidentified plasmid	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	topA	activator	21276095	14	ver/dev	Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare Figs 3A -RRB- .	219	Although topA promoter function has routinely been studied using plasmid-based systems ( Tse-Dinh , 1985 ; Tse-Dinh and Beran , 1988 ; Lesley et al. , 1990 ; Marshall et al. , 2000 ; Weinstein-Fischer and Altuvia , 2007 ) , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS ( compare Figs 3A and 4A ) .	7	CONTROL OF TOPA TRANSCRIPTION BY FIS DIFFERS BETWEEN E. COLI AND S. ENTERICA	unidentified plasmid;Escherichia coli;unidentified plasmid	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
Hha	gene	hilA	activator	21680637	19	ver/dev	The double hns hha-mutant showed the highest b-galactosidase activities at low-temperature , indicating that Hha enhances H-NS-mediated hilA silen-cing .	204	The double hns hha mutant showed the highest b-galactosidase activities at both low osmolarity and low temperature , indicating that Hha enhances H-NS-mediated hilA silen-cing .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Hha	gene	hilA	activator	21680637	19	ver/dev	The double hns hha-mutant showed the highest b-galactosidase activities at both low-osmolarity , indicating that Hha enhances H-NS-mediated hilA silen-cing .	204	The double hns hha mutant showed the highest b-galactosidase activities at both low osmolarity and low temperature , indicating that Hha enhances H-NS-mediated hilA silen-cing .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Hha	gene	hilA	activator	21680637	68	ver/dev	The Hha protein enhances the silencing effect of H-NS on hilA .	350	The Hha protein enhances the silencing effect of H-NS on hilA .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	dsrA	activator	16816180	5	att	To study the role of dsrA and rprA in S. enterica , we characterized the effect of the deletion of each gene separately , or both genes together , on expression of the RpoS-dependent reporter , katE-lac [ op ] .	205	To study the role of dsrA and rprA in S. enterica , we characterized the effect of the deletion of each gene separately , or both genes together , on expression of the RpoS-dependent reporter , katE-lac [ op ] .	4	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Investigation	OTHER	New	Level 2
RpoS	gene	dsrA	activator	25123657	9	att	This is due to an increase in the expression of the untranslated mRNA dsrA , which activates RpoS translation and cause induced expression of RpoS-dependent genes such as bolA [ 19 ] .	94	This is due to an increase in the expression of the untranslated mRNA dsrA , which activates RpoS translation and cause induced expression of RpoS-dependent genes such as bolA [ 19 ] .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	dsrA	activator	25123657	9	ver/dev	the untranslated mRNA dsrA activates cause induced expression of RpoS-dependent genes	94	This is due to an increase in the expression of the untranslated mRNA dsrA , which activates RpoS translation and cause induced expression of RpoS-dependent genes such as bolA [ 19 ] .	6	RESULT AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	fur	regulator	30682134	30	ver/dev	However , CsrA did not regulate the expression of fur in S2 Table .	265	However , CsrA did not regulate the expression of fur in mLPM or LB ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	fur	regulator	30682134	30	ver/dev	However , CsrA did not regulate the expression of fur in LB .	265	However , CsrA did not regulate the expression of fur in mLPM or LB ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	fur	regulator	30682134	30	ver/dev	However , CsrA did not regulate the expression of fur in mLPM .	265	However , CsrA did not regulate the expression of fur in mLPM or LB ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	nan	1	L3	OTHER	Other	NEG	New	Level 1
McbR	gene	yciGFE	activator	20713450	8	ver/dev	that McbR are both able to induce expression of the yciGFE locus in E. coli K-12	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
McbR	gene	yciGFE	activator	20713450	8	ver/dev	that McbR are both able to induce expression of the yciGFE locus in Salmonella	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
Fur	gene	feoB	activator	18790861	45	ver/dev	Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .	238	Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
sigma-28	TU	flhDC	regulator	26442936	8	ver/dev	Transcriptional regulation of flhDC by sigma-28 ( FliA ) in enterohaemorrhagic Esche-richia coli .	844	Transcriptional regulation of flhDC by QseBC and sigma 28 ( FliA ) in enterohaemorrhagic Esche-richia coli .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
sigma-28	TU	flhDC	regulator	26443762	6	ver/dev	Transcriptional regulation of flhDC by sigma-28 ( FliA ) in enterohaemorrhagic Escherichia coli .	626	Transcriptional regulation of flhDC by QseBC and sigma 28 ( FliA ) in enterohaemorrhagic Escherichia coli .	27	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hlyE	activator	24885225	12	att	PhoP-dependent up-regulation of hlyE was reported when bacteria were cultured simultaneously under low pH and low concentration of Mg2 + [ 11 ] .	50	PhoP-dependent up-regulation of hlyE was reported when bacteria were cultured simultaneously under low pH and low concentration of Mg2 + [ 11 ] .	3	BACKGROUND	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hlyE	activator	24885225	3	att	Moreover , PhoP-dependent hlyE up-regulation has been reported in bacteria cultured simultaneously under low pH and low concentration of Mg2 + .	12	Moreover , PhoP-dependent hlyE up-regulation has been reported in bacteria cultured simultaneously under low pH and low concentration of Mg2 + .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	hlyE	activator	24885225	37	att	Nevertheless , considering that the low pH is an environmental signal that activates both the RpoS - and PhoP-dependent up-regulation of hlyE , it is not clear the relative contribution of each glo-bal regulator to the up-regulation of this gene .	130	Nevertheless , considering that the low pH is an environmental signal that activates both the RpoS - and PhoP-dependent up-regulation of hlyE , it is not clear the relative contribution of each glo-bal regulator to the up-regulation of this gene .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	hlyE	activator	24885225	37	ver/dev	Nevertheless , considering that the low pH is PhoP-dependent up-regulation of hlyE , it is not clear the relative contribution of each glo-bal regulator to the up-regulation of this gene .	130	Nevertheless , considering that the low pH is an environmental signal that activates both the RpoS - and PhoP-dependent up-regulation of hlyE , it is not clear the relative contribution of each glo-bal regulator to the up-regulation of this gene .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsB	gene	dps	activator	25028458	20	att	( b ) Alignment of the RcsB-dependent regulatory sequences of dps S. enterica ( Se ) , ugd S. enterica ( Se ) and fts E. coli ( Ec ) genes .	175	( b ) Alignment of the RcsB-dependent regulatory sequences of dps S. enterica ( Se ) , ugd S. enterica ( Se ) and fts E. coli ( Ec ) genes .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	Salmonella;Salmonella;Salmonella;Salmonella;Escherichia coli	0.5	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	dps	activator	25028458	25	att	These results suggest that the increased resistance of the rcsC11 mutant to H2O2 treatment is the result of dps gene induction in an RcsB-dependent manner .	263	These results suggest that the increased resistance of the rcsC11 mutant to H2O2 treatment is the result of dps gene induction in an RcsB-dependent manner .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	dps	activator	25028458	26	att	This rcsB dps phenotype could be explained assuming that expression of other RcsB-dependent genes is required for H2O2 resistance .	267	This rcsB dps phenotype could be explained assuming that expression of other RcsB-dependent genes is required for H2O2 resistance .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	dps	activator	25028458	27	att	The dps -- RcsB-dependent induction is required for oxidative-stress resistance	275	The dps -- RcsB-dependent induction is required for oxidative stress resistance	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	dps	activator	25028458	4	att	Using a list of RcsB-dependent genes obtained from a microarray assay , we demonstrate experimentally that the dps gene is a new member of the RcsB regulon .	43	Using a list of RcsB-dependent genes obtained from a microarray assay , we demonstrate experimentally that the dps gene is a new member of the RcsB regulon .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	dps	activator	25028458	43	att	Accordingly , we conclude that this phenotype is due to the dps RcsB-dependent induction , because under our conditions the rcsC11 dps double mutant displayed less resistance to H2O2 than the wild-type and rcsC11 strains ( Fig. 4b ) .	357	Accordingly , we conclude that this phenotype is due to the dps RcsB-dependent induction , because under our conditions the rcsC11 dps double mutant displayed less resistance to H2O2 than the wild-type and rcsC11 strains ( Fig. 4b ) .	7	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	dps	activator	25028458	16	ver/dev	These data confirmed that RcsB positively controls dps expression , mainly playing the role of an inductor during the exponential phase .	137	These data confirmed that RcsB positively controls dps expression , mainly playing the role of an inductor during the exponential phase when the bacteria sense new changes in their environment .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	dps	activator	25028458	18	ver/dev	These results indicated that the most important contribution of RcsB in dps induction is produced when the PrcsDB promoter is activated during the exponential phase .	144	These results indicated that the most important contribution of RcsB in dps induction is produced when the PrcsDB promoter is activated during the exponential phase .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	dps	activator	25028458	24	ver/dev	Nevertheless , our data suggest that activation of the PrcsB promoter controlling RcsB production also contri-butes to dps expression during a more prolonged stationary-phase .	254	Nevertheless , our data suggest that activation of the PrcsB promoter controlling RcsB production also contri-butes to dps expression during a more prolonged stationary phase .	6	INDUCTION OF DPS IN THE EXPONENTIAL PHASE DEPENDS ON PRCSDB ACTIVATION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	dps	activator	25028458	31	ver/dev	In this sense , our micro-array results showed that RcsB induces transcription of dps in an RcsA-independent pathway , because gene expression was not affected in the rcsC11 rcsA mutant relative to those levels .	327	In this sense , our micro-array results showed that RcsB induces transcription of dps in an RcsA-independent pathway , because gene expression was not affected in the rcsC11 rcsA mutant relative to those levels observed in rcsC11 ( C. Mouslim et al. , unpublished data ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsB	gene	dps	activator	27206164	24	att	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	dps	activator	27206164	9	ver/dev	RcsB activates transcription of genes responsible for the dps gene .	65	RcsB activates transcription of genes involved in physiological processes like the wzzst gene responsible for correct LPS O-antigen formation and the dps gene involved in oxidative stress resistance ( Delgado et al. , 2006 ; Farizano et al. , 2014 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	dps	activator	30510144	30	att	To confirm the SlyA repression effect on rcsB , we used another RcsB-dependent gene , dps ( 32 ) .	136	To confirm the SlyA repression effect on rcsB , we used another RcsB-dependent gene , dps ( 32 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	dps	activator	30510144	42	att	A similar effect was observed using another RcsB-dependent gene , dps ; slyA overexpression decreased the levels of dps in the wild type but not in the rcsB strain .	186	A similar effect was observed using another RcsB-dependent gene , dps ; slyA overexpression decreased the levels of dps in the wild type but not in the rcsB strain .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsB	gene	dps	activator	31486760	4	att	As a negative control , we used a 234 bp PCR product containing a variant of the RcsB-dependent dps promoter , which lacked the RcsB-binding sequence [ 13 ] .	140	As a negative control , we used a 234 bp PCR product containing a variant of the RcsB-dependent dps promoter , which lacked the RcsB-binding sequence [ 13 ] .	5	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HilD	gene	gtgE	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the gtgE genes , independently of InvF .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	gtgE	activator	27886269	6	ver/dev	These results show that HilD positively controls the expression of the gtgE genes , independently of HilA .	81	These results show that HilD positively controls the expression of the gtgE , phoH , sinR , lpxR , SL1896 and SL4247 genes , independently of HilA and InvF .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	gtgE	activator	27886269	7	ver/dev	HilD induces the expression of gtgE , in the absence of other Salmonella-specific regulators .	82	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not that of SL1896 , in the absence of other Salmonella-specific regulators .	3	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	gtgE	activator	27886269	21	ver/dev	Thus , HilD positively regulates the expression of the gtgE genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	gtgE	activator	27886269	22	ver/dev	HilD positively regulates gtgE in S. Typhimurium .	132	HilD positively regulates gtgE , phoH , sinR , lpxR , SL1896 and SL4247 in S. Typhimurium .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	gtgE	activator	27886269	23	ver/dev	HilD induces the expression of gtgE , in E. coli MC4100 .	151	HilD induces the expression of gtgE , phoH , sinR , lpxR and SL4247 , but not SL1896 , in E. coli MC4100 .	4	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
LysR	gene	oxyR	regulator	20460466	0	ver/dev	the oxyR gene encodes a DNA binding , transcriptional dual regulator of the LysR family	404	StyR-243 ( 135 nt ) is expressed in an antisense orientation to ORF of the oxyR gene , which encodes a DNA binding , transcriptional dual regulator of the LysR family ( 58 ) .	16	CLASS 2: ANTISENSE S. TYPHI NPCRNAS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	STM2585A	activator	17379730	8	att	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	449	51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 )	15	CONCLUDING REMARKS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
STM4417	gene	iolE	regulator	19011032	7	ver/dev	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolH were cloned into the promoter probe vector pDEW201 .	197	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 , iolC1 , iolD1 , iolG2 , iolI2 , and iolH were cloned into the promoter probe vector pDEW201 carrying the luxCDABE cassette .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM4417	gene	iolE	regulator	19011032	7	ver/dev	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolI2 were cloned into the promoter probe vector pDEW201 .	197	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 , iolC1 , iolD1 , iolG2 , iolI2 , and iolH were cloned into the promoter probe vector pDEW201 carrying the luxCDABE cassette .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM4417	gene	iolE	regulator	19011032	7	ver/dev	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG2 were cloned into the promoter probe vector pDEW201 .	197	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 , iolC1 , iolD1 , iolG2 , iolI2 , and iolH were cloned into the promoter probe vector pDEW201 carrying the luxCDABE cassette .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM4417	gene	iolE	regulator	19011032	7	ver/dev	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolD1 were cloned into the promoter probe vector pDEW201 .	197	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 , iolC1 , iolD1 , iolG2 , iolI2 , and iolH were cloned into the promoter probe vector pDEW201 carrying the luxCDABE cassette .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM4417	gene	iolE	regulator	19011032	7	ver/dev	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolC1 were cloned into the promoter probe vector pDEW201 .	197	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 , iolC1 , iolD1 , iolG2 , iolI2 , and iolH were cloned into the promoter probe vector pDEW201 carrying the luxCDABE cassette .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
STM4417	gene	iolE	regulator	19011032	7	ver/dev	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 were cloned into the promoter probe vector pDEW201 .	197	In order to investigate the regulation of the genes in GEI4417 / 4436 , fragments of approximately 300 bp located upstream of the start codons of STM4417 , iolA , iolE , iolG1 , iolC1 , iolD1 , iolG2 , iolI2 , and iolH were cloned into the promoter probe vector pDEW201 carrying the luxCDABE cassette .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	lacZ	regulator	11260470	1	ver/dev	Thirty-eight unique mutants _ carrying transcriptional lacZ gene fusions positively regulated by RpoS	67	Thirty-eight unique mutants carrying transcriptional lacZ gene fusions positively regulated by RpoS were selected , and 21 of them were subjected to preliminary characterization ( Ibanez-Ruiz et al. , 2000 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	lacZ	regulator	22356617	9	att	Vijayakumar , S.R. , Kirchhof , M.G. , Patten , C.L. , and Schellhorn , H.E. ( 2004 ) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .	812	Vijayakumar , S.R. , Kirchhof , M.G. , Patten , C.L. , and Schellhorn , H.E. ( 2004 ) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .	57	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	lacZ	regulator	23893734	1	ver/dev	To further examine the SraL regulation by RpoS , we analyzed sraL promoter response in a transcriptional-fusion to lacZ reporter gene in both rpoS mutant genetic backgrounds .	102	To further examine the SraL regulation by RpoS , we analyzed sraL promoter response in a transcriptional fusion to lacZ reporter gene in both wild-type and rpoS mutant genetic backgrounds .	7	SRAL SRNA IS DIRECTLY REGULATED BY ΣS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
RpoS	gene	lacZ	regulator	23893734	1	ver/dev	To further examine the SraL regulation by RpoS , we analyzed sraL promoter response in a transcriptional-fusion to lacZ reporter gene in both wild-type .	102	To further examine the SraL regulation by RpoS , we analyzed sraL promoter response in a transcriptional fusion to lacZ reporter gene in both wild-type and rpoS mutant genetic backgrounds .	7	SRAL SRNA IS DIRECTLY REGULATED BY ΣS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
RpoS	gene	lacZ	regulator	24985365	5	att	Vijayakumar SRV , Kirchhof MG , Patten CL & Schellhorn HE ( 2004 ) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .	265	Vijayakumar SRV , Kirchhof MG , Patten CL & Schellhorn HE ( 2004 ) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .	23	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	lacZ	regulator	25313216	0	att	RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .	468	RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .	47	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
RpoS	gene	lacZ	regulator	32193977	1	att	RpoS-regulated genes of Escherichia coli Identified by random lacZ fusion mutagenesis .	671	RpoS-regulated genes of Escherichia coli Identified by random lacZ fusion mutagenesis .	39	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	tpx	regulator	18156266	44	ver/dev	Interestingly , the results indicate that H-NS is a positive regulator of tpx ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	354	Interestingly , the results presented here indicate that H-NS is a positive regulator of tpx and STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	STM4257	activator	23419780	7	ver/dev	InvF are transcription activators of effectors downregulates the first gene of SPI-4 , STM4257 .	239	HilA and InvF are transcription activators of effectors secreted by SPI-1 ( Darwin and Miller , 2001 ) and HilA directly downregulates sopA , sopB , and siiA ( the first gene of SPI-4 , STM4257 ) ( Thijs et al. , 2007 ) .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	ansB	activator	18559530	0	ver/dev	In E. coli , ansB is positively coregulated by Fnr .	145	In E. coli , ansB is positively coregulated by Fnr and by CRP ( cyclic AMP receptor protein ) , a carbon source utilization regulator ( 24 ) .	6	RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	recA	repressor	20457791	0	ver/dev	Transcription of the Salmonella enterica recA gene is negatively controlled by the LexA protein , the repressor of the SOS response .	7	Transcription of the Salmonella enterica recA gene is negatively controlled by the LexA protein , the repressor of the SOS response .	1	ABSTRACT	Salmonella;Salmonella enterica;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	rpoS	repressor	11489123	11	ver/dev	In support of this explanation , inactivation of the histone-like protein H-NS , has been shown to abrogate the requirement of the rpoS gene for expression of curli by E. coli K-12 .	309	In support of this explanation , inactivation of the histone-like protein H-NS , which induces negative DNA supercoiling and binds to curved DNA regions , has been shown to abrogate the requirement of the rpoS gene for expression of curli by E. coli K-12 ( Olsén et al. , 1993 ; Arnqvist et al. , 1994 ) .	14	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	era	regulator	15703297	0	att	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5-7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8-10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in-vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	12	A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Because the preva- lent mechanisms controlling gene expression operate at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features (1, 2) and map such features into expression patterns (3, 4) to classify genes into distinct networks. However, these methods are not focused on the more challenging problem of distinguishing between differ- entially regulated genes within a network. Here, we use a unsupervised machine learning method (5–7), Gene Promoter Scan (GPS), to investigate the regulatory interactions governed by the PhoP PhoQ two-component system, a central element in one of the most interconnected bacterial genetic networks thus far described. The PhoQ protein is a sensor for extracytoplasmic Mg2 that modifies the phosphorylated state of the DNA-binding protein PhoP (8–10). The PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2 environ- ments and or virulence in several bacterial species including Salmonella enterica, Shigella flexneri, Yersinia pestis, Erwinia carotovora, Neisseria meningitidis, Photorhabdus luminescens and Escherichia coli (see ref. 11 for a review). It has been proposed that the PhoP protein recognizes the direct hexanucleotide repeat (T G)GTTTA, separated by five nucleotides, which has been termed the PhoP box (12). Indeed, experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in vitro (13). However, there is uncertainty about what consti- tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model (14, 15). Moreover, the identification of PhoP-regulated targets is con- founded by the fact that many genes are indirectly regulated by	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Shigella flexneri;Yersinia pestis;Pectobacterium carotovorum;Neisseria meningitidis;Photorhabdus luminescens;Escherichia coli;Escherichia coli	0.5	L3	SPEC	Analysis	NEG	Other	Level 1
HilA	gene	sirA	activator	15765064	18	ver/dev	Some reports suggest that overexpression of sirA can also overcome the requirement for HilA activation of the inv operon .	106	Some reports suggest that overexpression of sirA can also overcome the requirement for HilA activation of the inv operon ( Eichelberg and Galán , 1999 ; Rakeman et al. , 1999 ) .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	3	ver/dev	HilD , regulates the expression of lpxR .	61	HilD , but not HilA or InvF , regulates the expression of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	regulator	27886269	11	ver/dev	that HilD directly controls the expression of the lpxR genes	94	Thus , these data strongly support that HilD directly controls the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly , through a regulator found in S. Typhimurium but not in E. coli MC4100 , that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	regulator	27886269	12	ver/dev	HilD binds to the regulatory regions of lpxR .	110	HilD binds to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of lpxR is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lpxR	regulator	27886269	13	ver/dev	To further define whether the HilD-mediated regulation of lpxR is direct , we analyzed the interaction of HilD with the regulatory region of these genes .	111	To further define whether the HilD-mediated regulation of gtgE , phoH , sinR , lpxR , SL1896 and SL4247 is direct or indirect , we analyzed the interaction of HilD with the regulatory region of these genes .	3	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lpxR	regulator	27886269	16	ver/dev	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the lpxR genes .	120	Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and indirectly that of the SL1896 gene .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	lpxR	regulator	27886269	17	ver/dev	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : lpxR .	125	In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes that are co-expressed with SPI-1 were identified : gtgE , phoH , sinR , SL1028 , lpxR , SL1896 , SL3812 , SL4247 and SL4433 .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Escherichia coli	0	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus	0	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	19	ver/dev	Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of lpxR .	128	Additionally , we show that HilD can induce the expression of gtgE-cat , phoH-cat , sinR-cat , lpxR-cat , SL3812-cat and SL4247-cat , but not SL1896-cat , transcriptional fusions , in the E. coli MC4100 strain , and thus in the absence of other Salmonella-specific regulators or FlhDC ; consistently , HilD bound to the regulatory regions of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	Felis catus;Salmonella;Salmonella	0.5	L2	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	lpxR	regulator	27886269	21	ver/dev	Thus , HilD directly regulates the expression of the lpxR genes , and positively .	130	Thus , HilD positively and directly regulates the expression of the gtgE , phoH , sinR , lpxR and SL4247 genes , and positively but indirectly controls the expression of the SL1896 gene .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	lpxR	regulator	27886269	27	ver/dev	In addition to HilD , the expression of lpxR in SPI-1-inducing conditions is positively regulated by a MarR-like regulator63 .	169	In addition to HilD , the expression of lpxR in SPI-1-inducing conditions is positively regulated by SlyA , a MarR-like regulator63 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	lpxR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the lpxR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lpxR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the lpxR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lpxR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the lpxR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lpxR	regulator	27886269	30	ver/dev	Whether the regulation by HilD implies that the lpxR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .	175	Whether the regulation by HilD implies that the gtgE , lpxR and sinR genes also have a role in the Salmonella invasion of host cells and thus in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .	4	DISCUSSION	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	lpxR	regulator	27886269	31	ver/dev	HilD binds to the regulatory region of lpxR .	177	HilD binds to the regulatory region of gtgE , phoH , sinR , lpxR and SL4247 , but not to that of SL1896 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in sopE229 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in sopE , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in sopF28 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sigE , located in SPI-527 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in sopE229 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in sopE , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in sopF28 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; siiB , siiC , siiD 26 ; sopB , located in SPI-527 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in sopE229 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in sopE , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in sopF28 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sigE , located in SPI-527 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in sopE229 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in sopE , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in sopF28 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lpxR	regulator	33299016	4	ver/dev	We identified 10 genes known either to be regulated by HilD ; 3 SPI-4 genes 26 ; sopB , located in SPI-527 , encoding for lpxR , encoding for an LPS-modifying enzyme30 .	146	We identified 30 SPI-1 genes and 10 genes encoded elsewhere but known either to be regulated by HilD or to have an expression profile comparable to those of SPI-1 genes ( Fig. 4h ) , namely rtsA , involved in SPI-1 regulation25 ; 3 SPI-4 genes ( siiB , siiC , siiD ) 26 ; sopB and sigE , located in SPI-527 , sopF28 , sopE and sopE229 , encoding for T3SS-1 effectors ; lpxR , encoding for an LPS-modifying enzyme30 .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	gene	malT	activator	14996792	54	ver/dev	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both the malT in E. coli is stimulated by H-NS .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
StpA	gene	crp	activator	19843227	24	att	Indeed , a StpA-dependent decrease of crp expression was observed in our experiment ( 1.6-fold ) .	141	Indeed , a StpA-dependent decrease of crp expression was observed in our experiment ( 1.6-fold ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	crp	activator	19843227	25	att	However , the StpA-dependent reduction of the crp mRNA was highly statistically significant ( FDR 0.001 ) .	143	However , the StpA-dependent reduction of the crp mRNA was highly statistically significant ( FDR 0.001 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
StpA	gene	crp	activator	19843227	26	att	A similar low-level StpA-dependent decrease in crp was seen in E. coli ( Johansson et al. , 2000 ) .	144	A similar low-level StpA-dependent decrease in crp was seen in E. coli ( Johansson et al. , 2000 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	crp	activator	19843227	43	att	Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli ( Johansson et al. , 2000 ) .	303	Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli ( Johansson et al. , 2000 ) .	15	DISCUSSION	Escherichia coli	0	L2	SPEC	Other	OTHER	Other	Level 1
StpA	gene	crp	activator	19843227	23	ver/dev	This raised the possibility that StpA could directly induce the expression of crp at LEP , as had been observed in E. coli .	140	This raised the possibility that StpA could directly induce the expression of crp at LEP , as had been observed in E. coli ( Johansson et al. , 1998 ; 2000 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	Escherichia coli	0	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	crp	activator	19843227	43	ver/dev	Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli .	303	Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli ( Johansson et al. , 2000 ) .	15	DISCUSSION	Escherichia coli	0	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	hlyE	activator	14996792	3	ver/dev	Finally , the identification of a SlyA binding site suggests a mechanism to explain how SlyA overproduction enhances hlyE expression by antagonizing the negative effects of H-NS .	15	Finally , the identification of a SlyA binding site that overlaps the H-NS I site in PhlyE suggests a mechanism to explain how SlyA overproduction enhances hlyE expression by antagonizing the negative effects of H-NS .	0	Unknown	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	hlyE	activator	14996792	39	ver/dev	In contrast , in the absence of hns , SlyA overproduction did not enhance hlyE expression .	190	In contrast , in the absence of hns , SlyA overproduction did not enhance hlyE expression ( Table 2 ) .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	activator	14996792	40	ver/dev	indirectly , SlyA activates hlyE expression ultimately by counteracting the negative effects of H-NS	193	These results confirm and extend the observations of Westermark et al. ( 36 ) and suggest that , either directly or indirectly , SlyA activates hlyE expression by modulating H-NS binding and ultimately by counteracting the negative effects of H-NS .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	activator	14996792	40	ver/dev	indirectly , SlyA activates hlyE expression by modulating H-NS binding	193	These results confirm and extend the observations of Westermark et al. ( 36 ) and suggest that , either directly or indirectly , SlyA activates hlyE expression by modulating H-NS binding and ultimately by counteracting the negative effects of H-NS .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	activator	14996792	40	ver/dev	directly , SlyA activates hlyE expression ultimately by counteracting the negative effects of H-NS	193	These results confirm and extend the observations of Westermark et al. ( 36 ) and suggest that , either directly or indirectly , SlyA activates hlyE expression by modulating H-NS binding and ultimately by counteracting the negative effects of H-NS .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	activator	14996792	40	ver/dev	directly , SlyA activates hlyE expression by modulating H-NS binding	193	These results confirm and extend the observations of Westermark et al. ( 36 ) and suggest that , either directly or indirectly , SlyA activates hlyE expression by modulating H-NS binding and ultimately by counteracting the negative effects of H-NS .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	activator	14996792	48	ver/dev	in-vitro evidence suggests that SlyA activates hlyE expression by antagonizing H-NS-mediated repression .	238	In vivo and in vitro evidence suggests that SlyA activates hlyE expression by antagonizing H-NS-mediated repression .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	hlyE	activator	14996792	48	ver/dev	In vivo suggests that SlyA activates hlyE expression by antagonizing H-NS-mediated repression .	238	In vivo and in vitro evidence suggests that SlyA activates hlyE expression by antagonizing H-NS-mediated repression .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	hlyE	activator	14996792	56	ver/dev	that SlyA does not enhance hlyE expression in hns cultures	257	The findings that SlyA does not enhance hlyE expression in hns cultures grown in liquid medium under anaerobic conditions and that SlyA appears unable to activate hlyE expression in the absence of FNR and CRP and the determination of the location of the region of PhlyE occupied by SlyA ( Fig. 6 ) suggest that SlyA activates hlyE expression by antagonizing the negative action of H-NS .	8	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
SlyA	gene	hlyE	activator	19204896	4	ver/dev	SlyA activates hlyE expression by antagonising H-NS-mediated repression .	35	SlyA activates hlyE expression by antagonising H-NS-mediated repression [ 9 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	hlyE	activator	23790417	0	ver/dev	It was reported that hlyE could be activated by SlyA , an important regulator of virulence genes in Salmonella .	23	It was reported that hlyE could be activated by the Salmonella transcription factor SlyA ( Oscarsson et al. 2002 ; von Rhein et al. 2009 ) , an important regulator of virulence genes in Salmonella ( Ellison and Miller , 2006 ) .	3	ABSTRACT	Salmonella	1	L1	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	aroQ	activator	22921935	7	att	The L-Ara4N-mediated negative feedback is not limited to PmrA-dependent genes specifying LPS-modifying enzymes , because mRNA levels of the PmrA-activated aroQ ( Tamayo et al. , 2005b ) , which encodes a chorismate mutase , are lower in the wild-type than in the ugd mutant at 120 min , even though these strains produce similar amounts of aroQ transcript at 20 min ( Figure S4A ) .	142	The L-Ara4N-mediated negative feedback is not limited to PmrA-dependent genes specifying LPS-modifying enzymes , because mRNA levels of the PmrA-activated aroQ ( Tamayo et al. , 2005b ) , which encodes a chorismate mutase , are lower in the wild-type than in the ugd mutant at 120 min , even though these strains produce similar amounts of aroQ transcript at 20 min ( Figure S4A ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	pbgP	regulator	15205413	0	att	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid-A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	7	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	pbgP	regulator	15205413	16	att	We have now established that both of these PmrA-controlled modifications are required for polymyxin B resistance , as a pbgP pmrC1 double mutant is as susceptible to polymyxin B as a pmrA null mutant ( Fig. 3B ) and has a lipid-A profile that is identical to that of a pmrA null mutant , lacking both aminoarabinose and phosphoethanolamine ( Fig. 4 ) .	253	We have now established that both of these PmrA-controlled modifications are required for polymyxin B resistance , as a pbgP pmrC1 double mutant is as susceptible to polymyxin B as a pmrA null mutant ( Fig. 3B ) and has a lipid A profile that is identical to that of a pmrA null mutant , lacking both aminoarabinose and phosphoethanolamine ( Fig. 4 ) .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	pbgP	regulator	15205413	2	att	A pbgP pmrC double mutant resembled a pmrA mutant both in its lipid-A profile and in its susceptibility to polymyxin B , indicating that the PmrA-dependent modification of lipid-A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance .	11	A pbgP pmrC double mutant resembled a pmrA mutant both in its lipid A profile and in its susceptibility to polymyxin B , indicating that the PmrA-dependent modification of lipid A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
YqhC	gene	yqhD	regulator	22004521	10	ver/dev	Further , this study showed that yqhD activation was induced by direct binding of YqhC to the promoter region of the yqhD gene .	310	Further , this study showed that yqhD activation was induced by direct binding of YqhC to the promoter region of the yqhD gene ( 32 ) .	25	DISCUSSION	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
IlvY	gene	ilvC	regulator	29791499	3	ver/dev	IlvY binds to the ilvC operator but activates transcription only when IlvC substrates -LRB- either α-prote .	227	IlvY binds to the ilvC operator but activates transcription only when IlvC substrates ( either α-acetolactate or α-protein .	13	MUTATIONS IN ILVY SUPPRESS THIAMINE REQUIREMENT	nan	1	L3	OTHER	Other	NEG	New	Level 1
IlvY	gene	ilvC	regulator	29791499	3	ver/dev	IlvY binds to the ilvC operator but activates transcription only when IlvC substrates -LRB- either α-acetolactat .	227	IlvY binds to the ilvC operator but activates transcription only when IlvC substrates ( either α-acetolactate or α-protein .	13	MUTATIONS IN ILVY SUPPRESS THIAMINE REQUIREMENT	nan	1	L3	OTHER	Other	NEG	New	Level 1
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acet-ohydroxybutyra , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acet-ohydroxybutyra , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acetolactat , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acetolactat , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acet-ohydroxybutyra , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acet-ohydroxybutyra , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acetolactat , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	29791499	7	ver/dev	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription upon binding of a coinducer molecule -LRB- α-acetolactat , activates transcription of the ilvC gene .	304	The binding of IlvY to the ilvYC promoter region negatively auto-regu-lates transcription of ilvY , and upon binding of a coinducer molecule ( α-acetolactate or α-acet-ohydroxybutyrate ) , activates transcription of the ilvC gene .	17	CONCLUSIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
IlvY	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-valine .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IlvY	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IlvY	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to p.Glu206Lys .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IlvY	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to avian .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IlvY	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to p.Leu106Gln sources .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IlvY	gene	ilvC	regulator	31694533	1	ver/dev	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) was associated by different mutations to swine sources .	457	Organized as a LysR protein-regulated system , the HTH-type transcriptional activator IlvY ( i.e. missense SNP in ilvC ) is the transcriptional regulator of the ketol-acid reductoisomerase NADP + ( i.e. missense SNP in ilvC ) involved in the parallel pathway for the biosynthesis of L-isoleucine and L-valine [ 88 ] , and was associated by different mutations to avian ( p.Glu206Lys ) and swine ( p.Leu106Gln ) sources ( Table 4 ) .	9	SIGNATURES OF ADAPTATION TO THE AVIAN SOURCE	Sus scrofa	0	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	csrB	activator	12791144	3	ver/dev	CsrA also activates transcription of csrB , possibly through indirect regulation of a transcription factor .	32	CsrA also activates transcription of csrB , possibly through indirect regulation of a transcription factor ( Gudapaty et al. , 2001 ) .	4	INTRODUCTION	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CsrA	gene	csrB	activator	12791144	17	ver/dev	Romeo , the RNA binding protein CsrA activates csrB transcription in Escherichia coli .	424	Gudapaty , S. , Suzuki , K. , Wang , X. , Babitzke , P. , and Romeo , T. ( 2001 ) Regulatory interactions of Csr components : the RNA binding protein CsrA activates csrB transcription in Escherichia coli .	24	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	csrB	activator	16949866	17	ver/dev	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA .	301	However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA ( Suzuki et al. , 2002 ; Teplitski et al. , 2003 ) .	16	SIRA REGULATES CSRC	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	csrB	activator	23676436	30	ver/dev	Regulatory interactions of Csr components : the RNA binding protein CsrA activates csrB transcription in Escherichia coli .	551	Regulatory interactions of Csr components : the RNA binding protein CsrA activates csrB transcription in Escherichia coli .	10	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	sscB	activator	20221735	0	ver/dev	Most of these genes were induced at a higher level in the RpoS - sscB .	167	Most of these genes were induced at a higher level in the RpoS - mutant background with a few exceptions , such as sptP , sscB , sseB , and mgtC .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NadR	gene	nadA	repressor	15805524	3	ver/dev	The NadR protein was previously shown to repress transcription of the nadA , nadB in response to high levels of NAD .	173	The NadR protein was previously shown to repress transcription of the nadA , nadB , and pncB promoters in response to high levels of NAD ( 25 , 39 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SirA	gene	srgB	regulator	15130116	9	ver/dev	Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates other genes of srgB .	223	Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates accessory factors that may contribute to intestinal survival or colonization ( rck , pefI , srgA ) and other genes of unknown function ( srgB -- E ) .	5	THE SALMONELLA SDIA SYSTEM	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
NsrR	gene	tehA	regulator	20829289	2	att	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	120	To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .	4	AN NSRR KNOCKOUT IS HYPERSENSITIVE TO PEROXYNITRITE STRESS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Sigma28	gene	flk	repressor	9765570	0	ver/dev	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .	13	FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants ( flgA , flgH , and flgI ) by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. , J. Bacteriol .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	envZ	regulator	33952386	18	ver/dev	Interestingly , while the ompR mRNA level was not significantly influenced by the SNP in envZ , the total OmpR protein level was increased by the SNP in envZ -LRB- Fig .	425	Interestingly , while the ompR mRNA level was not significantly influenced by the SNP in envZ , the total OmpR protein level was increased by the SNP in envZ ( Fig .	10	DISCUSSION	nan	1	L2	OTHER	Other	NEG	Other	Level 1
HNS	gene	rpsB	regulator	23470992	2	ver/dev	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy -LRB- 2/6 copies required a in S. Typhi -RRB- ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	401	Required or ambiguous in both S. Typhi and S. Typhimurium SRP RF00169 RNA component of the signal recognition particle RNase P RF00010 RNA component of RNase P RFN RF00050 FMN-sensing riboswitch controlling the ribB gene SroE RF00371 Putative cis-regulatory element controlling the hisS gene ThrU Leader NA Putative cis-regulatory element controlling the ThrU tRNA operon t44 RF00127 Cis-regulatory element controlling the ribosomal rpsB gene S15 RF00114 Translational regulator of the ribosomal b S15 protein StyR-8 NA Putative cis-regulatory element controlling the ribosomal rpmB gene MicA RF00078 sRNA involved in cellular response to extracytoplasmic stress DsrA RF00014 sRNA regulator of H-NS b STnc10 NA Putative sRNA STnc60 NA Putative sRNA b STnc840 NA Verified sRNA derived from 3 ' UTR of the flgL gene IS0420 NA Putative ncRNA a , b RGO0 NA Putative sRNA identified in E. coli b Required or ambiguous in S. Typhimurium only rne5 RF00040 RNase E autoregulatory 5 ' element RydC RF00505 sRNA regulator of the yejABEF ABC transporter RydB RF00118 Putative ncRNA STnc510 NA Putative sRNA STnc460 NA Putative sRNA b STnc170 NA Putative sRNA STnc130 NA Putative sRNA RseX RF01401 sRNA regulator of OmpA and OmpC IsrJ RF01393 sRNA regulator of SPI-1 effector protein secretion IsrI RF01392 Island-encoded Hfq-binding sRNA Required or ambiguous in S. Typhi only RybB RF00110 sRNA involved in cellular response to extracytoplasmic stress tk5 NA Putative ncRNA a STnc750 NA Verified sRNA StyR-44 RF01830 Putative multicopy ( 2/6 copies required a in S. Typhi ) ncRNA associated with ribosomal RNA operon Putative ncRNA RdlD RNA anti-toxin , 1/2 copies required in S. Typhi Putative sRNA Putative ncRNA Phenylalanine peptide leader sequence associated with the required PheST operon RimP Leader RF01770 Putative cis-regulator of the rimP-nusA-infB operon GlmY RF00128 Trans-acting regulator of the GlmS gene	18	THE SRNAS REQUIRED FOR COMPETITIVE GROWTH	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	ssaJ	regulator	27601571	47	ver/dev	ssaJ are regulated by HilC	422	ssaG and ssaJ are regulated by HilC , and sifB is regulated by SprB .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	aniC	activator	10692151	4	ver/dev	TyrR are required for anaerobic induction of aniC in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	aniC	activator	10692151	4	ver/dev	TyrR are required for acid-pH induction of aniC in Salmonella typhimurium .	615	Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. ( 1999 ) Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	43	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	aniC	activator	17906148	9	ver/dev	TyrR are required for anaerobic induction of aniC in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
TyrR	gene	aniC	activator	17906148	9	ver/dev	TyrR are required for acid-pH induction of aniC in Salmonella typhimurium .	418	Cyclic AMP receptor protein and TyrR are required for acid pH and anaerobic induction of hyaB and aniC in Salmonella typhimurium .	34	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	csgD	repressor	25437188	1	ver/dev	Inactivation of Crl , results in reduced expression of csgD biofilm-related genes .	105	Inactivation of Crl , an RpoS-binding factor , results in downregulated biofilm formation in S. Typhimurium and reduced expression of csgD and other biofilm-related genes .	5	REGULATION OF THE RDAR PHENOTYPE IN S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NorR	gene	norV	regulator	27583250	2	att	Transient increased sensitivity of a norV mutant to NO suggests that the NorR-regulated NO reductase is part of a multiple enzyme response to NO stress during the infection process ( Mills et al. , 2005 ) .	258	Transient increased sensitivity of a norV mutant to NO suggests that the NorR-regulated NO reductase is part of a multiple enzyme response to NO stress during the infection process ( Mills et al. , 2005 ) .	14	NORR	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RpoS	gene	pnp	regulator	16597989	0	att	In E. coli , a decrease in RpoS-regulated transcripts was observed in a pnp mutant ( 8 ) , including the dps gene involved in acid resistance ( 12 ) .	294	In E. coli , a decrease in RpoS-regulated transcripts was observed in a pnp mutant ( 8 ) , including the dps gene involved in acid resistance ( 12 ) .	3	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	pnp	regulator	28943871	0	att	Moreover , pnp mutant in E. coli has a decrease in RpoS-regulated transcripts ( Bearson et al. , 2006 ) .	381	Moreover , pnp mutant in E. coli has a decrease in RpoS-regulated transcripts ( Bearson et al. , 2006 ) .	21	OTHER DESICCATION SURVIVAL GENES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	STM3138	activator	19843227	15	att	After comparing the list of StpA-dependent genes with the previously published H-NS regulon of S. Typhimurium ( Ono et al. , 2005 ) , only one gene was identified that displayed such behav-iour ( STM3138 ) .	79	After comparing the list of StpA-dependent genes with the previously published H-NS regulon of S. Typhimurium ( Ono et al. , 2005 ) , only one gene was identified that displayed such behav-iour ( STM3138 ) .	7	IDENTIFICATION OF THE STPA REGULON	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	mutH	regulator	9765570	10	ver/dev	Negative regulation of mutH RpoS global regulators of Escherichia coli K-12 .	940	Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12 .	46	REFERENCES	Escherichia coli	0	L3	OTHER	Other	NEG	New	Level 1
RpoS	gene	mutH	regulator	9765570	10	ver/dev	Negative regulation of mutH RpoS global regulators of Escherichia coli K-12 .	940	Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12 .	46	REFERENCES	Escherichia coli	0	L3	OTHER	Other	NEG	New	Level 1
RcsB	TU	flhDC	repressor	19745516	2	ver/dev	In addition , at low-osmolarity , RcsB , negatively controls the transcription of flhDC .	63	In addition , at low osmolarity , RcsB , acting in association with TviA , negatively controls the transcription of flhDC , which is apparently required for activation of iagA ( hilA ) , invF and sipB ( encoding proteins involved in cell invasion ) [ 25 , 34 ] .	9	REGULATION OF VI POLYSACCHARIDE SYNTHESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	22149171	39	ver/dev	the flhDC promoter is repressed by RcsB	316	To test a known output of Rcs activity , expression of the flhDC promoter , which is repressed by RcsB ( Francez-Charlot et al. 2003 ) , was measured in DrcsD and E12 .	17	THE RCS PHOSPHORELAY NEGATIVELY REGULATES SDIA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	23443158	5	ver/dev	In addition , RcsB inhibits flhDC expression .	62	In addition , RcsB inhibits flhDC expression and thereby exerts a negative effect on motility [ 45 ] .	4	1.2. REGULATION OF OTHER BIOFILM MATRIX COMPONENTS: COLANIC ACID AND PGA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	24706743	2	ver/dev	ecnR in turn results in repression of flhDC transcription in concert with the RcsB protein	128	The FlhD4C2 complex directs transcription of ecnR , which in turn results in repression of flhDC transcription in concert with the RcsB protein .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	24706743	3	ver/dev	RcsB , is a known repressor of flhDC transcription .	129	RcsB , which regulates capsular polysaccharide synthesis and a number of genes in response to membrane and cell wall damage , is a known repressor of flhDC transcription ( 23 , 24 ) .	4	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
RcsB	TU	flhDC	repressor	27206164	20	ver/dev	To test a putative link between RcsB in repression of flhDC , we performed an unbiased genetic screen using random transposon mutagenesis .	90	To test a putative link between RflM and RcsB in repression of flhDC , we performed an unbiased genetic screen using random transposon mutagenesis .	5	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	TU	flhDC	repressor	27206164	21	ver/dev	The transposon mutagenesis thus provided further evidence for a functional link between RcsB in repression of flhDC .	101	The transposon mutagenesis thus provided further evidence for a functional link between RcsB and RflM in repression of flhDC .	5	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RcsB	TU	flhDC	repressor	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to csgD were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to dps were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	24	ver/dev	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to wzzB were regulated by RcsB independently of the presence of	121	To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon ( wzzB , dps and csgD ) were regulated by RcsB independently of the presence of	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	25	ver/dev	This demonstrated that RcsB is indispensable for the rflM-dependent repression of flhDC	130	This demonstrated that RcsB is indispensable for the rflM-dependent repression of flhDC , which is consistent with previous	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	26	ver/dev	The role of RcsB in repression of flhDC expression was analyzed using several rcsB mutants .	131	The role of RcsB in repression of flhDC expression was analyzed using several rcsB mutants .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	28	ver/dev	Coordinated repression of flhDC transcription by RcsB .	170	Coordinated repression of flhDC transcription by RcsB and RflM .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	27206164	29	ver/dev	A. Schematic regulatory model of repression of the flagellar master regulator flhDC by coordinated action of RcsB .	171	A. Schematic regulatory model of repression of the flagellar master regulator flhDC by coordinated action of RcsB and RflM .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	27206164	32	ver/dev	Moreover , the results above indicated that rcsB overexpression bypassed the need for RcsB phosphorylation in repression of flhDC transcription .	187	Moreover , the results above indicated that rcsB overexpression bypassed the need for RcsB phosphorylation in repression of flhDC transcription .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	TU	flhDC	repressor	27206164	35	ver/dev	expression of flhC-lac _ providing further evidence for a cooperative action of RcsB in repression of flhDC	201	S6C , increasing levels of rflM decreased expression of flhC-lac , providing further evidence for a cooperative action of RflM and RcsB in repression of flhDC .	7	RCSB-RFLM COMPLEX COORDINATELY REPRESSES FLHDC TRANSCRIPTION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
RcsB	TU	flhDC	repressor	27206164	48	ver/dev	In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC	265	In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC	10	RFLM ENHANCES BINDING AFFINITY OF RCSB TO THE FLHDC TARGET PROMOTER DNA	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	27206164	49	ver/dev	In E. coli , it has been shown that RcsA , enhan-ces RcsB-dependent repression of flhDC .	268	In E. coli , it has been shown that an auxiliary regulatory protein , RcsA , enhan-ces RcsB-dependent repression of flhDC ( Francez-Charlot et al. , 2003 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	49	ver/dev	In E. coli , it has been shown that an auxiliary regulatory protein , enhan-ces RcsB-dependent repression of flhDC .	268	In E. coli , it has been shown that an auxiliary regulatory protein , RcsA , enhan-ces RcsB-dependent repression of flhDC ( Francez-Charlot et al. , 2003 ) .	11	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	27206164	52	ver/dev	We dem-onstrate that RflM mediates target specificity of unphosphoryl-ated RcsB for repression of flhDC .	282	We dem-onstrate that RflM functions as a novel co-regulator of RcsB and mediates target specificity of unphosphoryl-ated RcsB for repression of flhDC .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	27206164	54	ver/dev	RcsB-mediated repression of flhDC increased significantly in the presence of RflM	284	Overexpressed RcsB or a phosphomimetic RcsBD56E mutant were able to repress flhDC , but RcsB-mediated repression of flhDC increased significantly in the presence of RflM .	11	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RcsB	TU	flhDC	repressor	27206164	54	ver/dev	Overexpressed RcsB were able to repress flhDC	284	Overexpressed RcsB or a phosphomimetic RcsBD56E mutant were able to repress flhDC , but RcsB-mediated repression of flhDC increased significantly in the presence of RflM .	11	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RcsB	TU	flhDC	repressor	27206164	57	ver/dev	As mentioned , we found that phosphorylation of RcsB was not essential for repression of flhDC in the presence of RflM , but for RcsB-mediated repression of flhDC in the absence of RflM .	296	As mentioned , we found that phosphorylation of RcsB was not essential for repression of flhDC in the presence of RflM , but for RcsB-mediated repression of flhDC in the absence of RflM .	11	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsB	TU	flhDC	repressor	27206164	57	ver/dev	As mentioned , we found that phosphorylation of RcsB was not essential for repression of flhDC in the presence of RflM , but for RcsB-mediated repression of flhDC in the absence of RflM .	296	As mentioned , we found that phosphorylation of RcsB was not essential for repression of flhDC in the presence of RflM , but for RcsB-mediated repression of flhDC in the absence of RflM .	11	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RcsB	TU	flhDC	repressor	27206164	58	ver/dev	These results indicated that RflM directs RcsB to specifically repress flhDC gene transcription independently of external stimuli .	297	These results indicated that RflM directs RcsB to specifically repress flhDC gene transcription independently of external stimuli that would result in RcsB phosphorylation , similar to the mode of action of other RcsB co-regulator complexes such as BglJ-RcsB ( Venkatesh et al. , 2010 ) .	11	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	TU	flhDC	repressor	27206164	62	ver/dev	Phosphorylated RcsB would be able to repress flhDC with low affinity by binding to the RcsB box in the flhDC promoter region as a homodimer .	314	Phosphorylated RcsB would be able to repress flhDC with low affinity by binding to the RcsB box in the flhDC promoter region as a homodimer .	11	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	TU	flhDC	repressor	27206164	62	ver/dev	Phosphorylated RcsB would be able to repress flhDC with low affinity by binding to the RcsB box in the flhDC promoter region as a homodimer .	314	Phosphorylated RcsB would be able to repress flhDC with low affinity by binding to the RcsB box in the flhDC promoter region as a homodimer .	11	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	TU	flhDC	repressor	27601571	27	ver/dev	RcsB is known to repress transcription of flhDC in both S. enterica .	253	RcsB is known to repress transcription of flhDC in both E. coli ( 50 ) and S. enterica ( 19 ) .	3	RESULTS AND DISCUSSION	Salmonella;Salmonella	1	L3	OTHER	Fact	OTHER	Other	Level 3
RcsB	TU	flhDC	repressor	27601571	27	ver/dev	RcsB is known to repress transcription of flhDC in both E. coli .	253	RcsB is known to repress transcription of flhDC in both E. coli ( 50 ) and S. enterica ( 19 ) .	3	RESULTS AND DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
RcsB	TU	flhDC	repressor	29186528	0	ver/dev	For example , in Escherichia coli , RcsB inhibits transcription of the flhDC flagellar master operon by binding to the promoter region P1flhDC .	38	For example , in Escherichia coli and the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium ( S. Typhimurium ) , RcsB inhibits transcription of the flhDC flagellar master operon by binding to the promoter region P1flhDC ( 15 ) and , inversely , activates the expression of rprA , a small regulatory RNA that controls exopolysaccharide production required for biofilm formation ( 16 ) .	5	INTRODUCTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	29186528	0	ver/dev	For example , in the intracellular bacterial pathogen S. Typhimurium , RcsB inhibits transcription of the flhDC flagellar master operon by binding to the promoter region P1flhDC .	38	For example , in Escherichia coli and the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium ( S. Typhimurium ) , RcsB inhibits transcription of the flhDC flagellar master operon by binding to the promoter region P1flhDC ( 15 ) and , inversely , activates the expression of rprA , a small regulatory RNA that controls exopolysaccharide production required for biofilm formation ( 16 ) .	5	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	29186528	0	ver/dev	For example , in the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium , RcsB inhibits transcription of the flhDC flagellar master operon by binding to the promoter region P1flhDC .	38	For example , in Escherichia coli and the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium ( S. Typhimurium ) , RcsB inhibits transcription of the flhDC flagellar master operon by binding to the promoter region P1flhDC ( 15 ) and , inversely , activates the expression of rprA , a small regulatory RNA that controls exopolysaccharide production required for biofilm formation ( 16 ) .	5	INTRODUCTION	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	29186528	13	ver/dev	To note that the RcsA -- RcsB heterodimer is required to reach optimal production levels of colanic acid capsule -LRB- wca -RRB- operon whereas the RcsB homodimer is sufficient to represses transcription of flhDC master regulator .	341	To note that the RcsA -- RcsB heterodimer is required to reach optimal production levels of colanic acid capsule ( wca ) operon whereas the RcsB homodimer is sufficient to represses transcription of flhDC , encoding the flagella master regulator ( 10,15 ) .	18	EFFECT OF RCSB MUTATIONS IN COLANIC CAPSULE FORMATION AND MOTILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	33638994	2	ver/dev	Conversely , phosphorylated RcsB represses transcription of the flhDC flagellar operon .	44	Conversely , phosphorylated RcsB represses transcription of the flhDC flagellar operon required for motility ( 14,15 ) .	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of motor-binding protein YcgR on motor rotation and switching .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	TU	flhDC	repressor	34340061	8	ver/dev	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; relieving the inhibition of the second messenger c-di-GMP on motor rotation and switching .	322	In E. coli , H-NS was confirmed to play multiple positive regulatory roles in bacterial motility : ( 1 ) relieving the inhibition of transcriptional regulators HdfR and RcsB on the flagellar master operon flhDC ; ( 2 ) relieving the inhibition of the master biofilm regulator CsgD on fliA , fliE , and fliF operons , which were responsible for the expression of Class III flagellar genes and flagella assembly separately ; and ( 3 ) relieving the inhibition of the second messenger c-di-GMP and motor-binding protein YcgR on motor rotation and switching ( Kim and Blair , 2015 ) .	17	4. DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
InvF	gene	prgH	regulator	28335027	6	ver/dev	Notably , our observation that deletion of all of the IS200 copies in S. Typhimurium impacted on the expression of prgH not under the control of InvF is consistent with tnpA producing either a multi-functional regulatory RNA or , as in the case of IS1341 , multiple regulatory sRNAs .	737	Notably , our observation that deletion of all of the IS200 copies in S. Typhimurium impacted on the expression of an SPI-1 gene ( prgH ) not under the control of InvF is consistent with tnpA producing either a multi-functional regulatory RNA or , as in the case of IS1341 , multiple regulatory sRNAs .	22	RIBONUCLEOLYTIC PROCESSING OF TNPA MRNA GENERATES SRNA REGULATORS OF INVF EXPRESSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	prgH	regulator	28439039	9	ver/dev	It is known that prgH is under the regulation of InvF .	327	It is known that prgH is under the regulation of many global regulators , such as HilA , InvF , PhoP , and SirA .	5	DISCUSSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
AraC	gene	araA	regulator	24272778	14	att	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	201	As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , 220.9 whether this is the true AraC site upstream of ytfQ , we performed a ChIP experiment in a wild-type strain and in a strain in which the putative AraC binding site was mutated .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
AraC	gene	araA	regulator	24272778	6	att	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	88	AMD187 ( E. coli Enterobacteriaceae species , these data identify a conserved AraC MG1655 araC-3 FLAG ) , JTW010 ( E. coli MG1655 with ytfQ AraC site mutation , araC-3 FLAG ) , and CB005 ( S. enterica serovar Typhimurium regulon that includes 7 previously described AraC-regulated 14028s araC-3 FLAG ) were constructed using the FRUIT recombineergenes ( araB , araA , araD , araE , araF , araG , and araH ) as well as ing system ( 18 ) .	2	MAIN	Escherichia coli;Iris germanica;Escherichia coli;Iris germanica;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	14563863	16	ver/dev	PhoP binds to the promoter region of pagC .	155	PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL , and pmrC genes but not to the promoter region of phoN , pagC , or mgtC .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	regulator	15703297	12	att	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	128	( A ) Chromatin immunoprecipitation ( ChIP ) of PhoP-regulated promoters predicted by GPS demonstrates binding of the PhoP-HA protein to the PhoP-activated mgtA , mgtC , pagC , mig-14 , and ugd promoters , which are found in different profiles .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	15703297	5	att	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	105	The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pagC	regulator	17158330	15	att	mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .	158	mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .	10	REFERENCES	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	18221392	3	ver/dev	The pagC genes appear to be regulated by both PhoP , by a mechanism .	67	The mig-14 and pagC genes appear to be regulated by both SlyA and PhoP , by a mechanism that is not yet understood ( Navarre et al. , 2005 ) .	9	SALMONELLA VIRULENCE GENES ARE SPECIFICALLY EXPRESSED IN VIVO DURING INFECTION OF C. ELEGANS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagC	regulator	18270203	10	att	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	151	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	2	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pagC	regulator	18270203	10	att	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	151	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	2	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pagC	regulator	18270203	31	att	( Fig. 3A ) , at a position and orientation relative to the 10 RNA Polymerase Recruitment to the pagC and ugtL region that is shared with other PhoP-regulated promoters ( 26 ) .	201	( Fig. 3A ) , at a position and orientation relative to the 10 RNA Polymerase Recruitment to the pagC and ugtL region that is shared with other PhoP-regulated promoters ( 26 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	18270203	20	ver/dev	pagC genes entails binding of both the PhoP to the promoters of these two genes .	187	pagC and ugtL genes entails binding of both the PhoP and SlyA proteins to the promoters of these two genes .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	regulator	18270203	69	ver/dev	because PhoP bound to the pagC promoter in-vivo -LRB- Fig. 3D -RRB-	294	Indeed , we determined that the PhoP protein is directly involved in promoting pagC transcription , because PhoP bound to the pagC promoter in vitro ( Fig. 3 , B and C ) and in vivo ( Fig. 3D ) and because point mutations in the PhoP box that prevented PhoP binding ( Fig. 3 , C and D ) abolished pagC transcription ( Fig. 3E ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	regulator	18270203	69	ver/dev	because PhoP bound to the pagC promoter in-vitro -LRB- Fig. 3D -RRB-	294	Indeed , we determined that the PhoP protein is directly involved in promoting pagC transcription , because PhoP bound to the pagC promoter in vitro ( Fig. 3 , B and C ) and in vivo ( Fig. 3D ) and because point mutations in the PhoP box that prevented PhoP binding ( Fig. 3 , C and D ) abolished pagC transcription ( Fig. 3E ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	regulator	19202096	3	ver/dev	pagC were used as controls for PhoP - and SsrB-dependent expression , respectively .	335	pagC and sseB were used as controls for PhoP - and SsrB-dependent expression , respectively .	10	TAIA ENHANCES E. COLI INVASION OF HELA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	19843227	36	ver/dev	Two StpA-repressed PhoP-dependent genes _ bound by pagC	262	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	regulator	23774596	0	ver/dev	The PhoP-activated gene pagC _ regulated by the PhoP	303	The PhoP-activated gene pagC regulated by the PhoP / PhoQ system was identified as an IVI virulence protein in S. Typhi , and the PagC antibody was detected in sera from 11 of 14 patients , which shows that it has the potential to be developed as a diagnostic antigen ( 12 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pagC	regulator	25135218	80	ver/dev	pagC genes are regulated by a similar mechanism , involving the response regulator of the PhoP / PhoQ two-component system .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	25135218	80	ver/dev	pagC genes are regulated by a similar mechanism , involving the response regulator of the PhoP / PhoQ two-component system .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	25135218	80	ver/dev	pagC genes are regulated by a similar mechanism , involving PhoP .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagC	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	pagC	regulator	26943369	4	att	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	pagC	regulator	26943369	4	ver/dev	To determine whether acetylation affects the activity of PhoP as a transcription factor , pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	83	To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .	6	RESULTS PHOP IS A SUBSTRATE OF COBB AND PAT	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	pagC	regulator	29324231	11	att	We also compared the expression of other PhoP-regulated genes in the wild-type and Δhns / ΔphoPQ strains , including genes whose expression in S. Typhimurium is dependent ( pagC ) or independent ( slyB and mgtA ) of H-NS ( Perez et al. , 2008 ) .	161	We also compared the expression of other PhoP-regulated genes in the wild-type and Δhns / ΔphoPQ strains , including genes whose expression in S. Typhimurium is dependent ( pagC ) or independent ( slyB and mgtA ) of H-NS ( Perez et al. , 2008 ) .	5	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	16045614	1	ver/dev	that HilD are each capable of independently inducing expression of the hilD genes	14	We demonstrate that HilC , HilD and RtsA are each capable of independently inducing expression of the hilC , hilD and rtsA genes , and that each can independently activate hilA .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	16045614	20	ver/dev	We demonstrate that HilD are each capable of inducing expression of hilD .	82	We demonstrate that HilC , HilD and RtsA are each capable of inducing expression of hilC , hilD and rtsA .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	activator	16045614	21	ver/dev	HilD can independently induce expression of hilD	85	HilC , HilD and RtsA can independently induce expression of hilC , hilD and rtsA	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilD	activator	16045614	24	ver/dev	We wanted to determine if HilD could induce expression of hilD in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
HilD	gene	hilD	activator	16045614	28	ver/dev	HilD also induced expression of hilD .	131	RtsA , HilC and HilD also induced expression of hilC , hilD and rtsA ( Fig. 2 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	activator	16045614	29	ver/dev	HilD induced expression of hilD ~ 10 - to 12-fold .	133	RtsA , HilC and HilD induced expression of hilC approximately threeto fourfold and hilD ~ 10 - to 12-fold .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	activator	16045614	30	ver/dev	These data show that HilD are each capable of independently inducing expression of hilD , consistent with our model that HilD constitute a feed forward regulatory loop .	134	These data show that HilC , HilD and RtsA are each capable of independently inducing expression of hilC , hilD and rtsA , consistent with our model that HilC , HilD and RtsA constitute a feed forward regulatory loop ( Fig. 1 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	16045614	69	ver/dev	We show that HilD can each independently activate expression of the hilD genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilD	activator	17208038	31	ver/dev	HilD are clearly able to induce hilD transcription .	159	HilC , HilD and RtsA , when overproduced are clearly able to induce hilD transcription .	11	REGULATION OF HILD	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilD	activator	17993530	6	ver/dev	HilD are all also capable of activating expression of hilD independent of each other and comprise a complex feed forward regulatory loop .	39	HilC , HilD , and RtsA are all also capable of activating expression of hilC , hilD , and rtsA independent of each other and comprise a complex feed forward regulatory loop that controls hilA expression ( Fig. 1 ) ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD is consistent with our model for SPI1 regulation ; transcription of hilD were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	17993530	32	ver/dev	However , like hilA expression , this transcriptional induction required that HilD be present ; transcription of hilD were all increased upon activation of the system .	237	However , like hilA expression , this transcriptional induction required that HilD be present and is consistent with our model for SPI1 regulation ( Fig. 1 ) ; transcription of hilD , transcription of hilC , transcription of rtsA , and transcription of hilA were all increased upon activation of the system .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	activator	17993530	50	ver/dev	not indirectly is it absolutely required for HilD to activate hilD transcription	340	Fur does not directly or indirectly act as a simple activator , nor is it absolutely required for HilD to activate hilD transcription ; overproduction of Fur has no effect in a hilD null background ( Fig. 4 ) , and overproduction of HilD overcomes Fur regulation ( data not shown ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	17993530	50	ver/dev	not directly is it absolutely required for HilD to activate hilD transcription	340	Fur does not directly or indirectly act as a simple activator , nor is it absolutely required for HilD to activate hilD transcription ; overproduction of Fur has no effect in a hilD null background ( Fig. 4 ) , and overproduction of HilD overcomes Fur regulation ( data not shown ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	21573071	8	auto	This complex response might be explained by the fact that only when the HilD protein reaches a significant threshold it is able to activate the expression of hilA and further induce its own expression [ 69 ] .	278	This complex response might be explained by the fact that only when the HilD protein reaches a significant threshold it is able to activate the expression of hilA and further induce its own expression [ 69 ] .	15	FUR ACTIVATES HILD GENE EXPRESSION IN VIVO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	activator	22479568	0	ver/dev	HilD can activate expression of hilD of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilD	activator	24018968	10	auto	Since HilD can induce its own expression [ 15 , 16 ] , the decrease in HilD in ∆ hfq likely decreases the hilD promoter ( P ) activity .	204	Since HilD can induce its own expression [ 15 , 16 ] , the decrease in HilD in ∆ hfq likely decreases the hilD promoter ( P ) activity .	15	HFQ AND ARCA CAN AFFECT HILD PROMOTER ACTIVITY	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HilD	gene	hilD	activator	24018968	14	ver/dev	In addition , P hilD expression decreased in Fig. 3B because HilD is the positive regulator for hilD promoter activation .	237	In addition , P hilD expression decreased in hfq mutants ( Fig. 3B ) because HilD is the positive regulator for hilD promoter activation [ 6 , 15 ] .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	24018968	14	ver/dev	In addition , P hilD expression decreased in hfq mutants because HilD is the positive regulator for hilD promoter activation .	237	In addition , P hilD expression decreased in hfq mutants ( Fig. 3B ) because HilD is the positive regulator for hilD promoter activation [ 6 , 15 ] .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in the occurrence of autogenous activation of hilD transcription .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	activator	25991823	18	ver/dev	Transcription of hilD undergoes autogenous activation by the HilD protein .	268	Transcription of hilD undergoes autogenous activation by the HilD protein ( Ellermeier et al. 2005 ) .	14	L-ARABINOSE-DEPENDENT REPRESSION OF SPI-1 IS TRANSMITTED VIA HILD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	activator	26300871	17	att	In agreement with our results indicating that CpxR represses the HilD-dependent expression of hilD and hilA , both the overexpression of CpxR and the absence of CpxA drastically reduced the production of SsrB-FLAG and SseB proteins ( Figures 1C , 3B ) , which are encoded in SPI-2 and whose expression is also dependent of HilD in the condition tested .	389	In agreement with our results indicating that CpxR represses the HilD-dependent expression of hilD and hilA , both the overexpression of CpxR and the absence of CpxA drastically reduced the production of SsrB-FLAG and SseB proteins ( Figures 1C , 3B ) , which are encoded in SPI-2 and whose expression is also dependent of HilD in the condition tested .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	Iris germanica	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	activator	27185788	9	ver/dev	This regulated induction of hilD eliminates the autoinduction of hilD expression by the HilD protein .	224	This regulated induction of hilD eliminates the autoinduction of hilD expression by the HilD protein and thus ensures that the effects observed are not attrib-utable to the control of hilD transcription .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	activator	28426789	12	auto	Other features that need to be taken in account when assessing hilD transcription are the presence of an intact hilD ORF , as the HilD protein positively regulates its own expression [ 15 ] and the presence of the newly described regulatory motif hilD 3 ' - UTR , that modulates hilD mRNA stability by promoting its rapid degradation [ 29 ] .	248	Other features that need to be taken in account when assessing hilD transcription are the presence of an intact hilD ORF , as the HilD protein positively regulates its own expression [ 15 ] and the presence of the newly described regulatory motif hilD 3 ' - UTR , that modulates hilD mRNA stability by promoting its rapid degradation [ 29 ] .	7	THE 3’-UTR OF HILD IS REQUIRED FOR GRE-MEDIATED REGULATION OF HILD EXPRESSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	activator	28426789	6	auto	The transcriptional expression of hilA is tightly modulated by three AraC activators , HilD , HilC and RtsA , which form an auto-inducing regulatory loop where each protein can activate its own expression , as well as expression of the other two regulators [ 15 ] .	199	The transcriptional expression of hilA is tightly modulated by three AraC activators , HilD , HilC and RtsA , which form an auto-inducing regulatory loop where each protein can activate its own expression , as well as expression of the other two regulators [ 15 ] .	6	INVASION OF EPITHELIAL CELLS REQUIRES A BATTERY OF EFFECTOR PROTEINS ENCODED MAINLY BY GENES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HilD	gene	hilD	activator	29229736	1	auto	hilD expression from the strain complemented with HilD was significantly higher than hilD expression from both the reporter strain alone and the reporter carrying the empty vector ( Fig. 5 ) , indicating that in S. Typhi HilD positively regulates its own transcription , either directly or indirectly .	210	hilD expression from the strain complemented with HilD was significantly higher than hilD expression from both the reporter strain alone and the reporter carrying the empty vector ( Fig. 5 ) , indicating that in S. Typhi HilD positively regulates its own transcription , either directly or indirectly .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	activator	29378886	23	ver/dev	Saini et al. demonstrated that the interaction of HilD with the hilD promoter is the trigger for inducing the expression of SPI1 through a stepwise increase of autoactivation .	241	Saini et al. demonstrated that the interaction of HilD with the hilD promoter is the trigger for inducing the expression of SPI1 through a stepwise increase of hilD promoter activity and autoactivation ( 17 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	activator	29378886	23	ver/dev	Saini et al. demonstrated that the interaction of HilD with the hilD promoter is the trigger for inducing the expression of SPI1 through a stepwise increase of hilD promoter activity .	241	Saini et al. demonstrated that the interaction of HilD with the hilD promoter is the trigger for inducing the expression of SPI1 through a stepwise increase of hilD promoter activity and autoactivation ( 17 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	activator	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	activator	32041797	5	ver/dev	The AraC-like proteins HilD activate transcription of hilD , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilD	activator	33299016	9	ver/dev	Taken together , these results show that hilD demonstrate that the absence of a functional HilD causes the lack of activation of SPI-1 expression over time during human cell infection .	164	Taken together , these results show that hilD_a encodes for a non-functional regulator as observed in broth culture conditions and demonstrate that the absence of a functional HilD causes the lack of activation of SPI-1 expression over time during human cell infection .	3	RESULTS	Homo sapiens	0	L3	OTHER	Analysis	NEG	New	Level 1
HilD	gene	hilD	activator	34048498	34	ver/dev	Hence , the SirA/BarA-CsrB/C cascade exerts two opposite regulatory effects on HilD ; the activation of the hilD mRNA translation ,	286	Hence , the SirA/BarA-CsrB/C cascade exerts two opposite regulatory effects on HilD ; the activation of the hilD mRNA translation ,	11	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	44	att	These results suggest that SlyA controls expression of magainin 2 resistance determinants in addition to the ugtL gene , which appears to be the sole SlyA-regulated gene mediating polymyxin B resistance .	169	These results suggest that SlyA controls expression of magainin 2 resistance determinants in addition to the ugtL gene , which appears to be the sole SlyA-regulated gene mediating polymyxin B resistance .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ugtL	regulator	15208313	70	att	The polymyxin B susceptibility of the slyA mutant was the same as that exhibited by the ugtL mutant ( Fig. 5A ) and could be complemented to wild-type levels by a plasmid that expressed the ugtL gene from a heterologous promoter ( Fig. 5B ) , suggesting that ugtL is the only SlyA-regulated gene mediating polymyxin B resistance .	234	The polymyxin B susceptibility of the slyA mutant was the same as that exhibited by the ugtL mutant ( Fig. 5A ) and could be complemented to wild-type levels by a plasmid that expressed the ugtL gene from a heterologous promoter ( Fig. 5B ) , suggesting that ugtL is the only SlyA-regulated gene mediating polymyxin B resistance .	5	DISCUSSION	unidentified plasmid	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ugtL	regulator	15208313	6	ver/dev	We propose that the SlyA proteins control ugtL transcription .	14	We propose that the PhoP and SlyA proteins control ugtL transcription using a feed-for-ward loop design .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	11	ver/dev	that both SlyA proteins bind to the ugtL promoter , suggesting that these two proteins use a feed-forward loop to control ugtL expression	35	We establish that the PhoP protein binds to the slyA promoter and that both the PhoP and SlyA proteins bind to the ugtL promoter , suggesting that these two proteins use a feed-forward loop to control ugtL expression .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	ugtL	regulator	15208313	22	ver/dev	The SlyA Proteins Bind to the ugtL Promoter -- We conducted gel shift assays .	126	The SlyA and PhoP Proteins Bind to the ugtL Promoter -- We conducted gel shift assays using the purified SlyA-FLAG and PhoP-His6 proteins and a 536-bp DNA fragment corresponding to the intergenic region between the ugtL gene and the upstream sifB gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	22	ver/dev	The SlyA Proteins Bind to the ugtL Promoter -- We conducted a 536-bp DNA fragment .	126	The SlyA and PhoP Proteins Bind to the ugtL Promoter -- We conducted gel shift assays using the purified SlyA-FLAG and PhoP-His6 proteins and a 536-bp DNA fragment corresponding to the intergenic region between the ugtL gene and the upstream sifB gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	27	ver/dev	These results demonstrate that the SlyA proteins bind to the ugtL promoter .	131	These results demonstrate that the PhoP and SlyA proteins bind to the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	31	ver/dev	The SlyA proteins bind to the ugtL promoter .	138	The PhoP and SlyA proteins bind to the ugtL promoter and are required for ugtL transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	44	ver/dev	These results suggest that SlyA controls expression of magainin 2 resistance determinants in addition to the ugtL gene .	169	These results suggest that SlyA controls expression of magainin 2 resistance determinants in addition to the ugtL gene , which appears to be the sole SlyA-regulated gene mediating polymyxin B resistance .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	ugtL	regulator	15208313	45	ver/dev	We have established that transcription of polymyxin B resistance gene ugtL is controlled by the SlyA proteins in what appears to be a feedforward loop design .	172	We have established that transcription of the magainin 2 and polymyxin B resistance gene ugtL is controlled by the PhoP and SlyA proteins in what appears to be a feedforward loop design ( Fig. 6 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	ugtL	regulator	15208313	57	ver/dev	The SlyA protein bound to a region located downstream from the ugtL transcription start site for a regulatory protein -LRB- Fig. 1A -RRB- .	198	The SlyA protein bound to a region located downstream from the ugtL transcription start site ( Fig. 2B ) , which is unusual for a regulatory protein that is promoting gene transcription ( Fig. 1A ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	65	ver/dev	Taken together with the identification of binding sites for both the SlyA in Fig. 2C , these results support the notion of a feedforward design in the regulation of ugtL transcription .	210	Taken together with the identification of binding sites for both the SlyA and PhoP proteins in the ugtL promoter ( Fig. 2C ) , these results support the notion of a feedforward design in the regulation of ugtL transcription .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	65	ver/dev	Taken together with the identification of binding sites for both the SlyA in the ugtL promoter , these results support the notion of a feedforward design in the regulation of ugtL transcription .	210	Taken together with the identification of binding sites for both the SlyA and PhoP proteins in the ugtL promoter ( Fig. 2C ) , these results support the notion of a feedforward design in the regulation of ugtL transcription .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	15208313	66	ver/dev	Model _ illustrating the feed-forward regulation of the ugtL gene by the SlyA proteins	222	Model illustrating the feed-forward regulation of the ugtL gene by the PhoP and SlyA proteins .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	16413221	4	ver/dev	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	313	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	10	ACKNOWLEDGEMENTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	17259627	8	att	In several SlyA-regulated genes , DNA sequences ( TTTAGTTTTTGTCTTAA , located in the ugtL promoter ; TTTGGAATGTAA , located in the pagC promoter ; and TTAGCTGTTAA , located in the mig-14 promoter ) have been identified as SlyA-specific binding sites by DNase-I-protection assay ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	60	In several SlyA-regulated genes , DNA sequences ( TTTAGTTTTTGTCTTAA , located in the ugtL promoter ; TTTGGAATGTAA , located in the pagC promoter ; and TTAGCTGTTAA , located in the mig-14 promoter ) have been identified as SlyA-specific binding sites by DNase I protection assay ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ugtL	regulator	17259627	37	ver/dev	However , SlyA has also been shown to have binding sites downstream of the transcriptional start site in the ugtL promoters .	348	However , SlyA has also been shown to have binding sites downstream of the transcriptional start site in the pagC and ugtL promoters that are required for gene transcription ( Navarre et al. , 2005 ; Shi et al. , 2004 ) .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	ugtL	regulator	17259627	44	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	554	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	63	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	18270203	6	ver/dev	Model _ depicting transcriptional control of ugtL genes by SlyA	59	Model depicting transcriptional control of the horizontally acquired pagC and ugtL genes by the regulatory proteins H-NS , PhoP , and SlyA .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	18270203	20	ver/dev	ugtL genes entails binding of both SlyA proteins to the promoters of these two genes .	187	pagC and ugtL genes entails binding of both the PhoP and SlyA proteins to the promoters of these two genes .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	18270203	56	ver/dev	the pagC promoter els for the ugtL mRNAs are probably due to the less are bound by the SlyA proteins	254	The lower lev - footprinting to identify the regions of the pagC promoter that els for the pagC and ugtL mRNAs are probably due to the less are bound by the H-NS and SlyA proteins .	3	RESULTS	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	ugtL	regulator	18407759	5	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	776	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	54	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	18715828	2	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	675	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	27	A	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	18792679	11	att	It is noteworthy that ugtL , like other PhoP - and SlyA-regulated genes , is Salmonella-specific and/or exhibits a very limited phylogenetic distribution .	177	It is noteworthy that ugtL , like other PhoP - and SlyA-regulated genes , is Salmonella-specific and/or exhibits a very limited phylogenetic distribution .	8	TYPICAL AND ATYPICAL TRANSCRIPTIONAL CASCADES	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ugtL	regulator	19091955	0	ver/dev	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL , in Salmonella .	18	Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL and pagC , in Salmonella ( 2 , 3 , 9 -- 11 ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	21388802	10	ver/dev	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	558	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	18	13. KOX LF, WOSTEN MM, GROISMAN EA: A SMALL PROTEIN THAT MEDIATES THE ACTIVATION OF A TWO-COMPONENT SYSTEM BY ANOTHER TWO-COMPONENT SYSTEM. EMBO J 2000, 19:1861-1872.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	24021902	8	ver/dev	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	478	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	9	REFERENCES AND RECOMMENDED READING	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	25135218	80	ver/dev	The S. Typhimurium ugtL are regulated by a similar mechanism , involving the coordinated actions of SlyA .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	ugtL	regulator	26443522	1	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	1060	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	21	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	27564394	22	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	1320	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	30	ACKNOWLEDGMENTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	29324231	13	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	512	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	8	BD FACS ARIA II FLOW CYTOMETER. FOR SAMPLES ISOLATED FROM INFECTED CELLS, ONLY PARTICLES WITH MCHERRY LEVELS (532 NM EXCITATION, 610/20 WITH 600LP EMISSION) ABOVE THE BACKGROUND LEVELS OBSERVED FOR MCHERRY-NEGATIVE CONTROL SAMPLES WERE ANALYZED.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	29937757	19	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	565	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	24	THIS WORK WAS SUPPORTED BY FONDECYT GRANT 1130225 (TO SÁ). ONLINE AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB. CS WAS SUPPORTED BY FONDECYT GRANT 1140754 AND 1171844. 2018.01220/FULL#SUPPLEMENTARY-MATERIAL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	30510144	36	ver/dev	Accordingly , other authors also reported an functional palindrome for SlyA binding at the ugtL , indicating that those motifs might function as SlyA regulatory sites .	165	Accordingly , other authors also reported an imperfect but functional palindrome for SlyA binding at the ugtL and slyA promoter regions ( 15 , 40 ) , indicating that those motifs identified in the PrcsDB and PrcsB sequences might function as SlyA regulatory sites .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	ugtL	regulator	30510144	36	ver/dev	Accordingly , other authors also reported an imperfect palindrome for SlyA binding at the ugtL , indicating that those motifs might function as SlyA regulatory sites .	165	Accordingly , other authors also reported an imperfect but functional palindrome for SlyA binding at the ugtL and slyA promoter regions ( 15 , 40 ) , indicating that those motifs identified in the PrcsDB and PrcsB sequences might function as SlyA regulatory sites .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	ugtL	regulator	31333620	8	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	629	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	49	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	31484980	58	ver/dev	The previously defined regulation of ugtL by SlyA and/or PhoP is not depicted in the model	297	The previously defined regulation of ugtL and slrP by SlyA and/or PhoP is not depicted in the model but it is described in text .	4	METHODS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
SlyA	gene	ugtL	regulator	31484980	64	ver/dev	Shi , Y. , Latifi , T. , Cromie , M. J. & Groisman , E. A. Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	642	Shi , Y. , Latifi , T. , Cromie , M. J. & Groisman , E. A. Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	20	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	ugtL	regulator	33045730	110	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .	736	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	69	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	narJ	activator	29857034	19	ver/dev	narJ are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilD	regulator	17208038	26	ver/dev	Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE .	143	Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE [ 49 ] .	10	HILE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilD	regulator	24354910	16	ver/dev	Because HilE is a negative regulator of hilD , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level .	83	Because HilE is a negative regulator of hilD ( Baxter et al. , 2003 ) , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level , which in turn might inhibit HilD activity .	9	RESULTS	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Crl	gene	rpoS	activator	20008066	18	ver/dev	As previously shown , Crl production was increased by the rpoS mutation by a mechanism .	434	As previously shown ( 38 ) , Crl production was increased by the rpoS mutation ( Fig. 6C , lanes 10 , 12 , and 15 ) by a mechanism that likely operates at the posttranscriptional level ( Fig. 8D ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
IgaA	gene	rcsB	regulator	15387821	1	ver/dev	To decipher the mechanism by which IgaA exerts negative control of the RcsC-YojN-RcsB system , isogenic strains , rcsB genes were constructed .	103	To decipher the mechanism by which IgaA exerts negative control of the RcsC-YojN-RcsB system , isogenic strains carrying epitope tags in the 3 cents end of the chromosomal rcsC , rcsB and yojN genes were constructed .	7	IGAA CONTROLS THE RCSC-YOJN-RCSB SYSTEM AT A POST-TRANSLATIONAL LEVEL	nan	1	L3	OTHER	Other	NEG	Other	Level 1
YncC	gene	yciGFE	activator	20713450	8	ver/dev	that YncC are both able to induce expression of the yciGFE locus in E. coli K-12	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
YncC	gene	yciGFE	activator	20713450	8	ver/dev	that YncC are both able to induce expression of the yciGFE locus in Salmonella	340	Altogether , these results show that YncC and McbR are both able to induce expression of the yciGFE ( katN ) locus in Salmonella and E. coli K-12 , and that this locus is expressed at drastically lower levels in E. coli K-12 than in Salmonella .	6	PUTATIVE YNCC TARGETS REVEALED BY PROTEINCHIP SELDI-TOF	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
OmpR	gene	fljB	repressor	24031550	8	ver/dev	fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of fliA by OmpR .	268	fljB : z66 at low osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC and fliA by OmpR .	5	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
OmpR	gene	fljB	repressor	24031550	8	ver/dev	fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC by OmpR .	268	fljB : z66 at low osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC and fliA by OmpR .	5	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
FliZ	gene	ssrB	regulator	31262841	1	ver/dev	PinT also indirectly represses expression of FliZ , and directly represses translation of ssrB , encoding the primary regulator of the SPI2 T3SS .	15	PinT also indirectly represses expression of FliZ , a posttranslational regulator of HilD , and directly represses translation of ssrB , encoding the primary regulator of the SPI2 T3SS .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	spoT	activator	16905537	9	att	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	197	Because ssrA/B expression is dependent on OmpR , we also determined the expression levels of ompR as well as a nonvirulence related OmpR-dependent gene , ompC , in both the wild type and relA spoT strains .	3	EXPERIMENTAL PROCEDURES	Leiostomus xanthurus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	katE	regulator	11260470	4	ver/dev	In the rpoS mutant , the amount of KatE is also significantly decreased ; this confirms that katE expression is also controlled by RpoS .	171	In the rpoS mutant , the amount of KatE is also significantly decreased ; this confirms that katE expression is also controlled by RpoS ( Loewen et al. , 1998 ; Ibanez-Ruiz et al. , 2000 ) .	8	TRANSCRIPTION OF KATN IS RPOS AND GROWTH PHASE DEPENDENT	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	katE	regulator	11682190	0	ver/dev	Moreover , the comparison of katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .	141	Moreover , the comparison of rfaH and katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS [ 27 ] .	14	3.2. THE RFAH GENE PRODUCT IS REQUIRED FOR NORMAL EXPRESSION OF LPS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
RpoS	gene	katE	regulator	20600858	2	ver/dev	katE _ regulated by RpoS	41	katE , regulated by RpoS , encodes catalase II and has an established role in antioxidant defenses in early stationary phase growth ( Ackerley et al. , 2006 ; Aertsen et al. , 2005 ; Mulvey et al. , 1990 ; Schellhorn and Hassan , 1988 ) .	4	1. INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	regulator	23936152	1	ver/dev	the RpoS _ regulated katE	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	regulator	23936152	1	ver/dev	the RpoS _ regulated katE	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	regulator	23936152	1	ver/dev	the RpoS _ regulated katE	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	regulator	23936152	1	ver/dev	the RpoS _ regulated katE	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	katE	regulator	25549217	3	ver/dev	The katE gene ( encoding catalase hydroperoxidase II [ HPII ] ) , is under the control of RpoS .	225	The katE gene ( encoding catalase hydroperoxidase II [ HPII ] ) , which is involved in the resistance to H2O2 , is under the control of RpoS .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	katE	regulator	29507892	4	ver/dev	It is well known that in E. coli , RpoS controls the expression of katE to oxygen under nutrient-limiting conditions .	199	It is well known that in S. Typhimurium and E. coli , RpoS controls the expression of katE , which encodes hydroperoxidase II that is responsible for the deprotonation of hydrogen peroxide to water and oxygen under nutrient-limiting conditions ( 57 , 59 ) .	4	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	katE	regulator	29507892	4	ver/dev	It is well known that in E. coli , RpoS controls the expression of katE to water under nutrient-limiting conditions .	199	It is well known that in S. Typhimurium and E. coli , RpoS controls the expression of katE , which encodes hydroperoxidase II that is responsible for the deprotonation of hydrogen peroxide to water and oxygen under nutrient-limiting conditions ( 57 , 59 ) .	4	DISCUSSION	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	katE	regulator	29507892	4	ver/dev	It is well known that in S. Typhimurium , RpoS controls the expression of katE to oxygen under nutrient-limiting conditions .	199	It is well known that in S. Typhimurium and E. coli , RpoS controls the expression of katE , which encodes hydroperoxidase II that is responsible for the deprotonation of hydrogen peroxide to water and oxygen under nutrient-limiting conditions ( 57 , 59 ) .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Fact	OTHER	Other	Level 3
RpoS	gene	katE	regulator	29507892	4	ver/dev	It is well known that in S. Typhimurium , RpoS controls the expression of katE to water under nutrient-limiting conditions .	199	It is well known that in S. Typhimurium and E. coli , RpoS controls the expression of katE , which encodes hydroperoxidase II that is responsible for the deprotonation of hydrogen peroxide to water and oxygen under nutrient-limiting conditions ( 57 , 59 ) .	4	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Fact	OTHER	Other	Level 3
YdiV	gene	STM3611	activator	24127899	3	ver/dev	YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 .	47	YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 ( YhjH ) , which is part of the flagellar regulon ( Simm et al. , 2009 ) .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilA	gene	sopA	regulator	31428589	0	ver/dev	sopA are regulated cooperatively by HilA .	125	sopA , sopB , and sopE are regulated cooperatively by HilA and InvF ( Thijs et al. , 2007 ) .	3	THE ROLE OF SPI-1	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Crl	gene	rpoS	regulator	20008066	19	ver/dev	Thus , depending on the mechanisms of regulation of rpoS expression , Crl might be dispensable .	442	Thus , depending on the bacterial lifestyles and environment encountered , cellular physiology , and the mechanisms of regulation of rpoS expression , Crl might be dispensable .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
OmpR	TU	flhDC	repressor	26441883	5	ver/dev	OmpR represses flhDC in response to extracellular osmolarity .	209	OmpR represses flhDC in response to extracellular osmolarity .	8	SEQUENCE COVERAGE REPORTS THE LENGTH OF THE IDENTIFIED HOMOLOGOUS PROTEIN SEQUENCE WITH THE INDICATED AMINO ACID IDENTITY. IN THE MAJORITY, THE TRUE ORTHOLOGS OF THE QUERY PROTEIN SEQUENCES ARE LISTED, WHEREAS CLOSE HOMOLOGS WITH UNKNOWN REGULATORY FUNCTION AND LOW SEQUENCE IDENTITY ARE GIVEN IN ITALICS. NA = NOT AVAILABLE.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	TU	flhDC	repressor	32032766	2	ver/dev	The qRT-PCR results showed that both flhDC were downregulated by the regulators , OmpR and Fis .	176	The qRT-PCR results showed that both asfD and flhDC were downregulated by the regulators , OmpR and Fis , and upregulated by RpoS .	19	3.4. ASFD OVEREXPRESSION PROMOTES S. TYPHI BIOFILM FORMATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	sprB	regulator	27601571	10	ver/dev	We detected direct regulation of sprB by HilD from a binding site immediately upstream of sprB .	124	We detected direct regulation of sprB by HilD from a binding site immediately upstream of sprB .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	sprB	regulator	27601571	13	ver/dev	S1B ) , we conclude that HilD regulation of sprB occurs predominantly through regulation of the hilC-sprB transcript .	130	S1B ) , we conclude that HilD regulation of sprB occurs predominantly through regulation of the hilC-sprB transcript .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sprB	regulator	27601571	13	ver/dev	S1B ) , we conclude that HilD regulation of sprB occurs predominantly through regulation of the hilC-sprB transcript .	130	S1B ) , we conclude that HilD regulation of sprB occurs predominantly through regulation of the hilC-sprB transcript .	3	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HilD	gene	sprB	regulator	31484980	24	ver/dev	To investigate whether HilD regulates expression of sprB -LRB- by acting on the regulatory region upstream of this gene -RRB- directly , we determined the activity of the sprB-cat fusion in the WT E. coli MC4100 strain .	133	To investigate whether HilD regulates expression of sprB ( by acting on the regulatory region upstream of this gene ) directly or through an additional Salmonella-specific factor , we determined the activity of the sprB-cat fusion in the WT E. coli MC4100 strain carrying the pK6-HilD plasmid or the pMPM-K6Ω vector .	3	RESULTS	Felis catus;Escherichia coli	0	L3	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	sprB	regulator	31484980	26	ver/dev	Furthermore , previous results from ChIP-seq analyses indicate that HilD binds to the intergenic region upstream of sprB in-vivo28 ,38 .	153	Furthermore , previous results from ChIP-seq analyses indicate that HilD binds to the intergenic region upstream of sprB in vivo28 ,38 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	yqjA	regulator	15225317	14	att	PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes	168	PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	yqjA	regulator	15225317	27	att	In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .	276	In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	yqjA	regulator	15225317	2	ver/dev	the yqjA gene we show is PhoP regulated for resistance to polymyxin B or defensin HNP-1	13	Inactivation of both ugtL and the regulatory gene pmrA , which controls lipid A modifications required for resistance to polymxyin B ( but not to magainin 2 ) and is post-tran-scriptionally activated by the PhoP -- PhoQ system , resulted in a strain that was as susceptible to poly-myxin B as a phoP mutant.The most frequently recovered clone harboured the yqjA gene , which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP-1 .	1	SUMMARY	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	yqjA	regulator	15225317	2	ver/dev	the yqjA gene we show is PhoP regulated for resistance to magainin 2 HNP-1	13	Inactivation of both ugtL and the regulatory gene pmrA , which controls lipid A modifications required for resistance to polymxyin B ( but not to magainin 2 ) and is post-tran-scriptionally activated by the PhoP -- PhoQ system , resulted in a strain that was as susceptible to poly-myxin B as a phoP mutant.The most frequently recovered clone harboured the yqjA gene , which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP-1 .	1	SUMMARY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	yqjA	regulator	15225317	2	ver/dev	the yqjA gene we show is PhoP regulated for resistance to polymyxin B or defensin HNP-1	13	Inactivation of both ugtL and the regulatory gene pmrA , which controls lipid A modifications required for resistance to polymxyin B ( but not to magainin 2 ) and is post-tran-scriptionally activated by the PhoP -- PhoQ system , resulted in a strain that was as susceptible to poly-myxin B as a phoP mutant.The most frequently recovered clone harboured the yqjA gene , which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP-1 .	1	SUMMARY	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	yqjA	regulator	15225317	2	ver/dev	the yqjA gene we show is PhoP regulated for resistance to magainin 2 HNP-1	13	Inactivation of both ugtL and the regulatory gene pmrA , which controls lipid A modifications required for resistance to polymxyin B ( but not to magainin 2 ) and is post-tran-scriptionally activated by the PhoP -- PhoQ system , resulted in a strain that was as susceptible to poly-myxin B as a phoP mutant.The most frequently recovered clone harboured the yqjA gene , which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP-1 .	1	SUMMARY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	yqjA	regulator	15225317	18	ver/dev	This raised the possibility that the yqjA and/or yqjB genes might be regulated by the PhoP protein .	174	This raised the possibility that the yqjA and/or yqjB genes might be required for magainin 2 resistance and regulated by the PhoP protein .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L1	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	yqjA	regulator	15225317	23	ver/dev	two genes -- yqjA -- are both transcriptionally regulated by the PhoP	255	This strategy was validated with the recovery of two genes -- ugtL and yqjA -- that are both required for magainin 2 resistance ( Fig. 2A -- C , F and G ) and transcriptionally regulated by the PhoP -- PhoQ system ( Fig. 4 ; Hilbert et al. , 1999 ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	yqjA	regulator	15225317	24	ver/dev	Expression of the yqjA gene is controlled by the PhoP protein at the transcriptional level .	261	Expression of the yqjA gene is controlled by the PhoP protein at the transcriptional level .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	osmB	activator	33751923	21	ver/dev	When phosphorylated , RcsB binds RcsA to activate expression of osmB .	645	When phosphorylated , RcsB binds RcsA to activate expression of several genes , such as osmB , osmC , bdm , ftsZ , rprA , wza , and rcsA .	25	RCSBCD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hlyE	repressor	14996792	52	ver/dev	In the previous report , H-NS acted as a strong repressor of hlyE expression , whereas here H-NS appears to have a positive effect on hlyE expression in the absence of glucose but an negative effect on hlyE expression in the presence of glucose .	246	In the previous report ( 36 ) , H-NS acted as a strong repressor of hlyE expression , whereas here H-NS appears to have a positive effect on hlyE expression in the absence of glucose but an attenuated or negative effect on hlyE expression in the presence of glucose ( Fig. 1 ) .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hlyE	repressor	14996792	52	ver/dev	In the previous report , H-NS acted as a strong repressor of hlyE expression , whereas here H-NS appears to have a positive effect on hlyE expression in the absence of glucose but an attenuated effect on hlyE expression in the presence of glucose .	246	In the previous report ( 36 ) , H-NS acted as a strong repressor of hlyE expression , whereas here H-NS appears to have a positive effect on hlyE expression in the absence of glucose but an attenuated or negative effect on hlyE expression in the presence of glucose ( Fig. 1 ) .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hlyE	repressor	14996792	53	ver/dev	This suggests that , in general , H-NS inhibits FNR-driven hlyE expression .	247	This suggests that , in general , H-NS inhibits FNR-driven hlyE expression ( Fig. 1 ) but enhances CRP-driven expression in liquid cultures ( compare Fig. 1b and c ) .	8	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hlyE	repressor	19835951	17	ver/dev	In hlyE are transcriptionally repressed by the nucleoid-associated protein H-NS .	226	In addition , hlyABCD , ehxCABD and hlyE are transcriptionally repressed by the nucleoid-associated protein H-NS , a regulator that essentially exerts the opposite effects of RpoS [ 14,34,42 ] .	17	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hlyE	repressor	30778340	0	ver/dev	S. Typhi 1hns where the hlyE transcript was highly abundant compared with the WT , showing that H-NS contributes to the repression of hlyE expression	173	The only exception was observed with S. Typhi 1hns , where the hlyE transcript was highly abundant compared with the WT , showing that H-NS contributes to the repression of hlyE expression ( Figure 1D ) .	16	GENERATION OF S. TYPHI HEMOLYTIC MUTANTS BY RANDOM INSERTIONAL	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hlyE	repressor	30778340	3	ver/dev	Accordingly , H-NS acts as a repressor of hlyE , belonging to the SPI-18 , a genomic locus presumably acquired by horizontal transfer in S. Typhi .	472	Accordingly , H-NS acts as a repressor of hlyE , belonging to the SPI-18 , a genomic locus presumably acquired by horizontal transfer in S. Typhi ( Oscarsson et al. , 2002 ; Fuentes et al. , 2008 ) .	18	CHARACTERIZATION OF OUTER MEMBRANE	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Other	OTHER	Other	Level 1
HilD	gene	hilC	regulator	12535071	89	ver/dev	Although HilD regulate two promoters upstream of hilC , they activate one and repress the other , such that overall HilD appear to have no effect on hilC expression .	252	Although HilD and HilC regulate two promoters upstream of hilC , they activate one and repress the other , such that overall HilD and HilC appear to have no effect on hilC expression ( Olekhnovich and Kadner , 2002 ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
HilD	gene	hilC	regulator	15661008	15	ver/dev	These results indicate that Lon is involved in the autoregulation of hilC transcription by modulating amounts of HilD .	181	These results indicate that Lon is involved in the autoregulation of hilC and hilD transcription by modulating amounts of HilC and HilD .	7	LEVEL OF HILC AND HILD TRANSCRIPTION IN WILD-TYPE AND LON-DISRUPTED MUTANT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilC	regulator	17208038	34	ver/dev	This work demonstrates the regulation of hilC by HilD .	203	This work demonstrates the regulation of rtsA , hilC , hilD , and hilA by HilC , HilD and RtsA , and that each regulator has a role in the host during infection .	15	18. AHMER BM, VAN REEUWIJK J, WATSON PR, WALLIS TS, HEFFRON F: SALMONELLA SIRA IS A GLOBAL REGULATOR OF GENES MEDIATING ENTEROPATHOGENESIS. MOL MICROBIOL 1999, 31:971-982.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilC	regulator	17675384	4	ver/dev	The HilD proteins bind to the common DNA sites at hilC promoters .	44	The HilD and HilC proteins bind to the common DNA sites at the hilA , hilD , and hilC promoters ( 37 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilC	regulator	19537165	6	ver/dev	To check if both regulators are important , the regulation of hilC gene expression by HilD is considered to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	106	To check if both regulators are important , the regulation of hilC gene expression by HilD and SirA is considered to function as an AND gate , and to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilC	regulator	19537165	6	ver/dev	To check if both regulators are important , the regulation of hilC gene expression by HilD is considered to function as gate , this dependency is taken as an OR gate .	106	To check if both regulators are important , the regulation of hilC gene expression by HilD and SirA is considered to function as an AND gate , and to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	regulator	19537165	6	ver/dev	To check if both regulators are important , the regulation of hilC gene expression by HilD is considered to function as an , this dependency is taken as an OR gate .	106	To check if both regulators are important , the regulation of hilC gene expression by HilD and SirA is considered to function as an AND gate , and to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .	9	SCENARIO-1: REGULATION OF THE NETWORK BY SIRA VIA HILC AND HILA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilC	regulator	22479568	0	ver/dev	HilD can activate expression of hilC of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	gene	hilC	regulator	25135218	6	ver/dev	HilD also directly controls the expression of hilC .	23	HilD also directly controls the expression of the SPI-1 genes hilD , hilC , and invF , as well as other acquired and ancestral genes located outside SPI-1 , such as rtsA , flhDC , siiA , lpxR , ytfK , STM14_1282 , and STM14_2342 ( 2 , 25 -- 31 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilC	regulator	31484980	52	ver/dev	direct regulation of hilC by HilD is well documented28 ,30,38,48,51	241	Previous studies indicate that HilD can also control expression of sprB by acting on the hilC gene , located upstream of sprB ; a hilC-sprB transcript was detected in a previous study28 and direct regulation of hilC by HilD is well documented28 ,30,38,48,51 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	invH	activator	25991823	14	att	For this purpose , we analyzed the effect of L-arabinose on the expression of three HilD-activated genes ( hilC , rtsA , and invH ) .	249	For this purpose , we analyzed the effect of L-arabinose on the expression of three HilD-activated genes ( hilC , rtsA , and invH ) .	14	L-ARABINOSE-DEPENDENT REPRESSION OF SPI-1 IS TRANSMITTED VIA HILD	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	TU	flhDC	activator	16952964	1	ver/dev	The RNA-binding protein CsrA positively regulate class 2 expression through enhancing translation of flhDC mRNA .	34	The RNA-binding protein CsrA and the DnaK chaperone positively regulate class 2 expression through enhancing translation of flhDC mRNA ( 34 ) and through converting the native FlhD2C2 heterotetramer into a functional form ( 32 ) , respectively .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	4	ver/dev	CsrA , regulates flagellar gene expression by enhancing translation of flhDC mRNA	30	CsrA , an RNA-binding protein , regulates flagellar gene expression by enhancing translation of flhDC mRNA , and DnaK , a chaperone protein , converts the native FlhDC to a functional protein form ( 14 -- 16 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Babitzke , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	T. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Romeo , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	I. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Berezin , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	H. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Yakhnin , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	C.A. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Vakulskas , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	C.S. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Baker , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	A.V. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	28973452	81	ver/dev	Yakhnin , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	450	Yakhnin , A.V. , Baker , C.S. , Vakulskas , C.A. , Yakhnin , H. , Berezin , I. , Romeo , T. and Babitzke , P. ( 2013 ) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	TU	flhDC	activator	31488053	5	ver/dev	Acetate is believed to repress flagellar gene expression because CsrA is known to post-transcriptionally induce flhDC expression .	232	Acetate is believed to repress flagellar gene expression because CsrA is known to post-transcriptionally induce flhDC expression [ 40 -- 42 ] .	8	DISCUSSION	nan	1	L3	SPEC	Fact	OTHER	Other	Level 1
CpxR	gene	tsgA	activator	30760616	7	ver/dev	In addition , the major facilitator superfamily member tsgA were also positively regulated by CpxR in egg white .	292	In addition , the major facilitator superfamily member tsgA , the esterase yjfP , and a putative membrane-bound redox modulator alx were also positively regulated by CpxR in egg white ( 78 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	hilD	repressor	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	activator	29378886	16	att	As shown in Fig. 7 , we observed HilE-dependent hilA promoter activity consistent with our genetic model and with previous findings ( 20 ) .	170	As shown in Fig. 7 , we observed HilE-dependent hilA promoter activity consistent with our genetic model and with previous findings ( 20 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilE	gene	hilA	activator	33593291	3	ver/dev	HilE is necessary for activation of hilA expression by acetate We previously found that during-growth on the addition of yeast extract and acetate synergistically induce hilA expression .	62	HilE is necessary for activation of hilA expression by acetate We previously found that during growth on TB medium , the addition of yeast extract and acetate synergistically induce hilA expression [ 13 ] .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	activator	33593291	3	ver/dev	HilE is necessary for activation of hilA expression by acetate We previously found that during-growth on TB medium synergistically induce hilA expression .	62	HilE is necessary for activation of hilA expression by acetate We previously found that during growth on TB medium , the addition of yeast extract and acetate synergistically induce hilA expression [ 13 ] .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	activator	33593291	5	ver/dev	that HilE is necessary for activation of hilA expression by acetate	78	Collectively , these results suggest that HilE is necessary for activation of hilA expression by acetate and that results are not an artifact of the method used to measure gene expression .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilE	gene	hilA	activator	33593291	6	ver/dev	HilE is not necessary for activation of hilA expression by other short-chain-fatty-acids Short-chain fatty-acids are known to induce hilA expression .	79	HilE is not necessary for activation of hilA expression by other short-chain fatty acids Short-chain fatty acids are known to induce hilA expression [ 14 ] .	6	RESULTS	nan	1	L3	OTHER	Fact	NEG	Other	Level 1
HilE	gene	hilA	activator	33593291	8	ver/dev	Taken together , we conclude that the requirement of HilE for activation of hilA expression is specific for acetate though we can not discount that there is also minor contribution in the case of propionate .	91	Taken together , we conclude that the requirement of HilE for activation of hilA expression is specific for acetate though we can not discount that there is also minor contribution in the case of propionate .	6	RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	activator	33593291	14	ver/dev	Expression profiling suggest that the Rcs is involved in inducing hilA expression by yeast extract Our results suggest that HilE is necessary for activation of hilA expression by yeast extract under the growth-conditions .	120	Expression profiling suggest that the Rcs is involved in inducing hilA expression by acetate and yeast extract Our results suggest that HilE is necessary for activation of hilA expression by acetate and yeast extract under the growth conditions tested .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	activator	33593291	14	ver/dev	Expression profiling suggest that the Rcs is involved in inducing hilA expression by acetate extract Our results suggest that HilE is necessary for activation of hilA expression by acetate extract under the growth-conditions .	120	Expression profiling suggest that the Rcs is involved in inducing hilA expression by acetate and yeast extract Our results suggest that HilE is necessary for activation of hilA expression by acetate and yeast extract under the growth conditions tested .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilE	gene	hilA	activator	33593291	18	ver/dev	In particular , HilE prevents it from activating hilA expression .	124	In particular , HilE binds the upstream regulator HilD and prevents it from activating hilA expression [ 10 -- 12 ] .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NagC	gene	galP	regulator	24450479	8	ver/dev	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli , although the galP gene is controlled via a single operator with high affinity .	68	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli ( nagEBACD , glmUS , chbBCARFG , fimB ) , although the galP gene is controlled via a single operator with high affinity ( El Qaidi et al. , 2009 ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
NagC	gene	galP	regulator	24450479	8	ver/dev	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli , although the galP gene is controlled via a single operator with high affinity .	68	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli ( nagEBACD , glmUS , chbBCARFG , fimB ) , although the galP gene is controlled via a single operator with high affinity ( El Qaidi et al. , 2009 ) .	4	RESULTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
EmrR	gene	pagC	activator	30992361	18	att	We found that the EmrR-stimulated pagC transcription in the ΔemrR ΔslyA mutant carrying plasmid pemrR-FLAG was 7.1-fold reduced by 1 mM dopamine , whereas the SlyA-stimulated transcription in this mutant carrying pslyA-FLAG was not influenced ( Fig. 3D ) .	136	We found that the EmrR-stimulated pagC transcription in the ΔemrR ΔslyA mutant carrying plasmid pemrR-FLAG was 7.1-fold reduced by 1 mM dopamine , whereas the SlyA-stimulated transcription in this mutant carrying pslyA-FLAG was not influenced ( Fig. 3D ) .	3	RESULTS	unidentified plasmid;Iris germanica;Iris germanica	0.5	L3	OTHER	Other	NEG	Other	Level 1
EmrR	gene	pagC	activator	30992361	19	att	L-Tyrosine , a precursor for biosynthesis of dopamine ( 41 ) , did not affect the EmrR-stimulated pagC transcription even at a concentration as high as 40 mM ( Fig. 3D ) .	137	L-Tyrosine , a precursor for biosynthesis of dopamine ( 41 ) , did not affect the EmrR-stimulated pagC transcription even at a concentration as high as 40 mM ( Fig. 3D ) .	3	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	ydgR	regulator	23782700	11	att	Goh , E. B. , Siino , D. F. , and Igo , M. M. ( 2004 ) The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	491	Goh , E. B. , Siino , D. F. , and Igo , M. M. ( 2004 ) The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	21	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	ydgR	regulator	30524381	49	att	The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	502	The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
Lrp	gene	traJ	repressor	12067346	4	ver/dev	These observations support the model that Lrp acts as a conjugation activator by promoting traJ transcription , whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis .	17	These observations support the model that Lrp acts as a conjugation activator by promoting traJ transcription , whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis .	2	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; does not have a direct role in c-di-GMP turnover ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG Positive regulator of csgD transcription ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - an additional report states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of 3.58 ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
CsgD	gene	yjcC	regulator	25824832	6	ver/dev	Positive regulator of motility by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms states that the function is the exact opposite Stimulates invasion 3.18 Negative regulator of rdar morphotype ; positive regulator of motility 4.47 Positive effect on motility 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to negative regulator of motility ; represses expression of yhjH Outer membrane NlpI can negatively influence the expression of yjcC DGC Positive regulator of cellulose production 0.34 -LRB- STM1987 -RRB- DGC Positive effect on rdar morphotype , CsgD expression , and cellulose 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ; the S. Typhimurium LT2 gene names are listed in parentheses .	372	Positive regulator of motility and virulence by both c-di-GMP-dependent 4.05 TP2 , TP3 , TP4 and - independent mechanisms ( 49 ) ; an additional report states that the function is the exact opposite ( 48 ) Stimulates invasion ( 48 ) 3.18 Negative regulator of rdar morphotype ; positive regulator of motility ( 46 ) 4.47 Positive effect on motility ( 49 ) 3.13 Binds c-di-GMP through a high-affinity PilZ domain ; represses motility 4.07 by binding directly to FliG ( 51 , 52 ) Positive regulator of csgD transcription and negative regulator of motility , 3.58 but does not have a direct role in c-di-GMP turnover ; represses expression of yhjH ( 53 ) Outer membrane NlpI can negatively influence the expression of yjcC , which codes for a protein DGC affecting CsgD expression ( 50 ) adrA ( yaiC ) DGC Positive regulator of cellulose production ( 46 ) 0.34 STM14_2408 ( STM1987 ) DGC Positive effect on rdar morphotype , CsgD expression , and cellulose ( 45 ) 0.54 a Gene names are listed as they appear in the S. Typhimurium 14028 genome ( 39 ) ; the S. Typhimurium LT2 gene names are listed in parentheses .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	pepT	regulator	16855381	2	att	Based on available literature data , the FNR-regulated pepT gene promoter was chosen as a starting point for our investigations .16 pepT is transcribed from two promoters .	153	Based on available literature data , the FNR-regulated pepT gene promoter was chosen as a starting point for our investigations .16 pepT is transcribed from two promoters .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	pepT	regulator	18559530	3	ver/dev	5 The Salmonella endogenous promoter for pepT is regulated by Fnr .	187	5 The Salmonella endogenous promoter for pepT is regulated by CRP and Fnr ( 14 ) .	6	RESULTS AND DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	TU	cydAB	regulator	11238977	7	ver/dev	Cooperative interaction between Fnr in the regulation of the cydAB operon of Escherichia coli .	370	Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli .	14	O’NEAL, C. R., GABRIEL, W. M., TURK, A. K., LIBBY, S. J., FANG, F. C. &	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	11238977	8	ver/dev	Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in activation .	430	Aerobic regulation of cytochrome d oxidase ( cydAB ) operon expression in Escherichia coli : roles of Fnr and ArcA in repression and activation .	17	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	11238977	8	ver/dev	Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in repression .	430	Aerobic regulation of cytochrome d oxidase ( cydAB ) operon expression in Escherichia coli : roles of Fnr and ArcA in repression and activation .	17	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	11796570	0	ver/dev	Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in activation .	355	Aerobic regulation of cytochrome d oxidase ( cydAB ) operon expression in Escherichia coli : roles of Fnr and ArcA in repression and activation .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	11796570	0	ver/dev	Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in repression .	355	Aerobic regulation of cytochrome d oxidase ( cydAB ) operon expression in Escherichia coli : roles of Fnr and ArcA in repression and activation .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	12761123	0	ver/dev	Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in activation .	512	Aerobic regulation of cytochrome d oxidase ( cydAB ) operon expression in Escherichia coli : roles of Fnr and ArcA in repression and activation .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	12761123	0	ver/dev	Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in repression .	512	Aerobic regulation of cytochrome d oxidase ( cydAB ) operon expression in Escherichia coli : roles of Fnr and ArcA in repression and activation .	15	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
FNR	TU	cydAB	regulator	19136587	15	ver/dev	Cooperative interaction between Fnr in the regulation of the cydAB operon of Escherichia coli .	545	Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli .	20	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
STM3124	gene	STM3122	regulator	30648943	5	ver/dev	Taken together with the above-mentioned genetic analysis of sulfatase activity , these results demonstrate that STM3124 regulates STM3122 .	212	Taken together with the above-mentioned genetic analysis of sulfatase activity , these results demonstrate that STM3124 regulates STM3122 and suggests that the presence of dopamine leads to transcriptional activation of STM3124 that , in turn , increases the expression of STM3122 .	15	PUTATIVE LUXR-TYPE TRANSCRIPTIONAL REGULATOR STM3124 IS REQUIRED FOR DOPAMINE INDUCTION OF SULFATASE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	slrP	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilD independently of InvF .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	activator	17208038	7	ver/dev	The genes slrP and dsbA are also induced by HilD independently of both HilA .	69	The genes slrP and dsbA are also induced by HilC , HilD and RtsA independently of both HilA and InvF [ 25,28 ] .	5	A MODEL FOR SPI1 REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	activator	25182488	3	ver/dev	In this context , slrP is induced by overexpression of HilD independently of the central SPI1 regulator HilA , with RtsA .	38	In this context , slrP is induced by overexpression of HilC , HilD , and RtsA independently of the central SPI1 regulator HilA , with RtsA being the best inducer .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	activator	29555922	18	ver/dev	Additionally , HilD positively regulate the expression of the slrP gene .	270	Additionally , HilD and PhoP positively and independently regulate the expression of the slrP gene , in SPI-1-inducing growth conditions , PhoP directly and HilD by an unknown mechanism37 .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	slrP	activator	31484980	38	ver/dev	Previous RNA-seq analyses indicate that HilD positively controls slrP .	184	Previous RNA-seq analyses indicate that HilD and SprB positively controls expression of several other genes in common , in addition to yobH , including slrP and ugtL28 , which have been involved in Salmonella virulence55 -- 59 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	slrP	activator	31484980	46	ver/dev	In this regulatory cascade , HilD induces expression of the slrP virulence genes through SprB .	219	In this regulatory cascade , HilD induces expression of the yobH , slrP and ugtL virulence genes through SprB , a Salmonella-specific LuxR-like regulator encoded in SPI-1 .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	activator	31484980	46	ver/dev	In this regulatory cascade , HilD induces expression of the slrP virulence genes through a Salmonella-specific LuxR-like regulator .	219	In this regulatory cascade , HilD induces expression of the yobH , slrP and ugtL virulence genes through SprB , a Salmonella-specific LuxR-like regulator encoded in SPI-1 .	3	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	slrP	activator	31484980	47	ver/dev	Previous studies revealed that HilD induce expression of slrP by an undefined way62 ,63 .	220	Previous studies revealed that HilD and RtsA induce expression of slrP by an undefined way62 ,63 .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	mgrB	activator	12519186	28	att	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	93	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgrB	activator	18792679	1	att	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	113	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	5	DIRECT TRANSCRIPTIONAL CONTROL BYTHE PHOP PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	mgrB	activator	23504014	31	ver/dev	A gene homologous to mgrB in S. enterica has been shown to be activated by PhoP , suggesting that MgrB is part of a negative feedback loop in the PhoQ/PhoP signaling circuit .	378	A gene homologous to mgrB in S. enterica has been shown to be activated by PhoP , suggesting that MgrB is part of a negative feedback loop in the PhoQ/PhoP signaling circuit ( 58 ) .	7	DISCUSSION	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	mgrB	activator	32620947	5	ver/dev	PhoP _ resulting in increased transcription of mgrB , i.e. down-regulation of phoPQ-lacZ in the acrB - or/and cpxR-deleted strains	83	In the PhoPQ system , PhoQ stimulation leads to increased levels of phosphorylated PhoP , resulting in increased transcription of mgrB , i.e. positive feedback .24 The membrane peptide MgrB is known as a feedback inhibitor of PhoQ in different bacteria and its up-regulation results in decreased PhoP phosphorylation , i.e. negative feedback .24 Interestingly , we discovered a synchronous up - or down-regulation of mgrB-lacZ and phoPQ-lacZ in the acrB - or/and cpxR-deleted strains , which was quite different from the expected negative feedback loop between MgrB and PhoPQ .	9	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	mgrB	activator	32620947	5	ver/dev	PhoP _ resulting in increased transcription of mgrB , i.e. down-regulation of mgrB-lacZ in the acrB - or/and cpxR-deleted strains	83	In the PhoPQ system , PhoQ stimulation leads to increased levels of phosphorylated PhoP , resulting in increased transcription of mgrB , i.e. positive feedback .24 The membrane peptide MgrB is known as a feedback inhibitor of PhoQ in different bacteria and its up-regulation results in decreased PhoP phosphorylation , i.e. negative feedback .24 Interestingly , we discovered a synchronous up - or down-regulation of mgrB-lacZ and phoPQ-lacZ in the acrB - or/and cpxR-deleted strains , which was quite different from the expected negative feedback loop between MgrB and PhoPQ .	9	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	ssaN	regulator	32954419	3	ver/dev	tr , opvAB , and ssaN , is consistent with genetic evidence indicating regulation by OxyR	234	( ii ) Putative OxyR binding sites were found in gtr , opvAB , and ssaN , which is consistent with genetic evidence indicating regulation by OxyR ( Figure 3 ) .	16	IDENTIFICATION OF REGULATORS INVOLVED IN TRANSCRIPTIONAL CONTROL	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilC	gene	invF	regulator	12535071	16	ver/dev	We show that HilC can directly bind invF .	63	We show that HilD and HilC can directly bind and activate invF , which leads to the non-co-ordinate expression of a subset of SPI1 genes .	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilC	gene	invF	regulator	12535071	28	ver/dev	In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	regulator	12535071	28	ver/dev	In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilC , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	regulator	12535071	28	ver/dev	In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilD , respectively , under the control of the arabinose-inducible PBAD promoter .	93	In order to study the activation of invF by HilD and HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain transformed with pSA4 , pLS119 or pCH112 , which express HilD , HilC and HilA , respectively , under the control of the arabinose-inducible PBAD promoter .	5	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HilC	gene	invF	regulator	12535071	73	ver/dev	These results suggest that HilC might directly activate invF expression by binding to sequences upstream of invF .	188	These results suggest that HilD and HilC might directly activate invF expression by binding to sequences upstream of invF .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilC	gene	invF	regulator	12535071	76	ver/dev	HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilC	gene	invF	regulator	12535071	76	ver/dev	HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	195	HilD and HilC bind to the invF promoter fragment in vitro To examine whether HilD and HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .	7	A HILD- AND HILC-DEPENDENT INVF TRANSCRIPTION START SITE LIES FAR UPSTREAM OF THE HILA-DEPENDENT TRANSCRIPTION START SITE	nan	1	L1	SPEC	Investigation	OTHER	New	Level 1
HilC	gene	invF	regulator	12535071	87	ver/dev	In addition to binding upstream of invF , HilC also bind to sites upstream of hilC .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	regulator	12535071	87	ver/dev	In addition to binding upstream of invF , HilC also bind within S. Akbar , unpublished results .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	regulator	12535071	87	ver/dev	In addition to binding upstream of invF , HilC also bind within the prgH-hilD intergenic region .	249	In addition to binding upstream of hilA and invF , HilD and HilC also bind to sites upstream of hilC and within the prgH-hilD intergenic region ( Olekhnovich and Kadner , 2002 ) ( S. Akbar , unpublished results ) .	9	HILD AND HILC DIRECTLY ACTIVATE INVF EXPRESSION BY BINDING UPSTREAM AND DOWNSTREAM OF A HILD/C-DEPENDENT PROMOTER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	invF	regulator	20008574	6	ver/dev	Dam-dependent regulation of invF was still observed in HilC	152	In an analogous fashion , Dam-dependent regulation of invF was still observed in HilA , HilC , and RtsA backgrounds , and no information was obtained in a HilD background ( Figure 3 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilC	gene	invF	regulator	22479568	2	ver/dev	In addition , invF has been shown to be directly regulated by HilC through a HilA-independent pathway .	33	In addition , invF has been shown to be directly regulated by HilD and HilC through a HilA-independent pathway [ 18 ] .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilA	repressor	28335027	10	ver/dev	H-NS repression of hilA counteracts transcriptional activation by RtsA	767	In the case of hilD , post-translational repression by HilE dampens hilD activation , and H-NS repression of hilA counteracts transcriptional activation by HilD , HilC and RtsA ( 66 ) .	23	REGULATORY CROSS-TALK BETWEEN HORIZONTALLY ACQUIRED GENES AND THE S. TYPHIMURIUM CORE GENOME	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	repressor	31182495	46	ver/dev	H-NS represses hilA expression through repression of HilD/HilC / RtsA .	212	H-NS represses hilA expression directly and through repression of HilD/HilC / RtsA .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	repressor	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of rtsA .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilA	repressor	31262841	7	ver/dev	When we tested the overexpression of = lacZ in an rtsA null background , PinT caused only a 2-fold repression of Fig. 4A , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	repressor	31262841	7	ver/dev	When we tested the overexpression of = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	repressor	31262841	7	ver/dev	When we tested the overexpression of PinT on hilA = , PinT caused only a 2-fold repression of Fig. 4A , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	repressor	31262841	7	ver/dev	When we tested the overexpression of PinT on hilA = , PinT caused only a 2-fold repression of hilA expression , consistent with the contribution of RtsA in activation of hilA transcription .	121	When we tested the overexpression of PinT on hilA = - = lacZ in an rtsA null background , PinT caused only a 2-fold repression of hilA expression ( Fig. 4A ) , consistent with the contribution of RtsA in activation of hilA transcription ( 15 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilA	repressor	33593291	12	ver/dev	Nonetheless , we tested whether RtsA are necessary for repression of hilA expression by yeast extract in a ΔhilE mutant .	103	Nonetheless , we tested whether HilC or RtsA are necessary for repression of hilA expression by acetate and yeast extract in a ΔhilE mutant .	6	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RtsA	gene	hilA	repressor	33593291	12	ver/dev	Nonetheless , we tested whether RtsA are necessary for repression of hilA expression by acetate extract in a ΔhilE mutant .	103	Nonetheless , we tested whether HilC or RtsA are necessary for repression of hilA expression by acetate and yeast extract in a ΔhilE mutant .	6	RESULTS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CysB	gene	cysJIH	regulator	2105304	2	ver/dev	L-Cysteine did not affect in-vitro-transcription initiation or binding of CysB protein to the cysJIH promoter region .	14	L-Cysteine did not affect in vitro transcription initiation or binding of CysB protein to the cysJIH promoter region .	0	Unknown	nan	1	L3	OTHER	Other	NEG	New	Level 1
CysB	gene	cysJIH	regulator	2105304	7	ver/dev	CysB protein at concentrations as high as 25 jig/ml did bind a small contaminant of cysJIH promoter fragment .	144	CysB protein at concentrations as high as 25 jig/ml did not form detectable complexes with the control DNA fragment but did bind a small contaminant of cysJIH promoter fragment that was present in this preparation ( Fig. 2 , lanes 14 to 20 ) .	6	GLUTATHIONE NONE 0.36 4.8	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	2105304	10	ver/dev	The gel mobility-shift assay was used to study in-vitro effects of L-cysteine on the binding of CysB protein to cysJIH promoter DNA .	158	The gel mobility shift assay was used to study in vitro effects of sulfide and L-cysteine on the binding of CysB protein to cysJIH promoter DNA .	6	GLUTATHIONE NONE 0.36 4.8	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	2105304	10	ver/dev	The gel mobility-shift assay was used to study in-vitro effects of sulfide on the binding of CysB protein to cysJIH promoter DNA .	158	The gel mobility shift assay was used to study in vitro effects of sulfide and L-cysteine on the binding of CysB protein to cysJIH promoter DNA .	6	GLUTATHIONE NONE 0.36 4.8	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	2105304	20	ver/dev	that CysB protein binds to the cysJIH promoter region in-vitro	221	The studies reported here demonstrate that CysB protein binds to the cysJIH promoter region in vitro and that such binding is stimulated by the inducers N-acetyl-L-serine and O-acetyl-L-serine .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	2105304	25	ver/dev	The ability of sulfide to inhibit binding of CysB protein to the cysJIH promoter is competitive with N-acetyl-L-serine .	312	The ability of sulfide to inhibit binding of CysB protein to the cysJIH promoter parallels its effects on transcription initiation and is competitive with N-acetyl-L-serine .	7	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CysB	gene	cysJIH	regulator	2105304	25	ver/dev	The ability of sulfide to inhibit binding of CysB protein to the cysJIH promoter parallels its effects on transcription initiation .	312	The ability of sulfide to inhibit binding of CysB protein to the cysJIH promoter parallels its effects on transcription initiation and is competitive with N-acetyl-L-serine .	7	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	22804842	33	ver/dev	Hryniewicz , M.M. , and Kredich , N.M. Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	672	Hryniewicz , M.M. , and Kredich , N.M. ( 1994 ) Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	30	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	24659766	26	ver/dev	Stoichiometry of binding of CysB to the cysJIH .	559	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	44	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	25637663	1	ver/dev	CysB , in turn , is a positive regulator of cysJIH .	10	CysB , in turn , is a positive regulator of cysJIH .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	25637663	5	ver/dev	Taken together , our results suggests that CysB regulates expression of cysJIH operon to produce H2S as a cellular protector during oxidative-stress in S. Typhimurium .	44	Taken together , our results suggests that CysB regulates expression of cysJIH operon to produce H2S , which could acts as a cellular protector during oxidative stress in S. Typhimurium .	6	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	8	ver/dev	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .	112	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ , cysI and cysH genes in wild type and DcysB strains in sulfate medium .	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	8	ver/dev	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .	112	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ , cysI and cysH genes in wild type and DcysB strains in sulfate medium .	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	8	ver/dev	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .	112	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ , cysI and cysH genes in wild type and DcysB strains in sulfate medium .	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	8	ver/dev	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .	112	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ , cysI and cysH genes in wild type and DcysB strains in sulfate medium .	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	8	ver/dev	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .	112	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ , cysI and cysH genes in wild type and DcysB strains in sulfate medium .	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	8	ver/dev	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .	112	In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ , cysI and cysH genes in wild type and DcysB strains in sulfate medium .	18	3.3. CYSJIH EXPRESSION IS UPREGULATED BY CYSB IN RESPONSE TO CEFTRIAXONE OR MENADIONE	nan	1	L1	SPEC	Other	OTHER	New	Level 1
CysB	gene	cysJIH	regulator	25637663	13	ver/dev	olecular characterization of the cysJIH promoters of Salmonella typhimurium : regulation by CysB protein and N-acetyl-L-serine , J. Bacteriol .	220	[ 13 ] J. Ostrowski , N.M. Kredich , Molecular characterization of the cysJIH promoters of Salmonella typhimurium and Escherichia coli : regulation by CysB protein and N-acetyl-L-serine , J. Bacteriol .	24	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	25637663	15	ver/dev	M.M. Hryniewicz , N.M. Kredich , Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium , J. Bacteriol .	224	[ 15 ] M.M. Hryniewicz , N.M. Kredich , Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium , J. Bacteriol .	24	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	27530757	4	ver/dev	Stoichiometry of binding of CysB to the cysJIH .	315	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	18	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	30538683	1	ver/dev	Transcription of cysJIH is upregulated upon binding of CysB .	65	Transcription of cysJIH and cysK is upregulated upon binding of CysB and acetyl-serine .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	30538683	3	ver/dev	Transcription of cysJIH is upregulated upon binding of CysB .	91	Transcription of cysJIH and cysK is upregulated upon binding of CysB and acetyl-serine .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	30538683	7	ver/dev	We found that DAS altered the binding of CysB to cysJIH , although the effects were small .	361	We found that DAS altered the binding of CysB to cysJIH , although the effects were small and therefore determined to be non-significant ( data not shown ) .	22	DAS DOES NOT CHANGE CYSB BINDING PATTERNS IN VITRO	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	30538683	7	ver/dev	We found that DAS altered the binding of CysB to cysJIH , although the effects were therefore determined to be data not shown .	361	We found that DAS altered the binding of CysB to cysJIH , although the effects were small and therefore determined to be non-significant ( data not shown ) .	22	DAS DOES NOT CHANGE CYSB BINDING PATTERNS IN VITRO	unidentified	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CysB	gene	cysJIH	regulator	30538683	7	ver/dev	We found that DAS altered the binding of CysB to cysJIH , although the effects were therefore determined to be non-significant .	361	We found that DAS altered the binding of CysB to cysJIH , although the effects were small and therefore determined to be non-significant ( data not shown ) .	22	DAS DOES NOT CHANGE CYSB BINDING PATTERNS IN VITRO	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
CysB	gene	cysJIH	regulator	30538683	11	ver/dev	Stoichiometry of binding of CysB to the cysJIH .	444	Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .	26	FUNDING	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	30538683	13	ver/dev	Molecular characterization of the cysJIH promoters of Escherichia coli : regulation by CysB protein and N-acetyl-L-serine .	505	Molecular characterization of the cysJIH promoters of Salmonella typhimurium and Escherichia coli : regulation by CysB protein and N-acetyl-L-serine .	26	FUNDING	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	regulator	30538683	13	ver/dev	Molecular characterization of the cysJIH promoters of Salmonella typhimurium : regulation by CysB protein and N-acetyl-L-serine .	505	Molecular characterization of the cysJIH promoters of Salmonella typhimurium and Escherichia coli : regulation by CysB protein and N-acetyl-L-serine .	26	FUNDING	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	hns	activator	17630976	6	ver/dev	We used qRT-PCR to demonstrate that SsrB has a modest effect in activating transcription in an hns background .	83	We used quantitative reverse transcription polymerase chain reaction ( qRT-PCR ) to demonstrate that SsrB has a modest effect in activating transcription in an hns background .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hns	activator	17630976	6	ver/dev	We used quantitative reverse transcription polymerase chain reaction to demonstrate that SsrB has a modest effect in activating transcription in an hns background .	83	We used quantitative reverse transcription polymerase chain reaction ( qRT-PCR ) to demonstrate that SsrB has a modest effect in activating transcription in an hns background .	3	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	hns	activator	17630976	41	ver/dev	The lower transcript levels in an hns/ssrB double mutant compared with an hns single mutant may reflect either direct activation by SsrB to H-NS .	336	The lower transcript levels in an hns/ssrB double mutant compared with an hns single mutant may reflect either direct activation by SsrB or the SsrB-mediated antagonism of silencers in addition to H-NS .	11	SSRB-DEPENDENT PROMOTERS ARE DIVERSE AND LACK A WELL-DEFINED CONSENSUS BINDING SITE	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
CsrA	gene	hilE	repressor	34048498	1	ver/dev	CsrA directly represses the expression of hilE	115	CsrA directly represses the expression of hilE	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	hilE	repressor	34048498	2	ver/dev	In a current project to analyze the global effect of CsrA on Salmonella we obtained circumstantial evidence that CsrA could negatively regulate the expression of hilE .	116	In a current project to analyze the global effect of CsrA on Salmonella we obtained circumstantial evidence that CsrA could negatively regulate the expression of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	Salmonella	1	L1	OTHER	Analysis	OTHER	New	Level 1
CsrA	gene	hilE	repressor	34048498	4	ver/dev	These results indicate that CsrA negatively controls the expression of hilE .	121	These results indicate that CsrA negatively controls the expression of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsrA	gene	hilE	repressor	34048498	11	ver/dev	Together , our results indicate that CsrA directly represses the expression of hilE .	131	Together , our results indicate that CsrA directly represses the expression of hilE .	7	CSRA DIRECTLY REPRESSES THE EXPRESSION OF HILE	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsrA	gene	hilE	repressor	34048498	14	ver/dev	CsrA represses expression of hilE .	142	CsrA represses expression of hilE .	8	SIRA/BARA INDUCES THE EXPRESSION OF HILE THROUGH CSRB/C	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	narG	activator	29857034	19	ver/dev	-RRB- , narG -LRB- are positively regulated by SlyA	319	Thus , our results suggest a different target for the NarX/NarL TCS including narJ ( STM14_2130 ) , narH ( STM14_2131 ) , narG ( STM14_2132 ) , and narK ( STM14_2134 ) , which are positively regulated by SlyA .	25	3.4. INFLUENCE OF SLYA IN BACTERIAL PHYSIOLOGY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	invA	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxS	gene	tolC	regulator	11036033	1	ver/dev	Like marRAB , tolC are positively regulated by SoxS .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hemX	regulator	27564394	18	ver/dev	the hemX gene were used as negative control regions , respectively , as H-NS does not bind to the hemX gene .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hemX	regulator	27564394	18	ver/dev	the hemX gene were used as positive control regions , respectively , as H-NS does not bind to the hemX gene .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hemX	regulator	27564394	18	ver/dev	The proV promoter were used as negative control regions , respectively , as H-NS does not bind to the hemX gene .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hemX	regulator	27564394	18	ver/dev	The proV promoter were used as positive control regions , respectively , as H-NS does not bind to the hemX gene .	535	The proV promoter and the hemX gene were used as positive and negative control regions , respectively , as H-NS binds to the proV promoter and does not bind to the hemX gene [ 71 ] .	9	TRANSCRIPTIONAL REGULATION OF THE STNC1480 SRNA	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CRP	gene	pepT	regulator	18559530	3	ver/dev	5 The Salmonella endogenous promoter for pepT is regulated by CRP .	187	5 The Salmonella endogenous promoter for pepT is regulated by CRP and Fnr ( 14 ) .	6	RESULTS AND DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	ssrA	regulator	29930310	9	ver/dev	These findings indicate that DksA does not appear to regulate ssrA gene transcription .	83	These findings indicate that DksA does not appear to regulate ssrA or ssrB gene transcription .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
PhoP	gene	yobG	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SirA	gene	crp	regulator	16949866	24	ver/dev	SirA does not regulate crp	392	SirA does not regulate crp or cya	17	SIRA DOES NOT REGULATE CRP OR CYA	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsgD	gene	bscA	regulator	16707690	23	ver/dev	CsgD controls the expression of bscA .	402	CsgD depends on RpoS and Crl and controls the expression of csgBAC and adrA but not the expression of bscA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CspA	gene	hns	activator	16940079	0	ver/dev	CspA is involved in the cold-shock response by stimulating the transcription of the cold-shock-inducible promoters of hns .	410	CspA is involved in the cold shock response by binding to and stimulating the transcription of the cold shock-inducible promoters of hns and gyrA .	6	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	acnA	regulator	23637460	0	ver/dev	that acnA expression was regulated by FNR , oxygen starvation .	17	that acnA expression was regulated by the cyclic-AMP receptor protein ( CRP , glucose starvation ) , the fumarate nitrate reduction regulator ( FNR , oxygen starvation ) , the ferric uptake regulator ( Fur , iron starvation ) and the superoxide response protein ( SoxR , oxidative stress ) .	0	Unknown	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	fhuA	repressor	18790861	19	att	Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB-medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .	155	Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	srfN	repressor	28674150	29	ver/dev	It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB may come into play .	325	It is interesting to speculate that srfN is initially repressed by H-NS in vitro , whereas during infection of host cells YdcR ( and SsrB ) may come into play and activate the expression of srfN .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	leuO	activator	21398529	8	ver/dev	However , LeuO could increase transcriptional activity in N-minimal-medium , as overexpression of the leuO gene resulted in a 2-fold induction of casA transcription compared to an absence of overexpression in the wild-type Sal-monella strain -LRB- data not shown -RRB- .	301	However , LeuO could increase transcriptional activity in N-minimal medium , as overexpression of the leuO gene resulted in a 2-fold induction of casA transcription compared to an absence of overexpression in the wild-type Sal-monella strain ( data not shown ) .	4	RESULTS	Salmonella;Salmonella;unidentified	1	L1	OTHER	Analysis	OTHER	New	Level 1
LeuO	gene	leuO	activator	21398529	8	ver/dev	However , LeuO could increase transcriptional activity in N-minimal-medium , as overexpression of the leuO gene resulted in a 2-fold induction of casA transcription compared to an absence of overexpression in the wild-type Sal-monella strain -LRB- data not shown -RRB- .	301	However , LeuO could increase transcriptional activity in N-minimal medium , as overexpression of the leuO gene resulted in a 2-fold induction of casA transcription compared to an absence of overexpression in the wild-type Sal-monella strain ( data not shown ) .	4	RESULTS	Salmonella;Salmonella;unidentified	1	L1	OTHER	Analysis	OTHER	New	Level 1
LeuO	gene	leuO	activator	22343301	1	att	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal-medium which is used for induction of Salmonella SPI-2 ( 16 ) .	27	A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich medium , whereas transcriptional start sites were determined for assT and the dsbL-dsbI transcriptional units in the absence of cloned leuO and in a leuO background , in N-minimal medium which is used for induction of Salmonella SPI-2 ( 16 ) .	2	MAIN	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	leuO	activator	24354910	46	att	To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .	190	To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .	12	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
LeuO	gene	leuO	activator	24354910	7	ver/dev	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the absence of LeuO .	53	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO ( Dillon et al. , 2012 ) , we compared the expression of selected SPI-1 genes in the presence and in the absence of LeuO .	9	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	leuO	activator	24354910	7	ver/dev	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the presence .	53	Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO ( Dillon et al. , 2012 ) , we compared the expression of selected SPI-1 genes in the presence and in the absence of LeuO .	9	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LeuO	gene	leuO	activator	24354910	14	ver/dev	Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of OFF subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -	79	Single cell analysis of gene expression by flow cytometry ( Fig. 2 ) confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : ( i ) activation of leuO expression decreased the activity of a sipB : : GFP fusion , abolishing bistable SPI-1 expression ; ( ii ) lack of LeuO restored the wild type pattern of sipB : : GFP expression , indicating that SPI-1 downregulation was caused by LeuO indeed ; ( iii ) a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 ( OFF ) subpopulation , in agreement with the role of HilE as a SPI-1 repressor ( Baxter et al. , 2003 ) ; ( iv ) activation of leuO expression in a HilE − background yielded a small subpopulation of sipB - : : GFP ( OFF ) cells ; and ( v ) absence of both LeuO and HilE restored the wild type pattern of sipB : : GFP expression .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	leuO	activator	24354910	14	ver/dev	Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -	79	Single cell analysis of gene expression by flow cytometry ( Fig. 2 ) confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : ( i ) activation of leuO expression decreased the activity of a sipB : : GFP fusion , abolishing bistable SPI-1 expression ; ( ii ) lack of LeuO restored the wild type pattern of sipB : : GFP expression , indicating that SPI-1 downregulation was caused by LeuO indeed ; ( iii ) a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 ( OFF ) subpopulation , in agreement with the role of HilE as a SPI-1 repressor ( Baxter et al. , 2003 ) ; ( iv ) activation of leuO expression in a HilE − background yielded a small subpopulation of sipB - : : GFP ( OFF ) cells ; and ( v ) absence of both LeuO and HilE restored the wild type pattern of sipB : : GFP expression .	9	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
LeuO	gene	leuO	activator	24354910	39	ver/dev	In the absence of HilE , activation of leuO transcription reduced Fig. 7B , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	147	In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three - to fourfold ( Fig. 7B ) , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	11	ACTIVATION OF LEUO TRANSCRIPTION INHIBITS EPITHELIAL CELL INVASION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
LeuO	gene	leuO	activator	24354910	39	ver/dev	In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three - to fourfold , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	147	In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three - to fourfold ( Fig. 7B ) , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .	11	ACTIVATION OF LEUO TRANSCRIPTION INHIBITS EPITHELIAL CELL INVASION	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
CRP	gene	ompF	activator	28874380	0	ver/dev	These data suggest that CRP activates ompF expression in exponential-growth .	108	These data suggest that CRP activates ompF expression in exponential growth and activates ompF and ompA expression during stationary phase but does not directly regulate ompC under these conditions .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	ompF	activator	28874380	0	ver/dev	These data suggest that CRP activates ompF expression during stationary-phase .	108	These data suggest that CRP activates ompF expression in exponential growth and activates ompF and ompA expression during stationary phase but does not directly regulate ompC under these conditions .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
AraC	gene	araJ	regulator	24272778	36	att	With the exception of xylA , the last AraC-regulated gene to be identified was araJ , more than 30 years ago ( 27 ) .	375	With the exception of xylA , the last AraC-regulated gene to be identified was araJ , more than 30 years ago ( 27 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
DksA	gene	icdA	activator	20851888	5	att	Genes encoding glucose-6-phosphate dehydrogenase ( zwf ) , isocitrate dehydrogenase ( icdA ) , and malic enzyme ( maeB ) responsible for the generation of NADPH , and the sucAB-encoded subunits of - oxaloacetate dehydrogenase associated with generation of NADH all showed DksA-dependent regulation ( Fig. 3A , bold red font ) .	178	Genes encoding glucose-6-phosphate dehydrogenase ( zwf ) , isocitrate dehydrogenase ( icdA ) , and malic enzyme ( maeB ) responsible for the generation of NADPH , and the sucAB-encoded subunits of - oxaloacetate dehydrogenase associated with generation of NADH all showed DksA-dependent regulation ( Fig. 3A , bold red font ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CpxR	gene	scsC	activator	29866803	9	att	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper-stress .	211	Our results indicate that , like scsA transcription , transcription of scsB , scsC , and scsD is driven by the CpxR-dependent scsA promoter , at least during copper stress .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	tum	activator	12399494	17	att	LexA-dependent control of a Fels-2 tum : : lac fusiona	469	LexA-dependent control of a Fels-2 tum : : lac fusiona	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	yciG	regulator	25375226	36	ver/dev	four H-NS _ regulated yciG	436	Transcript levels of four H-NS regulated genes , proV , ssrA , yciG and hilA , were measured by reverse transcriptase QPCR in a Dhns/DstpA strain expressing StpAWT or the variants StpAM4T , StpAA77D and StpAF21C .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RstA	gene	csgD	regulator	25437188	21	ver/dev	As the RstA binding site is identical apart from a single nucleotide , the RstA ortholog STM1475 might directly control csgD transcription in S. Typhimurium .	212	As the RstA binding site is identical apart from a single nucleotide ( Figure 3 ) , the RstA ortholog STM1475 might directly control csgD transcription in S. Typhimurium .	8	REGULATION OF CSGD TRANSCRIPTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	ssrB	repressor	16301528	7	ver/dev	Inactivation of ssrB in the ydgT background resulted in complete loss of virulence during systemic infection , consistent with the finding that deletion of ydgT does not override the requirement of SsrB for transcriptional activation of the SPI-2 pathogenicity island .	92	Inactivation of ssrB in the ydgT background resulted in complete loss of virulence during systemic infection , consistent with the finding that deletion of ydgT does not override the requirement of SsrB for transcriptional activation of the SPI-2 pathogenicity island .	5	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SsrB	gene	ssrB	repressor	24643535	9	ver/dev	Taken together , these lines of evidence suggest that the Fur repressor could interfere with binding of the SsrB activator to the ssrB promoter , leading to repression of ssrB transcription .	213	Taken together , these lines of evidence suggest that the Fur repressor could interfere with binding of the SsrB activator to the ssrB promoter , leading to repression of ssrB transcription .	6	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	yjfP	activator	30760616	7	ver/dev	In addition , the esterase yjfP were also positively regulated by CpxR in egg white .	292	In addition , the major facilitator superfamily member tsgA , the esterase yjfP , and a putative membrane-bound redox modulator alx were also positively regulated by CpxR in egg white ( 78 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ydgT	regulator	16301528	4	ver/dev	To test whether the loss of ydgT could overcome the requirement for positive regulation of SPI-2 , we introduced the ydgT deletion into an ssrB mutant lacking the response regulator of the SsrA SsrB two-component regulatory system .	86	To test whether the loss of ydgT could overcome the requirement for positive regulation of SPI-2 , we introduced the ydgT deletion into an ssrB mutant lacking the response regulator of the SsrA SsrB two-component regulatory system .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
SsrB	gene	ydgT	regulator	16301528	4	ver/dev	To test whether the loss of ydgT could overcome the requirement for positive regulation of SPI-2 , we introduced the ydgT deletion into an ssrB mutant lacking the response regulator of the SsrA SsrB two-component regulatory system .	86	To test whether the loss of ydgT could overcome the requirement for positive regulation of SPI-2 , we introduced the ydgT deletion into an ssrB mutant lacking the response regulator of the SsrA SsrB two-component regulatory system .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
UvrY	gene	csrA	regulator	15765064	22	ver/dev	It appears that csrA is necessary to regulate the activity of UvrY .	125	It appears that csrA is necessary to regulate the activity of UvrY , which in turn activates the expression of csrB ( Suzuki et al. , 2002 ) .	6	OTHER INVASION GENE ACTIVATORS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	sipC	regulator	24018968	6	att	The Hfq-dependent stationary-phase expression of SPI1 genes was also clearly observed in an InvF-regulated gene , sipC : a sipC : : lacZ chromosomal fusion expressed 3,761 ± 292 and 1,120 ± 12 Miller units of β-galactosidase at 4 and 12 h p.i. , respectively , in wild-type cells , whereas the sipC : : lacZ fusion in ∆ hfq cells expressed 1,486 ± 192 and 830 ± 67 Miller units of β-galactosidase at the same time points ( data	177	The Hfq-dependent stationary-phase expression of SPI1 genes was also clearly observed in an InvF-regulated gene , sipC : a sipC : : lacZ chromosomal fusion expressed 3,761 ± 292 and 1,120 ± 12 Miller units of β-galactosidase at 4 and 12 h p.i. , respectively , in wild-type cells , whereas the sipC : : lacZ fusion in ∆ hfq cells expressed 1,486 ± 192 and 830 ± 67 Miller units of β-galactosidase at the same time points ( data	14	STATIONARY PHASE UNDER SHAKING CULTURE CONDITIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	hilC	activator	15765064	17	ver/dev	Overexpression of hilC can overcome the requirement for HilA activation of the inv operon	105	Overexpression of hilC ( sirC/sprA ) can overcome the requirement for HilA activation of the inv operon , and subsequent transcription of genes encoding secreted effector proteins ( Eichelberg and Galán , 1999 ; Rakeman et al. , 1999 ) .	5	TRANSCRIPTIONAL ACTIVATORS OF HILA	nan	1	L2	OTHER	Other	OTHER	New	Level 1
Fur	gene	ryhB	regulator	17208038	23	ver/dev	Another ` Fur-activated ' gene , is controlled at the level of translation by the small RNA ryhB , with the help of the RNA binding protein Hfq , in Escherichia coli .	131	Another ` Fur-activated ' gene , sodB , is controlled at the level of translation by the small RNA ryhB , with the help of the RNA binding protein Hfq , in Escherichia coli [ 45 -- 48 ] .	9	FUR	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	ryhB	regulator	18554972	0	att	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	215	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	15	3.1. TRANSPOSON MUTAGENESIS IDENTIFIES IRON RESPONSE GENES INVOLVED IN NOREPINEPHRINE-ENHANCED GROWTH OF SALMONELLA TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SoxS	gene	mntH	activator	10844693	3	ver/dev	The failure of mntH : : lacZ-fusions to be induced by paraquat is consistent with the absence of a SoxS promoter element .	303	The failure of mntH : : lacZ fusions to be induced by paraquat is consistent with the absence of a SoxS promoter element .	18	MNTH REGULATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	spvR	repressor	29763647	0	ver/dev	twenty six compounds were re-tested for inhibition of expression of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .	66	One hundred and twenty six compounds that inhibited light production by > 3 standard deviations above the mean ( cutoff > 64 % inhibition ) were re-tested for inhibition of growth and expression of the RpoS-dependent spvR gene ( Kowarz et al. , 1994 ) in Samonella strain SL1344 ( data not shown ) .	0	Unknown	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	spvR	repressor	29763647	0	ver/dev	twenty six compounds were re-tested for inhibition of growth of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .	66	One hundred and twenty six compounds that inhibited light production by > 3 standard deviations above the mean ( cutoff > 64 % inhibition ) were re-tested for inhibition of growth and expression of the RpoS-dependent spvR gene ( Kowarz et al. , 1994 ) in Samonella strain SL1344 ( data not shown ) .	0	Unknown	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	spvR	repressor	29763647	0	ver/dev	One hundred were re-tested for inhibition of expression of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .	66	One hundred and twenty six compounds that inhibited light production by > 3 standard deviations above the mean ( cutoff > 64 % inhibition ) were re-tested for inhibition of growth and expression of the RpoS-dependent spvR gene ( Kowarz et al. , 1994 ) in Samonella strain SL1344 ( data not shown ) .	0	Unknown	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
RpoS	gene	spvR	repressor	29763647	0	ver/dev	One hundred were re-tested for inhibition of growth of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .	66	One hundred and twenty six compounds that inhibited light production by > 3 standard deviations above the mean ( cutoff > 64 % inhibition ) were re-tested for inhibition of growth and expression of the RpoS-dependent spvR gene ( Kowarz et al. , 1994 ) in Samonella strain SL1344 ( data not shown ) .	0	Unknown	Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified	0.5	L3	OTHER	Analysis	NEG	Other	Level 1
NsrR	gene	STM1808	regulator	23651595	18	att	These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .	625	These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
NsrR	gene	STM1808	regulator	23651595	19	ver/dev	STM1808 is regulated by NsrR , whilst STM1808 mutants have a growth impairment upon exposure to NO .	626	STM1808 is regulated by NsrR , whilst STM1808 mutants have a growth impairment upon exposure to NO .	32	3.3.2. NO PROTECTION AND DETOXIFICATION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NsrR	gene	STM1808	regulator	33024855	11	att	A role in virulence has been identified for the NsrR-regulated STM1808 and ytfE ( Karlinsey et al. , 2012 ) .	452	A role in virulence has been identified for the NsrR-regulated STM1808 and ytfE ( Karlinsey et al. , 2012 ) .	12	3.3. NITROSATIVE AND OXIDATIVE STRESS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
FlhDC	gene	fliE	activator	34450657	1	ver/dev	In E. coli , the fliE promoter is directly activated by FlhDC .	399	In Salmonella and E. coli , the fliE promoter is directly activated by FlhDC , the master transcriptional regulator of the flagellar network ( Figure 1B ) ( 51 -- 54 ) .	26	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
FlhDC	gene	fliE	activator	34450657	1	ver/dev	In Salmonella , the fliE promoter is directly activated by FlhDC .	399	In Salmonella and E. coli , the fliE promoter is directly activated by FlhDC , the master transcriptional regulator of the flagellar network ( Figure 1B ) ( 51 -- 54 ) .	26	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilA	gene	barA	regulator	10672185	3	ver/dev	If regulation by barA was mediated exclusively by modulating the level of HilA , null mutations in barAB would be without effect in these two settings because , in the ® rst case , HilA is absent and , in the second case , it is maintained at a constant level .	140	If regulation by barA and csr was mediated exclusively by modulating the level of HilA , null mutations in barA and csrB would be without effect in these two settings because , in the ® rst case , HilA is absent and , in the second case , it is maintained at a constant level .	8	INTEGRATION OF MULTIPLE INVASION REGULATORS	nan	1	L1	SPEC	Other	NEG	Other	Level 1
CsrA	gene	artI	regulator	30682134	53	ver/dev	Similarly , CLIP-seq identified a CsrA binding site on on the artI gene , encoding a component of an arginine transporter , although their regulation by CsrA was not observed under the conditions .	432	Similarly , CLIP-seq identified a CsrA binding site on the nagA gene encoding N-acetylglucosamine-6-phosphate deacetylase , and on the artI gene , encoding a component of an arginine transporter , although their regulation by CsrA was not observed under the conditions used here .	15	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
Fur	gene	feoB	repressor	18790861	45	att	Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .	238	Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	feoB	repressor	18790861	45	ver/dev	Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .	238	Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	feoB	repressor	18790861	55	ver/dev	the RstA-dependent activation of feoAB transcription increased Fe uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	feoB	repressor	18790861	55	ver/dev	Third increased Fe uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells .	272	Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SprB	gene	sptP	regulator	21168230	2	ver/dev	SprB , regulates the expression of sptP .	212	SprB , a transcriptional regulator , is encoded within the SPI1 and regulates the expression of sipC , sptP , avrA , sopB and sopE ( Eichelberg et al. , 1999 ) .	18	3.3. SPI1 ENCODED GENES DOWN-REGULATED BY NARINGENIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhDC	gene	repA	regulator	27727307	0	ver/dev	activators suggested that repA is not controlled by FlhDC SGI1	181	The promoter activity in pMSZ956 was around the detection limit ( 2.3 ± 0.7 units ) independently of the presence of activators , which suggested that S003 ( repA ) is not controlled by AcaCD or FlhDC SGI1 and expressed from a weak promoter probably located in S004 .	12	INDUCTION OF THE PREDICTED ACACD-DEPENDENT SGI1 PROMOTERS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	rpoD	activator	18350168	2	att	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	294	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilA	gene	spaS	activator	10692170	12	att	HilA-activated expression also results in readthrough transcription of sicAsipBCDA from a promoter upstream of spaS ( Darwin and Miller , 1999b ) .	285	HilA-activated expression also results in readthrough transcription of sicAsipBCDA from a promoter upstream of spaS ( Darwin and Miller , 1999b ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilA	gene	spaS	activator	10844688	10	att	For example , sipC has two promoters : a HilA-dependent promoter upstream of spaS and an InvF-dependent promoter downstream of spaS ( Darwin and Miller , 1999b ) .	275	For example , sipC has two promoters : a HilA-dependent promoter upstream of spaS and an InvF-dependent promoter downstream of spaS ( Darwin and Miller , 1999b ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	pagC	repressor	19091955	12	ver/dev	H-NS controls transcriptional repression of pagC , by acting on the up-52 fragment	72	Thus , SlyA should antagonize H-NS , which controls transcriptional repression of pagC ( 3 , 13 , 14 ) , by acting on the up-52 fragment .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	pagC	repressor	25375226	10	ver/dev	Multiple studies have shown that expression of pagC is strongly repressed by H-NS	102	Multiple studies have shown that expression of pagC is strongly repressed by H-NS , and the spontaneous loss of these genes from the Dhns isolate suggested that hns mutants are genetically unstable and may shed horizontally acquired sequences during passage [ 21,22,60 ] .	6	PASSAGING OF S. TYPHIMURIUM HNS MUTANTS FOR 30 DAYS LEADS TO STRAINS WITH IMPROVED FITNESS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	osmY	repressor	30682134	27	ver/dev	CsrA also repressed translation of osmY 5.1-and 2.3-fold in LB , respectively , which gives E. coli enhanced resistance to osmotic-stress in S2 Table .	254	CsrA also repressed translation of osmY 5.1-and 2.3-fold in mLPM and LB , respectively , which gives E. coli enhanced resistance to osmotic stress in rich media [ 93 ] ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	osmY	repressor	30682134	27	ver/dev	CsrA also repressed translation of osmY 5.1-and 2.3-fold in LB , respectively , which gives E. coli enhanced resistance to osmotic-stress in rich media .	254	CsrA also repressed translation of osmY 5.1-and 2.3-fold in mLPM and LB , respectively , which gives E. coli enhanced resistance to osmotic stress in rich media [ 93 ] ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	osmY	repressor	30682134	27	ver/dev	CsrA also repressed translation of osmY 5.1-and 2.3-fold in mLPM , respectively , which gives E. coli enhanced resistance to osmotic-stress in S2 Table .	254	CsrA also repressed translation of osmY 5.1-and 2.3-fold in mLPM and LB , respectively , which gives E. coli enhanced resistance to osmotic stress in rich media [ 93 ] ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CsrA	gene	osmY	repressor	30682134	27	ver/dev	CsrA also repressed translation of osmY 5.1-and 2.3-fold in mLPM , respectively , which gives E. coli enhanced resistance to osmotic-stress in rich media .	254	CsrA also repressed translation of osmY 5.1-and 2.3-fold in mLPM and LB , respectively , which gives E. coli enhanced resistance to osmotic stress in rich media [ 93 ] ( S2 Table ) .	13	CSRA REPRESSES GENES REQUIRED FOR RESISTANCE TO STRESSES ENCOUNTERED DURING INFECTION	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	proP	activator	11123690	31	ver/dev	Johnson , R.C. Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .	378	Xu , J. , and Johnson , R.C. ( 1995 ) Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	proP	activator	11123690	31	ver/dev	J. , R.C. Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .	378	Xu , J. , and Johnson , R.C. ( 1995 ) Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	proP	activator	11123690	31	ver/dev	Xu , R.C. Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .	378	Xu , J. , and Johnson , R.C. ( 1995 ) Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .	34	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	proP	activator	16332813	1	ver/dev	Fis activates the RpoS-dependent station-ary-phase expression of proP in Escherichia coli .	618	Fis activates the RpoS-dependent station-ary-phase expression of proP in Escherichia coli .	33	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	TU	fliDST	activator	21143315	3	att	This suggests that the s28 : FlgM and FliT regulatory circuits play distinct roles in regulating flagellar assembly , albeit that they are interlinked by s28-dependent transcription of the fliDST operon .	135	This suggests that the s28 : FlgM and FliT regulatory circuits play distinct roles in regulating flagellar assembly , albeit that they are interlinked by s28-dependent transcription of the fliDST operon .	7	OVEREXPRESSION OF FLIT DOES NOT HALT FLAGELLAR GENE EXPRESSION COMPLETELY	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	regulator	16949866	13	ver/dev	Expression of both crp and cya are autoregulated by CRP-cAMP so that when glucose concentrations decrease , the concentrations of both CRP increase .	84	Expression of both crp and cya are autoregulated by CRP-cAMP so that when glucose concentrations decrease , the concentrations of both cAMP and CRP increase ( Fandl et al. , 1990 ; Reverchon et al. , 1997 ) .	5	CORRESPONDING AUTHOR. TEL.: +1 352 392 1951X254; FAX: +1 352 392 3902.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	crp	regulator	16949866	13	ver/dev	Expression of both crp and cya are autoregulated by CRP-cAMP so that when glucose concentrations decrease , the concentrations of both cAMP .	84	Expression of both crp and cya are autoregulated by CRP-cAMP so that when glucose concentrations decrease , the concentrations of both cAMP and CRP increase ( Fandl et al. , 1990 ; Reverchon et al. , 1997 ) .	5	CORRESPONDING AUTHOR. TEL.: +1 352 392 1951X254; FAX: +1 352 392 3902.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	crp	regulator	21148209	8	ver/dev	In order to determine whether CRP is involved in the genetic control of this operon , transcriptional-fusions were transformed into the into an isogenic S. Typhi crp mutant strain .	165	In order to determine whether CRP is involved in the genetic control of this operon , transcriptional fusions containing the full-length promoter region were transformed into the wildtype and into an isogenic S. Typhi crp mutant strain .	8	CRP POSITIVELY REGULATES THE EXPRESSION OF THE YIHU–YSHA OPERON	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	regulator	2168849	1	ver/dev	P-galac-tosidase activities were determined in a constitutively derepressed crp mutant background in order to quantitate promoter activities independent of regulation by CAMP-CRP -LRB- the results were unaffected by addition of CAMP-data not shown -RRB- .	235	P-galac-tosidase activities were determined in a constitutively derepressed crp mutant background in order to quantitate promoter activities independent of regulation by CAMP-CRP ( the results were unaffected by addition of CAMP-data not shown ) .	5	A22642 CYAP+ 706 (559)B A22638 CYAP702 147	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
CRP	gene	crp	regulator	22149171	63	att	As a regulator of central carbon metabolism , CRP is important during infection ; crp mutants are avirulent and many CRP-regulated genes have been identified as important for virulence during infection ( Curtiss and Kelly 1987 ; Kennedy et al. 1999 ) .	395	As a regulator of central carbon metabolism , CRP is important during infection ; crp mutants are avirulent and many CRP-regulated genes have been identified as important for virulence during infection ( Curtiss and Kelly 1987 ; Kennedy et al. 1999 ) .	21	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	crp	regulator	26441883	44	ver/dev	Mechanism of the down-regulation of cAMP-receptor-protein by glucose in Escherichia coli : role of autoregulation of the crp gene .	1006	Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli : role of autoregulation of the crp gene .	56	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ssrB	regulator	19229334	11	ver/dev	Thus , one explanation for the transcription we observe following overexpression of ssrB may be that both SlyA and SsrB counteract binding of both H-NS and YdgD/Hha in this A+T rich SPI-2 region .	519	Thus , one explanation for the transcription we observe following overexpression of ssrB or slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins including both H-NS and YdgD/Hha in this A+T rich SPI-2 region [ 70 ] .	15	WHAT ARE THE SIGNALS BEING SENSED DURING SYSTEMIC INFECTION AND HOW ARE THEY INTEGRATED TO EXPRESS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
FimZ	gene	ssrB	activator	27564394	6	att	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	248	PhoP negatively regulates hilA , via activation of hilE in a FimZ-dependent manner [ 29 ] , and positively regulates SPI2 expression through transcriptional activation of ssrB and post-transcriptional activation of ssrA [ 113 ] .	6	RESULTS AND DISCUSSION RNA-SEQ ANALYSIS OF REGULATORY MUTANTS OF S. TYPHIMURIUM UNDER	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	1	ver/dev	In the absence of these negative cis elements , ssrAB was no longer repressed by the global regulator H-NS .	8	In the absence of these negative cis elements , ssrAB was expressed in a HilD-independent manner and was no longer repressed by the global regulator H-NS .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	11	ver/dev	that H-NS directly represses ssrAB	41	Furthermore , it has been shown that H-NS directly represses ssrAB and that HilD is required for the expression of ssrAB but only if H-NS is present ( 21 , 42 , 43 , 50 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	14	ver/dev	In this work , by combining biochemical strategies , we determined that H-NS represses the expression of ssrAB by initially binding to sequences located downstream of the promoter of this operon .	44	In this work , by combining genetic and biochemical strategies , we determined that H-NS represses the expression of ssrAB by initially binding to sequences located downstream of the promoter of this operon .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	14	ver/dev	In this work , by combining genetic strategies , we determined that H-NS represses the expression of ssrAB by initially binding to sequences located downstream of the promoter of this operon .	44	In this work , by combining genetic and biochemical strategies , we determined that H-NS represses the expression of ssrAB by initially binding to sequences located downstream of the promoter of this operon .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	25	ver/dev	cis elements required for the repression of ssrAB by H-NS .	111	cis elements required for the repression of ssrAB by H-NS .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	26	ver/dev	H-NS represses ssrAB as well as many other Salmonella genes .	112	H-NS represses ssrAB as well as many other Salmonella genes ( 21 , 39 , 42 , 43 , 50 ) .	4	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	30	ver/dev	This indicates that the 302 / 478 region contains the cis elements necessary for the repression of ssrAB by H-NS .	120	This indicates that the 302 / 478 region contains the cis elements necessary for the repression of ssrAB by H-NS .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	25135218	31	ver/dev	the regulatory sequences _ required for the repression of ssrAB by H-NS	121	To further localize the regulatory sequences required for the repression of ssrAB by H-NS , we analyzed the effect of dominant negative H-NSQ92am on the expression of the different ssrAB-cat fusions in the absence of HilD .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	32	ver/dev	ssrAB-cat 69 indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	Felis catus	0	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	TU	ssrAB	repressor	25135218	32	ver/dev	ssrAB-cat 119 indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	Felis catus	0	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	TU	ssrAB	repressor	25135218	32	ver/dev	ssrABcat Fig. 4B indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	TU	ssrAB	repressor	25135218	32	ver/dev	ssrABcat 10 fusions indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	TU	ssrAB	repressor	25135218	33	ver/dev	further _ supporting the role of HilD as an antagonist of H-NS-mediated repression of ssrAB	132	In addition , they show that in the absence of these negative cis elements , or when H-NS is inactivated , the expression of ssrAB becomes independent of HilD , further supporting the role of HilD as an antagonist of H-NS-mediated repression of ssrAB .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	33	ver/dev	further _ supporting the role of HilD as an antagonist of H-NS-mediated repression of ssrAB	132	In addition , they show that in the absence of these negative cis elements , or when H-NS is inactivated , the expression of ssrAB becomes independent of HilD , further supporting the role of HilD as an antagonist of H-NS-mediated repression of ssrAB .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	49	ver/dev	In the absence of the 119 / 336 region , the expression of ssrAB was no longer repressed by H-NS , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of ssrAB -LRB- Fig. 3 and	164	In the absence of the 119 / 336 region , the expression of ssrAB was no longer repressed by H-NS ( Fig. 4 ) , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of ssrAB ( Fig. 3 and	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	49	ver/dev	In the absence of the 119 / 336 region , the expression of ssrAB was no longer repressed by H-NS , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of ssrAB -LRB- Fig. 3 and	164	In the absence of the 119 / 336 region , the expression of ssrAB was no longer repressed by H-NS ( Fig. 4 ) , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of ssrAB ( Fig. 3 and	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	25135218	56	ver/dev	Taken together , these results indicate that H-NS represses the expression of ssrAB by acting on the 55 / 287 region .	184	Taken together , these results indicate that H-NS represses the expression of ssrAB by acting on the 55 / 287 region .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	TU	ssrAB	repressor	25135218	58	ver/dev	the model in which H-NS represses the expression of ssrAB initially by binding by forming a nucleoprotein filament on the promoter	191	Taken together , these results favor the model in which H-NS represses the expression of ssrAB initially by binding to two nucleation sites and then by forming a nucleoprotein filament on the promoter ( Fig. 7 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	58	ver/dev	the model in which H-NS represses the expression of ssrAB initially by binding to two nucleation sites	191	Taken together , these results favor the model in which H-NS represses the expression of ssrAB initially by binding to two nucleation sites and then by forming a nucleoprotein filament on the promoter ( Fig. 7 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	61	ver/dev	H-NS represses ssrAB by binding to multiple sites located in a region .	201	H-NS represses ssrAB by binding to multiple sites located in a region spanning the promoter and downstream sequence , which may form an H-NS filament complex that blocks the access of the RNA polymerase to the ssrAB promoter .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	25135218	67	ver/dev	another regulator may act along with HilD to counteract a double mechanism of H-NS-mediated repression of ssrAB	210	Thus , some of these H-NS binding sites may be unproductive for the repression of ssrAB , or another regulator may act along with HilD to counteract a double mechanism of H-NS-mediated repression of ssrAB .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	25135218	67	ver/dev	some of these H-NS binding sites may be unproductive for the repression of ssrAB	210	Thus , some of these H-NS binding sites may be unproductive for the repression of ssrAB , or another regulator may act along with HilD to counteract a double mechanism of H-NS-mediated repression of ssrAB .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	30718301	3	ver/dev	Interestingly , our results indicate that OmpR is required for the expression of ssrAB independently of the growth-conditions , even in the absence of repression by H-NS .	14	Interestingly , our results indicate that OmpR is required for the expression of ssrAB independently of the growth conditions , even in the absence of repression by H-NS .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	30718301	14	ver/dev	In both cases , the expression of ssrAB also requires the action of OmpR , even in the absence of the repression by H-NS .	54	In both cases , the expression of ssrAB also requires the action of OmpR , even in the absence of the repression by H-NS .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	21	ver/dev	Furthermore , we have shown that H-NS directly represses the expression of ssrAB when S. Typhimurium is grown in LB .	68	Furthermore , we have shown that H-NS directly represses the expression of ssrAB when S. Typhimurium is grown in LB ( 18 , 19 ) .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	26	ver/dev	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed EMSAs to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	83	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed competitive electrophoretic mobility shift assays ( EMSAs ) to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	3	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	26	ver/dev	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed competitive electrophoretic-mobility-shift assays to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	83	To investigate if SlyA counteracts directly the repression of H-NS on ssrAB , we performed competitive electrophoretic mobility shift assays ( EMSAs ) to examine the effect of SlyA on H-NS bound to the region 302 / 478 of ssrAB .	3	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	30	ver/dev	HilD additively antagonize repression of H-NS on ssrAB during-growth in LB .	102	SlyA and HilD additively antagonize repression of H-NS on ssrAB during growth in LB .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	30	ver/dev	SlyA additively antagonize repression of H-NS on ssrAB during-growth in LB .	102	SlyA and HilD additively antagonize repression of H-NS on ssrAB during growth in LB .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	32	ver/dev	To confirm that both SlyA and HilD act as antirepressors of H-NS to induce the expression of ssrAB , we analyzed if the inactivation of H-NS leads to the expression of ssrAB independently of both SlyA and HilD .	104	To confirm that both SlyA and HilD act as antirepressors of H-NS to induce the expression of ssrAB , we analyzed if the inactivation of H-NS leads to the expression of ssrAB independently of both SlyA and HilD .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	34	ver/dev	We next analyzed the expression of ssrAB in the absence of both , when the repression of ssrAB by H-NS is not blocked .	108	We next analyzed the expression of ssrAB in the absence of each SlyA or HilD , or both , when the repression of ssrAB by H-NS is blocked or not blocked .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	34	ver/dev	We next analyzed the expression of ssrAB in the absence of both , when the repression of ssrAB by H-NS is blocked .	108	We next analyzed the expression of ssrAB in the absence of each SlyA or HilD , or both , when the repression of ssrAB by H-NS is blocked or not blocked .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	34	ver/dev	We next analyzed the expression of ssrAB in the absence of each SlyA or HilD , when the repression of ssrAB by H-NS is not blocked .	108	We next analyzed the expression of ssrAB in the absence of each SlyA or HilD , or both , when the repression of ssrAB by H-NS is blocked or not blocked .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	34	ver/dev	We next analyzed the expression of ssrAB in the absence of each SlyA or HilD , when the repression of ssrAB by H-NS is blocked .	108	We next analyzed the expression of ssrAB in the absence of each SlyA or HilD , or both , when the repression of ssrAB by H-NS is blocked or not blocked .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	35	ver/dev	H-NS-binding sites _ required for repression of ssrAB by H-NS	110	The ssrAB-cat 302 / 10 fusion lacks H-NS-binding sites required for the repression by H-NS ; repression of ssrAB by H-NS involves the H-NS-binding sites located on the promoter as well as those located on the translational start codon of ssrA ( Fig. 4 ) ( 19 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δsl mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in y -LRB- Fig compared with D or ΔslyA single m , supporting the idea that A an have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δsl mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in y -LRB- Fig compared with D or ΔslyA single m , supporting the idea that tha have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δsl mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in in this acti compared with D or ΔslyA single m , supporting the idea that A an have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δsl mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in in this acti compared with D or ΔslyA single m , supporting the idea that tha have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δhil mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in y -LRB- Fig compared with D or ΔslyA single m , supporting the idea that A an have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δhil mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in y -LRB- Fig compared with D or ΔslyA single m , supporting the idea that tha have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δhil mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in in this acti compared with D or ΔslyA single m , supporting the idea that A an have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	37	ver/dev	The activity of the ssrAB-cat 302 / 478 fusion -LRB- repressed by H-NS -RRB- was reduced around 4-fold in the Δhil mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction -LRB- 40-fold -RRB- in in this acti compared with D or ΔslyA single m , supporting the idea that tha have an additive effect on ssrAB .	112	The activity of the ssrAB-cat 302 / 478 fusion ( repressed by H-NS ) was reduced around 4-fold in the ΔhilD and ΔslyA mutants , with respect to the WT strain ; interestingly , the ΔhilD ΔslyA double mutant showed a higher reduction ( 40-fold ) in this activity ( Fig. 5A ) compared with the ΔhilD or ΔslyA single mutants , supporting the idea that SlyA and HilD have an additive effect on ssrAB .	3	RESULTS	Felis catus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the ΔslyA mutan , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the ΔslyA mutan , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the ΔslyA mutan , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the ΔslyA mutan , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the WT S. Typhimurium strain , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the WT S. Typhimurium strain , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the ΔslyA mutan , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the ΔslyA mutan , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the ΔslyA mutan , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the ΔslyA mutan , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus	0	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the WT S. Typhimurium strain , grown in 37 °C , growth-conditions that somehow resemble the intracellular environment where S. enterica surviv .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	45	ver/dev	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in a growth-condition , the activities of the ssrAB-cat 302 / 478 / 10 fusions were tested in the WT S. Typhimurium strain , grown in N-MM at pH-5. .	138	In order to investigate if SlyA also antagonizes repression of ssrAB by H-NS in N-MM , a growth condition where HilD is not involved in the expression of ssrAB ( 18 , 19 ) , the activities of the ssrAB-cat 302 / 478 and ssrAB-cat 302 / 10 fusions were tested in the WT S. Typhimurium strain and the ΔslyA mutant , grown in N-MM at pH 5.8 and 37 °C , growth conditions that somehow resemble the intracellular environment where S. enterica survives ( 11 ) .	3	RESULTS	Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Other	OTHER	Other	Level 2
HNS	TU	ssrAB	repressor	30718301	46	ver/dev	These results show that HilD , counteracts the repression of ssrAB by H-NS during-growth in N-MM .	143	These results show that SlyA , but not HilD , counteracts the repression of ssrAB by H-NS during growth in N-MM .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	46	ver/dev	These results show that SlyA , counteracts the repression of ssrAB by H-NS during-growth in N-MM .	143	These results show that SlyA , but not HilD , counteracts the repression of ssrAB by H-NS during growth in N-MM .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	repressor	30718301	47	ver/dev	On the other hand , OmpR is also required for the expression of ssrAB in N-MM ; however , it is unknown whether , under these growth-conditions , OmpR is still needed for the expression of ssrAB in the absence of repression by H-NS .	144	On the other hand , OmpR is also required for the expression of ssrAB in N-MM ( 18 ) ; however , it is unknown whether , under these growth conditions , OmpR is still needed for the expression of ssrAB in the absence of repression by H-NS .	3	RESULTS	unidentified	1	L3	SPEC	Fact	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	30718301	48	ver/dev	These results indicate that OmpR is required for the expression of ssrAB during-growth in N-MM , independently of the repression by H-NS .	148	These results indicate that OmpR is required for the expression of ssrAB during growth in N-MM , independently of the repression by H-NS .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	30718301	59	ver/dev	However , our results indicate that the additive action of HilD is required to antagonize the repression of ssrAB by H-NS during-growth in LB .	177	However , our results indicate that the additive action of SlyA and HilD is required to antagonize the repression of ssrAB by H-NS during growth in LB .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	30718301	59	ver/dev	However , our results indicate that the additive action of SlyA is required to antagonize the repression of ssrAB by H-NS during-growth in LB .	177	However , our results indicate that the additive action of SlyA and HilD is required to antagonize the repression of ssrAB by H-NS during growth in LB .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	TU	ssrAB	repressor	30718301	63	ver/dev	Our data show that even when the repression by H-NS is displaced , the expression of ssrAB requires OmpR .	183	Our data show that even when the repression by H-NS is displaced , the expression of ssrAB requires OmpR .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	sitA	regulator	22149171	49	att	For comparison , expression of sitA , a Fur-regulated promoter , was greater in iron-limiting conditions ( Fig .	348	For comparison , expression of sitA , a Fur-regulated promoter , was greater in iron-limiting conditions ( Fig .	18	ILVY, NHAR, AND FUR ARE INDIRECT ACTIVATORS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DksA	gene	rpoS	regulator	12673058	2	ver/dev	DksA Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether HF-I , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	DksA Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether HF-I , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	Hfq Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	Hfq Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	DksA Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether Hfq , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	DksA Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	DksA Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether Hfq , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	2	ver/dev	DksA Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .	129	DksA and Hfq Are Required for Maximal Expression of rpoS but Not for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA or Hfq ( HF-I ) , two potent regulators of rpoS translation [ Brown and Elliott , 1996 ; Muffler et al. , 1996b ; Webb et al. , 1999 ] , were required for acid shock control .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	rpoS	regulator	12673058	10	ver/dev	Since DksA , two potent regulators of rpoS translation , were not absolutely required for acid shock induction , other factors must be involved in resolving the secondary structure .	303	Since DksA and Hfq , two potent regulators of rpoS translation , were not absolutely required for acid shock induction ( fig. 3 ) , other factors must be involved in resolving the secondary structure that limits rpoS translation ( discussed below ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
DksA	gene	mdh	regulator	20851888	6	ver/dev	mdh , , do not appear to be regulated by DksA .	179	Several other genes of the pentose phosphate pathway , glycolysis , and tricarboxylic acid cycle such as gnd , aceEF , and mdh , which are also associated with production of reductive power , do not appear to be regulated by DksA .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	New	Level 1
CadC	gene	STM4538	regulator	23066934	16	ver/dev	In addition , the PTS permease STM4538 is positively involved in regulation of CadC proteolysis through an unknown mechanism .	234	In addition , the PTS permease STM4538 is positively involved in regulation of CadC proteolysis through an unknown mechanism .	17	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	Other	Level 3
YdcR	gene	srfN	activator	28674150	0	att	Immunoblotting , qRT-PCR , and - galactosidase assays further dem-onstrate YdcR-dependent transcription and expression of srfN .	12	Immunoblotting , qRT-PCR , and - galactosidase assays further dem-onstrate YdcR-dependent transcription and expression of srfN .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YdcR	gene	srfN	activator	28674150	1	ver/dev	Moreover , we found physical interaction of YdcR with the promoter region of srfN , suggesting direct activation of its transcription .	13	Moreover , we found physical interaction of YdcR with the promoter region of srfN , suggesting direct activation of its transcription .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
YdcR	gene	srfN	activator	28674150	12	ver/dev	YdcR activates the expression of srfN at the transcriptional level .	218	YdcR activates the expression of srfN at the transcriptional level .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YdcR	gene	srfN	activator	28674150	19	ver/dev	YdcR activates the expression of srfN at the transcriptional level .	257	YdcR activates the expression of srfN at the transcriptional level .	5	PROFOUND INDUCTION OF YDCR IN INTRACELLULAR SALMONELLA DUR-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	hmp	regulator	17024490	0	ver/dev	Multiple regulators of the Flavohaemoglobin ( hmp ) gene of Salmonella enterica serovar Typhimurium include RamA	2	Multiple regulators of the Flavohaemoglobin ( hmp ) gene of Salmonella enterica serovar Typhimurium include RamA , a transcriptional regulator conferring the multidrug resistance phenotype	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	hmp	regulator	17024490	12	ver/dev	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp genes that PQ regulation of the hmpSt is mainly mediated by RamA .	227	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp and hmp genes and Ec St that PQ regulation of the hmpSt is mainly mediated by RamA .	16	CONCLUSIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	hmp	regulator	17024490	12	ver/dev	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp genes that PQ regulation of the hmpSt is mainly mediated by RamA .	227	Our results demonstrate for the Wrst time that Fur is a weak repressor of both hmp and hmp genes and Ec St that PQ regulation of the hmpSt is mainly mediated by RamA .	16	CONCLUSIONS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	hmp	regulator	17024490	13	ver/dev	It is important to note that the transcriptional regulation of hmp by PQ in E. coli is still obscure as RamA is not present in the E. coli chromosome .	228	It is important to note that the transcriptional regulation of hmp by PQ in E. coli is still obscure as RamA is not present in the E. coli chromosome .	16	CONCLUSIONS	Escherichia coli;Escherichia coli	0	L3	OTHER	Analysis	NEG	Other	Level 1
sigma-70	gene	yihU	activator	21148209	6	att	The initiation site is associated with a 210 ( 59-TACAAA-39 ) and a 235 box ( 59-CTGTCA-39 ) , suggesting a sigma-70-dependent promoter that drives yihU transcription , such as that predicted with the Bacterial Promoter Prediction program .	159	The initiation site is associated with a 210 ( 59-TACAAA-39 ) and a 235 box ( 59-CTGTCA-39 ) , suggesting a sigma 70-dependent promoter that drives yihU transcription , such as that predicted with the Bacterial Promoter Prediction program .	7	FUNCTIONAL ORGANIZATION OF THE YIHU–YSHA GENES OF S. TYPHI	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	flhDC	regulator	26267246	1	ver/dev	Transcription of flhDC is also activated by the master regulator of the Salmonella pathogenicity island-1 encoded Spi-1 , HilD .	64	Transcription of flhDC is also activated by the ironregulatory protein Fur [ 21 ] and the master regulator of the Salmonella pathogenicity island-1 encoded injectisome ( Spi-1 ) , HilD .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	regulator	26267246	1	ver/dev	Transcription of flhDC is also activated by the master regulator of the Salmonella pathogenicity island-1 encoded injectisome , HilD .	64	Transcription of flhDC is also activated by the ironregulatory protein Fur [ 21 ] and the master regulator of the Salmonella pathogenicity island-1 encoded injectisome ( Spi-1 ) , HilD .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	flhDC	regulator	27206164	6	ver/dev	The main regulator of HilD , thereby activates flhDC transcription .	47	The main regulator of the Spi-1 injectisome system , HilD , binds upstream of the flhDC P5 transcriptional start site and thereby activates flhDC transcription ( Singer et al. , 2014 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	regulator	27206164	6	ver/dev	The main regulator of HilD , binds upstream of the flhDC P5 transcriptional start site .	47	The main regulator of the Spi-1 injectisome system , HilD , binds upstream of the flhDC P5 transcriptional start site and thereby activates flhDC transcription ( Singer et al. , 2014 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	regulator	27206164	7	ver/dev	Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV .	48	Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV ( Chubiz et al. , 2010 ; Wada et al. , 2011 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	regulator	27886269	1	ver/dev	Furthermore , HilD directly controls the expression of the flhDC operon encoding FlhDC .	32	Furthermore , HilD directly controls the expression of the flhDC operon encoding FlhDC , the master transcriptional complex required for the expression of flagellar and chemotaxis genes30 ,35 .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	regulator	29866910	2	ver/dev	Likewise , HilD binds the flhDC promoter to activate the flagellar regulon .	154	Likewise , HilD binds the flhDC promoter to activate the flagellar regulon ( 47 , 48 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	flhDC	regulator	30355489	5	ver/dev	Although we found that purified HilD bound equally well to SBG flhDC promoters , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa , thus ruling out a competitive inhibition by SsrB .	97	Although we found that purified HilD bound equally well to the STM and SBG flhDC promoters ( Figure S3B ) , this interaction did not affect the binding of SsrBc to the STM flhDC promoter or vice versa ( Figure S3C ) , thus ruling out a competitive inhibition by SsrB .	7	SSRB BINDS TO THE FLHDC PROMOTER IN STM	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HilD	TU	flhDC	regulator	31484980	45	ver/dev	A previous study indicates that HilD directly regulates expression of the flhDC operon .	211	A previous study indicates that HilD directly regulates expression of the flhDC operon , encoding the master regulator of the flagellar genes , which is also conserved in E. coli K-12 and many other bacteria32 ,33 .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FlhDC	gene	ydiV	activator	26267246	9	ver/dev	Accordingly , a ydiV deletion resulted in increased motility due to upregulation of FlhDC activity .	161	Accordingly , a ydiV deletion resulted in increased motility due to upregulation of FlhDC activity .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsB	regulator	15469511	6	att	of the RcsC/YojN/RcsB regulatory system due to the rcsC11 allele in the sensor RcsC renders Salmonella avirulent , and that inactivation of the response regulator gene rcsB restores full virulence to the rcsC11 mutant , indicative that its attenuated phenotype results from aberrant expression of RcsB-regulated genes .	192	of the RcsC/YojN/RcsB regulatory system due to the rcsC11 allele in the sensor RcsC renders Salmonella avirulent , and that inactivation of the response regulator gene rcsB restores full virulence to the rcsC11 mutant , indicative that its attenuated phenotype results from aberrant expression of RcsB-regulated genes .	9	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsB	regulator	15469511	7	att	Both an rcsB single mutant and an rcsC11 rcsB double mutant exhibited wild-type virulence ( Table 1 ; Fig. 1 ) , indicating that the attenuated phenotype of the rcsC11 mutant is entirely dependent on RcsB-regulated genes and ruling out cross-talk of the mutant RcsC11 protein to other two-component systems as responsible for attenuation .	216	Both an rcsB single mutant and an rcsC11 rcsB double mutant exhibited wild-type virulence ( Table 1 ; Fig. 1 ) , indicating that the attenuated phenotype of the rcsC11 mutant is entirely dependent on RcsB-regulated genes and ruling out cross-talk of the mutant RcsC11 protein to other two-component systems as responsible for attenuation .	10	THE GENETIC BASIS FOR THE ATTENUATION PHENOTYPE OF THE RCSC11 MUTANT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	rcsB	regulator	28588134	4	att	We did not observe a decrease in Δ in a wza yjb rcsB mutant beyond what is observed in the rcsB mutant , suggesting that no additional RcsB-regulated factors are required for PMF maintenance ( see Fig .	256	We did not observe a decrease in Δ in a wza yjb rcsB mutant beyond what is observed in the rcsB mutant , suggesting that no additional RcsB-regulated factors are required for PMF maintenance ( see Fig .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CueR	gene	lacZ	regulator	23645605	4	att	( B ) - Galactosidase activity from GolS - or CueR-regulated transcriptional-fusions golB : : lacZ ( PgolB ) or copA-lacZ ( PcopA ) , respectively , on cells carrying either wild-type golS and cueR , or golSL , golSsL , or golSC111S , replacing the wild-type copy of golS , or cueRL , replacing cueR .	140	( B ) - Galactosidase activity from GolS - or CueR-regulated transcriptional fusions golB : : lacZ ( PgolB ) or copA-lacZ ( PcopA ) , respectively , on cells carrying either wild-type golS and cueR , or golSL , golSsL , or golSC111S , replacing the wild-type copy of golS , or cueRL , replacing cueR .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
CsrA	gene	slyA	regulator	30682134	19	ver/dev	This suggests that regulation of slyA by CsrA affects the expression of its downstream regulatory targets .	226	This suggests that regulation of slyA by CsrA affects the expression of its downstream regulatory targets .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	slyA	regulator	30682134	20	ver/dev	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the regulator of SPI-2 encoded effectors , slyA in LB .	227	Thus , in addition to the effects of CsrA on hilD expression , CsrA controlled the expression of regulators of other aspects of Salmonella virulence including repressing the activator of plasmid-encoded effectors spvR in mLPM and repressing the regulator of SPI-2 encoded effectors , slyA in LB .	12	CORE AND CONDITION-SPECIFIC ROLES OF CSRA IDENTIFIED BY FUNCTIONAL ENRICHMENT	Salmonella	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	crp	activator	19103774	0	att	PphoPQ107 : : TT araC PBAD phoPQ and 9108 with the PphoPQ107 : : TT araC PBAD phoPQ and Pcrp527 : : TT araC PBAD crp mutations when streaked on X-P plates without and with 0.2 % arabinose reveal acid phosphatase activity due to expression of the PhoP-activated phoN gene only when grown in the presence of arabinose ( Fig. 2c ) .	130	PphoPQ107 : : TT araC PBAD phoPQ and 9108 with the PphoPQ107 : : TT araC PBAD phoPQ and Pcrp527 : : TT araC PBAD crp mutations when streaked on X-P plates without and with 0.2 % arabinose reveal acid phosphatase activity due to expression of the PhoP-activated phoN gene only when grown in the presence of arabinose ( Fig. 2c ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	crp	activator	33563986	9	att	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , as well as SPI-2 genes when STM is inside macrophages65 , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence-factors .	346	However , it is worth noticing that a PhoP-activated small RNA PinT has been shown to repress sopE2 , crp , as well as SPI-2 genes when STM is inside macrophages65 , suggesting the pre-sence of negative regulatory mechanism to repress the overexpression of these virulence factors .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	cstA	regulator	23774596	1	ver/dev	CsrA regulates translation of cstA , by blocking ribosome access to the cstA transcript .	722	CsrA regulates translation of the Escherichia coli carbon starvation gene , cstA , by blocking ribosome access to the cstA transcript .	44	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilC	gene	sipA	activator	21168230	5	ver/dev	In addition , HilC directly activate sipA in non-HilA dependent manner .	344	In addition , HilD and HilC directly activate invF , sipA and sipC in non-HilA dependent manner ( Akbar et al. , 2003 ) .	25	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CytR	gene	udp	repressor	14499937	9	ver/dev	the V. cholerae CytR protein is able to repress transcription of the udp gene of E. coli in-vivo	279	This is in contrast to what has been found recently for the V. cholerae CytR protein , that is able to repress transcription of the udp gene of E. coli in vivo [ 10 ] .	20	4. DISCUSSION	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
Fis	gene	fis	repressor	17784910	2	ver/dev	the fis promoter is repressed by the Fis protein	42	This expression pattern reflects the activity of the fis promoter which is repressed by the Fis protein and requires negative DNA supercoiling for optimal activity ( Schneider et al. , 2000 ) .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	cRP	repressor	1624426	2	auto	Autoregulator of the Escherichia coli crp gene : CRP is a transcriptional repressor for its own gene .	299	Autoregulator of the Escherichia coli crp gene : CRP is a transcriptional repressor for its own gene .	7	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	cRP	repressor	3525518	3	auto	Autoregulation of the Escherichia coli crp gene : CRP is a transcriptional repressor for its own gene .	450	Autoregulation of the Escherichia coli crp gene : CRP is a transcriptional repressor for its own gene .	7	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Fur	gene	fhuF	regulator	12486045	0	att	Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein .	435	Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein .	16	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	fhuF	regulator	12652904	0	att	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	123	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	12	RESULTS AND DISCUSSIONS	unidentified plasmid;Escherichia coli	0.5	L2	OTHER	Analysis	OTHER	Other	Level 1
Fur	gene	fhuF	regulator	12652904	0	att	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	123	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	12	RESULTS AND DISCUSSIONS	unidentified plasmid;Escherichia coli	0.5	L2	OTHER	Analysis	OTHER	Other	Level 1
Fur	gene	fhuF	regulator	15790293	21	att	Members of the Fur protein family regulate iron and zinc transport in Escherichia coli and characteristics of the Fur-regulated fhuF protein .	661	Members of the Fur protein family regulate iron and zinc transport in Escherichia coli and characteristics of the Fur-regulated fhuF protein .	60	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	fhuF	regulator	18441067	1	att	Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein .	361	Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Fur	gene	fhuF	regulator	21952637	0	att	Regardless of the explanation , these results appear at odds with previous studies , which established that cells exposed to Co contain less iron and reported up-regulation of Fur-controlled entB and fhuF also directly destabilize particularly labile Fe -- S clusters such as those present on Fe -- S scaffolds .	135	Regardless of the explanation , these results appear at odds with previous studies , which established that cells exposed to Co contain less iron and reported up-regulation of Fur-controlled entB and fhuF also directly destabilize particularly labile Fe -- S clusters such as those present on Fe -- S scaffolds .	11	1. TRANSCRIPTOMIC ANALYSIS OF E. COLI RESPONSE TO CO	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	crp	activator	17906148	6	ver/dev	This repression was mediated by CRP , since , in a crp mutant , levels of isoenzyme 2 could not be increased by the addition of cAMP .	314	This repression was mediated by CRP , since , in a crp mutant , levels of isoenzyme 2 could not be increased by the addition of cAMP ( Jamieson et al. , 1986 ) .	9	DISCUSSION	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
CRP	gene	crp	activator	20585446	7	att	The change in identification is the result of the lack of fermentation of all Crp-dependent sugars ( crp is not expressed in the absence-of-arabinose ) .	577	The change in identification is the result of the lack of fermentation of all Crp-dependent sugars ( crp is not expressed in the absence of arabinose ) .	25	VACCINE CONSTRUCTION AND CHARACTERIZATION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pmrD	activator	12753201	33	ver/dev	In the case of PmrA/B regulation , the response regulator PhoP activates pmrD .	213	In the case of PmrA/B regulation , the response regulator PhoP activates pmrD .	10	A TWO-COMPONENT REGULATORY SYSTEM REGULATES A TWO-COMPONENT REGULATORY SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrD	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	15225317	3	att	PhoP-activated pmrD gene as well as the PmrA and PmrB proteins ( Kox et al. , 2000 ) .	32	PhoP-activated pmrD gene as well as the PmrA and PmrB proteins ( Kox et al. , 2000 ) .	3	2 ND POLYMYXIN B	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrD	activator	15569938	5	ver/dev	However , the E. coli pmrD gene was induced in low Mg2 in a phoP-dependent manner , like other members of the E. coli PhoP regulon .	109	However , the E. coli pmrD gene was induced in low Mg2 in a phoP-dependent manner ( Fig. 5A , which is published as supporting information on the PNAS web site ) , like other members of the E. coli PhoP regulon ( 25 ) and the Salmonella pmrD gene ( 22 ) .	4	RESULTS	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	15569938	5	ver/dev	However , the E. coli pmrD gene was induced in low Mg2 in Fig. 5A , like other members of the E. coli PhoP regulon .	109	However , the E. coli pmrD gene was induced in low Mg2 in a phoP-dependent manner ( Fig. 5A , which is published as supporting information on the PNAS web site ) , like other members of the E. coli PhoP regulon ( 25 ) and the Salmonella pmrD gene ( 22 ) .	4	RESULTS	Escherichia coli;Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	15703297	9	att	We have previously identified a multicomponent loop in Sal-monella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA , and activated PmrA represses transcription from the pmrD promoter , which harbors binding sites for both the PhoP and PmrA proteins ( 18 ) ( Fig. 1D ) .	115	We have previously identified a multicomponent loop in Sal-monella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA , and activated PmrA represses transcription from the pmrD promoter , which harbors binding sites for both the PhoP and PmrA proteins ( 18 ) ( Fig. 1D ) .	4	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	18792679	1	att	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	113	The prototypical PhoP-activated promoter harbors the PhoP box 11-13 bp upstream of the consensus -10 region for RNA polymerase .8,29.44,45.51.52 This includes the promoters for the phoPf6 pmrD , slyB , pagP , mgrB and rstAgenes , as well as that correspondingto the mgtAgene .	5	DIRECT TRANSCRIPTIONAL CONTROL BYTHE PHOP PROTEIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	18792679	21	att	This is the case of the E. coli PrnrD protein , which is only 55.3 % identical to the Salmonella PrnrD and unable to activate the PrnrA/PmrB system in E. coli ; yet , the two pmrD genes are similarly induced in low Mg '' + in a PhoP-dependent fashion . ''	273	This is the case of the E. coli PrnrD protein , which is only 55.3 % identical to the Salmonella PrnrD and unable to activate the PrnrA/PmrB system in E. coli ; yet , the two pmrD genes are similarly induced in low Mg '' + in a PhoP-dependent fashion . ''	9	PHOP AS A CO-ACTIVATOR PROTEIN	Escherichia coli;Salmonella;Escherichia coli	0.5	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	pmrD	activator	18792679	22	att	In Salmonella , PhoP-activated genes regulated via the PrnrD protein are induced to higher levels than those that are directly controlled by the PhoP protein.V Signal amplification is also detected when one compares expression ofthe same gene ( s ) in two isogenic strains : one harboring the PrnrD-mediated pathway operating in wild-type Salmonella and one lacking the pmrD gene and harboring a PhoP box in place of the PrnrA box at the target prornorerfs ) . ?	279	In Salmonella , PhoP-activated genes regulated via the PrnrD protein are induced to higher levels than those that are directly controlled by the PhoP protein.V Signal amplification is also detected when one compares expression ofthe same gene ( s ) in two isogenic strains : one harboring the PrnrD-mediated pathway operating in wild-type Salmonella and one lacking the pmrD gene and harboring a PhoP box in place of the PrnrA box at the target prornorerfs ) . ?	9	PHOP AS A CO-ACTIVATOR PROTEIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	18792679	21	ver/dev	This is the case of the E. coli PrnrD protein ; yet , the two pmrD genes are similarly induced in in a PhoP-dependent fashion . ''	273	This is the case of the E. coli PrnrD protein , which is only 55.3 % identical to the Salmonella PrnrD and unable to activate the PrnrA/PmrB system in E. coli ; yet , the two pmrD genes are similarly induced in low Mg '' + in a PhoP-dependent fashion . ''	9	PHOP AS A CO-ACTIVATOR PROTEIN	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	20593264	2	att	For example , despite the absence of the pmrD gene , Yersinia pestis ( Y. pestis ) can mediate PhoP-dependent modification of lipid-A with Ara4N through transcription of the pbgP and ugd genes ( Winfield et al. , 2005 ) .	226	For example , despite the absence of the pmrD gene , Yersinia pestis ( Y. pestis ) can mediate PhoP-dependent modification of lipid A with Ara4N through transcription of the pbgP and ugd genes ( Winfield et al. , 2005 ) .	12	5.3 ADDITIONAL BACTERIA CAPABLE OF MODIFYING LPS	Yersinia pestis	0	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	pmrD	activator	23504014	16	att	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	277	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	25182488	12	att	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	250	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	27381382	0	att	In S. Typhimurium , the PhoPQ TCS indirectly activates the PmrAB TCS via PhoP-activated pmrD expression ( Kox et al. , 2000 ) .	42	In S. Typhimurium , the PhoPQ TCS indirectly activates the PmrAB TCS via PhoP-activated pmrD expression ( Kox et al. , 2000 ) .	5	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrD	activator	29739882	0	att	The latter activation entails PhoQ-mediated phosphorylation of its cognate response regulator PhoP ( 20 ) , transcription of the PhoP-activated gene pmrD ( 18 ) , and protection of phosphorylated PmrA by the PmrD protein ( 21 ) ( Fig. 1B ) .	44	The latter activation entails PhoQ-mediated phosphorylation of its cognate response regulator PhoP ( 20 ) , transcription of the PhoP-activated gene pmrD ( 18 ) , and protection of phosphorylated PmrA by the PmrD protein ( 21 ) ( Fig. 1B ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrD	activator	29739882	14	att	When Salmonella experiences low Mg2 + , the PhoP/PhoQ system is activated before the PmrA/PmrB system because , under this inducing condition , PmrA activation is dependent on the PhoP-activated pmrD gene ( Fig. 1B ) ( 18 ) .	169	When Salmonella experiences low Mg2 + , the PhoP/PhoQ system is activated before the PmrA/PmrB system because , under this inducing condition , PmrA activation is dependent on the PhoP-activated pmrD gene ( Fig. 1B ) ( 18 ) .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	29739882	20	att	PmrA is also activated in low Mg2 + by the PhoP-activated pmrD gene product .	634	PmrA is also activated in low Mg2 + by the PhoP-activated pmrD gene product .	10	FUNDING: THIS RESEARCH WAS SUPPORTED BY NATIONAL INSTITUTES OF HEALTH GRANT R01 AI120558 TO E.A.G‥	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrD	activator	29739882	8	att	We reasoned that the kinetics with which a mildly acidic pH induces PmrA - and PhoP-activated genes might differ from that taking place in low Mg2 + because low Mg2 + activation requires the PhoP-dependent transcription of the pmrD gene ( 18 ) , which specifies a protein that protects phosphorylated PmrA from dephosphorylation by its cognate sensor PmrB ( 21 ) , and results in transcription of genes directly activated by PmrA .	125	We reasoned that the kinetics with which a mildly acidic pH induces PmrA - and PhoP-activated genes might differ from that taking place in low Mg2 + because low Mg2 + activation requires the PhoP-dependent transcription of the pmrD gene ( 18 ) , which specifies a protein that protects phosphorylated PmrA from dephosphorylation by its cognate sensor PmrB ( 21 ) , and results in transcription of genes directly activated by PmrA .	5	RESULTS	nan	1	L1	SPEC	Other	OTHER	New	Level 1
PhoP	gene	pmrD	activator	30967459	9	att	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	144	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	3	RESULTS	Salmonella;unidentified plasmid;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to activate transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	E. , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to activate transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	E. , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	Mathew , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to activate transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	Mathew , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	J. , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to activate transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	J. , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	Zhi , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to activate transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
Lrp	TU	dadAX	regulator	29021529	2	ver/dev	Zhi , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress transcription directly .	480	Zhi , J. , Mathew , E. & Freundlich , M. Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .	13	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	STM1485	activator	30763640	17	att	B ) The putative RcsB binding site on STM1485 was identified by alignment of the conserved RcsB box identified in other RcsB-dependent genes : ugd S. enterica ( Se ) and ams E. amylovora ( Ea ) genes .	146	B ) The putative RcsB binding site on STM1485 was identified by alignment of the conserved RcsB box identified in other RcsB-dependent genes : ugd S. enterica ( Se ) and ams E. amylovora ( Ea ) genes .	12	3.2. BIOINFORMATICS SEARCH OF A PUTATIVE RCSB CIS-ACTING ELEMENT ON STM1485 PROMOTER	Salmonella;Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RcsB	gene	STM1485	activator	30763640	0	ver/dev	We demonstrated that acid-induced activation of the RcsB represses STM1485 transcription by directly binding to the promoter .	13	We demonstrated that acid-induced activation of the RcsB represses STM1485 transcription by directly binding to the promoter .	0	Unknown	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	STM1485	activator	30763640	7	ver/dev	Since RcsB is involved in acid stress response , we decided to study the effect of RcsB in the pH-dependent activation of S. Typhimurium STM1485 gene .	104	Since RcsB is involved in acid stress response , we decided to study the effect of RcsB in the pH-dependent activation of S. Typhimurium STM1485 gene .	11	3.1. RCSB MODULATES THE STM1485 EXPRESSION IN A PH-DEPENDENT PATHWAY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Investigation	OTHER	Other	Level 2
RcsB	gene	STM1485	activator	30763640	10	ver/dev	These data confirmed that activation of the RcsB regulator inhibits STM1485 gene expression .	136	These data confirmed that activation of the RcsB regulator inhibits STM1485 gene expression .	11	3.1. RCSB MODULATES THE STM1485 EXPRESSION IN A PH-DEPENDENT PATHWAY	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	STM1485	activator	30763640	51	ver/dev	Since the RcsCDB system is activated at moderate acidity , we asked ourselves whether in Salmonella the STM1485 gene could be controlled by RcsB activation .	250	Since the RcsCDB system is activated at moderate acidity ( pH 5 ) and considering that this condition induces the asr gene expression in E. coli , we asked ourselves whether in Salmonella the STM1485 gene could be controlled by RcsB activation .	16	4. DISCUSSION	Salmonella	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression in the rcsB mutant was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RcsB	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression under PhoP-dependent RstA activation was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is inactive , since an induction of STM1485 expression under magnesium starvation conditions was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	OTHER	Other	Level 1
RcsB	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression under PhoP-dependent RstA activation was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	SPEC	Other	NEG	Other	Level 1
RcsB	gene	STM1485	activator	30763640	60	ver/dev	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent , since an induction of STM1485 expression under magnesium starvation conditions was observed .	286	In addition , we found that RstA could bind to this promoter sequence only when RcsB is absent or inactive , since an induction of STM1485 expression in the rcsB mutant or under magnesium starvation conditions ( PhoP-dependent RstA activation ) was observed .	16	4. DISCUSSION	nan	1	L1	OTHER	Other	NEG	Other	Level 1
SlyA	gene	pmrC	regulator	24021902	2	ver/dev	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid-A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits modification of lipid-A STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	93	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits LpxO function ( modification of lipid A ) STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	6	INTRODUCTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
SlyA	gene	pmrC	regulator	24021902	2	ver/dev	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid-A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits LpxO function STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	93	cptA STM4118 Necessary for the addition of phosphoethanolamine to the LPS core lpxR STM1328 Lipid 0 A 3 - O-deacylase pmrC STM4293 Inner membrane protein required for incorporation of phosphoethanolamine into lipid A ugtL STM1601 Resistance to Polymyxin B , regulated by SlyA visP STM3176 Inhibits LpxO function ( modification of lipid A ) STM1301 Gene likely to be involved in motility STM2314 CheV homologues STM2343 STM3154 Genes likely to be involved in motility STM3156	6	INTRODUCTION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
NtrC	gene	glnK	regulator	30201777	9	att	To ensure that NtrC was activated by the nitrogen-limiting conditions , expression of NtrC-regulated glnK ( 41 ) was measured by qRT-PCR ( see Fig .	118	To ensure that NtrC was activated by the nitrogen-limiting conditions , expression of NtrC-regulated glnK ( 41 ) was measured by qRT-PCR ( see Fig .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Cra	gene	fbp	activator	20676398	2	ver/dev	Cra protein activates ppsA , pckA , fbp	277	Under the conditions investigated , it is assumed that carbon flux is controlled by the catabolite repressor/activator ( Cra ) protein , which activates gluconeogenesis enzymes ( ppsA , pckA , fbp ) and represses sugar catabolism enzymes [ 61 ] .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilC	activator	15661008	26	ver/dev	In the present study , the expression from lac fusion was retained after disruption in hilC in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilC	activator	15661008	26	ver/dev	In the present study , the expression from the hilA was retained after disruption in hilC in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	325	In the present study , the expression from the hilA -- lac fusion was retained after disruption in hilC and hilD ( Fig. 2A ) in the lon + cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .	9	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilC	activator	16045614	1	ver/dev	that RtsA are each capable of independently inducing expression of the hilC genes	14	We demonstrate that HilC , HilD and RtsA are each capable of independently inducing expression of the hilC , hilD and rtsA genes , and that each can independently activate hilA .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilC	activator	16045614	20	ver/dev	We demonstrate that RtsA are each capable of inducing expression of hilC .	82	We demonstrate that HilC , HilD and RtsA are each capable of inducing expression of hilC , hilD and rtsA .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilC	activator	16045614	21	ver/dev	RtsA can independently induce expression of hilC	85	HilC , HilD and RtsA can independently induce expression of hilC , hilD and rtsA	5	RESULTS	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilC	activator	16045614	23	ver/dev	We had previously demonstrated that RtsA increased expression of hilC .	88	We had previously demonstrated that RtsA increased expression of hilC and hilD ( Ellermeier and Slauch , 2003 ) .	5	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RtsA	gene	hilC	activator	16045614	24	ver/dev	We wanted to determine if RtsA could induce expression of hilC in the absence of the other regulators .	90	We wanted to determine if HilC , HilD and RtsA could induce expression of hilC , hilD , rtsA and hilA in the absence of the other regulators .	5	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
RtsA	gene	hilC	activator	16045614	28	ver/dev	RtsA also induced expression of hilC .	131	RtsA , HilC and HilD also induced expression of hilC , hilD and rtsA ( Fig. 2 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilC	activator	16045614	29	ver/dev	RtsA induced expression of hilC approximately threeto fourfold 12-fold .	133	RtsA , HilC and HilD induced expression of hilC approximately threeto fourfold and hilD ~ 10 - to 12-fold .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RtsA	gene	hilC	activator	16045614	30	ver/dev	These data show that RtsA are each capable of independently inducing expression of hilC , consistent with our model that RtsA constitute a feed forward regulatory loop .	134	These data show that HilC , HilD and RtsA are each capable of independently inducing expression of hilC , hilD and rtsA , consistent with our model that HilC , HilD and RtsA constitute a feed forward regulatory loop ( Fig. 1 ) .	5	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilC	activator	16045614	69	ver/dev	We show that RtsA can each independently activate expression of the hilC genes .	462	We show that HilD , HilC and RtsA can each independently activate expression of the hilD , hilC , rtsAB and hilA genes .	8	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilC	activator	17993530	6	ver/dev	RtsA are all also capable of activating expression of hilC independent of each other and comprise a complex feed forward regulatory loop .	39	HilC , HilD , and RtsA are all also capable of activating expression of hilC , hilD , and rtsA independent of each other and comprise a complex feed forward regulatory loop that controls hilA expression ( Fig. 1 ) ( 16 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilC	activator	22479568	0	ver/dev	RtsA can activate expression of hilC of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA .	30	HilD , HilC , and RtsA are able to regulate their own gene expression and can activate expression of hilD , hilC and rtsA independent of each other to constitute a regulatory circuit for the control of the SPI1 central regulator hilA [ 17 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
RtsA	gene	hilC	activator	27601571	4	ver/dev	Indeed , this is the case for activation of hilC by HilD/HilC / RtsA .	72	Indeed , this is the case for activation of hilD , hilC , rtsA , and hilA by HilD/HilC / RtsA ( 29 , 30 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RtsA	gene	hilC	activator	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilC .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RtsA	gene	hilC	activator	32041797	5	ver/dev	RtsA activate transcription of hilC , the last T3SS structural genes .	61	The AraC-like proteins HilD , HilC , and RtsA activate transcription of hilD , hilC , rtsA , and hilA , the last encoding the transcriptional activator of the SPI1 T3SS structural genes ( 20 , 26 ) .	3	KEYWORDS SPI1, HILD, HILC, RTSA, DIMERIZATION, SALMONELLA, PATHOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	steB	regulator	24021902	5	ver/dev	a c deubiquitinase in-vivo _ regulated by SlyA steB STM1629 Type III secretion system effector protein c steC STM1698 Type III secretion system effector protein c STM2239 SPI-12-encoded genes	127	pipB2 STM2780 Type III secretion system effector protein , regulated by SlyA siiA STM4257 SPI-4 genes that encode an adhesin system siiB STM4258 siiC STM4259 siiD STM4260 siiE STM4261 siiF STM4262 sopD2 STM0972 Type III secretion system effector protein , regulated by SlyA c srcA STM2138 SPI-2 effector chaperone required for systemic infection in c mice sseK2 STM2137 Type III secretion system effector protein c sseL STM2287 Type III secretion system effector protein , functions as a c deubiquitinase in vivo , regulated by SlyA steB STM1629 Type III secretion system effector protein c steC STM1698 Type III secretion system effector protein c STM2239 SPI-12-encoded genes regulated by SsrB , enhance fitness in c vivo , STM2239 encodes a transcriptional regulator STM2340 STM3117 SPI-13-encoded genes with suggested function in c biosynthesis of the cell wall peptidoglycan layer STM3118 c STM3119	6	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	repressor	11123690	30	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	370	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	32	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	repressor	17908208	86	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	519	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	24	ACKNOWLEDGEMENTS	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	repressor	24354910	64	ver/dev	Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	507	Tobe , T. , Yoshikawa , M. , Mizuno , T. , and Sasakawa , C. ( 1993 ) Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF and repression by H-NS .	46	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	virB	repressor	25566242	22	ver/dev	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .	455	Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF and repression by H-NS .	54	REFERENCES	Shigella flexneri	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	mgtC	regulator	30524381	41	att	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter ( Quinn et al. , 2014 ) , although microarray and qRT-PCR analysis of OmpR-regulated genes at acid-pH did not identify mgtC as a target of OmpR regulation , nor did mgtC contribute to intracellular acidification ( Chakraborty et al. , 2015 ) .	382	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter ( Quinn et al. , 2014 ) , although microarray and qRT-PCR analysis of OmpR-regulated genes at acid pH did not identify mgtC as a target of OmpR regulation , nor did mgtC contribute to intracellular acidification ( Chakraborty et al. , 2015 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	mgtC	regulator	30524381	41	att	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter ( Quinn et al. , 2014 ) , although microarray and qRT-PCR analysis of OmpR-regulated genes at acid-pH did not identify mgtC as a target of OmpR regulation , nor did mgtC contribute to intracellular acidification ( Chakraborty et al. , 2015 ) .	382	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter ( Quinn et al. , 2014 ) , although microarray and qRT-PCR analysis of OmpR-regulated genes at acid pH did not identify mgtC as a target of OmpR regulation , nor did mgtC contribute to intracellular acidification ( Chakraborty et al. , 2015 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	mgtC	regulator	30524381	41	ver/dev	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter , although qRT-PCR analysis of OmpR-regulated genes at acid-pH did not identify mgtC as a target of OmpR regulation	382	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter ( Quinn et al. , 2014 ) , although microarray and qRT-PCR analysis of OmpR-regulated genes at acid pH did not identify mgtC as a target of OmpR regulation , nor did mgtC contribute to intracellular acidification ( Chakraborty et al. , 2015 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
OmpR	gene	mgtC	regulator	30524381	41	ver/dev	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter , although microarray analysis of OmpR-regulated genes at acid-pH did not identify mgtC as a target of OmpR regulation	382	ChIP-on-chip results with OmpR showed increased binding of OmpR at the mgtC promoter ( Quinn et al. , 2014 ) , although microarray and qRT-PCR analysis of OmpR-regulated genes at acid pH did not identify mgtC as a target of OmpR regulation , nor did mgtC contribute to intracellular acidification ( Chakraborty et al. , 2015 ) .	25	A CAUTION REGARDING C-TERMINAL FUSIONS TO OMPR	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PmrA	gene	pmrB	activator	15205413	17	att	It has been hypothesized that two promoters mediate the transcription of the pmrA and pmrB genes : a PmrA-activated promoter located upstream of the pmrC gene in the pmrCAB operon and a constitutive promoter located within the pmrC open reading frame .	271	It has been hypothesized that two promoters mediate the transcription of the pmrA and pmrB genes : a PmrA-activated promoter located upstream of the pmrC gene in the pmrCAB operon and a constitutive promoter located within the pmrC open reading frame .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrB	activator	15205413	8	att	The generated mutation ( designated pmrC1 ) was not polar on the pmrA and pmrB genes because the same levels of transcription of the PmrA-activated pbgP gene were displayed by isogenic wildtype and pmrC1 strains ( Fig. 1B ) .	149	The generated mutation ( designated pmrC1 ) was not polar on the pmrA and pmrB genes because the same levels of transcription of the PmrA-activated pbgP gene were displayed by isogenic wildtype and pmrC1 strains ( Fig. 1B ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	pmrB	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrB	activator	22921935	0	att	We identified a PmrA-activated promoter immediately downstream of and transcribed towards the pmrB coding region that had not been reported in previous experimental and computational searches of PmrA-activated targets ( Aguirre et al. , 2000 ; Marchal et al. , 2004 ; Wosten and Groisman , 1999 ) ( Figure 2A ) .	62	We identified a PmrA-activated promoter immediately downstream of and transcribed towards the pmrB coding region that had not been reported in previous experimental and computational searches of PmrA-activated targets ( Aguirre et al. , 2000 ; Marchal et al. , 2004 ; Wosten and Groisman , 1999 ) ( Figure 2A ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PmrA	gene	pmrB	activator	22921935	0	att	We identified a PmrA-activated promoter immediately downstream of and transcribed towards the pmrB coding region that had not been reported in previous experimental and computational searches of PmrA-activated targets ( Aguirre et al. , 2000 ; Marchal et al. , 2004 ; Wosten and Groisman , 1999 ) ( Figure 2A ) .	62	We identified a PmrA-activated promoter immediately downstream of and transcribed towards the pmrB coding region that had not been reported in previous experimental and computational searches of PmrA-activated targets ( Aguirre et al. , 2000 ; Marchal et al. , 2004 ; Wosten and Groisman , 1999 ) ( Figure 2A ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	pmrA	activator	12480883	4	ver/dev	PhoP -RCB- PhoQ activates transcription of pmrA -RCB- B .	411	PhoP } PhoQ activates transcription of pmrA } B , encoding a two-component system involved in Salmonella typhimurium antimicrobial peptide resistance .	14	FAREWELL, A., BRAZAS, R., DAVIE, E., MASON, J. & ROTHFIELD, L. I.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrA	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	pmrA	activator	15225317	28	att	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	338	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	pmrA	activator	15225317	2	ver/dev	the regulatory gene pmrA is post-tran-scriptionally activated by the PhoP	13	Inactivation of both ugtL and the regulatory gene pmrA , which controls lipid A modifications required for resistance to polymxyin B ( but not to magainin 2 ) and is post-tran-scriptionally activated by the PhoP -- PhoQ system , resulted in a strain that was as susceptible to poly-myxin B as a phoP mutant.The most frequently recovered clone harboured the yqjA gene , which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP-1 .	1	SUMMARY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pmrA	activator	17693506	6	att	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid-A modifications explain most of the alterations in the passive permeability of the OM bilayer .	208	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid A modifications explain most of the alterations in the passive permeability of the OM bilayer .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	pmrA	activator	32209674	25	att	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	206	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrA	activator	32209674	34	att	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	292	Strains defective in the PhoP-activated rstA and pmrA genes retained wild-type H-NS amounts ( SI Appendix , Fig .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	hlyE	regulator	30020426	0	ver/dev	In S. Typhi , the expression of hlyE is under the control of the transcriptional regulatory protein PhoP , a master regulator of intracellular survival of S. enterica .	172	In S. Typhi , the expression of hlyE is under the control of the transcriptional regulatory protein PhoP [ 17 , 37 ] , a master regulator of intracellular survival of S. enterica .	14	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	hlyE	regulator	30020426	0	ver/dev	In S. Typhi , the expression of hlyE is under the control of the transcriptional regulatory protein PhoP , a master regulator of intracellular survival of S. enterica .	172	In S. Typhi , the expression of hlyE is under the control of the transcriptional regulatory protein PhoP [ 17 , 37 ] , a master regulator of intracellular survival of S. enterica .	14	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ompF	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-2 genes by SsrB resembles the reciprocal control of ompF transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ompF	regulator	28704543	50	ver/dev	The inverse regulation of the SPI-1 genes by SsrB resembles the reciprocal control of ompF transcription by OmpR .	307	The inverse regulation of the SPI-1 and SPI-2 genes by SsrB resembles the reciprocal control of ompC and ompF transcription by OmpR .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssaR	regulator	17630976	11	ver/dev	There was no evidence of SsrB binding at ssaR .	116	There was no evidence of SsrB binding at ssaH and ssaR .	5	THE ISOLATED C-TERMINUS OF SSRB (SSRBC) BINDS TO MULTIPLE TARGETS WITHIN SPI-2	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
SsrB	gene	ssrB	activator	11918798	1	ver/dev	Intracellular induction of HA-tagged PipB expression is not detected for an SsrB mutant ( ssrB : : kan ) .	131	Intracellular induction of HA-tagged PipB expression is not detected for an SsrB mutant ( ssrB : : kan ) .	5	SPI-5 GENES HAVE A DIFFERENTIAL EXPRESSION PATTERN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SsrB	gene	ssrB	activator	14641178	0	ver/dev	The activation of the reporter fusion was dependent on the function of SsrB , as no induction was observed in the ssrB background .	86	The activation of the reporter fusion was dependent on the function of SsrB , as no induction was observed in the ssrB background .	7	BM-DC WERE INFECTED WITH S. TYPHIMURIUM STRAINS HARBOURING GFP REPORTER PLASMIDS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SsrB	gene	ssrB	activator	15491370	4	ver/dev	The response regulator SsrB , in turn , is autoregulated , activating ssrB	37	The response regulator SsrB , in turn , is autoregulated , activating ssrB , ssrA and spiC ( Feng et al. , 2003 ) , as well as other genes located both inside and outside of	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssrB	activator	15491370	9	ver/dev	SsrB , in turn , activates ssrB .	88	SsrB , in turn , activates ssrB , ssrA and spiC ( ssaB ) as well as additional genes , including srfH .	7	SSRB AND OMPR ACTIVATE SRFH	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssrB	activator	17630976	31	att	SsrB-dependent gene expression in-vivo was determined by measuring b-galactosidase activity of wild-type and ssrB null Salmonella Typhimurium strains growing in macrophages at various time points post infection .	256	SsrB-dependent gene expression in vivo was determined by measuring b-galactosidase activity of wild-type and ssrB null Salmonella Typhimurium strains growing in macrophages at various time points post infection .	8	ACTIVATION OF SPI-2 GENES IN VITRO REQUIRES SSRB AND ACIDIC PH	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssrB	activator	23690578	4	att	An ssrB null mutant is highly attenuated for virulence in mice inoculated by the i.p. route ( 23 ) , consistent with the notion that the SsrB-dependent Spi/Ssa system is required for pathogen growth in deep tissues .	30	An ssrB null mutant is highly attenuated for virulence in mice inoculated by the i.p. route ( 23 ) , consistent with the notion that the SsrB-dependent Spi/Ssa system is required for pathogen growth in deep tissues .	3	SALMONELLA PATHOGENICITY ISLAND 2 | CYTOTOXICITY	Mus sp.	0	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssrB	activator	23690578	24	ver/dev	PmrA 's action at the ssrB promoter is not simply to antagonize activation of ssrB transcription by the SsrB protein because the levels of β-galactosidase activit were higher in the pmrA mutant than in the wild-type strai even though this fusion was driven by the heterologous lac promoter derivative plac1 -- 6 .	93	PmrA 's action at the ssrB promoter is not simply to antagonize activation of ssrB transcription by the SsrB protein because the levels of β-galactosidase activity originating from a plasmid-linked ssrB-lacZ transcriptional fusion were higher in the pmrA mutant than in the wild-type strain and the ssrB mutant ( Fig. 4D ) even though this fusion was driven by the heterologous lac promoter derivative plac1 -- 6 ( 35 ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Other	NEG	Other	Level 1
SsrB	gene	ssrB	activator	23690578	26	ver/dev	These results demonstrated that SsrB is necessary to activate the ssrB promoter even in the absence of PmrA repression .	98	These results demonstrated that SsrB is necessary to activate the ssrB promoter even in the absence of PmrA repression .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SsrB	gene	ssrB	activator	24643535	14	ver/dev	Because the putative 19-bp Fur box is located only 5 bp because Fur binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .	265	Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site ( 7 , 33 ) on the ssrB promoter ( Fig. 4A ) , and because Fur binds to regions larger than the Fur box ( 31 bp ) ( 11 ) , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .	7	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	ssrB	activator	24643535	14	ver/dev	Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site on Fig. 4A binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .	265	Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site ( 7 , 33 ) on the ssrB promoter ( Fig. 4A ) , and because Fur binds to regions larger than the Fur box ( 31 bp ) ( 11 ) , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .	7	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	ssrB	activator	24643535	14	ver/dev	Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site on the ssrB promoter binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .	265	Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site ( 7 , 33 ) on the ssrB promoter ( Fig. 4A ) , and because Fur binds to regions larger than the Fur box ( 31 bp ) ( 11 ) , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .	7	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
SsrB	gene	ssrB	activator	29930310	17	ver/dev	ssrB genes led to enhanced expression of SsrB protein	160	Salmonella expressing ssrADsc overexpressed ssrA and ssrB genes , which led to enhanced expression of SsrB protein and the downstream ssaG gene .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SsrB	gene	ssrB	activator	33045730	68	att	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type or defective SsrB binding site in the ugtL-sifB intergenic region ( ugtL-sifBmu ; Figure 3B ) , and , as controls , mutants lacking the ssrB or sifB genes .	288	To determine whether the SsrB-dependent activation of PhoP in mildly acidic pH is necessary for virulence , we compared a set of isogenic strains with a wild-type or defective SsrB binding site in the ugtL-sifB intergenic region ( ugtL-sifBmu ; Figure 3B ) , and , as controls , mutants lacking the ssrB or sifB genes .	29	SSRB-DEPENDENT ACTIVATION OF THE UGTL GENE IS NECESSARY FOR VIRULENCE	nan	1	L3	SPEC	Analysis	NEG	Other	Level 1
SsrB	gene	ssrB	activator	33045730	76	att	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	333	The behavior of the ugtL and pagC genes is in contrast to that of ssrB and the SsrB-activated ssaG gene ( 58 ) .	31	PHOP AND SSRB EXHIBIT DIFFERENT ACTIVATION KINETICS WHEN S. TYPHIMURIUM IS INSIDE MACROPHAGES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SsrB	gene	ssrB	activator	33045730	7	ver/dev	S. Typhimurium acquired the ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in purple , enables activation of virulence .	65	S. Typhimurium acquired the spiR and ssrB genes by horizontal gene transfer , which , together with the evolution of an SsrB binding site in the ugtL promoter ( purple ) , enables activation of PhoP/PhoQ in mildly acidic pH ( by promoting transcription of ugtL and phoP genes ) and virulence .	8	QUANTITATIVE RT-PCR (QRT-PCR)	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
TdcR	gene	tdcA	activator	21464594	0	ver/dev	These results suggest that the induction of tdcA expression by anaerobic conditions is observable when tdcA expression is low owing to the absence of TdcR .	15	These results suggest that the induction of tdcA expression by anaerobic conditions is observable when tdcA expression is low owing to the absence of TdcR .	2	RECEIVED: OCTOBER 11, 2010 / REVISED: DECEMBER 24, 2010 / ACCEPTED: DECEMBER 25, 2010	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
TdcR	gene	tdcA	activator	21464594	3	ver/dev	In S. Typhimurium , TdcR overexpression increased tdcA expression under both conditions .	55	In S. Typhimurium , TdcR overexpression increased tdcA expression under both conditions .	2	RECEIVED: OCTOBER 11, 2010 / REVISED: DECEMBER 24, 2010 / ACCEPTED: DECEMBER 25, 2010	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ssrA	regulator	25375226	36	ver/dev	four H-NS _ regulated ssrA	436	Transcript levels of four H-NS regulated genes , proV , ssrA , yciG and hilA , were measured by reverse transcriptase QPCR in a Dhns/DstpA strain expressing StpAWT or the variants StpAM4T , StpAA77D and StpAF21C .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ssrA	regulator	30718301	71	ver/dev	Under inducing HilD -LRB- as during-growth in LB -RRB- or only SlyA -LRB- as during-growth in N-MM -RRB- displace the H-NS complex bound to the promoter upstream of ssrA .	213	Under inducing conditions , SlyA and HilD ( as during growth in LB ) or only SlyA ( as during growth in N-MM ) displace the H-NS complex bound to the promoter upstream of ssrA .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ssrA	regulator	30718301	71	ver/dev	Under inducing SlyA -LRB- as during-growth in LB -RRB- or only SlyA -LRB- as during-growth in N-MM -RRB- displace the H-NS complex bound to the promoter upstream of ssrA .	213	Under inducing conditions , SlyA and HilD ( as during growth in LB ) or only SlyA ( as during growth in N-MM ) displace the H-NS complex bound to the promoter upstream of ssrA .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	ssrA	regulator	30718301	71	ver/dev	Under inducing conditions -LRB- as during-growth in LB -RRB- or only SlyA -LRB- as during-growth in N-MM -RRB- displace the H-NS complex bound to the promoter upstream of ssrA .	213	Under inducing conditions , SlyA and HilD ( as during growth in LB ) or only SlyA ( as during growth in N-MM ) displace the H-NS complex bound to the promoter upstream of ssrA .	5	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PocR	gene	pduF	repressor	8636018	1	ver/dev	Additionally , since it has been suggested that insertions in pduF may exert polarity onto the downstream pocR gene , pduF mutants may also have decreased amounts of PocR protein .	167	Additionally , since it has been suggested that insertions in pduF may exert polarity onto the downstream pocR gene , pduF mutants may also have decreased amounts of PocR protein ( 8 ) .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CadC	gene	ompC	activator	33854491	14	ver/dev	In this respect , CadC transcriptional factors have been reported to positively regulate ompC .	293	In this respect , the CpxRA and CadC transcriptional factors have been reported to positively regulate ompC ( Batchelor et al. , 2005 ; Lee et al. , 2007 ; De la Cruz and Calva , 2010 ) .	20	B	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	orby , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	.L. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	rown , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	.J. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	arshall , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	lank , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	awley , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	.L. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	obman , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	.R. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	12023084	2	ver/dev	rocklehurst , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	215	[ 13 ] Brocklehurst , K.R. , Hobman , J.L. , Lawley , B. , Blank , L. , Marshall , S.J. , Brown , N.L. and Morby , A.P. ( 1999 ) ZntR is a Zn ( II ) - respon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .	22	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	21722794	14	ver/dev	ZntR is responsive MerR-like transcriptional regulator of zntA in Escherichia coli .	898	ZntR is a Zn ( II ) - responsive MerR-like transcriptional regulator of zntA in Escherichia coli .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	24858080	1	ver/dev	zntA , _ predicted to be regulated by ZntR , , as shown in E. coli	43	Salmonella also encodes a cytoplasmic Zn ( II ) exporter , zntA , predicted to be regulated by a MerR-like sensor , ZntR , and to be expressed during Zn overload , as shown in E. coli ( Brocklehurst et al. , 1999 ) .	2	3THESE TWO AUTHORS CONTRIBUTED EQUALLY TO THIS WORK.	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	24858080	13	ver/dev	ZntR is responsive MerR-like transcriptional regulator of zntA in Escherichia coli .	591	ZntR is a Zn ( II ) - responsive MerR-like transcriptional regulator of zntA in Escherichia coli .	19	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	24970347	0	ver/dev	The zntA gene is under the control of the transcriptional activator ZntR .	35	The zntA gene is under the control of the transcriptional activator ZntR , which is a member of the MerR-like proteins ( Brocklehurst et al. 1999 ) that senses in vivo nano-molar variation of intracellular free zinc ( Wang et al. 2012 ) and can also bind cadmium and lead ( Binet and Poole 2000 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
ZntR	gene	zntA	regulator	24970347	2	ver/dev	Toxicol Appl Pharmacol 204 :274 -- 308 Brocklehurst KR , Hobman JL , Lawley B , Blank L , Marshall SJ , Brown NL , Morby AP ZntR is responsive MerR-like transcriptional regulator of zntA in Escherichia coli .	244	Toxicol Appl Pharmacol 204 ( 3 ) :274 -- 308 Brocklehurst KR , Hobman JL , Lawley B , Blank L , Marshall SJ , Brown NL , Morby AP ( 1999 ) ZntR is a Zn ( II ) - responsive MerR-like transcriptional regulator of zntA in Escherichia coli .	20	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
Hha	gene	ssrA	regulator	29751061	2	ver/dev	Hha , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated .	236	Other SPI-2 regulators , such as YdgT , Hha and IHF , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated [ 21,24,25 ] .	19	4. DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Fis	gene	dnaA	regulator	22911678	2	ver/dev	Besides , Fis can bind to the transcription start site of dnaA operon to suppress its expression .	39	Besides , Fis can bind to the transcription start site of dnaA operon to suppress its expression [ 12 ] .	3	INTRODUCTION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
OmpR	gene	cadB	repressor	25875623	8	ver/dev	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadB .	248	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC and cadB .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	cadB	repressor	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in SCV of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadB	repressor	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in the Salmonellacontaining vacuole of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadB	repressor	29214489	15	ver/dev	Activated OmpR then represses the cadC/BA operon by directly binding to both cadB promo-ters , leading to cytoplasmic acidification .	163	Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC and cadB promo-ters , leading to cytoplasmic acidification and reduced flagellation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	sbmC	regulator	21102598	3	ver/dev	The Escherichia coli SOS gene sbmC is regulated by RpoS during stationary growth phase .	412	The Escherichia coli SOS gene sbmC is regulated by H-NS and RpoS during the SOS induction and stationary growth phase .	13	ACKNOWLEDGEMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	sbmC	regulator	21102598	3	ver/dev	The Escherichia coli SOS gene sbmC is regulated by RpoS during the SOS-induction .	412	The Escherichia coli SOS gene sbmC is regulated by H-NS and RpoS during the SOS induction and stationary growth phase .	13	ACKNOWLEDGEMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
CysB	gene	cysJIH	repressor	2105304	16	ver/dev	Inhibition of CysB protein binding to a cysJIH promoter fragment by sulfide .	205	Inhibition of CysB protein binding to a cysJIH promoter fragment by sulfide .	6	GLUTATHIONE NONE 0.36 4.8	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CysB	gene	cysJIH	repressor	25637663	3	ver/dev	Unexpectedly , CysB downregulated cysJIH operon .	18	Unexpectedly , CysB downregulated cysJIH operon when cysteine was used instead of sulfate , suggesting a complex regulation of this system .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	tolC	activator	11036033	1	ver/dev	Like marRAB , tolC are positively regulated by MarA .	17	Like marRAB , acrAB and tolC are positively regulated by MarA , SoxS , and Rob ( 2 , 7 , 25 , 32 ) .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	tolC	activator	16842216	0	ver/dev	The global regulatory proteins MarA are primarily responsible for activation of tolC transcription .	343	The global regulatory proteins MarA , SoxS and Rob are primarily responsible for activation of acrAB and tolC transcription .	6	3.2. ACRAB-TOLC EFFLUX SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	tolC	activator	18984645	1	ver/dev	8 -- 13 _ shown that MarA , play a role in antimicrobial resistance by activating tolC	21	Studies in Escherichia coli have 8 -- 13 shown that transcriptional activators , such as MarA , SoxS and Rob , play a role in antimicrobial resistance by activating transcription of efflux pumps , including acrAB and tolC .	4	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	tolC	activator	19230852	21	ver/dev	Martin , Transcriptional activation by MarA of two tolC promoters using a complex promoter configuration for tolC in Escherichia coli , Mol .	635	Martin , Transcriptional activation by MarA of two tolC promoters using one binding site : a complex promoter configuration for tolC in Escherichia coli , Mol .	40	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	tolC	activator	19230852	21	ver/dev	Martin , Transcriptional activation by MarA of two tolC promoters using one binding site in Escherichia coli , Mol .	635	Martin , Transcriptional activation by MarA of two tolC promoters using one binding site : a complex promoter configuration for tolC in Escherichia coli , Mol .	40	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MarA	gene	tolC	activator	23493314	0	ver/dev	MarA is induced following tolC .5,9,10	23	MarA is induced following salicylate treatment ,5 SoxS in response to superoxide and Rob following treatment with bile salts and dipyridyl .6 -- 8 Up-regulation of these transcription factors has been shown to increase the expression of several genes , including acrAB and tolC .5,9,10	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	tolC	activator	34202800	6	ver/dev	MarA , , are involved in activating tolC expression .	254	Three homologous transcriptional activators , RamA , SoxS , and MarA , controlled by RamR , SoxR , and MarR , are involved in activating acrB and tolC expression [ 68 ] .	6	3.1. THE TETR FAMILY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	flhD	regulator	24031550	14	ver/dev	However , translational regulator for flhD expression in E. coli in z66 revealed that OmpR did condition .	351	However , translational regulator for flhD expression in E. coli in the high osmolarity expression investigation of fljB : z66 revealed that OmpR did condition ( 22 ) .	6	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	flhD	regulator	24031550	14	ver/dev	However , translational regulator for flhD expression in E. coli in the high-osmolarity expression investigation of fljB revealed that OmpR did condition .	351	However , translational regulator for flhD expression in E. coli in the high osmolarity expression investigation of fljB : z66 revealed that OmpR did condition ( 22 ) .	6	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
RamA	gene	tolC	regulator	18577510	23	ver/dev	RamA binds to the upstream region of tolC .	222	RamA binds to the upstream region of acrA and tolC .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	tolC	regulator	18577510	27	ver/dev	Bile RamA directly controls the expression of tolC .	236	Bile RamA directly controls the expression of acrAB and tolC .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RamA	gene	tolC	regulator	21858134	2	ver/dev	It has been confirmed that RamA can bind to the upstream promoter region of tolC .	48	It has been confirmed that RamA can bind to the upstream promoter region of acrAB and tolC and increase the expression level of the efflux [ 16 ] .	4	INTRODUCTION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RamA	gene	tolC	regulator	23230062	0	ver/dev	Activation of tolC gene transcription is achieved through the direct binding of RamA , to the operator regions of these genes .	27	Activation of the acrAB operon and tolC gene transcription is achieved through the direct binding of RamA , a positive regulator of the AraC/XylS family , to the operator regions of these genes [ 13 , 14 ] .	4	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhD	gene	flhD	activator	16430704	6	ver/dev	The FlhD levels were determined by immunoblotting analysis at various times after flhD transcription was induced by 50 µM IPTG .	171	The FlhD and FlhC levels were determined by immunoblotting analysis at various times after flhD and flhC transcription was induced by 50 µM IPTG .	6	THE DNAK CHAPERONE MACHINERY IS NOT ESSENTIAL FOR ASSEMBLING OF FLHD AND FLHC PROTEINS INTO THE FLHD2C2 COMPLEX	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	fadD	regulator	23782700	10	att	These findings also indicate that the basal down-regulation in the PhoP-regulated gene expression observed in the fadD mutant strain ( Fig. 6 ) is attrib-utable to a reduction in PhoQ autokinase activity caused by accumulation of LCUFAs together with a decrease in PhoQ protein levels due to phoPQ autoregulation combined with diminished PhoQ or stability in the fadD background .	326	These findings also indicate that the basal down-regulation in the PhoP-regulated gene expression observed in the fadD mutant strain ( Fig. 6 ) is attrib-utable to a reduction in PhoQ autokinase activity caused by accumulation of LCUFAs together with a decrease in PhoQ protein levels due to phoPQ autoregulation combined with diminished PhoQ or stability in the fadD background .	4	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MarA	gene	acrR	repressor	18407759	2	ver/dev	Although MarA can act as an activator or repressor depending on the gene it is regulating , the repression of acrR allows expression of acrAB .	255	Although MarA can act as an activator or repressor depending on the orientation of the mar box and the gene it is regulating , the repression of acrR allows expression of acrAB .	19	EFFLUX SYSTEMS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
MarA	gene	acrR	repressor	18407759	2	ver/dev	Although MarA can act as an activator or repressor depending on the orientation of the mar box , the repression of acrR allows expression of acrAB .	255	Although MarA can act as an activator or repressor depending on the orientation of the mar box and the gene it is regulating , the repression of acrR allows expression of acrAB .	19	EFFLUX SYSTEMS	nan	1	L2	OTHER	Other	NEG	Other	Level 1
HNS	gene	cadC	repressor	25566242	5	ver/dev	Both cadC and dsrA are repressed by H-NS .	68	Both cadC and dsrA are repressed by H-NS ( 55 , 56 ) .	4	LEUO HISTORY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	spaS	activator	10692170	6	att	Because sicA has an InvF-dependent promoter , we wanted to determine whether , in addition to cis-polar effects , the spaS mutations could affect sicAsipBCDA expression in trans .	93	Because sicA has an InvF-dependent promoter , we wanted to determine whether , in addition to cis-polar effects , the spaS mutations could affect sicAsipBCDA expression in trans .	7	THE EXPRESSION OF GENES ENCODING SECRETED PROTEINS IS REDUCED IN A SPAS MUTANT	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
InvF	gene	spaS	activator	10844688	10	att	For example , sipC has two promoters : a HilA-dependent promoter upstream of spaS and an InvF-dependent promoter downstream of spaS ( Darwin and Miller , 1999b ) .	275	For example , sipC has two promoters : a HilA-dependent promoter upstream of spaS and an InvF-dependent promoter downstream of spaS ( Darwin and Miller , 1999b ) .	15	MODELS FOR INVASION GENE REGULATION IN VITRO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
FlhC	gene	fliA	activator	16430704	0	ver/dev	In turn , fliA is positively controlled by FlhC .	79	In turn , fliA is positively controlled by the gene products FlhD and FlhC , which are encoded by the sole operon lying at the apex of the hierarchy .	5	THE SALMONELLA DNAK MUTANT IS DEFECTIVE IN FLAGELLUM BIOGENESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FlhC	gene	fliA	activator	16430704	1	ver/dev	The FlhC proteins act together in an FlhD2C2 hetero-tetramer to activate the σ70 promoter of fliA gene .	86	The FlhD and FlhC proteins act together in an FlhD2C2 hetero-tetramer to activate the σ70 promoter of fliA gene ( Ikebe et al. , 1999 ) .	5	THE SALMONELLA DNAK MUTANT IS DEFECTIVE IN FLAGELLUM BIOGENESIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	regulator	17555437	1	ver/dev	In the presence of Mn , MntR represses the expression of mntH , through direct binding of specific sites within the promoter regions of these genes .	270	In the presence of Mn ( 2 + ) , MntR represses the expression of mntH and sitABCD , through direct binding of specific sites within the promoter regions of these genes .	8	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	regulator	24596096	0	ver/dev	MntR , plays a major role in regulating mntH expression in Bacillus subtilis .	45	MntR , plays a major role in regulating mntH expression in Bacillus subtilis .	4	MAIN	Bacillus subtilis	0	L3	OTHER	Other	OTHER	New	Level 2
MntR	gene	mntH	regulator	24596096	6	ver/dev	Expression of Salmonella mntH gene is regulated by both MntR-dependent .	183	Expression of Salmonella mntH gene is regulated by both MntR-dependent and - independent mechanisms .	5	MATERIALS AND METHODS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
MntR	gene	mntH	regulator	28553268	0	att	The Fur - and MntR-controlled mntH gene , also involved in Mn2 + and Fe2 + uptake ( with a preference for Mn2 + ) , was also induced but in lesser extent ( up to 2.1-fold at 45 min ) .	207	The Fur - and MntR-controlled mntH gene , also involved in Mn2 + and Fe2 + uptake ( with a preference for Mn2 + ) , was also induced but in lesser extent ( up to 2.1-fold at 45 min ) .	19	HIGHLIGHTED FOLD CHANGES CORRESPOND TO UP-REGULATED (DARK GRAY) AND DOWN-REGULATED (LIGHT GRAY) GENES. (N.S., NON-SIGNIFICANT), FOLD CHANGES WITH P > 0.05.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	def	regulator	19525399	5	att	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	175	However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .	3	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
LexA	gene	def	regulator	20421601	1	att	The increase in mutation rates in the lexA ( def ) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho .	9	The increase in mutation rates in the lexA ( def ) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	def	regulator	20421601	6	att	To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .	121	To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .	4	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
InvF	gene	sipBCDA	activator	25128737	0	ver/dev	Along with InvF , SicA is required for transcription activation of several virulence genes like sipBCDA .	187	Along with InvF , SicA is required for transcription activation of several virulence genes like sigDE ( sopB , pipC ) , sipBCDA , and sopE ( Darwin et al. , 2001 ) .	19	3.3. THE FIVE INDIVIDUAL SPI AND COMBINED INTERACTOMES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
InvF	gene	sipBCDA	activator	25128737	2	ver/dev	As had already been mentioned earlier , along with SicA , InvF helps in the transcriptional activation of several virulence genes , out of which sipBCDA are noteworthy .	345	As had already been mentioned earlier , along with SicA , InvF helps in the transcriptional activation of several virulence genes , out of which sipBCDA are noteworthy .	23	3.8. COMPARATIVE ANALYSES OF INDISPENSABLE SICA	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	tdcA	repressor	20396961	6	ver/dev	The four PhoP-dependent genes were not strongly downregulated by the tdcA mutation in cultures , whereas the gene , showed significantly reduced expression in the tdcA mutant strains inside macrophages .	296	The four PhoP-dependent genes tested were not strongly downregulated by the tdcA mutation in cultures , whereas the gene encoding the SPI2-associated apparatus protein SsaG , which was induced by about 400-fold in the intracellular environment ( Valdivia and Falkow , 1997 ) , showed significantly reduced expression in the tdcA mutant strains inside macrophages ( Figs. 5F and 6 ) .	12	DISCUSSION	nan	1	L2	OTHER	Analysis	NEG	Other	Level 1
CadC	gene	cadC	regulator	18487329	12	ver/dev	ACYC184-HA-CadC , was expressed under the control of the cadC promoter in the cadC strain .	228	( A ) pACYC184-HA-CadC , encoding a CadC derivative with an N-terminal HA tag ( HA-CadC ) , was expressed under the control of the cadC promoter in the cadC strain .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	hns	regulator	19406898	7	ver/dev	This smaller effect could be due to the lowering of the affinity of the binding of StpA in an hns background , as shown in Fig. 5D .	103	This smaller effect could be due to the lowering of the affinity of the binding of StpA in an hns background , as shown in Fig. 5D .	10	DNA CURVATURE IS REQUIRED FOR THE NEGATIVE REGULATION OF OMPS1 EXPRESSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
StpA	gene	hns	regulator	19843227	13	ver/dev	It has been reported that StpA can negatively regulate expression of a reporter gene under the control of the hns promoter in E. coli ; although this could only be observed in the absence of hns , this raised the possibility that StpA-dependent gene expression could simply reflect changes in the level of H-NS .	77	It has been reported that StpA can negatively regulate expression of a reporter gene under the control of the hns promoter in E. coli ( Zhang et al. , 1996 ) ; although this could only be observed in the absence of hns , this raised the possibility that StpA-dependent gene expression could simply reflect changes in the level of H-NS .	7	IDENTIFICATION OF THE STPA REGULON	Escherichia coli	0	L1	SPEC	Analysis	OTHER	Other	Level 1
PutA	gene	putA	repressor	33593945	4	auto	PutA also contains a DNA binding domain that controls , via repression , its own expression ( putA ) as well as that of the divergently transcribed putP gene , encoding the proline importer PutP .	208	PutA also contains a DNA binding domain that controls , via repression , its own expression ( putA ) as well as that of the divergently transcribed putP gene , encoding the proline importer PutP .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	lacZ	activator	12753201	29	att	The b-galac-tosidase activity of ssrA -- lacZ in J774 mouse macrophages ( from Fig. 2A ) is also included in the rightmost columns ( n = 6 ) for a comparison of OmpR-dependent ssrA activation observed in Salmonella-infected macrophages but not in Salmonella cultures in-vitro .	195	The b-galac-tosidase activity of ssrA -- lacZ in J774 mouse macrophages ( from Fig. 2A ) is also included in the rightmost columns ( n = 6 ) for a comparison of OmpR-dependent ssrA activation observed in Salmonella-infected macrophages but not in Salmonella cultures in vitro .	9	PHOSPHORYLATION OF OMPR INCREASES ITS AFFINITY FOR SSRA	Mus musculus;Salmonella;Salmonella;Salmonella	0.5	L3	OTHER	Other	NEG	Other	Level 1
OmpR	gene	lacZ	activator	12753201	7	att	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	73	The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .	5	CLONING OF THE SPIC-SSRA/B REGULATORY REGION AND IDENTIFICATION OF THE REGULATORY REGIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	fliA	regulator	11237608	0	ver/dev	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by ¯ iA * mutan .	50	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino acid residues of s28 that interact with FlgM , we carried out a selection for ¯ iA mutants defective for negative regulation by FlgM ( ¯ iA * mutants ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	fliA	regulator	11237608	0	ver/dev	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by ¯ iA * mutan .	50	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino acid residues of s28 that interact with FlgM , we carried out a selection for ¯ iA mutants defective for negative regulation by FlgM ( ¯ iA * mutants ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	fliA	regulator	11237608	0	ver/dev	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by Flg .	50	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino acid residues of s28 that interact with FlgM , we carried out a selection for ¯ iA mutants defective for negative regulation by FlgM ( ¯ iA * mutants ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Sigma28	gene	fliA	regulator	11237608	0	ver/dev	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by Flg .	50	Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino acid residues of s28 that interact with FlgM , we carried out a selection for ¯ iA mutants defective for negative regulation by FlgM ( ¯ iA * mutants ) .	4	RESULTS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	lacZ	regulator	12652904	0	att	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	123	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	12	RESULTS AND DISCUSSIONS	unidentified plasmid;Escherichia coli	0.5	L2	OTHER	Analysis	OTHER	Other	Level 1
Fur	gene	lacZ	regulator	12652904	0	att	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	123	Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .	12	RESULTS AND DISCUSSIONS	unidentified plasmid;Escherichia coli	0.5	L2	OTHER	Analysis	OTHER	Other	Level 1
StpA	gene	stpA	regulator	25375226	44	ver/dev	The StpA were incorporated into pHSG576 in the opposite orientation of such that stpA expression levels were controlled by the native stpA promoter .	565	The StpA coding sequence and promoter region were incorporated into pHSG576 in the opposite orientation of the lac promoter , such that stpA expression levels were controlled by the native stpA promoter .	13	PLASMID AND STRAIN CONSTRUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	stpA	regulator	25375226	44	ver/dev	The StpA were incorporated into pHSG576 in the opposite orientation of the lac promoter that stpA expression levels were controlled by the native stpA promoter .	565	The StpA coding sequence and promoter region were incorporated into pHSG576 in the opposite orientation of the lac promoter , such that stpA expression levels were controlled by the native stpA promoter .	13	PLASMID AND STRAIN CONSTRUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	ams	activator	12519186	27	att	C. Alignment of the RcsB-dependent regulatory sequences of S. enterica ( Se ) ugd , P. stewartii ( Ps ) cps , Erwinia amylovora ( Ea ) ams , E. coli ( Ec ) cps and E. coli ( Ec ) fts genes .	91	C. Alignment of the RcsB-dependent regulatory sequences of S. enterica ( Se ) ugd , P. stewartii ( Ps ) cps , Erwinia amylovora ( Ea ) ams , E. coli ( Ec ) cps and E. coli ( Ec ) fts genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	Salmonella;Salmonella;Erwinia amylovora;Escherichia coli;Escherichia coli	0.5	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	regulator	22149171	3	ver/dev	LeuO directly binds the sdiA promoter	10	We demonstrate that LeuO directly binds the sdiA promoter and the Rcs phosphorelay represses sdiA expression .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	regulator	22149171	25	ver/dev	LeuO binds the sdiA promoter	264	LeuO binds the sdiA promoter and is an activator of sdiA	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	regulator	22149171	27	ver/dev	LeuO bound the sdiA promoter , whereas no binding was detected with a negative control , the cysJ promoter -LRB- Fig. 4A , left -RRB- .	271	LeuO bound the sdiA promoter , whereas no binding was detected with a negative control , the cysJ promoter for which no predicted LeuO binding sites exist ( Fig. 4A , left ) .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	sdiA	regulator	22149171	28	ver/dev	LeuO was found to bind the region of sdiA between Fig. 4A , right .	272	LeuO was found to bind the region of sdiA between sdiA2 and sdiA3 ( Fig. 4A , right ) .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	sdiA	regulator	22149171	28	ver/dev	LeuO was found to bind the region of sdiA between sdiA3 .	272	LeuO was found to bind the region of sdiA between sdiA2 and sdiA3 ( Fig. 4A , right ) .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	sdiA	regulator	22149171	28	ver/dev	LeuO was found to bind the region of sdiA between sdiA2 .	272	LeuO was found to bind the region of sdiA between sdiA2 and sdiA3 ( Fig. 4A , right ) .	16	IDENTIFICATION OF THE SDIA TRANSCRIPTION START SITE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	sdiA	regulator	22149171	34	ver/dev	LeuO binds the sdiA promoter .	300	LeuO binds the sdiA promoter .	17	THE RCS PHOSPHORELAY NEGATIVELY REGULATES SDIA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	regulator	22149171	35	ver/dev	Middle panel : LeuO binds sdiA in two binding sites .	302	Middle panel : LeuO binds sdiA in two binding sites .	17	THE RCS PHOSPHORELAY NEGATIVELY REGULATES SDIA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LeuO	gene	sdiA	regulator	25566242	23	ver/dev	Transcriptional regulation of sdiA by LeuO in Salmonella enterica serovar Typhimurium .	531	Transcriptional regulation of sdiA by cAMP-receptor protein , LeuO , and environmental signals in Salmonella enterica serovar Typhimurium .	65	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OxyR	gene	dps	regulator	14742565	0	ver/dev	Expression of dps in E. coli has been shown to be regulated by OxyR .	15	Expression of dps in E. coli has been shown to be regulated by the stationary-phase sigma factor RpoS ( 38 ) , OxyR , and IHF ( 3 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
OxyR	gene	dps	regulator	18166161	0	ver/dev	Moreover , while in E. coli the expression of dps in logarithmic phase is modulated by the exposition to sources of hydrogen-peroxide -LRB- mediated by OxyR -RRB- , in the stationary-phase its expression is regulated by σ .	155	Moreover , while in E. coli the expression of dps in logarithmic phase is modulated by the exposition to sources of hydrogen peroxide ( mediated by OxyR ) , in the stationary phase its expression is regulated by σs and is not induced by this reactive oxygen species [ 34 ] .	13	3.2. SUSCEPTIBILITY OF S. TYPHIMURIUM TO SUPEROXIDE	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
OxyR	gene	dps	regulator	25028458	35	ver/dev	In addition , Yoo et al. suggested that , as in E. coli , the Salmonella dps gene could also be controlled by OxyR during exponential-growth .	336	In addition , Yoo et al. ( 2007 ) suggested that , as in E. coli , the Salmonella dps gene could also be controlled by OxyR during exponential growth .	7	DISCUSSION	Escherichia coli;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoB	gene	dnaK	activator	16574345	0	att	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	179	Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; stress-related dnaK , which encodes heat-shock protein Hsp70 ; cpxP , a periplasmic repressor of Cpx regulon ; and phoH , a PhoB-dependent , ATP-binding Pho regulon ( Table 2 ) .	15	3.1. MICROARRAY ANALYSIS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PhoP	gene	pmrAB	activator	15145463	8	ver/dev	I. PhoP activates ranscription of pmrAB .	354	[ 16 ] Gunn , J.S. and Miller , S.I. ( 1996 ) PhoP -- PhoQ activates transcription of pmrAB , encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrAB	activator	15145463	8	ver/dev	I. PhoP activates ranscription of pmrAB .	354	[ 16 ] Gunn , J.S. and Miller , S.I. ( 1996 ) PhoP -- PhoQ activates transcription of pmrAB , encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrAB	activator	15145463	8	ver/dev	I. PhoP activates ranscription of pmrAB .	354	[ 16 ] Gunn , J.S. and Miller , S.I. ( 1996 ) PhoP -- PhoQ activates transcription of pmrAB , encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrAB	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	pmrAB	activator	16023758	17	ver/dev	I. PhoP activates ranscription of pmrAB .	1161	[ 202 ] Gunn , J.S. and Miller , S.I. ( 1996 ) PhoP -- PhoQ activates transcription of pmrAB , encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance .	151	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrAB	activator	16023758	17	ver/dev	I. PhoP activates ranscription of pmrAB .	1161	[ 202 ] Gunn , J.S. and Miller , S.I. ( 1996 ) PhoP -- PhoQ activates transcription of pmrAB , encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance .	151	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pmrAB	activator	16023758	17	ver/dev	I. PhoP activates ranscription of pmrAB .	1161	[ 202 ] Gunn , J.S. and Miller , S.I. ( 1996 ) PhoP -- PhoQ activates transcription of pmrAB , encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance .	151	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
YafQ	gene	rho	regulator	30201777	24	ver/dev	tRNA-Val tRNA-Glu Transcriptional regulator of maltose regulon Toxin of YafQ-DinJ TA system Antitoxin to YafQ RNA repair , RNA 3 = - terminal-phosphate cyclase RNA repair , RNA-splicing ligase RNA repair , Ro 60-related ribonucleoprotein tRNA-Glu Pseudogene in rho operon leader region tRNA-Glu	234	tRNA-Val tRNA-Glu Transcriptional regulator of maltose regulon Toxin of YafQ-DinJ TA system Antitoxin to YafQ RNA repair , RNA 3 = - terminal-phosphate cyclase RNA repair , RNA-splicing ligase RNA repair , Ro 60-related ribonucleoprotein tRNA-Glu Pseudogene in rho operon leader region tRNA-Glu	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	pepT	activator	16855381	0	att	We therefore tested the potential hypoxic induction of a promoter ( HIP ) derived from the FNR-dependent pepT promoter in attenuated Salmonella typhimurium .19 Here , we demonstrate that Salmonella grow as efficiently in both normoxic and hypoxic conditions and show that hypoxia induced bacterial promoters have the potential to increase the specificity of the Salmonella mediated gene delivery system by establishing spatial control of gene expression .	61	We therefore tested the potential hypoxic induction of a promoter ( HIP ) derived from the FNR-dependent pepT promoter in attenuated Salmonella typhimurium .19 Here , we demonstrate that Salmonella grow as efficiently in both normoxic and hypoxic conditions and show that hypoxia induced bacterial promoters have the potential to increase the specificity of the Salmonella mediated gene delivery system by establishing spatial control of gene expression .	4	INTRODUCTION D	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella;Salmonella	1	L1	OTHER	Analysis	OTHER	Other	Level 1
IHF	gene	dps	regulator	14742565	0	ver/dev	Expression of dps in E. coli has been shown to be regulated by IHF .	15	Expression of dps in E. coli has been shown to be regulated by the stationary-phase sigma factor RpoS ( 38 ) , OxyR , and IHF ( 3 ) .	2	MAIN	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
IHF	gene	dps	regulator	19223478	1	ver/dev	dps transcription is regulated in IHF-dependent manner	358	In E. coli , dps transcription is regulated in a sigma S - and IHF-dependent manner , and the IHF protein has been shown to bind upstream of the dps promoter ( 3 ) .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	yciG	activator	20713450	1	ver/dev	In Salmonella , YncC acts in concert with S to activate transcription at the yciG promoter .	13	In Salmonella , YncC acts in concert with S to activate transcription at the yciG promoter ( pyciG ) .	0	Unknown	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
YncC	gene	yciG	activator	20713450	21	ver/dev	The position of the YncC binding site , centered at -- 101 with respect to the transcription start site of yciG , is 10 bp upstream of the most distant transcription activators at simple 70-dependent promoters .	468	The position of the YncC binding site , centered at -- 101 with respect to the transcription start site of yciG , is 10 bp upstream of the most distant transcription activators at simple 70-dependent promoters .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
H	gene	fil	regulator	23515315	24	att	The 25 , primers , and the transcript levels of three H-NS-regulated 75 , and 100 M H-NS samples eluted from the S200 gel fil - genes were assessed by qPCR .	249	The 25 , primers , and the transcript levels of three H-NS-regulated 75 , and 100 M H-NS samples eluted from the S200 gel fil - genes were assessed by qPCR .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsrA	gene	csrB	repressor	16949866	43	ver/dev	While crp increases the expression of this report , the regulatory RNAs csrB and csrC inhibit the activity of CsrA protein .	520	While crp increases the expression of csrA ( this report ) , the regulatory RNAs csrB and csrC inhibit the activity of CsrA protein ( data from E. coli ; Liu and Romeo , 1997 ; Weilbacher et al. , 2003 ) .	19	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both the csrB/C genes are required , we hypothesize that fim gene expression requires the csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both the csrB/C genes are required , we hypothesize that fim gene expression requires the csrB RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both the csrB/C genes are required , we hypothesize that hilC gene expression requires the csrB RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both the csrB/C genes are required , we hypothesize that hilA gene expression requires the csrB RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both sirA are required , we hypothesize that fim gene expression requires the csrB RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both sirA are required , we hypothesize that hilC gene expression requires the csrB RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CsrA	gene	csrB	repressor	17074910	20	ver/dev	Given that both sirA are required , we hypothesize that hilA gene expression requires the csrB RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	511	Given that both sirA and the csrB/C genes are required , we hypothesize that hilA , hilC and fim gene expression requires SirA for transcription initiation , and requires the csrB and csrC RNAs for stabilization and/or translation of the messages ( via inhibition of CsrA activity ) .	10	CONCLUSIONS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	invH	repressor	26810370	0	att	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	202	Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( STM14_3470 to STM14_3473 ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( STM14_3481 approximately STM14_3484 ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( STM14_3491 approximately STM14_3499 ) , which were essential for invasion of cells ( Supplementary Table 4 ) .	10	RESULTS	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YgaE	gene	ompC	regulator	24592164	3	ver/dev	The regulation of YgaE to ompC seems more obvious than ompF due to the more abundant expression of ompC than ompF .	215	The regulation of YgaE to ompC seems more obvious than ompF , which may due to the more abundant expression of ompC than ompF .	8	3.2. YGAE REPRESSES THE EXPRESSION OF OMPF/OMPC AT THE	nan	1	L2	SPEC	Other	OTHER	New	Level 1
YgaE	gene	ompC	regulator	24592164	4	ver/dev	whether the regulation of YgaE to ompC is direct	216	However , whether the regulation of YgaE to ompC and ompF is direct and the concrete regulation mechanism still need further experiments to explore .	8	3.2. YGAE REPRESSES THE EXPRESSION OF OMPF/OMPC AT THE	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
YgaE	gene	ompC	regulator	24592164	6	ver/dev	This result suggested that YgaE does not influence the growth of S. Typhi by the regulation of ompC .	230	This result suggested that YgaE does not influence the growth of S. Typhi by the regulation of ompC and ompF .	9	3.3. YGAE DOES NOT AFFLFFLUENCE GROWTH AND ANTIBIOTIC SUSCEP-	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
StpA	gene	mgtA	regulator	23936152	1	ver/dev	mgtA genes _ known to be regulated by StpA respectively	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
StpA	gene	mgtA	regulator	23936152	1	ver/dev	mgtA genes _ known to be regulated by StpA respectively	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
StpA	gene	mgtA	regulator	23936152	1	ver/dev	mgtA genes _ known to be regulated by StpA respectively	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
StpA	gene	mgtA	regulator	23936152	1	ver/dev	mgtA genes _ known to be regulated by StpA respectively	347	To test whether the mutations in StpA and a PhoQ were affecting protein function positively or negatively , we tested how the reconstructed mutations affected expression of the RpoS regulated katE and the PhoQ regulated mgtA genes known to be regulated by StpA and PhoQ respectively [ 24,30 ] .	22	REGULATION OF VIRULENCE-GENE EXPRESSION	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
CpxR	gene	sseB	regulator	26300871	18	ver/dev	Taken together , these results show that CpxR represses the autoregulation of sseB located in SPI-2 .	390	Taken together , these results show that CpxR represses the autoregulation of HilD , which in turn affects the expression of hilA and thus the SPI-1 genes , as well as of other virulence genes regulated by HilD , such as ssrB and sseB located in SPI-2 .	16	T5-LAC PROMOTER OF PLASMID PCA-CPXR WAS INDUCED BY ADDING 50 ΜM IPTG AT THE BEGINNING OF THE BACTERIAL CULTURES.	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	invF	repressor	11123690	16	ver/dev	kan parent strain _ indicating that HilD can overcome the decreased expression of invF	136	The introduction of plasmid pJB1 , which carries hilD , into the S. typhimurium DhilA fis : : kan double mutant increased invF : : Tn5lacZY b-galacto-sidase levels 50-fold ( 94 Miller units ) compared with the DhilA fis : : kan parent strain ( 2 Miller units ) , indicating that HilD can overcome the decreased expression of invF : : Tn5lacZY in a fis mutant in a HilA-independent manner .	8	MOUSE VIRULENCE OF A S. TYPHIMURIUM FIS MUTANT IS DIMINISHED	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RpoS	gene	narU	regulator	21311887	2	att	The narUZY reported are RpoS-regulated , narU gene is involved in nitrite transport and is known to be necessary for the survival of E. coli during severe nutrient-starvation [ 33 ] , narZY is necessary for carbon-starvation-inducible thermotolerance and acid tolerance in S. typhimurium [ 32 ] .	128	The narUZY reported are RpoS-regulated , narU gene is involved in nitrite transport and is known to be necessary for the survival of E. coli during severe nutrient starvation [ 33 ] , narZY is necessary for carbon-starvation-inducible thermotolerance and acid tolerance in S. typhimurium [ 32 ] .	9	RESULTS AND DISCUSSION	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	0.5	L3	OTHER	Fact	OTHER	Other	Level 3
Hha	gene	hilD	regulator	17675384	10	ver/dev	Interestingly , Hha played no role in the regulation of the hilD promoter .	162	Interestingly , Hha played no role in the regulation of the hilD promoter .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
MviA	gene	rpoS	activator	12673058	6	ver/dev	Therefore , entry into stationary-phase does appear to regulate MviA activity , whereas upregulation of rpoS translation alone is responsible for acid shock accumulation .	199	Therefore , entry into stationary phase does appear to regulate MviA activity , whereas upregulation of rpoS translation alone is responsible for acid shock accumulation .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MviA	gene	rpoS	activator	12673058	7	ver/dev	Induction of ÛS in Nonstressed Cells Is Sufficient to Increase Half-Life The results presented thus far suggest that increases in rpoS expression can lead to increased ÛS half-li without affecting the activity of MviA .	200	Induction of ÛS in Nonstressed Cells Is Sufficient to Increase Half-Life The results presented thus far suggest that increases in rpoS expression can overwhelm the degradation complex and lead to increased ÛS half-life without affecting the activity of MviA .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MviA	gene	rpoS	activator	12673058	7	ver/dev	Induction of ÛS in Nonstressed Cells Is Sufficient to Increase Half-Life The results presented thus far suggest that increases in rpoS expression can overwhelm the degradation comple without affecting the activity of MviA .	200	Induction of ÛS in Nonstressed Cells Is Sufficient to Increase Half-Life The results presented thus far suggest that increases in rpoS expression can overwhelm the degradation complex and lead to increased ÛS half-life without affecting the activity of MviA .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
MviA	gene	rpoS	activator	12673058	8	ver/dev	Instead , increased rpoS translation produces an imbalance between the limited amount of MviA recognition protein in the cel , thus decreasing ÛS turnover .	212	Instead , increased rpoS translation produces an imbalance between the levels of ÛS and the limited amount of MviA recognition protein in the cell , thus decreasing ÛS turnover .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Rho	gene	chiP	activator	22895254	0	att	By studying the mechanism by which ChiX , upon pairing near the 59 end of the transcript , represses the distal gene in the operon , we discovered that the action of the sRNA induces Rho-dependent transcription termination within the chiP cistron .	7	By studying the mechanism by which ChiX , upon pairing near the 59 end of the transcript , represses the distal gene in the operon , we discovered that the action of the sRNA induces Rho-dependent transcription termination within the chiP cistron .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	chiP	activator	22895254	1	att	Mutational studies identified the chiP sequences responsible for Rho-dependent effects and revealed a requirement for NusG protein in the termination event .	43	Mutational studies identified the chiP sequences responsible for Rho-dependent effects and revealed a requirement for NusG protein in the termination event .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Rho	gene	chiP	activator	22895254	2	att	Altogether , the above results suggest that ChiX action on the nascent mRNA induces Rho-dependent transcription termination within the chiP portion of the chiPQ operon .	129	Altogether , the above results suggest that ChiX action on the nascent mRNA induces Rho-dependent transcription termination within the chiP portion of the chiPQ operon .	4	CHIX ACTIVITY INDUCES RHO-DEPENDENT POLARITY	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
Rho	gene	chiP	activator	22895254	3	att	To map the presumptive sites of Rho-dependent transcription termination , tandem UAA stop codons were introduced at several positions in the chromosomal chiP gene , and chiQ-lacZ expression was measured in the resulting strains .	131	To map the presumptive sites of Rho-dependent transcription termination , tandem UAA stop codons were introduced at several positions in the chromosomal chiP gene , and chiQ-lacZ expression was measured in the resulting strains .	5	PROFILING THE CHIP POLARITY GRADIENT BY STOP CODON SCANNING	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	chiP	activator	22895254	4	att	A significant part of this variation occurs within the interval between codons 63 and 108 , corresponding to the +275 to +410 segment of chiP mRNA ( Fig. 3B ) , suggesting the presence of a Rho-dependent polarity site within this segment .	135	A significant part of this variation occurs within the interval between codons 63 and 108 , corresponding to the +275 to +410 segment of chiP mRNA ( Fig. 3B ) , suggesting the presence of a Rho-dependent polarity site within this segment .	5	PROFILING THE CHIP POLARITY GRADIENT BY STOP CODON SCANNING	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	chiP	activator	22895254	5	att	Among these data are the detection of residual Rho-dependent polarity in the interval between codons 108 and 256 ( Fig. 3A ) , the increase in chiQ-lacZY expression in a chiP deletion mutant lacking a segment downstream from the rut site ( between base pairs 595 and 1203 ) ( see above ) , and the termination patterns from the in-vitro-transcription study described below .	157	Among these data are the detection of residual Rho-dependent polarity in the interval between codons 108 and 256 ( Fig. 3A ) , the increase in chiQ-lacZY expression in a chiP deletion mutant lacking a segment downstream from the rut site ( between base pairs 595 and 1203 ) ( see above ) , and the termination patterns from the in vitro transcription study described below .	6	A FUNCTIONAL RUT SITE IN THE EARLY PORTION OF THE CHIP GENE	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	chiP	activator	22895254	6	att	NusG requirement for Rho-dependent termination at the chiP rut site in-vitro	158	NusG requirement for Rho-dependent termination at the chiP rut site in vitro	7	NUSG REQUIREMENT FOR RHO-DEPENDENT TERMINATION AT THE CHIP RUT SITE IN VITRO	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	chiP	activator	22895254	7	att	We next examined whether chiP would be similarly susceptible to Rho-dependent termination in-vitro .	159	We next examined whether chiP would be similarly susceptible to Rho-dependent termination in vitro .	7	NUSG REQUIREMENT FOR RHO-DEPENDENT TERMINATION AT THE CHIP RUT SITE IN VITRO	nan	1	L1	SPEC	Investigation	OTHER	Other	Level 1
Rho	gene	chiP	activator	24450479	2	att	In addition , the repression of chiP translation by ChiX induces premature Rho-dependent transcription termination within the chiP gene , preventing expression of the chiQ gene ( encoding a putative lipoprotein of unknown function ) located immediately downstream of chiP and normally cotranscribed with the latter ( Bossi et al. , 2012 ) .	40	In addition , the repression of chiP translation by ChiX induces premature Rho-dependent transcription termination within the chiP gene , preventing expression of the chiQ gene ( encoding a putative lipoprotein of unknown function ) located immediately downstream of chiP and normally cotranscribed with the latter ( Bossi et al. , 2012 ) .	3	INTRODUCTION	unidentified	1	L2	SPEC	Fact	OTHER	New	Level 1
Rho	gene	chiP	activator	24450479	2	att	In addition , the repression of chiP translation by ChiX induces premature Rho-dependent transcription termination within the chiP gene , preventing expression of the chiQ gene ( encoding a putative lipoprotein of unknown function ) located immediately downstream of chiP and normally cotranscribed with the latter ( Bossi et al. , 2012 ) .	40	In addition , the repression of chiP translation by ChiX induces premature Rho-dependent transcription termination within the chiP gene , preventing expression of the chiQ gene ( encoding a putative lipoprotein of unknown function ) located immediately downstream of chiP and normally cotranscribed with the latter ( Bossi et al. , 2012 ) .	3	INTRODUCTION	unidentified	1	L2	SPEC	Fact	OTHER	New	Level 1
OmpR	gene	tviA	regulator	20363312	3	ver/dev	So , it is possible that OmpR independently regulate the expression of tviA in S. typhi at osmotic-stress .	118	So , it is possible that Hfq and OmpR independently regulate the expression of tviA in S. typhi at osmotic stress .	4	3. DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	Other	Level 1
OmpR	gene	tviA	regulator	23982073	0	ver/dev	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of CD11c dendritic cells in the lamina .	309	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR and RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes and CD11c dendritic cells in the lamina ( 37 -- 39 ) .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	tviA	regulator	23982073	0	ver/dev	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes dendritic cells in the lamina .	309	Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR and RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes and CD11c dendritic cells in the lamina ( 37 -- 39 ) .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
OmpR	gene	tviA	regulator	29417203	0	ver/dev	OmpR binds to the promoters of tviA to activate their transcription ; however , it negatively regulates hfq in an indirect manner .	9	OmpR binds to the promoters of tviA and its own genes to activate their transcription ; however , it positively regulates tviB and negatively regulates hfq in an indirect manner .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	tviA	regulator	29417203	0	ver/dev	OmpR binds to the promoters of tviA to activate their transcription ; however , it positively regulates tviB .	9	OmpR binds to the promoters of tviA and its own genes to activate their transcription ; however , it positively regulates tviB and negatively regulates hfq in an indirect manner .	2	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	tviA	regulator	29417203	2	ver/dev	OmpR also binds to the promoter of tviA to activate its transcription .	34	OmpR also binds to the promoter of tviA to activate its transcription , and thus act as an activator of Vi antigen [ 15 , 19 ] .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	tviA	regulator	29417203	5	ver/dev	These results indicated that the transcription of tviA was under negative control of OmpR , respectively .	92	These results indicated that the transcription of tviA and tviB was under positive and negative control of OmpR and Hfq , respectively .	12	REGULATION OF TVIA AND TVIB BY OMPR AND HFQ	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	tviA	regulator	29417203	5	ver/dev	These results indicated that the transcription of tviA was under positive control of OmpR , respectively .	92	These results indicated that the transcription of tviA and tviB was under positive and negative control of OmpR and Hfq , respectively .	12	REGULATION OF TVIA AND TVIB BY OMPR AND HFQ	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	tviA	regulator	29417203	7	ver/dev	Fig. 3 OmpR regulate tviA transcription under osmotic-stress condition .	101	Fig. 3 OmpR and Hfq regulate tviA and tviB transcription under osmotic stress condition .	13	AUTOREGULATION AND RECIPROCAL REGULATION OF OMPR AND HFQ	nan	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	tviA	regulator	29417203	9	ver/dev	Thus , OmpR only directly regulates two , i.e. , tviA , of the four genes .	112	Thus , OmpR only directly regulates two , i.e. , tviA and ompR , of the four genes tested .	13	AUTOREGULATION AND RECIPROCAL REGULATION OF OMPR AND HFQ	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PmrA	gene	pmrA	activator	15205413	0	att	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid-A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	7	The aminoarabinose modification is required for resistance to the antibiotic polymyxin B , as mutations of the PmrA-activated pbg operon or ugd gene result in strains that lack aminoarabinose in their lipid A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance , as pbgP and ugd mutants are not as sensitive to polymyxin B as a pmrA mutant .	1	ABSTRACT	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PmrA	gene	pmrA	activator	15205413	17	att	It has been hypothesized that two promoters mediate the transcription of the pmrA and pmrB genes : a PmrA-activated promoter located upstream of the pmrC gene in the pmrCAB operon and a constitutive promoter located within the pmrC open reading frame .	271	It has been hypothesized that two promoters mediate the transcription of the pmrA and pmrB genes : a PmrA-activated promoter located upstream of the pmrC gene in the pmrCAB operon and a constitutive promoter located within the pmrC open reading frame .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrA	activator	15205413	8	att	The generated mutation ( designated pmrC1 ) was not polar on the pmrA and pmrB genes because the same levels of transcription of the PmrA-activated pbgP gene were displayed by isogenic wildtype and pmrC1 strains ( Fig. 1B ) .	149	The generated mutation ( designated pmrC1 ) was not polar on the pmrA and pmrB genes because the same levels of transcription of the PmrA-activated pbgP gene were displayed by isogenic wildtype and pmrC1 strains ( Fig. 1B ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	pmrA	activator	15205413	9	att	To examine whether the pmrC gene is necessary for the incorporation of phosphoethanolamine into lipid-A , we used negative-ion-mode MALDI-TOF mass spectrometry to analyze the lipid-A species from wild-type pbgP , pmrC1 .1 , and pmrA strains and strains grown at a low pH and with a low level of Mg2 , which are conditions that promote the transcription of PmrA-activated genes ( 41 ) .	155	To examine whether the pmrC gene is necessary for the incorporation of phosphoethanolamine into lipid A , we used negative-ion-mode MALDI-TOF mass spectrometry to analyze the lipid A species from wild-type pbgP , pmrC1 .1 , and pmrA strains and strains grown at a low pH and with a low level of Mg2 , which are conditions that promote the transcription of PmrA-activated genes ( 41 ) .	4	RESULTS	nan	1	L3	SPEC	Investigation	OTHER	Other	Level 1
PmrA	gene	pmrA	activator	15681155	6	att	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	190	Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .	11	3. RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PmrA	gene	pmrA	activator	19076233	3	att	To investigate whether the increased PM resistance observed in the DrpoN strain was linked to the PmrA-dependent pathway , double DrpoN pmrA505 and DrpoN pmrA : : CmR mutant strains were constructed and their resistance to PM were compared with the wild-type strain as well as with the single DrpoN , pmrA505 , and pmrA : : Cm mutants ( Fig. 2 ) .	104	To investigate whether the increased PM resistance observed in the DrpoN strain was linked to the PmrA-dependent pathway , double DrpoN pmrA505 and DrpoN pmrA : : CmR mutant strains were constructed and their resistance to PM were compared with the wild-type strain as well as with the single DrpoN , pmrA505 , and pmrA : : Cm mutants ( Fig. 2 ) .	14	INACTIVATION OF RPON INDUCES PM RESISTANCE	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrA	activator	20833808	2	att	On the other hand , the influx rate of the pmrA pagL mutant strain was higher than that of the wild-type strain , suggesting that PmrA-dependent lipid-A modifications , such as aminoarabinose and phosphoethano-lamine attachment , are also involved in generating a robust permeation barrier ( Fig. 2 ) .	59	On the other hand , the influx rate of the pmrA pagL mutant strain was higher than that of the wild-type strain , suggesting that PmrA-dependent lipid A modifications , such as aminoarabinose and phosphoethano-lamine attachment , are also involved in generating a robust permeation barrier ( Fig. 2 ) .	3	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrA	activator	23690578	0	att	PmrA-dependent LPS modifications confer resistance to serum , Fe3 + , and several antimicrobial peptides , suggesting that the pmrA gene is required for Salmonella virulence .	6	PmrA-dependent LPS modifications confer resistance to serum , Fe3 + , and several antimicrobial peptides , suggesting that the pmrA gene is required for Salmonella virulence .	1	ABSTRACT	Salmonella	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	pmrA	activator	23690578	45	att	Indeed , we could decrease SPI-2 expression by increasing the iron concentration in the growth media ( Fig. 3A ) ; this effect was PmrA-dependent because it was not observed in the pmrA null mutant ( Fig. 3B ) .	174	Indeed , we could decrease SPI-2 expression by increasing the iron concentration in the growth media ( Fig. 3A ) ; this effect was PmrA-dependent because it was not observed in the pmrA null mutant ( Fig. 3B ) .	6	FREELY AVAILABLE ONLINE THROUGH THE PNAS OPEN ACCESS OPTION. 1TO WHOM CORRESPONDENCE SHOULD BE ADDRESSED. E-MAIL: EDUARDO.GROISMAN@YALE.EDU.	nan	1	L1	OTHER	Other	NEG	Other	Level 1
OmpR	gene	cadC	repressor	25875623	8	ver/dev	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC .	248	Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC and cadB .	8	CYTOPLASMIC ACIDIFICATION OCCURS IMMEDIATELY AFTER ENTRY INTO THE MACROPHAGE SCV	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	cadC	repressor	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in SCV of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadC	repressor	29214489	7	ver/dev	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in the Salmonellacontaining vacuole of macrophages .	97	Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC and cadB promoters in the Salmonellacontaining vacuole ( SCV ) of macrophages ( Chakraborty et al. , 2015 ) , which acidifies to between pH 4.0 and 5.0 soon after formation ( Rathman et al. , 1996 ) .	12	INVERSE CORRELATION BETWEEN THE ACID-SENSING REGULATOR CADC AND THE RESPONSE REGULATOR OMPR	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	cadC	repressor	29214489	15	ver/dev	Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC , leading to cytoplasmic acidification .	163	Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC and cadB promo-ters , leading to cytoplasmic acidification and reduced flagellation .	13	CADC INTERACTS DIRECTLY WITH OMPR	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	repressor	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	hilE	repressor	24354910	18	ver/dev	We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE .	85	We also observed that a hilE null mutation increased the HilD levels in the presence and in the absence of LeuO ( Fig. 3 ) , in accordance with two well known facts : the inhibition of HilD activity by HilE ( Baxter et al. , 2003 ) and the occurrence of autogenous activation of hilD transcription ( Ellermeier et al. , 2005 ) .	9	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	activator	25135218	32	ver/dev	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat ssrAB-cat 240 fusions in the hilD mutant to levels similar to those .	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	Felis catus;Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	activator	25135218	32	ver/dev	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 240 fusions in the hilD mutant to levels similar to those .	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	Felis catus	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	TU	ssrAB	activator	25135218	32	ver/dev	Moreover , Q92am induction of H-NS did not affect the expression of ssrAB-cat 69 .	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	Felis catus	0	L3	OTHER	Other	NEG	New	Level 1
HNS	TU	ssrAB	activator	25135218	32	ver/dev	Moreover , Q92am induction of H-NS did not affect the expression of ssrAB-cat 119 .	129	Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 and ssrAB-cat 240 fusions in the hilD mutant to levels similar to those shown in the WT strain ( Fig. 3B and 4B ) but did not affect the expression of ssrAB-cat 119 , ssrAB-cat 69 , and ssrABcat 10 fusions ( Fig. 4B ) , which indicates that when H-NS is inactivated , the 119 / 336 region is not able to mediate repression of ssrAB .	4	RESULTS	Felis catus	0	L3	OTHER	Other	NEG	New	Level 1
HNS	TU	ssrAB	activator	32021316	6	ver/dev	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of invasion against the cell and entrance , SPI-2 suppresses the expression of SPI-1 through SsrB .	202	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of SPI-1 and invasion against the cell and entrance , SPI-2 activates and suppresses the expression of SPI-1 through SsrB .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HNS	TU	ssrAB	activator	32021316	6	ver/dev	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of invasion against the cell and entrance , SPI-2 activates .	202	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of SPI-1 and invasion against the cell and entrance , SPI-2 activates and suppresses the expression of SPI-1 through SsrB .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HNS	TU	ssrAB	activator	32021316	6	ver/dev	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of SPI-1 against the cell and entrance , SPI-2 suppresses the expression of SPI-1 through SsrB .	202	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of SPI-1 and invasion against the cell and entrance , SPI-2 activates and suppresses the expression of SPI-1 through SsrB .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HNS	TU	ssrAB	activator	32021316	6	ver/dev	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of SPI-1 against the cell and entrance , SPI-2 activates .	202	HilD can counteract the repressive effect of H-NS in the regulatory region of ssrAB operon .163 In summary , following the activation of SPI-1 and invasion against the cell and entrance , SPI-2 activates and suppresses the expression of SPI-1 through SsrB .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L2	OTHER	Other	OTHER	New	Level 1
PhoP	gene	phoP	repressor	10816543	1	att	Previously , a Salmonella enterica sero-var Typhimurium phoP locus mutant ( pho24 ) was isolated that constitutively expressed PhoP-activated genes ( pag ) and repressed PhoP-repressed genes ( prg ) ( 21 , 24 ) .	38	Previously , a Salmonella enterica sero-var Typhimurium phoP locus mutant ( pho24 ) was isolated that constitutively expressed PhoP-activated genes ( pag ) and repressed PhoP-repressed genes ( prg ) ( 21 , 24 ) .	2	MAIN	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	repressor	12492857	0	att	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	144	Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .	8	REGULATORY GENE EXPRESSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	repressor	16359323	0	ver/dev	Moreover , the macB genes were expressed to higher levels in a phoP mutant than in Fig. 4A , suggesting that these genes are repressed by PhoP as low Mg2 .	200	Moreover , the macA and macB genes were expressed to higher levels in a phoP mutant than in the wild-type strain ( Fig. 4A ) , suggesting that these genes are repressed by PhoP as low Mg2 + is the signal that activates the PhoP/PhoQ system ( Groisman , 2001 ) .	9	THE PHOP-PHOQ VIRULENCE REGULATORY SYSTEM CONTROLS TRANSCRIPTION OF THE MACAB DRUG EXPORTER GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	repressor	16359323	0	ver/dev	Moreover , the macB genes were expressed to higher levels in a phoP mutant than in the wild-type strain , suggesting that these genes are repressed by PhoP as low Mg2 .	200	Moreover , the macA and macB genes were expressed to higher levels in a phoP mutant than in the wild-type strain ( Fig. 4A ) , suggesting that these genes are repressed by PhoP as low Mg2 + is the signal that activates the PhoP/PhoQ system ( Groisman , 2001 ) .	9	THE PHOP-PHOQ VIRULENCE REGULATORY SYSTEM CONTROLS TRANSCRIPTION OF THE MACAB DRUG EXPORTER GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	repressor	16359323	0	ver/dev	Moreover , the macA genes were expressed to higher levels in a phoP mutant than in Fig. 4A , suggesting that these genes are repressed by PhoP as low Mg2 .	200	Moreover , the macA and macB genes were expressed to higher levels in a phoP mutant than in the wild-type strain ( Fig. 4A ) , suggesting that these genes are repressed by PhoP as low Mg2 + is the signal that activates the PhoP/PhoQ system ( Groisman , 2001 ) .	9	THE PHOP-PHOQ VIRULENCE REGULATORY SYSTEM CONTROLS TRANSCRIPTION OF THE MACAB DRUG EXPORTER GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	repressor	16359323	0	ver/dev	Moreover , the macA genes were expressed to higher levels in a phoP mutant than in the wild-type strain , suggesting that these genes are repressed by PhoP as low Mg2 .	200	Moreover , the macA and macB genes were expressed to higher levels in a phoP mutant than in the wild-type strain ( Fig. 4A ) , suggesting that these genes are repressed by PhoP as low Mg2 + is the signal that activates the PhoP/PhoQ system ( Groisman , 2001 ) .	9	THE PHOP-PHOQ VIRULENCE REGULATORY SYSTEM CONTROLS TRANSCRIPTION OF THE MACAB DRUG EXPORTER GENES	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	repressor	17575908	2	ver/dev	The expression profile of phoP is rather consistent with the proposed role of PhoP as a repressor of SPI-1 genes since phoP was expressed when the SPI-1 regulators have become to decline .	149	The expression profile of phoP is rather consistent with the proposed role of PhoP as a repressor of SPI-1 genes ( Behlau and Miller 1993 ; Bajaj et al. 1996 ) since phoP was expressed when the SPI-1 regulators have become to decline .	5	DISCUSSION	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	repressor	32209674	44	ver/dev	PhoP are responsible for decreasing H-NS amounts in phoP lon Salmonella grown to midlog phase in N-minimal media with 1 mM Mg2 .	361	Lon and PhoP are responsible for decreasing H-NS amounts in acidic pH. ( A -- C and E ) Western blot analysis of crude extracts prepared from ( A ) wildtype ( JC805 ) , phoP ( JC837 ) , lon ( JC864 ) , and phoP lon ( JC1223 ) Salmonella grown to midlog phase in N-minimal media with 1 mM Mg2 + at pH 4.9 ( acidic pH ) .	5	PUBLISHED UNDER THE PNAS LICENSE. 1TO WHOM CORRESPONDENCE MAY BE ADDRESSED. EMAIL: EDUARDO.GROISMAN@YALE.EDU.	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	repressor	33318137	5	ver/dev	The results showed that PhoP K88Ac had lower DNA-binding affinity with the phoP promoter than Fig. 3C .	153	The results showed that PhoP K88Ac had lower DNA-binding affinity with the phoP promoter than nonacetylated PhoP ( Fig. 3C ) .	2	KEYWORDS PHOP, SALMONELLA ENTERICA SEROVAR TYPHIMURIUM, ACETYL PHOSPHATE, ACETYLATION, VIRULENCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	repressor	33318137	5	ver/dev	The results showed that PhoP K88Ac had lower DNA-binding affinity with the phoP promoter than nonacetylated PhoP .	153	The results showed that PhoP K88Ac had lower DNA-binding affinity with the phoP promoter than nonacetylated PhoP ( Fig. 3C ) .	2	KEYWORDS PHOP, SALMONELLA ENTERICA SEROVAR TYPHIMURIUM, ACETYL PHOSPHATE, ACETYLATION, VIRULENCE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	csgD	regulator	29163440	12	ver/dev	CRP-cAMP regulates csgD formation by uropathogenic Escherichia coli .	441	CRP-cAMP regulates csgD and biofilm formation by uropathogenic Escherichia coli .	18	AUTHOR	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HilD	gene	lon	repressor	27341691	19	ver/dev	the protease _ known to affect HilD , as in mutants of lon , sipC remained repressed by Fig. 4B	297	However , this effect apparently is not mediated through Lon , the protease known to affect HilD , as in mutants of lon , sipC remained repressed by Pat ( Fig. 4B ) .	11	SALMONELLA TO MAXIMIZE ITS VIRULENCE.	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HilD	gene	lon	repressor	27341691	19	ver/dev	the protease _ known to affect HilD , as in mutants of lon , sipC remained repressed by Pat	297	However , this effect apparently is not mediated through Lon , the protease known to affect HilD , as in mutants of lon , sipC remained repressed by Pat ( Fig. 4B ) .	11	SALMONELLA TO MAXIMIZE ITS VIRULENCE.	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
FadD	gene	hilA	regulator	27936347	0	ver/dev	In line with these observations , Lucas et al. 66 have shown that FadD is a positive regulator of the hilA expression .	280	In line with these observations , Lucas et al. 66 have shown that FadD is a positive regulator of the hilA expression , which is a central player for the host invasion process .	9	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	fliZ	activator	30941426	14	ver/dev	Down-regulation of fliZ reduces SPI-1 expression in rpsD * Previous work has shown that a flagellar gene fliZ activates HilD post-translationally to enhance hilA expression .	254	Down-regulation of fliZ reduces SPI-1 expression in rpsD * Previous work has shown that a flagellar gene fliZ activates HilD post-translationally to enhance hilA expression ( 64 ) .	25	NON-OPTIMAL TRANSLATIONAL FIDELITY PROMOTES DEGRADATION OF HILD BY LON	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarR	TU	acrAB	regulator	26446080	0	ver/dev	Mutations in AcrR have been shown to impair its repressive effect , hence leading to derepression of the acrAB genes .16 -- 18 The repressors MarR and RamR are regulators of transcriptional factors MarA , RamA and SoxS , respectively .	257	Mutations in AcrR have been shown to impair its repressive effect , hence leading to derepression of the acrAB genes .16 -- 18 The repressors MarR and RamR and the activator SoxR are regulators of transcriptional factors MarA , RamA and SoxS , respectively .	22	EFFLUX AND PERMEABILITY ARE ALTERED IN TY_C2	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
DksA	gene	sipC	activator	26039089	5	att	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	activator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at LSP according to measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	activator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP according to measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	activator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at LSP according to ChIP-chip data : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	activator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at LSP according to the microarray : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	activator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP according to ChIP-chip data : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
DksA	gene	sipC	activator	26039089	5	ver/dev	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP according to the microarray : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary-phase .	152	The observations that intracellular SipC was undetectable by western blotting , yet sipC transcripts were elevated at MSP and LSP according to the microarray and ChIP-chip data , and measurement of sipC : : lacZ activity revealed only a slight decrease in the ΔdksA strain compared to the parent strain ( Fig 3 ) , suggests that the stability of SipC is regulated by a DksA-dependent post-transciptional mechanism during late-log/stationary phase .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
IHF	gene	csgD	regulator	28148244	0	ver/dev	IHF regulate the transcription of csgD in S. typhimurium .	33	Global transcriptional regulators such as RpoS , OmpR , H-NS and IHF regulate the transcription of csgD in S. typhimurium [ 25 ] .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
IHF	gene	csgD	regulator	31827464	0	ver/dev	The transcription of csgD is regulated by IHF to metabolic stress .	56	The transcription of csgD is regulated by ompR , integration host factor ( IHF ) , and histone-like nucleoid structuring ( H-NS ) proteins in response to environmental cues and metabolic stress .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	csgD	regulator	31827464	0	ver/dev	The transcription of csgD is regulated by IHF to environmental cues .	56	The transcription of csgD is regulated by ompR , integration host factor ( IHF ) , and histone-like nucleoid structuring ( H-NS ) proteins in response to environmental cues and metabolic stress .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SoxR	TU	acrAB	activator	32468234	6	ver/dev	SoxS induces acrAB expression in response to SoxR activation by a superoxide generating agent .	126	SoxS induces acrAB expression in response to SoxR activation by methyl viologen , a superoxide generating agent ( Nikaido et al. 2011 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxR	TU	acrAB	activator	32468234	6	ver/dev	SoxS induces acrAB expression in response to SoxR activation by methyl viologen .	126	SoxS induces acrAB expression in response to SoxR activation by methyl viologen , a superoxide generating agent ( Nikaido et al. 2011 ) .	6	ARAC/XYLS FAMILY; MASTER REGULATOR OF ACRAB‑TOLC SYSTEM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	pbgP	regulator	18792679	23	ver/dev	a Salmonella pmrD mutant where PhoP controls expression of the polymyxin B resistance pbgP directly	282	We contrasted the polymxyin B resistance exhibited by a Salmonella pmrD mutant where PhoP controls expression of the polymyxin B resistance pbgP and ugdgenes directly to that of a Salmonella with the PrnrD-mediated pathway .	9	PHOP AS A CO-ACTIVATOR PROTEIN	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
IHF	gene	envZ	regulator	14643403	27	ver/dev	For example , in E. coli , IHF has been shown to regulate envZ operon .	208	For example , in E. coli , IHF has been shown to regulate transcription of the ompR -- envZ operon [ 49 ] , while rpoS , on the other hand , regulates the two spatially distant IHF subunits , especially ihfA at a transcriptional level [ 2 ] .	20	6.5. MLRA	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
YjjQ	TU	flhDC	repressor	32032766	5	ver/dev	H. Wiebe , D. Gurlebeck , J. Gross , K. Dreck , D. Pannen , C. Ewers , L.H. Wieler , K. Schnetz , YjjQ represses ranscription of flhDC .	303	[ 28 ] H. Wiebe , D. Gurlebeck , J. Gross , K. Dreck , D. Pannen , C. Ewers , L.H. Wieler , K. Schnetz , YjjQ represses transcription of flhDC and additional loci in Escherichia coli , J. Bacteriol .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
DeoR	gene	tsx	activator	16489221	0	ver/dev	Repression by DeoR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
DeoR	gene	tsx	activator	16489221	0	ver/dev	Repression by DeoR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .	182	Repression by DeoR and CytR is relieved by adenosine or cytidine ( Valentin-Hansen et al. 1978 ) ; these nucleosides are inducers of the tsx gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	tppB	regulator	10568808	3	ver/dev	OmpR are positive regulation of tppB of Salmonella typhimu-rium .	197	OmpR and EnvZ are pleiotropic regulatory proteins : positive regulation of the tripeptide permease ( tppB ) of Salmonella typhimu-rium .	9	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	tppB	regulator	16045614	93	ver/dev	C.F. OmpR are positive regulation of tppB of Salmonella typhimurium .	712	Gibson , M.M. , Ellis , E.M. , Graeme-Cook , K.A. , and Higgins , C.F. ( 1987 ) OmpR and EnvZ are pleiotropic regulatory proteins : positive regulation of the tripeptide permease ( tppB ) of Salmonella typhimurium .	23	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	tppB	regulator	22179129	7	ver/dev	Gibson MM , Ellis EM , Graeme-Cook KA et al OmpR are pleiotropic regulatory proteins : positive regulation of tppB of Salmonella typhimurium .	224	Gibson MM , Ellis EM , Graeme-Cook KA et al ( 1987 ) OmpR and EnvZ are pleiotropic regulatory proteins : positive regulation of the tripeptide permease ( tppB ) of Salmonella typhimurium .	18	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	tppB	regulator	23782700	11	att	Goh , E. B. , Siino , D. F. , and Igo , M. M. ( 2004 ) The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	491	Goh , E. B. , Siino , D. F. , and Igo , M. M. ( 2004 ) The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	21	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	New	Level 2
OmpR	gene	tppB	regulator	24185747	8	ver/dev	OmpR are positive regulation of tppB of Salmonella typhimurium .	163	OmpR and EnvZ are pleiotropic regulatory proteins : positive regulation of the tripeptide permease ( tppB ) of Salmonella typhimurium .	17	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	tppB	regulator	30524381	27	att	Three of these were ompF , ompC and tppB , i.e. , known OmpR-regulated genes .	295	Three of these were ompF , ompC and tppB , i.e. , known OmpR-regulated genes .	21	OMPR DOWN-REGULATES A METABOLIC PATHWAY THAT PRODUCES TOXIC	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
OmpR	gene	tppB	regulator	30524381	49	att	The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	502	The Escherichia coli tppB ( ydgR ) gene represents a new class of OmpR-regulated genes .	37	REFERENCES	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
StpA	gene	stpA	activator	19843227	17	att	To test the phenotypic consequences of StpA-dependent gene regulation , we analysed the effects of deleting or overexpressing stpA on survival of PmB challenge .	86	To test the phenotypic consequences of StpA-dependent gene regulation , we analysed the effects of deleting or overexpressing stpA on survival of PmB challenge .	8	STPA REPRESSES GENES REQUIRED FOR CELL ENVELOPE MODIFICATION AND RESISTANCE TO CATIONIC PEPTIDES	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
StpA	gene	stpA	activator	19843227	29	att	This was exemplified by the expression profile of the s38-dependent gene osmY ; the expression of osmY is StpA-dependent ( i.e. altered in the stpA deletion strain ) during mid-exponential-growth ( Fig. 7C ) .	188	This was exemplified by the expression profile of the s38-dependent gene osmY ; the expression of osmY is StpA-dependent ( i.e. altered in the stpA deletion strain ) during mid-exponential growth ( Fig. 7C ) .	13	STPA MODULATES S38 STABILITY	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
StpA	gene	stpA	activator	31661351	12	att	Our results can not be attributed to a reduced expression of H-NS in the stpA mutant as no significant StpA-dependent changes in hns expression was observed at any S. Typhimurium growth time point [ 29 ] in accordance with other transcriptomic studies in Shigella flexneri or E. coli [ 48,50 ] .	297	Our results can not be attributed to a reduced expression of H-NS in the stpA mutant as no significant StpA-dependent changes in hns expression was observed at any S. Typhimurium growth time point [ 29 ] in accordance with other transcriptomic studies in Shigella flexneri or E. coli [ 48,50 ] .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella flexneri;Escherichia coli	0.5	L2	OTHER	Other	OTHER	Other	Level 1
CpxR	gene	tsgA	regulator	30760616	7	ver/dev	In addition , the major facilitator superfamily member tsgA were also positively regulated by CpxR in egg white .	292	In addition , the major facilitator superfamily member tsgA , the esterase yjfP , and a putative membrane-bound redox modulator alx were also positively regulated by CpxR in egg white ( 78 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompR	regulator	12068808	30	ver/dev	Figure 8 illustrates that H-NS is , indeed , a negative regulator of ompR .	188	Figure 8 illustrates that H-NS is , indeed , a negative regulator of ompR .	10	OMPR FOOTPRINT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ompR	regulator	12068808	32	ver/dev	The evidence suggested that H-NS bound to the ompR promoter represses transcription .	193	The evidence suggested that H-NS bound to the ompR promoter represses transcription .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	ompR	regulator	12080060	30	ver/dev	Figure 8 illustrates that H-NS is , indeed , a negative regulator of ompR .	188	Figure 8 illustrates that H-NS is , indeed , a negative regulator of ompR .	10	OMPR FOOTPRINT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	ompR	regulator	12080060	32	ver/dev	The evidence suggested that H-NS bound to the ompR promoter represses transcription .	193	The evidence suggested that H-NS bound to the ompR promoter represses transcription .	11	ACID SHOCK CONTROL OF OMPR EXPRESSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	ompR	regulator	33854491	10	ver/dev	Due to the fact that only a few transcriptional factors have been implicated in the control of ompR in Salmonella , such as H-NS , the data contribute to the understanding of the regulatory network .	261	Due to the fact that only a few transcriptional factors have been implicated in the control of ompR in Salmonella , such as LtrR , H-NS , and OmpR ( autoregulation ; Bang et al. , 2002 ; Villarreal et al. , 2014 ) , the data obtained contribute to the understanding of the regulatory network that controls the activity of this master regulator .	19	DISCUSSION	Salmonella	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	mlrA	activator	24735176	7	ver/dev	mlrA expression itself is positively regulated by RpoS .	410	mlrA expression itself is positively regulated by RpoS , the stationary phase and stress response sigma-factor ( Hengge-Aronis 2002 ) .	16	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15208313	56	att	These features of the ugtL promoter are atypical for PhoP-regulated promoters and could be the reason that ugtL transcription also requires the SlyA protein ( Fig. 1A ) .	197	These features of the ugtL promoter are atypical for PhoP-regulated promoters and could be the reason that ugtL transcription also requires the SlyA protein ( Fig. 1A ) .	5	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	56	att	These features of the ugtL promoter are atypical for PhoP-regulated promoters and could be the reason that ugtL transcription also requires the SlyA protein ( Fig. 1A ) .	197	These features of the ugtL promoter are atypical for PhoP-regulated promoters and could be the reason that ugtL transcription also requires the SlyA protein ( Fig. 1A ) .	5	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	58	att	The PhoP and SlyA protein appear to be part of a feed-forward loop that controls transcription of the ugtL gene and possibly additional PhoP-regulated genes .	202	The PhoP and SlyA protein appear to be part of a feed-forward loop that controls transcription of the ugtL gene and possibly additional PhoP-regulated genes .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	6	ver/dev	We propose that the PhoP proteins control ugtL transcription .	14	We propose that the PhoP and SlyA proteins control ugtL transcription using a feed-for-ward loop design .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	22	ver/dev	The PhoP Proteins Bind to the ugtL Promoter -- We conducted gel shift assays .	126	The SlyA and PhoP Proteins Bind to the ugtL Promoter -- We conducted gel shift assays using the purified SlyA-FLAG and PhoP-His6 proteins and a 536-bp DNA fragment corresponding to the intergenic region between the ugtL gene and the upstream sifB gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	22	ver/dev	The PhoP Proteins Bind to the ugtL Promoter -- We conducted a 536-bp DNA fragment .	126	The SlyA and PhoP Proteins Bind to the ugtL Promoter -- We conducted gel shift assays using the purified SlyA-FLAG and PhoP-His6 proteins and a 536-bp DNA fragment corresponding to the intergenic region between the ugtL gene and the upstream sifB gene .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	24	ver/dev	Then , we found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region overlapping the potential 10 of the ugtL promoter .	128	Then , we conducted DNase I footprinting assays and found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring an imperfect hexanucleotide repeat resembling a PhoP box but located in the opposite strand , and a 1-proximal region with no resemblance to the PhoP box and overlapping the potential 10 of the ugtL promoter .	4	RESULTS	nan	1	L1	OTHER	Analysis	OTHER	New	Level 1
PhoP	gene	ugtL	regulator	15208313	24	ver/dev	Then , we found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring a 1-proximal region with no resemblance to the PhoP box .	128	Then , we conducted DNase I footprinting assays and found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring an imperfect hexanucleotide repeat resembling a PhoP box but located in the opposite strand , and a 1-proximal region with no resemblance to the PhoP box and overlapping the potential 10 of the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	ugtL	regulator	15208313	24	ver/dev	Then , we found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring an imperfect hexanucleotide repeat .	128	Then , we conducted DNase I footprinting assays and found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring an imperfect hexanucleotide repeat resembling a PhoP box but located in the opposite strand , and a 1-proximal region with no resemblance to the PhoP box and overlapping the potential 10 of the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	27	ver/dev	These results demonstrate that the PhoP proteins bind to the ugtL promoter .	131	These results demonstrate that the PhoP and SlyA proteins bind to the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either downstream PhoP binding sites in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either the upstream in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either downstream PhoP binding sites in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either the upstream in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either downstream PhoP binding sites in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either the upstream in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either downstream PhoP binding sites in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	28	ver/dev	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either the upstream in the ugtL promoter .	132	The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro and for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences or nucleotide substitutions at either the upstream or downstream PhoP binding sites in the ugtL promoter .	4	RESULTS	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15208313	30	ver/dev	These results demonstrate that binding of the PhoP protein to both PhoP binding sites in the ugtL promoter is required for ugtL transcription .	136	These results demonstrate that binding of the PhoP protein to both PhoP binding sites in the ugtL promoter is required for ugtL transcription .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15208313	31	ver/dev	The PhoP proteins bind to the ugtL promoter .	138	The PhoP and SlyA proteins bind to the ugtL promoter and are required for ugtL transcription .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	45	ver/dev	We have established that transcription of polymyxin B resistance gene ugtL is controlled by the PhoP proteins in what appears to be a feedforward loop design .	172	We have established that transcription of the magainin 2 and polymyxin B resistance gene ugtL is controlled by the PhoP and SlyA proteins in what appears to be a feedforward loop design ( Fig. 6 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP2 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP2 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP2 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP2 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP1 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP1 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP1 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	55	ver/dev	Mutation of the PhoP1 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .	196	Mutation of the PhoP1 or PhoP2 sites abolished ugtL transcription ( Fig. 3A ) , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results ( Fig. 3B ) .	5	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15208313	65	ver/dev	Taken together with the identification of binding sites for both PhoP proteins in Fig. 2C , these results support the notion of a feedforward design in the regulation of ugtL transcription .	210	Taken together with the identification of binding sites for both the SlyA and PhoP proteins in the ugtL promoter ( Fig. 2C ) , these results support the notion of a feedforward design in the regulation of ugtL transcription .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	65	ver/dev	Taken together with the identification of binding sites for both PhoP proteins in the ugtL promoter , these results support the notion of a feedforward design in the regulation of ugtL transcription .	210	Taken together with the identification of binding sites for both the SlyA and PhoP proteins in the ugtL promoter ( Fig. 2C ) , these results support the notion of a feedforward design in the regulation of ugtL transcription .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	66	ver/dev	Model _ illustrating the feed-forward regulation of the ugtL gene by the PhoP proteins	222	Model illustrating the feed-forward regulation of the ugtL gene by the PhoP and SlyA proteins .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	67	ver/dev	PhoP along with SlyA bind to the ugtL promoter	223	Transcription of the slyA gene is activated during growth in low Mg2 via the PhoP/PhoQ system , and PhoP along with SlyA bind to the ugtL promoter stimulating ugtL transcription .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15208313	69	ver/dev	Although full resist-ance to polymyxin B requires ugtL , these genes appear to be differentially regulated by PhoP in that transcription of Fig. 1A	232	Although full resist-ance to polymyxin B requires ugtL and pmrA , these genes appear to be differentially regulated by PhoP in that transcription of the former ( Fig. 1A ) , but not the latter ,1 is dependent on the SlyA protein .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	ugtL	regulator	15208313	69	ver/dev	Although full resist-ance to polymyxin B requires ugtL , these genes appear to be differentially regulated by PhoP in that transcription of the former	232	Although full resist-ance to polymyxin B requires ugtL and pmrA , these genes appear to be differentially regulated by PhoP in that transcription of the former ( Fig. 1A ) , but not the latter ,1 is dependent on the SlyA protein .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
PhoP	gene	ugtL	regulator	15225317	10	att	The PhoP-regulated ugtL gene is required for resistance to magainin 2 and other alpha-helical antimicrobial peptides	63	The PhoP-regulated ugtL gene is required for resistance to magainin 2 and other alpha-helical antimicrobial peptides	5	A SURVIVAL ENRICHMENT STRATEGY FOR RECOVERING PEPTIDE RESISTANCE GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15225317	11	att	Having demonstrated previously that ugtL is a PhoP-activated gene ( Hilbert et al. , 1999 ) , these results validated our strategy for the recovery of the PhoP-regulated peptide resistance determinants .	92	Having demonstrated previously that ugtL is a PhoP-activated gene ( Hilbert et al. , 1999 ) , these results validated our strategy for the recovery of the PhoP-regulated peptide resistance determinants .	6	1473104	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15225317	12	att	These results demonstrate that PhoP-regulated polymyxin B resistance is mediated by the ugtL gene and by some of the targets of PmrA -- PmrB regulation ( Groisman et al. , 1997 ; Gunn et al. , 1998 ) .	121	These results demonstrate that PhoP-regulated polymyxin B resistance is mediated by the ugtL gene and by some of the targets of PmrA -- PmrB regulation ( Groisman et al. , 1997 ; Gunn et al. , 1998 ) .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15225317	14	att	PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes	168	PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	15225317	15	att	Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .	169	Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L2	OTHER	Other	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	15225317	17	att	A ugtL pagP double mutant was more sensitive than either the ugtL or pagP single mutants but still more resistant than the phoP mutant ( Fig. 2C ) , indicating that the ugtL and pagP genes participate in different pathways of magainin 2 resistance and that additional PhoP-regulated genes contribute to magainin 2 resistance .	172	A ugtL pagP double mutant was more sensitive than either the ugtL or pagP single mutants but still more resistant than the phoP mutant ( Fig. 2C ) , indicating that the ugtL and pagP genes participate in different pathways of magainin 2 resistance and that additional PhoP-regulated genes contribute to magainin 2 resistance .	7	THE UGTL GENE MEDIATES POLYMYXIN B RESISTANCE INDEPENDENTLY OF THE PMRA–PMRB SYSTEM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15225317	22	att	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	192	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	8	UGTL IS AN INNER MEMBRANE PROTEIN THAT PROMOTES THE FORMATION OF MONOPHOSPHORYLATED LIPID A	Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15225317	22	att	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	192	The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .	8	UGTL IS AN INNER MEMBRANE PROTEIN THAT PROMOTES THE FORMATION OF MONOPHOSPHORYLATED LIPID A	Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15225317	27	att	In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .	276	In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	15225317	6	att	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid-A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	37	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	3	2 ND POLYMYXIN B	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	ugtL	regulator	15225317	23	ver/dev	two genes -- ugtL -- are both transcriptionally regulated by the PhoP	255	This strategy was validated with the recovery of two genes -- ugtL and yqjA -- that are both required for magainin 2 resistance ( Fig. 2A -- C , F and G ) and transcriptionally regulated by the PhoP -- PhoQ system ( Fig. 4 ; Hilbert et al. , 1999 ) .	9	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	16413221	4	ver/dev	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	313	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	10	ACKNOWLEDGEMENTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	17259627	44	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	554	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	63	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	18270203	10	att	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	151	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	2	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	18270203	10	att	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	151	The slyA gene is necessary to promote transcription of the horizontally acquired PhoP-regulated pagC and ugtL genes but not the ancestral PhoP-regulated mgtA gene .	2	MAIN	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	ugtL	regulator	18270203	31	att	( Fig. 3A ) , at a position and orientation relative to the 10 RNA Polymerase Recruitment to the pagC and ugtL region that is shared with other PhoP-regulated promoters ( 26 ) .	201	( Fig. 3A ) , at a position and orientation relative to the 10 RNA Polymerase Recruitment to the pagC and ugtL region that is shared with other PhoP-regulated promoters ( 26 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	18270203	6	ver/dev	Model _ depicting transcriptional control of ugtL genes by PhoP	59	Model depicting transcriptional control of the horizontally acquired pagC and ugtL genes by the regulatory proteins H-NS , PhoP , and SlyA .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	18270203	20	ver/dev	ugtL genes entails binding of both the PhoP to the promoters of these two genes .	187	pagC and ugtL genes entails binding of both the PhoP and SlyA proteins to the promoters of these two genes .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	18407759	5	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	776	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	54	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	18715828	2	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	675	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	27	A	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	19091955	36	ver/dev	Shi Y , Groisman E-A Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	226	Shi Y , Latifi T , Cromie M-J , Groisman E-A ( 2004 ) Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	19204896	11	ver/dev	Shi Y , Groisman EA Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	192	Shi Y , Latifi T , Cromie MJ , Groisman EA ( 2004 ) Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	8	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	19229334	12	ver/dev	Shi Y , Groisman EA Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	842	Shi Y , Latifi T , Cromie MJ , Groisman EA ( 2004 ) Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	25	AUTHOR CONTRIBUTIONS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	19843227	36	ver/dev	Two StpA-repressed PhoP-dependent genes _ bound by ugtL	262	Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) .	15	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	21388802	10	ver/dev	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	558	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	18	13. KOX LF, WOSTEN MM, GROISMAN EA: A SMALL PROTEIN THAT MEDIATES THE ACTIVATION OF A TWO-COMPONENT SYSTEM BY ANOTHER TWO-COMPONENT SYSTEM. EMBO J 2000, 19:1861-1872.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	24021902	8	ver/dev	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	478	Shi Y , Latifi T , Cromie MJ , Groisman EA : Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	9	REFERENCES AND RECOMMENDED READING	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	25135218	80	ver/dev	The S. Typhimurium ugtL are regulated by a similar mechanism , involving the response regulator of the PhoP / PhoQ two-component system .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	25135218	80	ver/dev	The S. Typhimurium ugtL are regulated by a similar mechanism , involving the response regulator of the PhoP / PhoQ two-component system .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	25135218	80	ver/dev	The S. Typhimurium ugtL are regulated by a similar mechanism , involving PhoP .	227	The S. Typhimurium ugtL and pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA , which antagonizes H-NS-mediated repression of these genes , and PhoP ( the response regulator of the PhoP / PhoQ two-component system ) , which acts as a conventional transcriptional activator ( 65 ) .	5	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	26443522	1	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	1060	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	21	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	27564394	22	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	1320	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	30	ACKNOWLEDGMENTS	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	29324231	13	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	512	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	8	BD FACS ARIA II FLOW CYTOMETER. FOR SAMPLES ISOLATED FROM INFECTED CELLS, ONLY PARTICLES WITH MCHERRY LEVELS (532 NM EXCITATION, 610/20 WITH 600LP EMISSION) ABOVE THE BACKGROUND LEVELS OBSERVED FOR MCHERRY-NEGATIVE CONTROL SAMPLES WERE ANALYZED.	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	29937757	19	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	565	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	24	THIS WORK WAS SUPPORTED BY FONDECYT GRANT 1130225 (TO SÁ). ONLINE AT: HTTPS://WWW.FRONTIERSIN.ORG/ARTICLES/10.3389/FMICB. CS WAS SUPPORTED BY FONDECYT GRANT 1140754 AND 1171844. 2018.01220/FULL#SUPPLEMENTARY-MATERIAL	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	30373755	8	att	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	ugtL	regulator	31333620	8	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	629	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	49	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	31484980	64	ver/dev	Shi , Y. , Latifi , T. , Cromie , M. J. & Groisman , E. A. Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	642	Shi , Y. , Latifi , T. , Cromie , M. J. & Groisman , E. A. Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	20	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	32209674	60	ver/dev	Y. Shi , Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	705	Y. Shi , T. Latifi , M. J. Cromie , E. A. Groisman , Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	6	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	33045730	93	ver/dev	PhoP binds at two different sites in the ugtL promoter .	404	PhoP binds at two different sites in the ugtL promoter ( Supplemental Figure S6 ) ( 62 ) and is necessary to recruit RNA polymerase ( 63 ) .	35	CONTROL OF THE VIRULENCE REGULATOR PHOP BY THE SSRB PROTEIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	ugtL	regulator	33045730	110	ver/dev	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .	736	Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins .	69	REFERENCES	Salmonella	1	L3	OTHER	Other	OTHER	New	Level 2
StpA	gene	micF	activator	19843227	4	ver/dev	In addition to its RNA splicing role , StpA induces OmpF expression in E. coli by destabilizing the micF antisense RNA .	49	In addition to its RNA splicing role , StpA induces OmpF expression in E. coli by destabilizing the micF antisense RNA .	5	MAIN	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	iagA	repressor	17178790	15	ver/dev	In contrast , RcsB under low-osmolarity conditions , acting in association with the viaB locus-encoded TviA protein , negatively controls the transcription of iagA .	345	In contrast , RcsB under low-osmolarity conditions , acting in association with the viaB locus-encoded TviA protein , negatively controls the transcription of iagA , invF , and sipB ( encoding proteins involved in cell invasion ) ( 1 ) .	7	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	stpA	repressor	27407104	7	ver/dev	Hence , combined repression of stpA mRNAs by SdsR endorses down-regulation of the CRP regulon .	386	Hence , combined repression of crp and stpA mRNAs by SdsR fosters the expression of Sdependent genes and endorses down-regulation of the CRP regulon .	21	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
AraC	gene	sigD	activator	10692170	8	att	AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA .	207	AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA .	8	INVF AND SICA ARE SUFFICIENT TO ACTIVATE TRANSCRIPTION OF SICA- AND SIGD±LACZYA IN E:COLI CC118LPIR.	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	ftsZ	regulator	12519186	48	att	RcsB-regulated genes can be divided into those that are RcsA dependent , such as the cps genes ( Gottesman et al. , 1985 ) ( Fig. 3 ) , and those that are RcsA independent , such as the ftsZ ( Carballes et al. , 1999 ; Costa and Anton , 2001 ) and osmC ( Davalos-Garcia et al. , 2001 ) genes .	136	RcsB-regulated genes can be divided into those that are RcsA dependent , such as the cps genes ( Gottesman et al. , 1985 ) ( Fig. 3 ) , and those that are RcsA independent , such as the ftsZ ( Carballes et al. , 1999 ; Costa and Anton , 2001 ) and osmC ( Davalos-Garcia et al. , 2001 ) genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	adrA	regulator	15458421	6	ver/dev	the response regulator CsgD in turn regulates the transcription of adrA	118	As stated before , MlrA is known to control the transcription of the response regulator CsgD , which in turn regulates the biosynthesis of thin aggregative fimbriae and the transcription of adrA .	6	STM1987 AND MLRA ACTIVATE CELLULOSE PRODUCTION AND BIOFILM FORMATION IN S. TYPHIMURIUM	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	16313619	2	att	In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 : : csgD ] , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of its own promoter , which exclusively activates cellulose	169	In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 : : csgD ] , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of its own promoter , which exclusively activates cellulose	8	RELATIONSHIP BETWEEN BAPA AND OTHER COMPONENTS OF THE BIOFILM MATRIX	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CsgD	gene	adrA	regulator	16313619	8	ver/dev	Altogether , these results show that bapA , like adrA , is regulated by CsgD , which plays a central role in biofilm formation in Salmonella strains .	249	Altogether , these results show that bapA , like adrA and csgAB , is regulated by CsgD and is therefore a new member of the CsgD regulon , which plays a central role in biofilm formation in Salmonella strains .	10	TRANSCRIPTIONAL REGULATION OF BAPA	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	regulator	16707690	23	ver/dev	CsgD controls the expression of adrA .	402	CsgD depends on RpoS and Crl and controls the expression of csgBAC and adrA but not the expression of bscA .	5	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	16707690	30	ver/dev	Indeed , it has been suggested , although it has never been shown , that CsgD binds to conserved 11-bp sequences upstream of the adrA promoters , activating transcription of these genes .	426	Indeed , it has been suggested , although it has never been shown , that CsgD binds to conserved 11-bp sequences upstream of the csgB and adrA promoters , activating transcription of these genes ( 9 , 16 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
CsgD	gene	adrA	regulator	20545866	5	ver/dev	CsgD binds directly to adrA promoter regions	55	CsgD binds directly to the csgBA and adrA promoter regions	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	20545866	6	ver/dev	In S. Typhimurium the expression of adrA is positively regulated by the transcriptional regulator CsgD .	56	In S. Typhimurium the expression of csgBA and adrA is positively regulated by the transcriptional regulator CsgD ( Hammar et al. , 1995 ; Romling et al. , 2000 ; Gerstel and Romling , 2003 ) .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	regulator	20545866	7	ver/dev	In order to demonstrate the direct binding of CsgD to the adrA promoter regions we performed EMSA with purified CsgD-His6 tagged protein ( Fig .	58	In order to demonstrate the direct binding of CsgD to the csgBA and adrA promoter regions we performed electrophoretic mobility shift assays ( EMSA ) with purified CsgD-His6 tagged protein ( Fig .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	adrA	regulator	20545866	7	ver/dev	In order to demonstrate the direct binding of CsgD to the adrA promoter regions we performed electrophoretic-mobility-shift assays with purified CsgD-His6 tagged protein ( Fig .	58	In order to demonstrate the direct binding of CsgD to the csgBA and adrA promoter regions we performed electrophoretic mobility shift assays ( EMSA ) with purified CsgD-His6 tagged protein ( Fig .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CsgD	gene	adrA	regulator	20545866	8	ver/dev	Since CsgD is highly integrated into the c-di-GMP signalling network , we investigated whether c-di-GMP affects the binding of CsgD-His6 to adrA promoter region .	63	Since CsgD is highly integrated into the c-di-GMP signalling network , we investigated whether c-di-GMP affects the binding of CsgD-His6 to the csgBA and adrA promoter region .	5	CSGD BINDS DIRECTLY TO THE CSGBA AND ADRA PROMOTER REGIONS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CsgD	gene	adrA	regulator	20545866	13	ver/dev	To investigate the binding of CsgD to the adrA promoter region , a 257 bp 32P-labelled fragment from bp -222 to +35 was subjected to Fig. 2E .	82	To investigate the binding of CsgD to the adrA promoter region , a 257 bp 32P-labelled fragment from bp -222 to +35 was subjected to DNase I footprint analysis ( Fig. 2E ) .	6	DETECTION OF THE CSGD BINDING SITES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	regulator	20545866	13	ver/dev	To investigate the binding of CsgD to the adrA promoter region , a 257 bp 32P-labelled fragment from bp -222 to +35 was subjected to DNase I footprint analysis .	82	To investigate the binding of CsgD to the adrA promoter region , a 257 bp 32P-labelled fragment from bp -222 to +35 was subjected to DNase I footprint analysis ( Fig. 2E ) .	6	DETECTION OF THE CSGD BINDING SITES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	regulator	20545866	24	ver/dev	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA , compared with Fig. 5A .	154	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA and the csgBA promoter fragments , compared with CsgD alone ( Fig. 5A ) .	8	EFFECTS OF ACP ON CSGD ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	20545866	24	ver/dev	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA , compared with CsgD alone .	154	Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA and the csgBA promoter fragments , compared with CsgD alone ( Fig. 5A ) .	8	EFFECTS OF ACP ON CSGD ACTIVITY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	20545866	25	ver/dev	Since the binding of CsgD to the adrA promoter regions is altered in the presence of the phosphodonor AcP , we investigated whether CsgD can be phosphorylated in-vitro .	181	Since the binding of CsgD to the csgBA and the adrA promoter regions is altered in the presence of the phosphodonor AcP , we investigated whether CsgD can be phosphorylated in vitro .	8	EFFECTS OF ACP ON CSGD ACTIVITY	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
CsgD	gene	adrA	regulator	20545866	49	ver/dev	However , we discovered that c-di-GMP , is not required for binding of CsgD to the adrA promoters .	294	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	9	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	regulator	20545866	49	ver/dev	However , we discovered that an integral part of the regulatory network , is not required for binding of CsgD to the adrA promoters .	294	However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .	9	DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	regulator	22164276	0	ver/dev	The rdar morphotype is positively regulated by the transcriptional regulator CsgD that in turn , activates adrA .	35	The rdar morphotype is positively regulated by the transcriptional regulator CsgD that in turn , activates the curli biosynthesis operon csgBAC and adrA , encoding a di-guanylate cyclase which mediates cellulose biosynthesis [ 14 ] .	5	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CsgD	gene	adrA	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene involved in bio-film formation , EPS production	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	adrA	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene involved in bio-film formation , transport production	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	adrA	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene involved in bio-film formation , virulence production	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	adrA	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of lpfE genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	adrA	regulator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of fimA genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	adrA	regulator	25437188	43	ver/dev	In contrast to the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .	525	In contrast to VpsT , the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA and csgBAC is unaffected by c-di-GMP in vitro [ 76 ] .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	Vibrio cholerae	0	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	regulator	25437188	43	ver/dev	In contrast to VpsT , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .	525	In contrast to VpsT , the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA and csgBAC is unaffected by c-di-GMP in vitro [ 76 ] .	11	REGULATION OF RDAR BIOFILM FORMATION BY THE REDOX STATUS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
CsgD	gene	adrA	regulator	27260360	2	ver/dev	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgB , coding for adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	315	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD and csgB , coding for curli fimbria production , and adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	27260360	2	ver/dev	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD , coding for adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	315	To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD and csgB , coding for curli fimbria production , and adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .	6	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	adrA	regulator	28889298	1	ver/dev	CsgD indirectly regulates cellulose production by transcriptional control over adrA .	48	CsgD indirectly regulates cellulose production by transcriptional control over adrA [ 23 , 24 ] .	2	MAIN	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	sifB	activator	15208313	10	att	The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .	33	The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .	2	MAIN	Salmonella;Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
RpoS	gene	fliZ	activator	22356617	4	att	Further , a mutation in the fliZ gene in E. coli has recently been shown to cause premature expression of RpoS-dependent genes ( Pesavento et al. , 2008 ) and in Salmonella overproduction of FliZ decreases expression of the RpoS-dependent genes , katE and sodCII ( Chubiz et al. , 2010 ) .	342	Further , a mutation in the fliZ gene in E. coli has recently been shown to cause premature expression of RpoS-dependent genes ( Pesavento et al. , 2008 ) and in Salmonella overproduction of FliZ decreases expression of the RpoS-dependent genes , katE and sodCII ( Chubiz et al. , 2010 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
RpoS	gene	fliZ	activator	22356617	5	att	Consequently , FliZ could be the link between the immobilization-specific downregulation of the flagellar regulon , including the fliZ gene , and the two other major phenotypes of the immobilized cells : increased expression of RpoS-dependent genes ( Fig. 5B ) and downregulation of SPI1 , SPI4 and SPI5 genes ( Fig. 7A ) .	343	Consequently , FliZ could be the link between the immobilization-specific downregulation of the flagellar regulon , including the fliZ gene , and the two other major phenotypes of the immobilized cells : increased expression of RpoS-dependent genes ( Fig. 5B ) and downregulation of SPI1 , SPI4 and SPI5 genes ( Fig. 7A ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	yciGFE	regulator	20713450	2	ver/dev	Our results indicate that differences between E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by H-NS in these two enterobacteria .	15	Our results indicate that differences between Salmonella and E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE ( katN ) genes by H-NS and YncC in these two enterobacteria .	0	Unknown	Escherichia coli	0	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	yciGFE	regulator	20713450	2	ver/dev	Our results indicate that differences between Salmonella , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by H-NS in these two enterobacteria .	15	Our results indicate that differences between Salmonella and E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE ( katN ) genes by H-NS and YncC in these two enterobacteria .	0	Unknown	Salmonella	1	L2	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	yciGFE	regulator	20713450	4	ver/dev	The results reveal differential regulation of the yciGFE locus by H-NS in these two closely related bacteria .	40	The results reveal differential regulation of the yciGFE ( katN ) locus by YncC and H-NS ( the Histone-like Nucleoid Structuring protein , 14 -- 16 ) in these two closely related bacteria .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	yciGFE	regulator	20713450	22	ver/dev	H-NS are also able to bind to the promoter region of the E. coli K-12 yciGFE genes .	478	YncC/McbR and H-NS are also able to bind to the promoter region of the E. coli K-12 yciGFE genes .	7	DISCUSSION	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	yciGFE	regulator	20713450	24	ver/dev	It is remarkable that in E. coli K-12 , regulation of yciGFE by H-NS are intimately linked , whereas in Salmonella , YncC directly activates transcription	480	It is remarkable that in E. coli K-12 , regulation of yciGFE by YncC and by H-NS are intimately linked , whereas in Salmonella , YncC directly activates transcription , and thus , activation by YncC is , at least partly , disconnected from the H-NS network .	7	DISCUSSION	Escherichia coli;Salmonella	0.5	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	spf	activator	18399940	6	ver/dev	However , unlike spf -- CRP complex , cyaR is activated by CRP .	394	However , unlike spf which is repressed by the cAMP -- CRP complex ( Polayes et al. , 1988 ) , cyaR is activated by CRP and has no apparent role in sugar metabolism .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	spf	activator	18399940	6	ver/dev	However , unlike spf -- CRP complex , cyaR is activated by CRP .	394	However , unlike spf which is repressed by the cAMP -- CRP complex ( Polayes et al. , 1988 ) , cyaR is activated by CRP and has no apparent role in sugar metabolism .	10	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	pgtP	regulator	33563986	8	ver/dev	a newly characterized regulator VrpA links the regulation of 3PG uptake gene pgtP to the classic bacterial cAMP-CRP regulatory system	271	This regulatory pathway contains a newly characterized regulator VrpA , which links the regulation of 3PG uptake gene pgtP to the classic bacterial cAMP-CRP regulatory system .	4	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
KdgR	gene	araH	regulator	26682862	1	ver/dev	kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	araH	regulator	26682862	1	ver/dev	kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	araH	regulator	26682862	1	ver/dev	kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	araH	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	araH	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
KdgR	gene	araH	regulator	26682862	1	ver/dev	Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .	230	Genes kduI ( encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase ) and kdgM ( encoding oligogalacturonate-specific porin ) appear to be most strongly controlled by KdgR , while kdgK ( 2-keto-3-deoxyg-luconate kinase ) , araH , and fruF likely are controlled by additional regulators ( Table 2 and Fig. 4 ) .	5	4	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MlrA	gene	csgD	activator	16313619	0	ver/dev	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	40	While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .	3	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MlrA	gene	csgD	activator	16313619	5	ver/dev	As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in mlrA mutant .	245	As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in the wild type , mlrA mutant and csgD mutant complemented with mlrA .	10	TRANSCRIPTIONAL REGULATION OF BAPA	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
MlrA	gene	csgD	activator	16313619	5	ver/dev	As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in the wild type .	245	As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in the wild type , mlrA mutant and csgD mutant complemented with mlrA .	10	TRANSCRIPTIONAL REGULATION OF BAPA	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
MlrA	gene	csgD	activator	16313619	5	ver/dev	As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in csgD mutant .	245	As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in the wild type , mlrA mutant and csgD mutant complemented with mlrA .	10	TRANSCRIPTIONAL REGULATION OF BAPA	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
MlrA	gene	csgD	activator	23443158	15	ver/dev	Ogasawara , H. ; Yamamoto , K. ; Ishihama , A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	353	Ogasawara , H. ; Yamamoto , K. ; Ishihama , A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	9	ACKNOWLEDGMENTS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MlrA	gene	csgD	activator	24735176	8	ver/dev	Under the influence of unknown environmental signals , MlrA induces the csgD expression .	411	Under the influence of unknown environmental signals , MlrA induces the csgD expression , which is the master regulator of the Salmonella ( and E. coli ) biofilm formation .	16	DISCUSSION	unidentified	1	L3	OTHER	Fact	OTHER	New	Level 3
MlrA	gene	csgD	activator	26293911	6	ver/dev	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	286	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	24	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
MlrA	gene	csgD	activator	29163440	2	ver/dev	Moreover , transcriptional expression of csgD , is activated by the regulator MlrA .	180	Moreover , transcriptional expression of csgD , which is tightly regulated in response to different environmental stimuli , is activated by the regulator MlrA ( Brown et al. , 2001 ) .	14	TRANSCRIPTIONAL EXPRESSION OF GENES INVOLVED IN CURLI AND CELLULOSE SYNTHESIS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MlrA	gene	csgD	activator	29163440	4	ver/dev	It has been described that csgD expression is stimulated by MlrA .	191	It has been described that csgD expression is stimulated by MlrA ( Brown et al. , 2001 ) .	14	TRANSCRIPTIONAL EXPRESSION OF GENES INVOLVED IN CURLI AND CELLULOSE SYNTHESIS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MlrA	gene	csgD	activator	31233504	12	ver/dev	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	778	Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .	46	44	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
PmrA	gene	rcsB	activator	12519186	22	att	On the other hand , the tolB mutant produced two S1 products : the large PmrA-dependent product , and a small product whose presence is RcsB dependent because it was produced at higher levels in a mutant harbouring a constitutive allele of rcsC -- rcsC11 ( Costa and Anton , 2001 ) , and it was not detected in RNA harvested from rcsB and tolB rcsB mutants ( Fig. 4A ) .	73	On the other hand , the tolB mutant produced two S1 products : the large PmrA-dependent product , and a small product whose presence is RcsB dependent because it was produced at higher levels in a mutant harbouring a constitutive allele of rcsC -- rcsC11 ( Costa and Anton , 2001 ) , and it was not detected in RNA harvested from rcsB and tolB rcsB mutants ( Fig. 4A ) .	5	THE RCSC–YOJN–RCSB TWO-COMPONENT SYSTEM IS RESPONSIBLE FOR THE TOLB MUTATION-PROMOTED UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hdfR	repressor	16763111	6	ver/dev	For example , the apparent activation of flagellar genes by H-NS most likely occurs by mediated repression of hdfR .	91	For example , the apparent activation of flagellar genes by H-NS most likely occurs by means of H-NS -- mediated repression of hdfR , a repressor of the flagellar regulators flhDC ( 1 ) .	4	6 FEBRUARY 2006; ACCEPTED 30 MAY 2006 10.1126/SCIENCE.1125878	nan	1	L2	SPEC	Other	OTHER	New	Level 1
HNS	gene	hdfR	repressor	25375226	20	ver/dev	H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly .	349	H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly [ 22,74 ] .	9	INACTIVATION OF SALMONELLA PATHOGENICITY ISLAND 1 IMPROVES GROWTH OF HNS MUTANTS	nan	1	L3	OTHER	Fact	OTHER	New	Level 3
CpxR	gene	acrD	regulator	23651595	8	ver/dev	Although CpxR also regulates transcription of acrD , cpxR deletion strains is critically required for S. Typhimurium resistance to Na2WO4 .	337	Although CpxR also regulates transcription of mdtA and acrD , cpxR deletion strains do not possess a tungstate-sensitive phenotype , suggesting that BaeR is the primary regulator of these genes in response to tungstate waste removal and is critically required for S. Typhimurium resistance to Na2WO4 ( Appia-Ayme et al. , 2011 ) .	18	2.3.2. THE BAE PATHWAY	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CpxR	gene	acrD	regulator	23651595	8	ver/dev	Although CpxR also regulates transcription of acrD , cpxR deletion strains do not possess a tungstate-sensitive phenotype .	337	Although CpxR also regulates transcription of mdtA and acrD , cpxR deletion strains do not possess a tungstate-sensitive phenotype , suggesting that BaeR is the primary regulator of these genes in response to tungstate waste removal and is critically required for S. Typhimurium resistance to Na2WO4 ( Appia-Ayme et al. , 2011 ) .	18	2.3.2. THE BAE PATHWAY	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	gene	pmrC	repressor	12507481	2	ver/dev	Mg2þ-dependent repression of the PhoP-activated pmrC gene requires the periplasmic domain of the PhoQ protein .	54	Mg2þ-dependent repression of the PhoP-activated pmrC gene requires the periplasmic domain of the PhoQ protein .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	15161921	1	ver/dev	Studies of bacteria have , to date , revealed that hilA expression is regulated by a complex array of hilC/sirC/sprA , hilD , sirA/barA , fis , csrAB , envZ / ompR , phoB , fadD , fliZ , hha , H-NS , .	35	Studies of bacteria grown under these conditions have , to date , revealed that hilA expression is regulated by a complex array of regulatory systems including hilC/sirC/sprA ( 13 -- 15 ) , hilD ( 15 ) , sirA/barA ( 16 , 17 ) , fis ( 18 , 19 ) , csrAB ( 16 , 20 ) , envZ / ompR ( 21 ) , phoB ( 7 ) , fadD ( 7 ) , fliZ ( 7 ) , hha ( 22 ) , H-NS ( 19 ) , and HU ( 19 ) .	2	MAIN	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hilA	regulator	16443238	19	ver/dev	Electrophoretic mobility-shift assays of he binding of H-NS of the hilA promoter .	188	( b ) Electrophoretic mobility shift assays of the binding of H-NS , and MBP-Hha to regions of the hilA promoter .	11	ACTION SITES OF H-NS AND HHA ON HILA FLANKING SEQUENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	21573071	12	ver/dev	Specifically , Fur is able to indirectly through H-NS ( in hilA ) , all the main regulators of SPI1 .	344	Specifically , Fur is able to control , either directly ( in the case of HilD ) or indirectly through H-NS ( in hilA , hilD , hilC , and rtsA ) , all the main regulators of SPI1 .	17	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	hilA	regulator	21573071	13	ver/dev	H-NS control of the hilA promoters is also shown .	358	H-NS control of the hilD , hilC , rtsA and hilA promoters is also shown [ 21,22,31 ] .	19	ACKNOWLEDGMENTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hilA	regulator	21680637	0	ver/dev	Integration host factor alleviates H-NS silencing the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA	2	Integration host factor alleviates H-NS silencing the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA	0	Unknown	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	21680637	46	ver/dev	In vitro binding of H-NS to the hilA regulatory region	269	In vitro binding of H-NS and IHF to the hilA regulatory region	9	IN VITRO BINDING OF H-NS AND IHF TO THE HILA REGULATORY REGION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	21680637	56	ver/dev	In spite of the fact that several reports have shown that H-NS influences hilA expression , information is not yet available .	311	In spite of the fact that several reports have shown that Hha , H-NS or an H-NS/Hha complex influences hilA expression ( Fahlen et al. , 2001 ; Olekhnovich & Kadner , 2006 ; Schechter et al. , 2003 ) , information integrating the role of H-NS/Hha-mediated hilA modulation in the bacterial response to different environmental inputs is not yet available .	11	DISCUSSION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
HNS	gene	hilA	regulator	23040276	11	ver/dev	M.H. Queiroz , C. Madrid , S. Paytubi , C. Balsalobre , A. Juárez , Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA , Microbiology	651	[ 95 ] M.H. Queiroz , C. Madrid , S. Paytubi , C. Balsalobre , A. Juárez , Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA , Microbiology ( Reading , England )	41	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	24018968	20	ver/dev	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	433	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	32	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	24079299	13	ver/dev	Queiroz MH , Madrid C , Paytubi S , Balsalobre C , Juárez A : Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	574	Queiroz MH , Madrid C , Paytubi S , Balsalobre C , Juárez A : Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	24	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	24368153	0	ver/dev	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	521	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	32	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	25135218	89	ver/dev	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	539	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	57	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	25375226	36	ver/dev	four H-NS _ regulated hilA	436	Transcript levels of four H-NS regulated genes , proV , ssrA , yciG and hilA , were measured by reverse transcriptase QPCR in a Dhns/DstpA strain expressing StpAWT or the variants StpAM4T , StpAA77D and StpAF21C .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	27601571	54	ver/dev	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	723	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	29	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	31182495	48	ver/dev	However , it has been hypothesized that RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	48	ver/dev	However , it has been hypothesized that RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	48	ver/dev	However , it has been hypothesized that HilC activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	48	ver/dev	However , it has been hypothesized that HilC activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	48	ver/dev	However , it has been hypothesized that HilD activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	48	ver/dev	However , it has been hypothesized that HilD activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	52	ver/dev	that these proteins directly activate hilA transcription rather than simply blocking H-NS binding at the hilA promoter	225	These data suggest that a primary effect of H-NS is to control expression of HilD , HilC , and/or RtsA and that these proteins directly activate hilA transcription rather than simply blocking H-NS binding at the hilA promoter .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	31182495	54	ver/dev	Together , these data suggest RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	54	ver/dev	Together , these data suggest HilC directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	regulator	33119619	1	ver/dev	H-NS represses the expression mainly by binding to the regulatory region of hilA	19	In SPI-1 , H-NS represses the expression mainly by binding to the regulatory region of hilA and derepression is exercised mainly by HilD .	7	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	regulator	34340061	10	ver/dev	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	560	Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .	33	REFERENCES	Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
DeoR	TU	deoCABD	repressor	1848842	2	ver/dev	three genetically separated operator elements are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor	750	DNA-protein recognition : demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor .	35	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	Other	Level 2
LexA	gene	ftsK	regulator	30201777	18	att	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	194	Five of the E. coli SOS response genes ( hokE , hlyE , molR , dinQ , and dinD ) have no homolog in S. Typhimurium 14028s , and expression of five E. coli LexA-regulated genes ( ybfE , ftsK , dinS , uvrD , and symE ) was not increased by 3-fold .	3	RESULTS AND DISCUSSION STRESS CONDITIONS AND BEBPS THAT INDUCE EXPRESSION OF THE RNA REPAIR OPERON.	Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Escherichia coli	0.5	L3	OTHER	Other	NEG	Other	Level 1
FabR	gene	fabA	regulator	27004424	12	ver/dev	Next to the two known E. coli targets , FabR is also known to control the expression of fabA in E. coli by binding to its promoter region .	194	Next to the two known E. coli targets , FabR is also known to control the expression of fabA in E. coli by binding to its promoter region [ 29 , 52 ] .	11	RESULTS	Escherichia coli;Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
FabR	gene	fabA	regulator	27004424	13	ver/dev	Although not detected on the tiling array , we could show binding of FabR to the fabA promoter by ChIP-qPCR , under biofilm conditions .	195	Although not detected on the tiling array , we could show binding of FabR to the fabA promoter by ChIP-qPCR , under TSB , LB and biofilm conditions .	11	RESULTS	nan	1	L1	OTHER	Analysis	NEG	New	Level 1
FabR	gene	fabA	regulator	27004424	13	ver/dev	Although not detected on the tiling array , we could show binding of FabR to the fabA promoter by ChIP-qPCR , under LB .	195	Although not detected on the tiling array , we could show binding of FabR to the fabA promoter by ChIP-qPCR , under TSB , LB and biofilm conditions .	11	RESULTS	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
FabR	gene	fabA	regulator	27004424	13	ver/dev	Although not detected on the tiling array , we could show binding of FabR to the fabA promoter by ChIP-qPCR , under TSB .	195	Although not detected on the tiling array , we could show binding of FabR to the fabA promoter by ChIP-qPCR , under TSB , LB and biofilm conditions .	11	RESULTS	nan	1	L1	SPEC	Analysis	NEG	New	Level 1
FabR	gene	fabA	regulator	27004424	14	ver/dev	In S. Typhimurium , this represents the first evidence for direct in-vivo binding of FabR to the fabA promoters .	196	In S. Typhimurium , this represents the first evidence for direct in vivo binding of FabR to the fabB , fabA and yqfA promoters .	11	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	OTHER	Analysis	OTHER	Other	Level 1
RpoS	gene	ydgP	activator	26039089	7	att	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	164	Other RpoS-dependent activators which have been shown to increase both SPI1 and SPI2 expression and were significantly elevated > 2-fold at LSP compared to ESP in the ΔrpoS relative to the parent strain included hupA , hupB , corA , rtsA , trkH , ydgP and STM2303 ( S3 Table , Fig 6 ) .	12	SIPC LEVELS ARE POST-TRANSCRIPTIONALLY REGULATED BY DKSA	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	16443238	12	ver/dev	In contrast , absence of H-NS showed 5.3-fold increase of hilA expression under low-osmolarity conditions .	166	In contrast , absence of H-NS showed 5.3-fold increase of hilA expression under low osmolarity conditions , but no effect in the high-salt medium ( line 3 ) .	10	SYNERGISTIC EFFECT OF H-NS AND HHA ON HILA PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilA	activator	21680637	34	ver/dev	in antagonizing H-NS silencing of hilA to promote its Stationary-phase induction of hilA in strain	249	in antagonizing H-NS silencing of hilA to promote its Stationary phase induction of hilA in strain	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	activator	21680637	36	ver/dev	Whereas hilA induction at antagonize H-NS hilA silencing account for hilA derepres should be abolished in sion in cells growing in LB-medium at 37 uC .	252	Whereas hilA induction at antagonize H-NS hilA silencing account for hilA derepres - the onset of the stationary phase should be abolished in sion in cells growing in LB medium at 37 uC and entering mutants lacking the hypothetical H-NS antagonist , the the stationary phase .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	hilA	activator	21680637	36	ver/dev	Whereas hilA induction at antagonize H-NS hilA silencing account for hilA derepres should be abolished in sion in cells entering mutants .	252	Whereas hilA induction at antagonize H-NS hilA silencing account for hilA derepres - the onset of the stationary phase should be abolished in sion in cells growing in LB medium at 37 uC and entering mutants lacking the hypothetical H-NS antagonist , the the stationary phase .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
HNS	gene	hilA	activator	21680637	44	ver/dev	Interestingly , a partial inhibition of H-NS activity in cells resulted in a signi-ficant induction of hilA expression , up to about 50 % of the expression .	267	Interestingly , a partial inhibition of H-NS activity in cells lacking IHF resulted in a signi-ficant induction of hilA expression , up to about 50 % of the expression obtained in the wt cells ( Table 2 ) .	8	TEMPERATURE, OSMOLARITY AND GROWTH PHASE- DEPENDENT SILENCING OF HILA BY H-NS AND HHA	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilA	activator	23515315	39	ver/dev	Notably , EMSAs revealed that H-NS DNA binding to hilA was also enhanced by the addition of HhaR14A/R17A , although this mutant was Fig. 7B .	334	Notably , EMSAs performed with the purified Hha arginine mutants revealed that H-NS DNA binding to hilA was also enhanced by the addition of HhaR14A/R17A , although this mutant was completely defective for gene silencing in vivo ( Fig. 7B ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hilA	activator	23515315	39	ver/dev	Notably , EMSAs revealed that H-NS DNA binding to hilA was also enhanced by the addition of HhaR14A/R17A , although this mutant was completely defective for gene silencing in-vivo .	334	Notably , EMSAs performed with the purified Hha arginine mutants revealed that H-NS DNA binding to hilA was also enhanced by the addition of HhaR14A/R17A , although this mutant was completely defective for gene silencing in vivo ( Fig. 7B ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hilA	activator	25375226	30	ver/dev	In the absence of H-NS it is possible that silencing complexes generated by M4T StpAA77D , although more effective than StpAWT , were unable to impede HilD-mediated activation of hilA .	403	In the absence of H-NS it is possible that silencing complexes generated by StpA and M4T StpAA77D , although more effective than StpAWT , were unable to impede the combined HilC and HilD-mediated activation of hilA .	10	AMINO ACID SUBSTITUTIONS M4T AND A77D ALTER STPA’S SILENCING PROPERTIES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
HNS	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilC activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilC activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilD activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting in small part as activators through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	31182495	48	ver/dev	However , it has been hypothesized that HilD activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors through direct stimulation of the polymerase .	214	However , it has been hypothesized that HilD , HilC , and RtsA activate hilA transcription mainly by disrupting binding of the global repressor H-NS , acting as antirepressors , and only in small part as activators through direct stimulation of the polymerase ( 21 , 68 ) .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hilA	activator	32571967	12	ver/dev	H-NS contributes to silencing of hilA	223	Rcs could , for example , be functioning through H-NS , which contributes to silencing of hilD , hilC , rtsA , and hilA ( 33 , 78 -- 80 ) .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilA	activator	34424033	36	ver/dev	As shown in Fig. 8A , in a wild-type background , production of simplest explanation for the effect of the H-NS DN in the wild type is that it activators of hilA expression	416	As shown in Fig. 8A , in a wild-type background , production of simplest explanation for the effect of the H-NS DN in the wild type is that it activators of hilA expression and that the primary role of H-NS in SPI1 regulation	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RcsB	gene	ugd	regulator	12519186	24	att	We analysed the 281 bp region upstream of the ugd start codon and identified a motif that could correspond to a potential RcsB binding site ( Fig. 4B ) because it resembled the upstream regulatory region of other RcsB-regulated genes ( Fig. 4C ) .	76	We analysed the 281 bp region upstream of the ugd start codon and identified a motif that could correspond to a potential RcsB binding site ( Fig. 4B ) because it resembled the upstream regulatory region of other RcsB-regulated genes ( Fig. 4C ) .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
RcsB	gene	ugd	regulator	12519186	49	att	The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .	137	The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	ugd	regulator	15387821	6	att	Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	463	Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	30	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	15469511	11	att	Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	460	Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	18467098	9	att	47 , 335 -- 344 62 Mouslim , C. et al. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	337	47 , 335 -- 344 62 Mouslim , C. et al. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	41	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	19780840	4	att	Mouslim C , Latifi T & Groisman EA ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	358	Mouslim C , Latifi T & Groisman EA ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	17	BORDETELLA PERTUSSIS MEDIATED BY THE VIR (BVG) LOCUS. MOLECULAR GENETICS OF BACTERIAL PATHOGENESIS (MILLER VL, KAPER JB, PORTNEY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	20593264	6	att	Mouslim , C. , Latifi , T. , Groisman , E. Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	466	Mouslim , C. , Latifi , T. , Groisman , E. Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	42	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	20724387	9	att	Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	284	Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	37	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	21487806	3	att	Mouslim C , Latifi T , Groisman EA ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	351	Mouslim C , Latifi T , Groisman EA ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	25	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	23019341	3	att	Mouslim , C. , Latifi , T. , and Groisman , E. A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	476	Mouslim , C. , Latifi , T. , and Groisman , E. A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	24	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	25028458	49	att	Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	504	Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	41	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	27206164	67	att	Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	513	Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .	41	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	27558204	6	att	in transcription of the RcsB-regulated ugd gene .	313	in transcription of the RcsB-regulated ugd gene .	25	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	30763640	64	att	[ 19 ] C. Mouslim , T. Latifi , E.A. Groisman , Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene , J. Biol .	366	[ 19 ] C. Mouslim , T. Latifi , E.A. Groisman , Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene , J. Biol .	25	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	ugd	regulator	31563538	19	att	[ 4 ] C. Mouslim , T. Latifi , E.A. Groisman , Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene , J. Biol .	332	[ 4 ] C. Mouslim , T. Latifi , E.A. Groisman , Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene , J. Biol .	21	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PtsJ	gene	pdxK	activator	27987384	3	ver/dev	When growth took place in LB-rich-medium , a significant 6.6-fold increase of expression of pdxK was observed in the DptsJ strain with respect to Fig. 1B , con-firming the repressor role of PtsJ .	193	When growth took place in LB-rich medium , a significant 6.6-fold increase of expression of pdxK was observed in the DptsJ strain with respect to wild-type ( Fig. 1B ) , con-firming the repressor role of PtsJ .	11	ROLE OF PTSJ IN THE EXPRESSION OF VITAMIN B6 SALVAGE PATHWAY GENES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
PtsJ	gene	pdxK	activator	27987384	3	ver/dev	When growth took place in LB-rich-medium , a significant 6.6-fold increase of expression of pdxK was observed in the DptsJ strain with respect to wild-type , con-firming the repressor role of PtsJ .	193	When growth took place in LB-rich medium , a significant 6.6-fold increase of expression of pdxK was observed in the DptsJ strain with respect to wild-type ( Fig. 1B ) , con-firming the repressor role of PtsJ .	11	ROLE OF PTSJ IN THE EXPRESSION OF VITAMIN B6 SALVAGE PATHWAY GENES	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
FliZ	gene	fliB	activator	22356617	6	att	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	358	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
Fis	gene	hlyE	regulator	24885225	36	ver/dev	Altogether , these results suggest that Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	125	Altogether , these results suggest that CRP and Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fis	gene	hlyE	regulator	25913156	0	ver/dev	RpoS integrates Fis to control Salmonella Typhi hlyE expression .	515	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	32	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	hlyE	regulator	27260307	1	ver/dev	RpoS integrates Fis to control Salmonella Typhi hlyE expression .	575	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	11	ESCHERICHIA COLI. INFECT IMMUN 72, 2879–2888.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	hlyE	regulator	27567490	0	ver/dev	RpoS integrates Fis to control Salmonella Typhi hlyE expression .	514	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	37	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Fis	gene	hlyE	regulator	30778340	5	ver/dev	RpoS integrates Fis to control Salmonella Typhi hlyE expression .	568	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	20	SUPPLEMENTARY MATERIAL	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoN	activator	12218035	0	att	Briefly , pNL3 is a pBR322-derived reporter plasmid in which the PhoP-activated phoN promoter region of S. enterica serovar Typhimurium is fused to the lacZ structural gene .	46	Briefly , pNL3 is a pBR322-derived reporter plasmid in which the PhoP-activated phoN promoter region of S. enterica serovar Typhimurium is fused to the lacZ structural gene .	3	MATERIALS AND METHODS	unidentified plasmid;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoN	activator	14563863	0	att	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	12	We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .	1	ABSTRACT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoN	activator	16023758	7	att	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	161	PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .	10	2.3. PHOPQ AND THE ACID STRESS RESPONSE	Prochilodus marggravii;Salmo platycephalus;Salmo ohridanus;Salmo obtusirostris;Salmonella	0.5	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	phoN	activator	18350168	2	att	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	294	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	phoN	activator	19103774	0	att	PphoPQ107 : : TT araC PBAD phoPQ and 9108 with the PphoPQ107 : : TT araC PBAD phoPQ and Pcrp527 : : TT araC PBAD crp mutations when streaked on X-P plates without and with 0.2 % arabinose reveal acid phosphatase activity due to expression of the PhoP-activated phoN gene only when grown in the presence of arabinose ( Fig. 2c ) .	130	PphoPQ107 : : TT araC PBAD phoPQ and 9108 with the PphoPQ107 : : TT araC PBAD phoPQ and Pcrp527 : : TT araC PBAD crp mutations when streaked on X-P plates without and with 0.2 % arabinose reveal acid phosphatase activity due to expression of the PhoP-activated phoN gene only when grown in the presence of arabinose ( Fig. 2c ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
PhoP	gene	phoN	activator	20396961	7	att	Considering that some PhoP-regulated genes such as pag loci and phoN , which encodes a nonspecific acid phosphatase , are maximally induced under starvation conditions ( Behlau and Miller , 1995 ; Kier et al. , 1997 ) , it is reasonable to conclude that induced synthesis of the tdc genes inside macrophages affects the expression of a subset of PhoP-dependent genes such as SPI2 .	329	Considering that some PhoP-regulated genes such as pag loci and phoN , which encodes a nonspecific acid phosphatase , are maximally induced under starvation conditions ( Behlau and Miller , 1995 ; Kier et al. , 1997 ) , it is reasonable to conclude that induced synthesis of the tdc genes inside macrophages affects the expression of a subset of PhoP-dependent genes such as SPI2 .	12	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoN	activator	23504014	19	att	Two additional PhoP-activated genes , slyB and phoN , were used as positive and negative controls , respectively , since previous experiments have shown direct interaction of PhoP with the promoter of slyB but not with the promoter of phoN ( 50 ) .	296	Two additional PhoP-activated genes , slyB and phoN , were used as positive and negative controls , respectively , since previous experiments have shown direct interaction of PhoP with the promoter of slyB but not with the promoter of phoN ( 50 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
CRP	gene	hlyE	regulator	14996792	54	att	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	254	While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .	8	DISCUSSION	Escherichia coli	0	L3	OTHER	Other	NEG	Other	Level 1
CRP	gene	hlyE	regulator	14996792	14	ver/dev	Thus , we concluded that CRP all contribute towards the regulation of hlyE expression .	83	Thus , we concluded that CRP , FNR , and H-NS all contribute towards the regulation of hlyE expression .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
CRP	gene	hlyE	regulator	14996792	23	ver/dev	In summary , the data suggest that CRP are positive regulators of hlyE expression in liquid culture in response to glucose-starvation , respectively .	124	In summary , the data presented here suggest that FNR and CRP are positive regulators of hlyE expression in liquid culture in response to oxygen and glucose starvation , respectively .	7	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	hlyE	regulator	14996792	23	ver/dev	In summary , the data suggest that CRP are positive regulators of hlyE expression in liquid culture in response to oxygen , respectively .	124	In summary , the data presented here suggest that FNR and CRP are positive regulators of hlyE expression in liquid culture in response to oxygen and glucose starvation , respectively .	7	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	14996792	51	ver/dev	This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .	242	This reciprocity of binding site recognition and transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals ( oxygen and glucose starvation ) rather than , for example , the much larger degree of upregulation when FNR and CRP act synergistically by binding at different sites within the ansB promoter ( 28 ) .	8	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	19835951	0	ver/dev	RpoS- and Crp-dependent transcriptional control of hlyE genes	2	RpoS- and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes: role of environmental conditions	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	21148209	36	ver/dev	RpoS-and Crp-dependent transcriptional control of hlyE genes : role of environmental conditions .	329	RpoS-and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	35	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	24885225	19	ver/dev	Nevertheless , genetic experiments showed that CRP participates in the negative regulation of hlyE in S. Typhi since crp deletion led to increased β-galactosidase activit .	61	Nevertheless , genetic experiments showed that CRP participates in the negative regulation of hlyE in S. Typhi since crp deletion led to increased β-galactosidase activity associated to the ΔhlyE : : lacZ strain [ 14 ] .	4	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	hlyE	regulator	24885225	36	ver/dev	Altogether , these results suggest that CRP are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	125	Altogether , these results suggest that CRP and Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	hlyE	regulator	24885225	65	ver/dev	Fuentes JA , Jofre MR , Villagra NA , Mora GC : RpoS - and Crp-dependent transcriptional control of hlyE genes : role of environmental conditions .	398	Fuentes JA , Jofre MR , Villagra NA , Mora GC : RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	25913156	0	ver/dev	RpoS integrates CRP to control Salmonella Typhi hlyE expression .	515	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	32	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	27260307	1	ver/dev	RpoS integrates CRP to control Salmonella Typhi hlyE expression .	575	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	11	ESCHERICHIA COLI. INFECT IMMUN 72, 2879–2888.	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	27260307	2	ver/dev	RpoS - and Crp-dependent transcriptional control of hlyE genes : role of environmental conditions .	739	RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	51	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	27567490	0	ver/dev	RpoS integrates CRP to control Salmonella Typhi hlyE expression .	514	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	37	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	30778340	4	ver/dev	RpoS - and Crp-dependent transcriptional control of hlyE genes : role of environmental conditions .	521	RpoS - and Crp-dependent transcriptional control of Salmonella Typhi taiA and hlyE genes : role of environmental conditions .	20	SUPPLEMENTARY MATERIAL	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	30778340	5	ver/dev	RpoS integrates CRP to control Salmonella Typhi hlyE expression .	568	RpoS integrates CRP , Fis , and PhoP signaling pathways to control Salmonella Typhi hlyE expression .	20	SUPPLEMENTARY MATERIAL	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	hlyE	regulator	33475482	5	ver/dev	In S. Typhi , Crp was identified as a regulator of hlyE , virulence genes .	194	In S. Typhi , Crp was identified as a regulator of hlyE and taiA , virulence genes encoded on SPI-18 [ 19 , 21 ] .	10	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	TU	flhDC	repressor	31501286	25	ver/dev	This approach allowed detection of possible posttranscriptional effects on flhDC expression , since reductions in flagellar expression and motility could not occur through transcriptional repression of the native flhDC promoter when RamA was ectopically expressed .	207	This approach allowed detection of possible posttranscriptional effects on flhDC expression , since reductions in flagellar expression and motility could not occur through transcriptional repression of the native flhDC promoter when MarA , SoxS , Rob , or RamA was ectopically expressed .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
RamA	TU	flhDC	repressor	31501286	36	ver/dev	FIG 3 Production of RamA _ resulting in posttranscriptional repression of flhDC	269	FIG 3 Production of MarA , SoxS , Rob , and RamA resulting in posttranscriptional repression of flhDC .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RpoS	gene	mgtC	activator	20221735	0	ver/dev	Most of these genes were induced at a higher level in the RpoS - mgtC .	167	Most of these genes were induced at a higher level in the RpoS - mutant background with a few exceptions , such as sptP , sscB , sseB , and mgtC .	7	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	pagN	regulator	25624475	7	att	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	77	To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .	7	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
Cra	gene	iscR	regulator	19136587	5	ver/dev	Cra binds to the iscR promoter region in-vitro .	341	Cra binds to the iscR promoter region in vitro .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cra	gene	iscR	regulator	19136587	8	ver/dev	If the effect of Cra were direct , Cra would bind to more nonconsensus sites within the iscR region .	346	If the effect of Cra were direct , Cra would bind to one or more nonconsensus sites within the iscR region .	4	RESULTS AND DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Cra	gene	iscR	regulator	19136587	8	ver/dev	If the effect of Cra were direct , Cra would bind to one nonconsensus sites within the iscR region .	346	If the effect of Cra were direct , Cra would bind to one or more nonconsensus sites within the iscR region .	4	RESULTS AND DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
Cra	gene	iscR	regulator	19136587	10	ver/dev	To determine whether Cra could bind to the iscR promoter region , EMSAs were performed with purified Cra protein .	349	To determine whether Cra could bind to the iscR promoter region , EMSAs were performed with purified Cra protein .	4	RESULTS AND DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
Cra	gene	iscR	regulator	19136587	12	ver/dev	Indeed , Cra bound to the iscR promoter region , albeit with relatively low affinity .	351	Indeed , Cra bound to the iscR promoter region , albeit with relatively low affinity ( Fig. 6 and 7 ) .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Cra	gene	iscR	regulator	19136587	13	ver/dev	The weak binding of Cra to the iscR promoter was not surprising given the lack of a consensus sequence .	353	The weak binding of Cra to the iscR promoter was not surprising given the lack of a consensus sequence .	4	RESULTS AND DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
RamA	gene	ramA	regulator	18984645	0	ver/dev	Mutations in the promoter region of ramA appear to play a role in the up-regulation of RamA	12	Conclusions : Mutations in the promoter region of ramA appear to play a role in the up-regulation of RamA and AcrAB , and RamA is an activator of the MDR regulation cascade in Salmonella Typhimurium .	2	ABSTRACT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
RamA	gene	ramA	regulator	18984645	8	ver/dev	bile-mediated 52 regulation of AcrAB in Salmonella is also that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium	315	Nikaido et al. showed that indole - and bile-mediated 52 regulation of AcrAB in Salmonella is also RamA-dependent , and that induction of ramA is required for overexpression of acrAB , indicating the important role of RamA in the regulation of efflux pumps in Salmonella Typhimurium .	17	DISCUSSION	Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	gene	ramA	regulator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in other Enterobacter-iaceae .11 -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	regulator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	regulator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in other Enterobacter-iaceae .11 -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	regulator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	regulator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in other Enterobacter-iaceae .11 -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	regulator	23493314	1	ver/dev	that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole	24	Although MarA , SoxS and Rob are present in Salmonella , studies have shown that the transcriptional activator RamA , which is not present in E. coli , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella and other Enterobacter-iaceae .11 -- 17 To date , few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole , and that acrAB induction by indole is dependent on RamA .	5	INTRODUCTION	Salmonella	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	gene	ramA	regulator	24816212	2	ver/dev	This derepression presumably results , as previously observed with other known ramA inducers , in increased levels of the RamA protein .27,28 Using in-vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .	214	This derepression presumably results , as previously observed with other known ramA inducers such as indole and chlorpromazine , in increased levels of the RamA protein .27,28 Using in vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .	12	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RamA	gene	ramA	regulator	24816212	2	ver/dev	This derepression presumably results , as previously observed with chlorpromazine , in increased levels of the RamA protein .27,28 Using in-vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .	214	This derepression presumably results , as previously observed with other known ramA inducers such as indole and chlorpromazine , in increased levels of the RamA protein .27,28 Using in vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .	12	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
RamA	gene	ramA	regulator	24816212	2	ver/dev	This derepression presumably results , as previously observed with indole , in increased levels of the RamA protein .27,28 Using in-vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .	214	This derepression presumably results , as previously observed with other known ramA inducers such as indole and chlorpromazine , in increased levels of the RamA protein .27,28 Using in vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .	12	DISCUSSION	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
FimZ	gene	hilA	repressor	25547794	7	ver/dev	We therefore hypothesized that the signals from PhoBR two-component regulators are processed through FimZ , leading to the repression of hilA .	66	We therefore hypothesized that the signals from the PhoPQ and PhoBR two-component regulators are processed through FimZ , leading to the repression of hilA .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FimZ	gene	hilA	repressor	25547794	7	ver/dev	We therefore hypothesized that the signals from the PhoPQ are processed through FimZ , leading to the repression of hilA .	66	We therefore hypothesized that the signals from the PhoPQ and PhoBR two-component regulators are processed through FimZ , leading to the repression of hilA .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Fur	gene	hfq	regulator	18554972	0	att	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	215	The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .	15	3.1. TRANSPOSON MUTAGENESIS IDENTIFIES IRON RESPONSE GENES INVOLVED IN NOREPINEPHRINE-ENHANCED GROWTH OF SALMONELLA TYPHIMURIUM	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	TU	ssrAB	regulator	30718301	52	ver/dev	Together , these results indicate that PhoP are not involved in the coordinated regulation of ssrAB revealed in this study .	155	Together , these results indicate that PhoP and SsrB are not involved in the coordinated regulation of ssrAB revealed in this study , mediated by SlyA , HilD , and OmpR .	3	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	TU	ssrAB	regulator	30718301	68	ver/dev	We found that SsrB do not play an evident role in transcription from the promoter upstream of ssrA ; however , PhoP controls the expression of ssrAB at the posttranscriptional level .	191	We found that PhoP and SsrB do not play an evident role in transcription from the promoter upstream of ssrA , which is consistent with findings from previous reports ( 23 , 26 ) ; however , PhoP controls the expression of ssrAB at the posttranscriptional level ( 26 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
PhoP	TU	ssrAB	regulator	30718301	68	ver/dev	We found that PhoP do not play an evident role in transcription from the promoter upstream of ssrA ; however , PhoP controls the expression of ssrAB at the posttranscriptional level .	191	We found that PhoP and SsrB do not play an evident role in transcription from the promoter upstream of ssrA , which is consistent with findings from previous reports ( 23 , 26 ) ; however , PhoP controls the expression of ssrAB at the posttranscriptional level ( 26 ) .	4	DISCUSSION	nan	1	L3	OTHER	Other	NEG	New	Level 1
FliZ	gene	STM3604	activator	22356617	6	att	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	358	Of the seven remaining FliZ-dependent genes , six were putative flagella class 2 or 3 genes , fliB , mcpA , mcpB , STM3154 , STM3156 , STM3604 ( Frye et al. , 2006 ; Wang et al. , 2006 ) .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	nan	1	L2	SPEC	Other	OTHER	Other	Level 1
NadR	gene	pncB	repressor	15805524	3	ver/dev	The NadR protein was previously shown to repress transcription of pncB promoters in response to high levels of NAD .	173	The NadR protein was previously shown to repress transcription of the nadA , nadB , and pncB promoters in response to high levels of NAD ( 25 , 39 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
NadR	gene	pncB	repressor	15968063	0	ver/dev	The NadR function represses transcription of the pncB genes .	37	The NadR ( R ) function represses transcription of the nadB and pncB genes and the nadA-pnuC operon when NAD levels are high ( 7 , 37 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CsgD	gene	lpfE	activator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of lpfE genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CsgD	gene	lpfE	activator	22803575	0	ver/dev	Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of lpfE genes	295	Typhimurium cells treated with polyphenol ( Fig. 1d and Table 3 ) , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons and adrA gene involved in bio-film formation , virulence , transport and EPS production ( Olsen et al. 1993 ; Hammar et al. 1995 ) and also the upregulation of expression of fimA and lpfE genes may affect the affinity and binding capacity of Salm .	20	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	TU	ssrAB	activator	25135218	7	ver/dev	Previously , we dem-onstrated that HilD directly induces the expression of the ssrAB operon .	24	Previously , we dem-onstrated that HilD directly induces the expression of the ssrAB operon , which is located in SPI-2 and codes for the SsrA/B two-component system , the central positive regulator of SPI-2 , thus establishing a transcriptional cross talk between SPI-1 and SPI-2 ( 21 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	25135218	12	ver/dev	This suggests that HilD induces the expression of ssrAB also by counteracting H-NS-me-diated repression of its promoter .	42	This suggests that HilD induces the expression of ssrAB also by counteracting H-NS-me-diated repression of its promoter .	2	MAIN	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	ssrAB	activator	25135218	68	ver/dev	All together , these results indicate that HilD induces the expression of ssrAB by displacing the H-NS nucleoprotein complex from the promoter of this operon .	211	All together , these results indicate that HilD induces the expression of ssrAB by displacing the H-NS nucleoprotein complex from the promoter of this operon ( Fig. 7 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	TU	ssrAB	activator	25135218	73	ver/dev	Furthermore , our results indicate that HilD induces the expression of ssrAB by binding to one located on .	216	Furthermore , our results indicate that HilD induces the expression of ssrAB by binding to at least two different AT-rich regions : one located on or close to the promoter and the other located far downstream ( Fig. 3 and 5 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	TU	ssrAB	activator	25135218	73	ver/dev	Furthermore , our results indicate that HilD induces the expression of ssrAB by binding to at least two different AT-rich regions .	216	Furthermore , our results indicate that HilD induces the expression of ssrAB by binding to at least two different AT-rich regions : one located on or close to the promoter and the other located far downstream ( Fig. 3 and 5 ) .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
HilD	TU	ssrAB	activator	26300871	1	ver/dev	Interestingly , when S. Typhimurium is grown to late stationary-phase in LB-medium , HilD directly induces the expression of the ssrAB operon .	73	Interestingly , when S. Typhimurium is grown to late stationary phase in LB medium , HilD directly induces the expression of the ssrAB operon that is located in SPI-2 and codes for the SsrA/B two-component system , the central positive regulator of the SPI-2 genes , thus establishing a transcriptional cross talk between SPI-1 and SPI-2 ( Bustamante et al. , 2008 ; Martínez et al. , 2014 ) .	1	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	26810370	2	ver/dev	HilD can activate the ssrAB operon by specifically interacting with its regulatory region to upregulate SPI-2 .	239	HilD can activate the ssrAB operon by specifically interacting with its regulatory region to upregulate SPI-2 [ 41 ] .	12	DISCUSSION	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	TU	ssrAB	activator	28329249	2	ver/dev	HilD can also induce expression of SPI-2 by direct binding to the promoter of ssrAB .	38	HilD can also induce expression of SPI-2 by direct binding to the promoter of ssrAB , which encodes a key regulator of SPI-2 [ 5 ] .	3	MAIN	nan	1	L2	OTHER	Other	OTHER	New	Level 1
HilD	TU	ssrAB	activator	30718301	11	ver/dev	For instance , HilD induces the expression of ssrAB by directly displacing H-NS-mediated repression on the promoter upstream of ssrA under in-vitro growth-conditions .	51	For instance , HilD induces the expression of ssrAB by directly displacing H-NS-mediated repression on the promoter upstream of ssrA under in vitro growth conditions that resemble the intestinal environment ( 18 , 19 ) .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HilD	TU	ssrAB	activator	30718301	12	ver/dev	In this work , we determine how the acquired regulator HilD induce the expression of the S. Typhimurium ssrAB operon under different growth-conditions .	52	In this work , we determine how the ancestral regulators SlyA and OmpR and the acquired regulator HilD induce the expression of the S. Typhimurium ssrAB operon under different growth conditions .	2	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	30718301	31	ver/dev	In previous studies , we demonstrated that HilD also induces the expression of ssrAB during the growth of S. Typhimurium in LB by antagonizing H-NS-mediated repression .	103	In previous studies , we demonstrated that HilD also induces the expression of ssrAB during the growth of S. Typhimurium in LB by antagonizing H-NS-mediated repression ( 18 , 19 ) .	3	RESULTS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	30718301	32	ver/dev	To confirm that both SlyA and HilD act as antirepressors of H-NS to induce the expression of ssrAB , we analyzed if the inactivation of H-NS leads to the expression of ssrAB independently of both SlyA and HilD .	104	To confirm that both SlyA and HilD act as antirepressors of H-NS to induce the expression of ssrAB , we analyzed if the inactivation of H-NS leads to the expression of ssrAB independently of both SlyA and HilD .	3	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	32021316	2	ver/dev	HilD also induce the expression of hilD genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	32021316	2	ver/dev	HilD also induce the expression of hilC genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	32021316	2	ver/dev	HilC also induce the expression of hilD genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	TU	ssrAB	activator	32021316	2	ver/dev	HilC also induce the expression of hilC genes that ultimately activate hilA .158 HilD first induces hilA and , then , induces ssrAB located in SPI-2 .	196	HilC and HilD also induce the expression of hilC and hilD genes that ultimately activate hilA .158 HilD first induces hilA that is located in SPI-1 and , then , induces ssrAB located in SPI-2 .	15	HOW TO ACTIVATE PATHOGENIC GENES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
SirA	gene	fimA	regulator	17074910	17	ver/dev	SirA csrC regulate the fimA promoter .	488	SirA and csrB csrC regulate the fimA promoter .	9	THE TYPE I FIMBRIAL OPERON IS REGULATED BY SIRA AND CSR, AND CONTRIBUTES TO BIOFILM FORMATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SirA	gene	fimA	regulator	17074910	19	ver/dev	However , this may seem unexpected , as SirA can directly bind fimA promoters , so SirA would be expected to activate these genes independently of csrC .	510	However , this may seem unexpected , as SirA can directly bind the hilA , hilC and fimA promoters , so SirA would be expected to activate these genes independently of csrB and csrC .	10	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
SirA	gene	fimA	regulator	17074910	19	ver/dev	However , this may seem unexpected , as SirA can directly bind fimA promoters , so SirA would be expected to activate these genes independently of csrB .	510	However , this may seem unexpected , as SirA can directly bind the hilA , hilC and fimA promoters , so SirA would be expected to activate these genes independently of csrB and csrC .	10	CONCLUSIONS	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	flhDC	regulator	31501286	18	ver/dev	For this reason , we hypothesized that RamA may bind to flhDC as well .	193	For this reason , we hypothesized that MarA , SoxS , and RamA may bind to flhDC as well .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
RamA	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test RamA-dependent control of the flhDC promoter , we replaced class I in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test RamA-dependent control of the flhDC promoter , we replaced class I in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	TU	flhDC	regulator	31501286	24	ver/dev	To genetically test RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter .	205	To genetically test MarA , SoxS , Rob , and RamA-dependent control of the flhDC promoter , we replaced the native flhDC promoter ( class I ) in situ with a tetracycline-inducible promoter cassette in an otherwise wild-type genetic background ; this genetic modification has been shown to remove all native transcriptional regulation of the flhDC promoter ( 11 , 13 ) .	4	RESULTS MARA, SOXS, ROB, AND RAMA INHIBIT MOTILITY AND DECREASE PRODUCTION OF FLAGEL-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
RamA	TU	flhDC	regulator	31501286	48	ver/dev	While RamA regulation of flhDC was not explored in detail here , our data indicated that it behaves similarly to SoxS .	449	While RamA regulation of flhDC was not explored in detail here , our data indicated that it behaves similarly to SoxS .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
Sigma54	gene	ant	activator	10629201	4	att	We examined the abilities of the deletion mutants to repress transcription from a phage P22 ant9-9lacZ reporter gene in which the s54-dependent Sinorhizobium meliloti nifH promoter overlapped the ant promoter ( 1 ) .	138	We examined the abilities of the deletion mutants to repress transcription from a phage P22 ant9-9lacZ reporter gene in which the s54-dependent Sinorhizobium meliloti nifH promoter overlapped the ant promoter ( 1 ) .	2	MAIN	Salmonella virus P22;Salmonella virus P22;Sinorhizobium meliloti	0.5	L2	OTHER	Investigation	OTHER	New	Level 1
PmrA	gene	STM1253	activator	15681155	28	att	Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .	334	Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .	14	4. DISCUSSION	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PmrA	gene	STM1253	activator	15681155	9	att	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	206	Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .	11	3. RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PmrA	gene	STM1253	activator	15681155	24	ver/dev	Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM0459 , AsnC family transcriptional regulator .	306	Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase , and STM0459 , AsnC family transcriptional regulator .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	STM1253	activator	15681155	24	ver/dev	Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; thymidine phosphorylase .	306	Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase , and STM0459 , AsnC family transcriptional regulator .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PmrA	gene	STM1253	activator	15681155	24	ver/dev	Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 .	306	Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase , and STM0459 , AsnC family transcriptional regulator .	14	4. DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	csgD	regulator	19759044	1	ver/dev	Prigent-Combaret et al. suggested that 51 52 E. coli OmpR is also a regulator of the csgD regulator .	374	Prigent-Combaret et al. suggested that 51 52 E. coli OmpR is also a regulator of the csgD regulator , which in turn activates curli formation and thus biofilm formation .	23	DISCUSSION	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
OmpR	gene	csgD	regulator	28148244	0	ver/dev	OmpR regulate the transcription of csgD in S. typhimurium .	33	Global transcriptional regulators such as RpoS , OmpR , H-NS and IHF regulate the transcription of csgD in S. typhimurium [ 25 ] .	5	BACKGROUND	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	csgD	regulator	30663891	1	ver/dev	csgD expression is controlled by the response regulator OmpR is also required for transcriptional activation of the csgD promoter	159	csgD expression is controlled by the alternative sigma factor rS and the response regulator OmpR is also required for transcriptional activation of the csgD promoter ( Ro $ mling et al. , 1998 )	8	4.1.1. SALMONELLA PROTECTIVE SURFACE STRUCTURES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	csgD	regulator	33952386	4	ver/dev	For example , the EnvZ / OmpR system controls the expression of csgD .	47	For example , the EnvZ / OmpR system controls the expression of csgD , which encodes a master regulator activating the biosynthesis of curli fimbriae and cellulose [ 19 -- 21 ] .	2	INTRODUCTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	activator	10816543	0	att	The constitutive phoP gene was placed under the control of an arabinose-inducible promoter to examine the kinetics of PhoP-activated gene induction and the resultant modifications of LPS .	10	The constitutive phoP gene was placed under the control of an arabinose-inducible promoter to examine the kinetics of PhoP-activated gene induction and the resultant modifications of LPS .	1	ABSTRACT	nan	1	L3	OTHER	Investigation	OTHER	Other	Level 2
PhoP	gene	phoP	activator	10816543	4	att	We placed the constitutive phoP gene under the control of an arabinose-inducible promoter and used this to determine the kinetics of activation of several pag genes as well as the modification of lipid-A with 2-hydroxymyristate , which can be added as a result of activation of an unknown PhoP-activated gene ( s ) .	121	We placed the constitutive phoP gene under the control of an arabinose-inducible promoter and used this to determine the kinetics of activation of several pag genes as well as the modification of lipid A with 2-hydroxymyristate , which can be added as a result of activation of an unknown PhoP-activated gene ( s ) .	2	MAIN	unidentified	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	11844755	0	att	To identify genes necessary for bile resistance , MudJ transposon mutagenesis was performed on a strain containing a phoP mutation that results in constitutive expression of PhoP-activated genes .	8	To identify genes necessary for bile resistance , MudJ transposon mutagenesis was performed on a strain containing a phoP mutation that results in constitutive expression of PhoP-activated genes .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	activator	11918812	1	att	A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence ( Miller and Mekalanos , 1990 ) .	249	A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence ( Miller and Mekalanos , 1990 ) .	8	DISCUSSION	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	phoP	activator	12507481	0	att	The PhoP/PhoQ two-component system governs the adaptation to low Mg2þ environments and virulence in several Gram-negative species .1 The PhoQ protein is a sensor for extra-cytoplasmic Mg2þ and Ca2þ that controls the activity of the response regulator PhoP : growth in millimolar concentrations of Mg2þ or Ca2þ represses transcription of PhoP-activated genes whereas growth in micromolar concentrations of these divalent cations results in transcription of PhoP-activated genes .2 A Salmonella phoQ null mutant exhibits the same phenotype as that of a phoP null mutant : the inability to promote transcription of PhoP -	23	The PhoP/PhoQ two-component system governs the adaptation to low Mg2þ environments and virulence in several Gram-negative species .1 The PhoQ protein is a sensor for extra-cytoplasmic Mg2þ and Ca2þ that controls the activity of the response regulator PhoP : growth in millimolar concentrations of Mg2þ or Ca2þ represses transcription of PhoP-activated genes whereas growth in micromolar concentrations of these divalent cations results in transcription of PhoP-activated genes .2 A Salmonella phoQ null mutant exhibits the same phenotype as that of a phoP null mutant : the inability to promote transcription of PhoP -	3	INTRODUCTION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	12519186	10	att	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	40	The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .	4	RESULTS	unidentified	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	phoP	activator	12519186	28	att	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	93	D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	phoP	activator	12519186	32	att	The ugd promoter was induced inside mammalian cells in a PhoP-dependent fashion because no expression was observed in a phoP mutant ( Fig. 6 ) .	103	The ugd promoter was induced inside mammalian cells in a PhoP-dependent fashion because no expression was observed in a phoP mutant ( Fig. 6 ) .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	14563863	3	att	Strains EG9523 ( mgtA : : MudJ phoP : : Tn10 ) , EG9313 ( slyB : : MudJ phoP : : Tn10 ) , EG9529 ( mgtC : : MudJ phoP : : Tn10 ) , EG9280 ( pmrC : : MudJ phoP : : Tn10 ) , and EG9332 ( pcgL : : MudJ phoP : : Tn10 ) ( 10 , 42 , 43 ) were transformed with plasmid pEG9014 or with the pUHE21-2lacIq vector ( 41 ) and were used for PhoP-dependent pag expression analysis .	52	Strains EG9523 ( mgtA : : MudJ phoP : : Tn10 ) , EG9313 ( slyB : : MudJ phoP : : Tn10 ) , EG9529 ( mgtC : : MudJ phoP : : Tn10 ) , EG9280 ( pmrC : : MudJ phoP : : Tn10 ) , and EG9332 ( pcgL : : MudJ phoP : : Tn10 ) ( 10 , 42 , 43 ) were transformed with plasmid pEG9014 or with the pUHE21-2lacIq vector ( 41 ) and were used for PhoP-dependent pag expression analysis .	3	MATERIALS AND METHODS	unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	15208313	35	att	As expected for a PhoP-activated gene , there was no slyA transcription when bacteria were grown under PhoP-repress-ing conditions ( i.e. 10 mM Mg2 ) , regardless of the presence of a functional phoP gene ( Fig. 4A ) .	150	As expected for a PhoP-activated gene , there was no slyA transcription when bacteria were grown under PhoP-repress-ing conditions ( i.e. 10 mM Mg2 ) , regardless of the presence of a functional phoP gene ( Fig. 4A ) .	4	RESULTS	nan	1	L3	OTHER	Other	NEG	Other	Level 1
PhoP	gene	phoP	activator	15225317	28	att	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	338	We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .	9	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S	1	L2	SPEC	Analysis	NEG	Other	Level 1
PhoP	gene	phoP	activator	15225317	6	att	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid-A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	37	We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid A. Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .	3	2 ND POLYMYXIN B	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	17158330	0	att	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4-6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	8	Urelatively constant environments, free- gene transcription taking place immediately after nlike obligate parasites, which live in b-galactosidase. To determine the changes in living organisms need to modulate their activation of the PhoP/PhoQ system, we in- gene expression patterns in response to environ- vestigated the expression kinetics of PhoP- mental cues. This is conspicuously true for bac- regulated genes by isolating RNA as early as terial pathogens, which must express (or silence) 5 min after Salmonella were shifted from media distinct sets of genes in the various tissues in- containing repressing (10 mM) to activating vaded during infection. This ensures that the (50 mM) Mg2+ concentrations. The mRNA lev- encoded products are produced in the correct els of the PhoP-activated mgtA, phoP, pmrD, locales, at the required amounts and for the ap- and mig-14 genes increased after the shift to low propriate extents of time. Consequently, a patho- Mg2+concentration, reached a peak, and then gen’s ability to colonize a particular niche and to decreased to attain steady-state levels that were cause disease is often compromised not only 20 to 50% of the maximum (Fig. 1, A to D). A when a virulence regulatory factor is removed but similar kinetic behavior was observed when also when it is constitutively activated (1, 2). Salmonella were induced in media with 200 mM The PhoP/PhoQ two-component system is a Mg2+, which activates the PhoP/PhoQ system major regulator of virulence in several Gram- less than does 50 mM Mg2+ (8): The mRNA negative species (3). Inactivation of the phoP or levels of the PhoP-activated genes increased, phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2+ virulent for mice and unable to proliferate within (except for the mgtA gene, which reached the phagocytic cells (4–6). The regulatory protein same levels), and then decreased (Fig. 1, A to PhoP governs expression of ~3% of the Sal- D). These results demonstrated that activation monella genome (7) in response to the Mg2+ of the PhoP/PhoQ system promotes a surge in levels sensed by the PhoQ protein: Transcription the mRNA levels of PhoP-regulated genes, of PhoP-activated genes is induced in low Mg2+ and that this surge is not specific to a par- concentrations and repressed in high Mg2+ ticular PhoP-activated gene or inducing con- concentrations (8), whereas the converse is true dition (11). for PhoP-repressed determinants. In addition to low Mg2+ concentrations, certain antimicrobial peptides have been shown to promote expres- Fig. 1. Induction of the sion of some PhoP-activated genes at inter- PhoP/PhoQ system by the 2+ mediate Mg2+ concentrations (9, 10). low-Mg signal results in Previously, the expression of PhoP-regulated a surge in PhoP-regulated gene transcription. (A to genes was examined hours after activation, D) The mRNA levels of often by means of stable reporters such as the mgtA, phoP, pmrD, and mig-14 genes deter- Department of Molecular Microbiology, Howard Hughes mined by real-time poly- Medical Institute, Washington University School of Medi- merase chain reaction cine, Campus Box 8230, 660 South Euclid Avenue, St. (PCR) analysis using RNA Louis, MO 63110, USA. prepared from wild-type *Present address: Center for Agricultural Biomaterials, Col- (EG13918) (10) cells that lege of Agriculture and Life Sciences, Seoul National Univer- 2+ sity, Seoul, 151-921, Korea. were grown in medium containing 10 mM Mg , shifte †To whom correspondence should be addresssed. E-mail: (blue lines) Mg2+, and harvested at the designated t groisman@borcim.wustl.edu the 16S ribosomal RNA gene.	0	Unknown	Salmonella;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.;Salmonella;Rickettsia sp. PAR	0.5	L2	OTHER	Investigation	OTHER	Other	Level 1
PhoP	gene	phoP	activator	17693506	6	att	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid-A modifications explain most of the alterations in the passive permeability of the OM bilayer .	208	In this experiment , the presence of all three mutations ( pmrA , pagP , and lpxO ) made the PhoP-constitutive strain almost as permeable as the phoP null strain , indicating that the known PhoP-dependent lipid A modifications explain most of the alterations in the passive permeability of the OM bilayer .	4	RESULTS	nan	1	L2	SPEC	Fact	OTHER	Other	Level 1
PhoP	gene	phoP	activator	18350168	2	att	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	294	RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .	18	RNS SUPPRESS PHOPQ-DEPENDENT SIGNALING	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	phoP	activator	19091955	23	ver/dev	Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by PhoP because the mRNA level of transcripts is reduced significantly in the phoP mutants grown in low-Mg2 conditions -LRB- Fig .	147	Our results from primer extension demonstrate that transcriptions of the identified loci are activated by PhoP and SlyA because the mRNA level of transcripts is reduced significantly in the phoP and slyA mutants grown in low-Mg2 conditions ( Fig .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	synthetic construct	0	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21511762	0	att	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	217	In vitro studies indicate that some PhoP-activated genes ( pags ) , including mig-14 , virK and pagP , increase resistance to AMPs such as polymyxin B and protegrin-1 ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ; Guo et al. , 1998 ) ; the partial rescue of growth of a phoP mutant strain in BMM lacking the AMP CRAMP suggests that this also occurs in the intramacrophage environment ( Rosenberger et al. , 2004 ) .	4	METHODS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	att	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnB .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnB .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrH .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP1 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrH .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP1 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnC .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnC .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrF .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP2 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrF .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	21563813	0	ver/dev	phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP2 .	157	phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .	6	’ RESULTS	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	23504014	16	att	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	277	As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .	6	RESULTS T-POP-BASED SCREENS IDENTIFY PHOP, PHOQ, AND MGRB AS REGU-	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	activator	23782700	4	att	The Transcriptional Activity of phoPQ Is Down-regulated by the Action of C18 :2 -- Taking into account that phoPQ expression is subjected to autoregulation as part of the PhoP/PhoQ regulon ( 40 ) , the concerted down-regulation in the expression of PhoP-activated genes allowed us to predict that the transcriptional activity of phoP would be turned off when bacteria are grown in the presence of LCUFAs .	203	The Transcriptional Activity of phoPQ Is Down-regulated by the Action of C18 :2 -- Taking into account that phoPQ expression is subjected to autoregulation as part of the PhoP/PhoQ regulon ( 40 ) , the concerted down-regulation in the expression of PhoP-activated genes allowed us to predict that the transcriptional activity of phoP would be turned off when bacteria are grown in the presence of LCUFAs .	3	EXPERIMENTAL PROCEDURES	nan	1	L1	SPEC	Other	OTHER	Other	Level 1
PhoP	gene	phoP	activator	25182488	12	att	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	250	A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	25362575	1	ver/dev	PhoP in turn is responsible for transcriptional activation of response systems .22 The phoP mutant	228	The PhoP/Q two-component regulatory system is controlled by environmental factors such as Mg2 + and pH levels .20,21 Under low Mg2 + levels PhoQ phosphorylates PhoP , which in turn is responsible for transcriptional activation of many different genes and response systems .22 The phoP mutant used here showed increased resistance to low pH and bile , indicative of a constitutive phenotype .	24	EXPRESSION LEVELS OF PAGP IN THE PHOP MUTANT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	25362575	1	ver/dev	PhoP in turn is responsible for transcriptional activation of many different genes .22 The phoP mutant	228	The PhoP/Q two-component regulatory system is controlled by environmental factors such as Mg2 + and pH levels .20,21 Under low Mg2 + levels PhoQ phosphorylates PhoP , which in turn is responsible for transcriptional activation of many different genes and response systems .22 The phoP mutant used here showed increased resistance to low pH and bile , indicative of a constitutive phenotype .	24	EXPRESSION LEVELS OF PAGP IN THE PHOP MUTANT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	25362575	1	ver/dev	PhoP in turn is responsible for transcriptional activation of response systems .22 The phoP mutant	228	The PhoP/Q two-component regulatory system is controlled by environmental factors such as Mg2 + and pH levels .20,21 Under low Mg2 + levels PhoQ phosphorylates PhoP , which in turn is responsible for transcriptional activation of many different genes and response systems .22 The phoP mutant used here showed increased resistance to low pH and bile , indicative of a constitutive phenotype .	24	EXPRESSION LEVELS OF PAGP IN THE PHOP MUTANT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	25362575	1	ver/dev	PhoP in turn is responsible for transcriptional activation of many different genes .22 The phoP mutant	228	The PhoP/Q two-component regulatory system is controlled by environmental factors such as Mg2 + and pH levels .20,21 Under low Mg2 + levels PhoQ phosphorylates PhoP , which in turn is responsible for transcriptional activation of many different genes and response systems .22 The phoP mutant used here showed increased resistance to low pH and bile , indicative of a constitutive phenotype .	24	EXPRESSION LEVELS OF PAGP IN THE PHOP MUTANT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	26943369	21	ver/dev	It has been shown that PhoP phosphorylation is required for activation of transcription of phoP genes .	447	It has been shown that PhoP phosphorylation is required for activation of transcription of phoP and PhoP-regulated genes [ 7 ] .	9	ACETYLATION OF PHOP K201 IS CRITICAL FOR REGULATION OF PHOP ACTIVITY	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	activator	30373755	12	att	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	221	( B ) qRT-PCR validation of RNA-seq data for upregulated genes ( phoP and PhoP-activated ugtL and pagD genes ) and downregulated genes ( rflM and rtsB ) in the Δ1829 mutant ( HL1233 ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	30373755	8	att	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	30373755	8	ver/dev	Using qRT-PCR , we validated the RNA-seq data for several PhoP-regulated genes and others , including upregulated phoP .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	30373755	8	ver/dev	Using quantitative real-time PCR , we validated the RNA-seq data for several PhoP-regulated genes and others , including upregulated phoP .	189	Using quantitative real-time PCR ( qRT-PCR ) , we validated the RNA-seq data for several PhoP-regulated genes and others that are differentially expressed in the ΔSTM14_1829 mutant , including upregulated genes ( phoP and PhoP-activated ugtL and pagD ) and downregulated genes ( rflM and rtsB , both encoding transcriptional repressors of the flhDC operon ) ( Fig. 6B ) .	4	RESULTS IDENTIFICATION OF THREE PARALOGOUS SMALL GENES REQUIRED FOR WILD-TYPE SWIM-	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	30967459	9	att	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	144	( A and B ) mRNA levels of PhoP-activated pmrD , pagD , mig-14 , and mgtA were determined in Salmonella wild-type , ptsN mutant , and ptsN mutant strains harboring a plasmid expressing EIIANtr , EIIANtr ( H73A ) , or EIIANtr ( H73E ) [ pPtsN , pPtsN ( H73A ) , or pPtsN ( H73E ) or an empty vector ( pVec ) ( A ) and Salmonella wild-type and isogenic mutants with deletions of the ptsN , phoP , or ptsN and phoP genes ( B ) .	3	RESULTS	Salmonella;unidentified plasmid;Salmonella	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	phoP	activator	33045730	39	att	Moreover , the site is necessary for PhoP activation in mildly acidic pH because the mRNA abundances of the PhoP-activated pagC and phoP genes were lower in an engineered strain deleted for the SsrB binding site ( Figure 3B ) than in the isogenic wild-type strain ( Figure 3E ) .	236	Moreover , the site is necessary for PhoP activation in mildly acidic pH because the mRNA abundances of the PhoP-activated pagC and phoP genes were lower in an engineered strain deleted for the SsrB binding site ( Figure 3B ) than in the isogenic wild-type strain ( Figure 3E ) .	26	SSRB ACTIVATES PHOP BY PROMOTING TRANSCRIPTION OF THE UGTL GENE	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
PhoP	gene	phoP	activator	33045730	56	att	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	255	SsrB appears to activate PhoP by means other than promoting ugtL transcription because inactivation of the ssrB gene decreases expression of the PhoP-activated phoP promoter in a strain in which the ugtL gene is transcribed from a heterologous promoter ( Figure 3C ) , and also because the ssrB mutant exhibited defective phoP expression in a phoP * phoQ strain ( Figure 3A ) even though UgtL activates PhoP in a PhoQ-dependent manner ( 25 ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
PhoP	gene	phoP	activator	33045730	58	att	DNase I footprinting analysis of the phoP promoter region ( ∼ 300 bp ) demonstrated that the purified DNA binding domain of SsrB protects a region 145 -- 167 nt upstream of the PhoP-dependent transcription start site ( P1 ) of the phoP gene ( Figure 4A and 4B ) .	257	DNase I footprinting analysis of the phoP promoter region ( ∼ 300 bp ) demonstrated that the purified DNA binding domain of SsrB protects a region 145 -- 167 nt upstream of the PhoP-dependent transcription start site ( P1 ) of the phoP gene ( Figure 4A and 4B ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	activator	33045730	58	att	DNase I footprinting analysis of the phoP promoter region ( ∼ 300 bp ) demonstrated that the purified DNA binding domain of SsrB protects a region 145 -- 167 nt upstream of the PhoP-dependent transcription start site ( P1 ) of the phoP gene ( Figure 4A and 4B ) .	257	DNase I footprinting analysis of the phoP promoter region ( ∼ 300 bp ) demonstrated that the purified DNA binding domain of SsrB protects a region 145 -- 167 nt upstream of the PhoP-dependent transcription start site ( P1 ) of the phoP gene ( Figure 4A and 4B ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PhoP	gene	phoP	activator	33045730	64	att	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	283	A double mutant with nucleotide substitutions in the SsrB binding site in the purB coding region upstream of the phoP promoter and the deletion of the SsrB binding region in the ugtL promoter was as defective in PhoP-dependent transcription as the ssrB null mutant ( Figure 4E ) .	28	SSRB PROMOTES PHOP TRANSCRIPTION BY BINDING TO THE PURB COD- ING REGION UPSTREAM OF THE PHOP PROMOTER	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
GatR	gene	gatZ	regulator	27956522	8	ver/dev	The promoters of gatZ are negatively regulated by GatR .	102	The promoters of gatZ , gatY , and gatR are negatively regulated by GatR .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	Pon , C.L. Antagonistic H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	C.O. H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	Gualerzi H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	A. H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	La Teana H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	A. H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	Brandi H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	M. H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	11123690	26	ver/dev	Falconi H-NS proteins in the transcriptional control of hns expression .	296	Falconi , M. , Brandi , A. , La Teana , A. , Gualerzi , C.O. , and Pon , C.L. ( 1996 ) Antagonistic involvement of Fis and H-NS proteins in the transcriptional control of hns expression .	23	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	15256548	28	ver/dev	Antagonistic involvement of H-NS proteins in the transcriptional control of hns expression .	937	Antagonistic involvement of FIS and H-NS proteins in the transcriptional control of hns expression .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	18156266	44	ver/dev	Interestingly , the results indicate that H-NS is a positive regulator of STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	354	Interestingly , the results presented here indicate that H-NS is a positive regulator of tpx and STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .	6	DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hns	regulator	19091955	24	ver/dev	As suggested by our previous study , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level remains high in high-Mg2 conditions in the hns mutant .	150	As suggested by our previous study ( 14 ) , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS , which antagonizes the functions of SlyA and PhoP ; thus the mRNA level is reduced greatly in the phoP or slyA mutants in PhoP-activating ( low-Mg2 ) conditions but remains high in PhoP-repressing ( high-Mg2 ) conditions in the hns mutant ( Fig. 4B ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hns	regulator	19091955	24	ver/dev	As suggested by our previous study , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level remains high in PhoP-repressing conditions in the hns mutant .	150	As suggested by our previous study ( 14 ) , establishing the Mg2 - responsive regulation of these loci requires the transcriptional repressor H-NS , which antagonizes the functions of SlyA and PhoP ; thus the mRNA level is reduced greatly in the phoP or slyA mutants in PhoP-activating ( low-Mg2 ) conditions but remains high in PhoP-repressing ( high-Mg2 ) conditions in the hns mutant ( Fig. 4B ) .	2	EDITED BY EMIL C. GOTSCHLICH, THE ROCKEFELLER UNIVERSITY, NEW YORK, NY, AND APPROVED NOVEMBER 12, 2008 (RECEIVED FOR REVIEW JULY 22, 2008)	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	hns	regulator	19843227	6	ver/dev	Consistent with the pleiotropic effects of hns mutations were regulated by H-NS in S. Typhimurium .	53	Consistent with the pleiotropic effects of hns mutations , 1439 genes were regulated by H-NS ( twofold cut-off , FDR 0.05 ) in S. Typhimurium ( Ono et al. , 2005 ; Lucchini et al. , 2006 ; Navarre et al. , 2006 ) .	5	MAIN	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	regulator	21059643	5	ver/dev	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sseJ loci .	148	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA , sifB , and sseJ loci ( 13 , 14 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	regulator	21059643	5	ver/dev	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sifB .	148	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA , sifB , and sseJ loci ( 13 , 14 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	regulator	21059643	5	ver/dev	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA .	148	SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA , sifB , and sseJ loci ( 13 , 14 ) .	6	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into F9 , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into F9 , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into F8 , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into F8 , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into two smaller fragments , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into two smaller fragments , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into two smaller fragments , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	22343301	27	ver/dev	Nevertheless , when F7 was divided into two smaller fragments , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .	226	Nevertheless , when F7 was divided into two smaller fragments ( F8 and F9 ) , containing the 5 = and 3 = regions of F7 , respectively , no H-NS affinity for both F8 ( 297 to 105 ) and F9 ( 1232 to 258 ) was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression ( Table 1 and Fig. 7 ) and suggesting that H-NS may act indirectly on the dsbL 297/dsbI 107 fusion ( Table 1 ) , which contains the whole dsbL gene and the initial portion of dsbI .	4	RESULTS	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
HNS	gene	hns	regulator	31487966	3	ver/dev	EMSAs revealed that H-NS bound specifically to the hns promoter , but 2.4 .	169	Electrophoretic mobility shift assays ( EMSAs ) revealed that H-NS bound specifically to the hns promoter ( positive control ) and yaeB promoter , but 2.4 .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hns	regulator	31487966	3	ver/dev	Electrophoretic mobility-shift assays revealed that H-NS bound specifically to the hns promoter , but 2.4 .	169	Electrophoretic mobility shift assays ( EMSAs ) revealed that H-NS bound specifically to the hns promoter ( positive control ) and yaeB promoter , but 2.4 .	7	2.4. YAEB WAS DIRECTLY REPRESSED BY H-NS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hns	regulator	32111072	7	ver/dev	To corroborate the involvement of H-NS in regulation of usp expression , we subsequently investigated activity of P3 usp-lacZ-fusions from E. coli hns .	273	To corroborate the involvement of H-NS in regulation of usp expression , we subsequently investigated activity of P3 usp-lacZ fusions from E. coli and S. bongori as well as Usp protein levels in an hns + ( JW1889 ) and hns - defective E. coli strain ( JW1225 ) .	15	3.5. REPRESSION OF E. COLI AND S. BONGORI USP EXPRESSION BY H-NS	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hns	regulator	32111072	7	ver/dev	To corroborate the involvement of H-NS in regulation of usp expression , we subsequently investigated activity of S. bongori as well as Usp protein levels in ( JW1889 ) and hns .	273	To corroborate the involvement of H-NS in regulation of usp expression , we subsequently investigated activity of P3 usp-lacZ fusions from E. coli and S. bongori as well as Usp protein levels in an hns + ( JW1889 ) and hns - defective E. coli strain ( JW1225 ) .	15	3.5. REPRESSION OF E. COLI AND S. BONGORI USP EXPRESSION BY H-NS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	regulator	32111072	7	ver/dev	To corroborate the involvement of H-NS in regulation of usp expression , we subsequently investigated activity of S. bongori as well as Usp protein levels in an hns and hns .	273	To corroborate the involvement of H-NS in regulation of usp expression , we subsequently investigated activity of P3 usp-lacZ fusions from E. coli and S. bongori as well as Usp protein levels in an hns + ( JW1889 ) and hns - defective E. coli strain ( JW1225 ) .	15	3.5. REPRESSION OF E. COLI AND S. BONGORI USP EXPRESSION BY H-NS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	hns	regulator	34340061	9	ver/dev	In addition , the contrary regulation by hns mRNA and H-NS might provide precise regulation of bacterial motility by hns .	324	In addition , the contrary regulation by hns mRNA and H-NS might provide precise regulation of bacterial motility by hns .	17	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
HNS	gene	hns	regulator	34340061	9	ver/dev	In addition , the contrary regulation by hns mRNA and H-NS might provide precise regulation of bacterial motility by hns .	324	In addition , the contrary regulation by hns mRNA and H-NS might provide precise regulation of bacterial motility by hns .	17	4. DISCUSSION	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
CspA	gene	cspB	activator	24056458	0	ver/dev	this effect was reflected by induction of cspB and proteins ( CspA ) in response to preadaptation to cold-stress	146	Cold stress genes and proteins regulate membrane fluidity and resume protein synthesis ( 18 ) , and this effect was reflected by induction of cold stress genes ( cspB and cspD ) and proteins ( CspA , CspE , and CspC ) in response to preadaptation to cold stress .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	yrbL	repressor	15703297	11	ver/dev	In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fig. 1F .	117	In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fe3 ( Fig. 1F ) , which is the specific signal that activates the PmrA protein ( 11 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
PmrA	gene	yrbL	repressor	15703297	11	ver/dev	In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fe3 .	117	In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fe3 ( Fig. 1F ) , which is the specific signal that activates the PmrA protein ( 11 ) .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	rob	repressor	22752112	5	ver/dev	In agreement with these results , the molecular mechanism of repression of rob by MarA was shown to be due to steric hindrance at the level of the promoter region .	30	In agreement with these results , the molecular mechanism of repression of rob by MarA was shown to be due to steric hindrance at the level of the promoter region ( McMurry and Levy 2010 ) .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	rob	repressor	22752112	6	ver/dev	Furthermore , we demonstrate that MarA mediate repression of rob by binding to its promoter region .	69	Furthermore , we demonstrate that MarA and SoxS mediate repression of rob by binding to its promoter region .	4	INTRODUCTION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
MarA	gene	rob	repressor	22752112	9	ver/dev	rob is negatively regulated by MarA	200	rob is negatively regulated by MarA and SoxS	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
MarA	gene	rob	repressor	22752112	10	ver/dev	This confirms our previous results that repression of rob in the must have been due to overexpression of MarA .	218	This confirms our previous results that repression of rob in the complemented strains in the presence of arabinose must have been due to overexpression of MarA or SoxS .	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	rob	repressor	22752112	11	ver/dev	The results above suggest that MarA could mediate together a repression of rob in response to NaOCl .	220	The results above suggest that MarA and SoxS could mediate together a repression of rob in response to NaOCl .	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
MarA	gene	rob	repressor	22752112	12	ver/dev	NaOCl _ supporting our hypothesis of a repression of rob by both MarA	230	NaOCl ( 0.86 ± 0.01-fold change , Fig. 3d ) , supporting our hypothesis of a repression of rob by both MarA and SoxS .	15	EXPRESSION OF ROB, MARA, AND SOXS IN RESPONSE TO HYPOCHLORITE TREATMENT	nan	1	L2	OTHER	Analysis	OTHER	New	Level 1
MarA	gene	rob	repressor	22752112	21	ver/dev	other studies _ performed in E. coli where rob was shown to be negatively regulated by both MarA by a direct interaction with its promoter region	304	Our results are in agreement with other studies performed in E. coli where rob was shown to be negatively regulated by both MarA and SoxS by a direct interaction with its promoter region ( Schneiders and Levy 2006 ; Michán et al. 2002 ) .	17	DISCUSSION	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
MarA	gene	rob	repressor	22752112	23	ver/dev	the expression of rob is repressed by the transcription factors MarA	309	Taken together , our results indicate that the expression of rob is repressed by the transcription factors MarA and SoxS in response to NaOCl due to a direct interaction with the promoter region .	17	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
LeuO	gene	tpx	activator	18156266	18	att	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	261	Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .	5	FIG. 2	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid	1	L3	OTHER	Other	OTHER	Other	Level 2
RamA	gene	hmp	activator	20829289	0	ver/dev	In Salmonella , five transcription factors have been implicated : hmp transcription is activated by RamA .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
RamA	gene	hmp	activator	20829289	0	ver/dev	In E. coli , five transcription factors have been implicated : hmp transcription is activated by RamA .	48	In E. coli and Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR ( Membrillo-Herna ́ndez et al. , 1998 ) and RamA ( Hernández - Urzúa et al. , 2007 ) and is repressed by NsrR ( Bodenmiller & Spiro , 2006 ) , FNR ( Cruz-Ramos et al. , 2002 ; Poole et al. , 1996 ) and Fur ( D'Autreaux et al. , 2002 ; Hernández - Urzúa et al. , 2007 ) .	1	INTRODUCTION	Escherichia coli	0	L2	OTHER	Other	OTHER	Other	Level 1
CsgD	gene	bcsZ	repressor	27756305	4	ver/dev	Equally , deletion of the major biofilm regulator CsgD , previously demonstrated to contribute to the inhibition of epithelial cell line invasion at high c-di-GMP levels , did not affect uptake of the bcsZ mutant .	382	Equally , deletion of the major biofilm regulator CsgD , previously demonstrated to contribute to the inhibition of epithelial cell line invasion at high c-di-GMP levels [ 14 , 18 ] , did not affect uptake of the bcsZ mutant ( Fig. 6b ) .	25	ROLE OF BCSZ IN HOST‑PATHOGEN INTERACTION	nan	1	L3	OTHER	Analysis	NEG	Other	Level 1
PhoP	gene	efp	activator	28181542	1	att	Indeed , when grown in media containing 500 μM Mg2 + for 1 h to initiate transcription from the PhoP-dependent promoter , the efp mutant increased mRNA levels of both the mgtC and mgtB genes by ~ 100 fold ( Fig .	61	Indeed , when grown in media containing 500 μM Mg2 + for 1 h to initiate transcription from the PhoP-dependent promoter , the efp mutant increased mRNA levels of both the mgtC and mgtB genes by ~ 100 fold ( Fig .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PhoP	gene	rpoS	activator	16763111	3	att	This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS - and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .	60	This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS - and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .	2	MAIN	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
YncC	gene	katN	regulator	20713450	4	ver/dev	The results reveal differential regulation of katN locus by YncC in these two closely related bacteria .	40	The results reveal differential regulation of the yciGFE ( katN ) locus by YncC and H-NS ( the Histone-like Nucleoid Structuring protein , 14 -- 16 ) in these two closely related bacteria .	3	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
YncC	gene	katN	regulator	20713450	23	ver/dev	However , the sequence , the length , , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / H-NS .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	katN	regulator	20713450	23	ver/dev	However , the sequence , the length , , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	katN	regulator	20713450	23	ver/dev	However , the position of H-NS binding regions , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / H-NS .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	katN	regulator	20713450	23	ver/dev	However , the position of H-NS binding regions , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	katN	regulator	20713450	23	ver/dev	However , the position of the McbR/YncC , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / H-NS .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
YncC	gene	katN	regulator	20713450	23	ver/dev	However , the position of the McbR/YncC , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR .	479	However , the sequence , the length , and the position of the McbR/YncC and H-NS binding regions , relative to the yciGFE ( katN ) promoter , are different in E. coli K-12 and Salmonella , resulting in differential mechanisms of regulation of these genes by YncC / McbR and H-NS .	7	DISCUSSION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
HNS	gene	ompC	regulator	12068808	28	ver/dev	However , another report indicated that the nucleoid protein H-NS , was a negative regulator of E. coli ompC .	186	However , another report indicated that the nucleoid protein H-NS , shown to regulate many genes , was a negative regulator of E. coli ompC ( Tsuzuki et al. , 1994 ) .	10	OMPR FOOTPRINT	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	ompC	regulator	12068808	29	ver/dev	We suspected that H-NS might regulate ompC indirectly , at least in part , by controlling ompR .	187	We suspected that H-NS might regulate ompC indirectly , at least in part , by controlling ompR .	10	OMPR FOOTPRINT	nan	1	L1	SPEC	Other	OTHER	New	Level 1
HNS	gene	ompC	regulator	12080060	28	ver/dev	However , another report indicated that the nucleoid protein H-NS , was a negative regulator of E. coli ompC .	186	However , another report indicated that the nucleoid protein H-NS , shown to regulate many genes , was a negative regulator of E. coli ompC ( Tsuzuki et al. , 1994 ) .	10	OMPR FOOTPRINT	Escherichia coli	0	L2	SPEC	Analysis	OTHER	Other	Level 1
HNS	gene	ompC	regulator	12080060	29	ver/dev	We suspected that H-NS might regulate ompC indirectly , at least in part , by controlling ompR .	187	We suspected that H-NS might regulate ompC indirectly , at least in part , by controlling ompR .	10	OMPR FOOTPRINT	nan	1	L1	SPEC	Other	OTHER	New	Level 1
OmpR	gene	ompF	activator	10692360	0	att	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	625	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	26	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	10712695	3	att	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	439	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	42	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	10913072	0	att	cis-Acting ompF mutations that result in OmpR-dependent constitutive expression .	894	cis-Acting ompF mutations that result in OmpR-dependent constitutive expression .	27	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	11133955	0	att	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	1035	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	40	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	11577150	3	att	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	477	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	15	GUZMAN, L. M., BELIN, D., CARSON, M. J. & BECKWITH, J. (1995).	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	11722742	4	att	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive	637	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive	32	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	14622426	1	att	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	564	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	33	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	16023758	9	att	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC and ompF [ 69 ] suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	176	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC and ompF [ 69 ] suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	11	2.4. OMPR/ENVZ AND THE ACID STRESS RESPONSE	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	ompF	activator	16023758	9	ver/dev	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompF suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	176	Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC and ompF [ 69 ] suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .	11	2.4. OMPR/ENVZ AND THE ACID STRESS RESPONSE	nan	1	L2	SPEC	Analysis	NEG	Other	Level 1
OmpR	gene	ompF	activator	16045614	99	att	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	781	Slauch , J.M. , and Silhavy , T.J. ( 1991 ) cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	29	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	17172341	4	att	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	933	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	60	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	19797361	1	att	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	512	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	53	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	22179129	6	ver/dev	Forst S , Delgado J , Rampersaud A et al In vivo phosphorylation of OmpR , the transcription activator of the ompF genes in Escherichia coli .	216	Forst S , Delgado J , Rampersaud A et al ( 1990 ) In vivo phosphorylation of OmpR , the transcription activator of the ompF and ompC genes in Escherichia coli .	18	REFERENCES	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
OmpR	gene	ompF	activator	25566242	25	att	Chatfield SN , Dorman CJ , Hayward C , Dougan G. Role of OmpR-dependent genes in Salmonella typhimurium virulence : mutants deficient in both ompC and ompF are attenuated in-vivo .	593	Chatfield SN , Dorman CJ , Hayward C , Dougan G. Role of OmpR-dependent genes in Salmonella typhimurium virulence : mutants deficient in both ompC and ompF are attenuated in vivo .	72	REFERENCES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
OmpR	gene	ompF	activator	33593291	24	att	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	344	cis-acting ompF mutations that result in OmpR-dependent constitutive expression .	25	REFERENCES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , others .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , a nutritional regulator .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , YdiV .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , a fimbrial regulator .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FliZ	TU	flhDC	repressor	31501286	5	ver/dev	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ , FimZ .	36	Repression of flhDC expression is also mediated through posttranslational regulation of FlhD4C2 by FliZ and FliT , YdiV ( a nutritional regulator ) , FimZ ( a fimbrial regulator ) , and others ( 12 , 13 , 28 , 29 ) .	3	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
FNR	gene	fnr	regulator	12420160	0	ver/dev	As both ArcA and Fnr contribute to regulation of respiration , the same explanation may be relevant for the GNS phenotype of the fnr mutants .	257	As both ArcA and Fnr contribute to regulation of respiration and therefore generation of a membrane potential , in addition to the regulatory effect on central metabolism , the same explanation may be relevant for the GNS phenotype of the arcA and fnr mutants .	22	GNS MUTANTS WHOSE PHENOTYPES MAY BE LINKED WITH A DECREASED CAPACITY TO UTILIZE NUTRIENTS REMAINING IN THE STATIONARY-PHASE BROTH CULTURES	nan	1	L1	SPEC	Analysis	OTHER	New	Level 1
FNR	gene	fnr	regulator	12761099	1	ver/dev	Our results also provide evidence that nipAB expression is regulated by Fnr , as induction is completely abolished in an fnr mutant background .	279	Our results also provide evidence that nipAB expression is regulated by Fnr , as induction is completely abolished in an fnr mutant background .	5	DISCUSSION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
FNR	gene	fnr	regulator	17906148	2	ver/dev	Likewise , b-galactosidase activity decreased fourfold for the hya fusion in the fnr mutant background , indicating that both hya are regulated by FNR .	199	Likewise , b-galactosidase activity decreased fourfold for the hya fusion in the fnr mutant background , indicating that both hyb and hya are regulated by FNR .	7	ANOXIC REGULATION OF HYDROGENASE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	fnr	regulator	17906148	2	ver/dev	Likewise , b-galactosidase activity decreased fourfold for the hya fusion in the fnr mutant background , indicating that both hyb are regulated by FNR .	199	Likewise , b-galactosidase activity decreased fourfold for the hya fusion in the fnr mutant background , indicating that both hyb and hya are regulated by FNR .	7	ANOXIC REGULATION OF HYDROGENASE PROMOTERS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
FNR	gene	fnr	regulator	21829527	4	ver/dev	As acrEF has been reported to be regulated by FNR in E. coli we investigated the level of fnr expression in our mutants	101	As acrEF has been reported to be regulated by FNR in E. coli [ 26 ] we investigated the level of fnr expression in our mutants but the level of expression was not significantly different between the mutants and wild-type .	15	TR 1% 32 8 2 0.12 0.06	Escherichia coli	0	L3	OTHER	Analysis	OTHER	Other	Level 2
FNR	gene	fnr	regulator	33341307	0	ver/dev	As Fnr are involved in the regulation of 120 genes in a similar fashion during anaerobiosis , we hypothesized that deletion of fnr simultaneously could cause maximum virulence attenuation of S. Typhimurium	55	As ArcA and Fnr are involved in the regulation of 120 genes in a similar fashion during anaerobiosis [ 22 ] , we hypothesized that deletion of arcA and fnr simultaneously could cause maximum virulence attenuation of S. Typhimurium , and the resulting mutant could have the potential to be a novel live vaccine strain .	3	1. INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	activator	26934594	0	att	Formation of the ` closed ' structure leads to Rho-dependent transcriptional termination of the tufB mRNA .	12	Formation of the ` closed ' structure leads to Rho-dependent transcriptional termination of the tufB mRNA .	2	SUMMARY	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	tufB	activator	26934594	1	att	The ` open ' structure facilitated expression of tufB and production of EF-TuB , while the ` closed ' structure decreased tufB expression by a Rho-dependent transcriptional termination mechanism .	45	The ` open ' structure facilitated expression of tufB and production of EF-TuB , while the ` closed ' structure decreased tufB expression by a Rho-dependent transcriptional termination mechanism .	4	1993A,B).	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	tufB	activator	26934594	10	att	The next 32 codons of the tufB gene contain a rut site-like sequence and our results indicate that this region is important for efficient Rho-dependent transcriptional termination ( Figs 6 and 7 ) .	283	The next 32 codons of the tufB gene contain a rut site-like sequence and our results indicate that this region is important for efficient Rho-dependent transcriptional termination ( Figs 6 and 7 ) .	13	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	activator	26934594	11	att	When ternary complex concentrations are high , rapid transcription and translation through the early part of tufB increases the probability that an initiation-inhibitory mRNA structure will form , and in the absence of ribosome coverage a rut site becomes accessible on the mRNA and Rho-dependent transcription termination will abort further tufB mRNA elongation .	303	When ternary complex concentrations are high , rapid transcription and translation through the early part of tufB increases the probability that an initiation-inhibitory mRNA structure will form , and in the absence of ribosome coverage a rut site becomes accessible on the mRNA and Rho-dependent transcription termination will abort further tufB mRNA elongation .	13	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	tufB	activator	26934594	11	att	When ternary complex concentrations are high , rapid transcription and translation through the early part of tufB increases the probability that an initiation-inhibitory mRNA structure will form , and in the absence of ribosome coverage a rut site becomes accessible on the mRNA and Rho-dependent transcription termination will abort further tufB mRNA elongation .	303	When ternary complex concentrations are high , rapid transcription and translation through the early part of tufB increases the probability that an initiation-inhibitory mRNA structure will form , and in the absence of ribosome coverage a rut site becomes accessible on the mRNA and Rho-dependent transcription termination will abort further tufB mRNA elongation .	13	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Rho	gene	tufB	activator	26934594	2	att	Our data support a model in which translational speed in the early part of the tufB mRNA is used to sense the cellular EF-Tu concentration and regulate tufB expression by modulating the probability of Rho-dependent transcription termination .	46	Our data support a model in which translational speed in the early part of the tufB mRNA is used to sense the cellular EF-Tu concentration and regulate tufB expression by modulating the probability of Rho-dependent transcription termination .	4	1993A,B).	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
Rho	gene	tufB	activator	26934594	3	att	Rho-dependent transcriptional termination regulates tufB expression	163	Rho-dependent transcriptional termination regulates tufB expression	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
Rho	gene	tufB	activator	26934594	4	att	Using this experimental system we tested two hypotheses : ( i ) that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; ( ii ) that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	168	Using this experimental system we tested two hypotheses : ( i ) that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; ( ii ) that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	activator	26934594	5	att	The tufB coding sequence does not contain a factor-independent transcriptional terminator , so we tested the role of Rho-dependent termination for tufB regulation .	183	The tufB coding sequence does not contain a factor-independent transcriptional terminator , so we tested the role of Rho-dependent termination for tufB regulation .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L3	OTHER	Other	NEG	New	Level 1
Rho	gene	tufB	activator	26934594	5	att	The tufB coding sequence does not contain a factor-independent transcriptional terminator , so we tested the role of Rho-dependent termination for tufB regulation .	183	The tufB coding sequence does not contain a factor-independent transcriptional terminator , so we tested the role of Rho-dependent termination for tufB regulation .	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L3	OTHER	Other	NEG	New	Level 1
Rho	gene	tufB	activator	26934594	6	att	Taken together our results support the hypothesis that Rho-dependent transcriptional termination is involved in the regulation of tufB gene expression and that there might be factors , addi -	193	Taken together our results support the hypothesis that Rho-dependent transcriptional termination is involved in the regulation of tufB gene expression and that there might be factors , addi -	9	FORMATION OF THE CLOSED STRUCTURE FACILITATES TRANSCRIPTIONAL TERMINATION	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
Rho	gene	tufB	activator	26934594	8	att	In this paper , we have shown that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination , modulated by the rate of translation elongation in the early part of the coding sequence , and that the mechanism depends on the nucleotide sequence in the early part of the tufB mRNA having the ability to form a closed secondary structure that hides the ribosome binding site .	265	In this paper , we have shown that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination , modulated by the rate of translation elongation in the early part of the coding sequence , and that the mechanism depends on the nucleotide sequence in the early part of the tufB mRNA having the ability to form a closed secondary structure that hides the ribosome binding site .	13	DISCUSSION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
Rho	gene	tufB	activator	26934594	8	att	In this paper , we have shown that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination , modulated by the rate of translation elongation in the early part of the coding sequence , and that the mechanism depends on the nucleotide sequence in the early part of the tufB mRNA having the ability to form a closed secondary structure that hides the ribosome binding site .	265	In this paper , we have shown that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination , modulated by the rate of translation elongation in the early part of the coding sequence , and that the mechanism depends on the nucleotide sequence in the early part of the tufB mRNA having the ability to form a closed secondary structure that hides the ribosome binding site .	13	DISCUSSION	Salmonella	1	L2	OTHER	Other	OTHER	Other	Level 1
RpoS	gene	rprA	activator	16816180	5	att	To study the role of dsrA and rprA in S. enterica , we characterized the effect of the deletion of each gene separately , or both genes together , on expression of the RpoS-dependent reporter , katE-lac [ op ] .	205	To study the role of dsrA and rprA in S. enterica , we characterized the effect of the deletion of each gene separately , or both genes together , on expression of the RpoS-dependent reporter , katE-lac [ op ] .	4	RESULTS	Salmonella;Salmonella	1	L3	OTHER	Investigation	OTHER	New	Level 2
SoxS	gene	micF	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates Mn-containing superoxide dismutase , micF .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	micF	activator	12379462	1	ver/dev	The SoxS protein , in turn , activates sodA , micF .	213	The SoxS protein , in turn , activates expression of several genes , including sodA ( Mn-containing superoxide dismutase ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( an efflux pump ) , micF ( antisense RNA to the porin OmpF mRNA ) , zwf ( glucose-6-phosphate dehydrogenase ) and fumC ( heat resistant fumarase C ) [ 46 ] .	16	4. DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	micF	activator	12886427	0	ver/dev	SoxS protein , activates Mn-containing superoxid dismutase , micF .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SoxS	gene	micF	activator	12886427	0	ver/dev	SoxS protein , activates sodA , micF .	111	SoxS protein , which is a member of the AraC / XylS family of transcriptional regulators , activates at least 15 genes including sodA ( Mn-containing superoxid dismutase ) , zwf ( glucose-6-phosphate dehydrogenase ) , micF ( antisense RNA to the porin OmpF mRNA ) , nfo ( DNA repair endonuclease IV ) , fpr ( NADPH : ferrodoxin oxidoreductase ) , acrAB ( efflux pump ) , acnA ( aconitase ) , fumC ( heat-resistant fumarase ) and nfsA ( nitroreductase A ) ( Pomposiello & Demple 2000 ) .	3	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
PocR	gene	hilA	repressor	16585772	4	ver/dev	This prompted us to investigate whether PocR is also involved in the PDL-dependent repression of hilA .	141	This prompted us to investigate whether PocR is also involved in the PDL-dependent repression of hilA .	2	MAIN	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
PocR	gene	hilA	repressor	16585772	6	ver/dev	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of the cofactor of PocR .	146	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of PDL , the cofactor of PocR .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
PocR	gene	hilA	repressor	16585772	6	ver/dev	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of PDL .	146	Thus , the simplest interpretation of the results was that PocR , through activation of its own DNA-binding capacity , directly repressed hilA expression in the presence of PDL , the cofactor of PocR .	2	MAIN	nan	1	L2	OTHER	Analysis	OTHER	Other	Level 1
SdiA	TU	acrAB	regulator	18577510	2	ver/dev	Other regulators of SdiA did not contrib-ute to acrAB induction by indole in Salmonella .	14	Other regulators of acrAB such as MarA , SoxS , Rob , SdiA , and AcrR did not contrib-ute to acrAB induction by indole in Salmonella .	1	ABSTRACT	Salmonella	1	L3	OTHER	Other	NEG	New	Level 1
CRP	gene	rpoS	repressor	19835951	23	ver/dev	Lee , H.J. , Park , S.J. , Choi , S.H. , Lee , K.H. Vibrio vulnificus rpoS expression is repressed by direct binding of cAMP-CRP complex to its two promoter regions .	323	[ 33 ] Lee , H.J. , Park , S.J. , Choi , S.H. , Lee , K.H. ( 2008 ) Vibrio vulnificus rpoS expression is repressed by direct binding of cAMP-CRP complex to its two promoter regions .	28	REFERENCES	Vibrio vulnificus	0	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	rpoS	repressor	19843227	27	ver/dev	In E. coli , CRP-cAMP represses rpoS transcription during logarithmic growth .	146	In E. coli , CRP-cAMP represses rpoS transcription during logarithmic growth ( Lange and Hengge-Aronis , 1994 ) .	11	STPA IS ESSENTIAL FOR LINKING S38 EXPRESSION TO GLUCOSE AVAILABILITY	Escherichia coli	0	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	rpoS	repressor	24885225	24	ver/dev	CRP participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .	103	CRP and Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay using purified CRP activated with cAMP and the DNA corresponding to the taiA -- hlyE promoter region .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	SPEC	Other	OTHER	Other	Level 1
CRP	gene	rpoS	repressor	24885225	26	ver/dev	Previously , it has been reported that rpoS expression is repressed by the cAMP-CRP complex in Vibrio vulnificus .	106	Previously , it has been reported that rpoS expression is repressed by the cAMP-CRP complex in Vibrio vulnificus [ 24 ] .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Vibrio vulnificus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
CRP	gene	rpoS	repressor	24885225	29	ver/dev	Thus , CRP might repress hlyE expression by repressing rpoS in S. Typhi .	109	Thus , CRP might repress hlyE expression by repressing rpoS in S. Typhi .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	rpoS	repressor	24885225	36	ver/dev	Altogether , these results suggest that CRP are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	125	Altogether , these results suggest that CRP and Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	Other	Level 1
CRP	gene	rpoS	repressor	24885225	40	ver/dev	Figure 2 CRP participate in the repression of rpoS .	149	Figure 2 CRP and Fis participate in the repression of rpoS .	5	GLUCOSE INCREASES TRANSCRIPTION OF FIS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
CRP	gene	rpoS	repressor	24885225	44	ver/dev	Here , we present genetic evidence indicating that CRP exerts down-regulation of hlyE by repressing rpoS in S. Typhi .	189	Here , we present genetic evidence indicating that CRP exerts down-regulation of hlyE by repressing rpoS ( Figures 1 and 2 ) , one of the most important hlyE activators in S. Typhi [ 14 ] .	6	DISCUSSION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	OTHER	New	Level 1
CRP	gene	rpoS	repressor	24885225	45	ver/dev	On the other hand , it has been reported that rpoS expression is repressed by direct binding of CRP-cAMP to its promoter region in Vibrio vulnificus .	192	On the other hand , it has been reported that rpoS expression is repressed by direct binding of CRP-cAMP to its promoter region in Vibrio vulnificus [ 24 ] .	6	DISCUSSION	Vibrio vulnificus	0	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	repressor	17993530	54	ver/dev	For example , hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	363	For example , hilA expression , rtsA expression , and hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
HilD	gene	hilD	repressor	22356617	7	ver/dev	However , HilD is auto-regulated , which could explain the observed downregulation of hilD in the DfliZ mutant during planktonic growth .	360	However , HilD is auto-regulated ( Ellermeier et al. , 2005 ) , which could explain the observed downregulation of hilD in the DfliZ mutant during planktonic growth .	10	THE FLIZ TRANSCRIPTIONAL REGULATOR AFFECTS VIRULENCE EXPRESSION	nan	1	L1	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	repressor	31182495	54	ver/dev	Together , these data suggest HilD directly stimulate the polymerase as a main mechanism of hilA activation in addition through repression of hilD .	228	Together , these data suggest HilD , HilC , and RtsA directly stimulate the polymerase as a main mechanism of hilA activation in addition to blocking the binding of H-NS , while H-NS represses hilA expression directly as well as through repression of hilD , hilC , and rtsA .	3	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
HilD	gene	hilD	repressor	34424033	4	ver/dev	NS-mediated repression of the hilA promoter , downstream of hilD , is through its control of HilD .	41	NS-mediated repression of the hilA promoter , downstream of hilD , is through its control of HilD , which directly activates hilA transcription .	2	MAIN	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
HilD	gene	hilD	repressor	34424033	34	ver/dev	This observation holds true in the absence of any of the overproduction of wild-type H-NS can outcompete HilD to repress hilD expression	400	This observation holds true in the absence of any of the overproduction of wild-type H-NS can outcompete HilD to repress hilD expression , but overexpression of the H-NS DN has no effect when HilD is overproduced .	4	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RcsB	gene	rprA	regulator	33638994	0	ver/dev	Our structural data reveal that RcsB binds promoters of rprA in a dimeric active conformation .	17	Our structural data reveal that RcsB binds promoters of target genes such as rprA and flhDC in a dimeric active conformation .	4	MAIN	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	rprA	regulator	33638994	4	ver/dev	In an effort to understand this , we analysed the impact of RcsB phosphorylation for DNA binding by solving the structures of S. Typhimurium RcsB bound to the rprA promoters .	57	In an effort to understand this , we analysed the impact of RcsB phosphorylation for DNA binding by solving the structures of S. Typhimurium RcsB bound to the rprA and P1flhDC promoters and the structures of the isolated REC domain in the absence and presence of phosphomimetic BeF − 3 .	6	INTRODUCTION	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rprA	regulator	33638994	9	ver/dev	RcsB bound to rprA promoters shows the phos	168	RcsB bound to rprA and P1 promoters shows the phos- flhDC phorylated active conformation	21	RCSB BOUND TO RPRA AND P1 PROMOTERS SHOWS THE PHOS- FLHDC PHORYLATED ACTIVE CONFORMATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
RcsB	gene	rprA	regulator	33638994	9	ver/dev	RcsB bound to rprA promoters shows flhDC	168	RcsB bound to rprA and P1 promoters shows the phos- flhDC phorylated active conformation	21	RCSB BOUND TO RPRA AND P1 PROMOTERS SHOWS THE PHOS- FLHDC PHORYLATED ACTIVE CONFORMATION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
HNS	gene	hilD	repressor	17675384	1	ver/dev	The data show that all three genes , hilD , were repressed by H-NS and/or Hha .	10	The data show that all three genes , hilD , hilC , and rtsA , were repressed by H-NS and/or Hha .	1	ABSTRACT	nan	1	L3	OTHER	Other	NEG	Other	Level 1
HNS	gene	hilD	repressor	31182495	49	ver/dev	Additionally , H-NS is known to repress hilD expression .	217	Additionally , H-NS is known to repress hilD expression ( 12 ) , which could affect how we interpret the H-NS repressive effect on hilA expression .	3	RESULTS	nan	1	L3	OTHER	Fact	OTHER	Other	Level 3
HNS	gene	hilD	repressor	34424033	1	ver/dev	Running H-NS repression of hilD	9	Running Title : H-NS repression of hilD	0	Unknown	nan	1	L3	OTHER	Other	OTHER	New	Level 2
HNS	gene	hilD	repressor	34424033	31	ver/dev	It is clear that HilD autoactivation is key to acting primarily to alleviate H-NS repression of the hilD promoter , as proposed also proposed .	393	It is clear that HilD autoactivation is key to acting primarily to alleviate H-NS repression of the hilD promoter , as proposed also proposed ( 43 , 45 ) .	4	RESULTS	nan	1	L3	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	rcsB	repressor	30510144	1	ver/dev	We demonstrated that SlyA overproduction negatively regulates rcsB transcription .	11	We demonstrated that SlyA overproduction negatively regulates rcsB transcription .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	rcsB	repressor	30510144	4	ver/dev	According to these results , SlyA represses rcsB transcription by direct binding to spe-cific sites located on the rcsB promoters , thus accounting for the attenuated/virulence antagonistic behaviors .	14	According to these results , SlyA represses rcsB transcription by direct binding to spe-cific sites located on the rcsB promoters , thus accounting for the attenuated/virulence antagonistic behaviors .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	rcsB	repressor	30510144	4	ver/dev	According to these results , SlyA represses rcsB transcription by direct binding to spe-cific sites located on the rcsB promoters , thus accounting for the attenuated/virulence antagonistic behaviors .	14	According to these results , SlyA represses rcsB transcription by direct binding to spe-cific sites located on the rcsB promoters , thus accounting for the attenuated/virulence antagonistic behaviors .	1	ABSTRACT	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	rcsB	repressor	30510144	11	ver/dev	We also found that the repression of rcsB transcription , produced by SlyA overproduction , affected Salmonella motility behavior .	59	We also found that the repression of rcsB transcription , produced by SlyA overproduction , affected Salmonella motility behavior .	3	KEYWORDS RCSCDB SYSTEM, SALMONELLA, SLYA, GENE REGULATION	Salmonella	1	L3	OTHER	Other	OTHER	Other	Level 2
SlyA	gene	rcsB	repressor	30510144	12	ver/dev	SlyA downregulates rcsB expression .	63	SlyA downregulates rcsB expression .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
SlyA	gene	rcsB	repressor	30510144	14	ver/dev	As shown in Fig. 1 , - galactosidase levels in the slyA mutant were 1.6-fold higher than those , suggesting that the SlyA regulator is able to repress transcription of the rcsB gene .	66	As shown in Fig. 1 , - galactosidase levels in the slyA mutant were 1.6-fold higher than those observed in the wild-type strain , suggesting that the SlyA regulator is able to repress transcription of the rcsB gene .	4	RESULTS	nan	1	L2	SPEC	Analysis	OTHER	Other	Level 1
SlyA	gene	rcsB	repressor	30510144	16	ver/dev	These results demonstrate that SlyA represses rcsB transcription .	71	These results demonstrate that SlyA represses rcsB transcription , suggesting that SlyA acts on one or both of the rcsB promoters .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	rcsB	repressor	30510144	29	ver/dev	We hypothesized that SlyA repression of rcsB transcription affects the motility behavior of Salmonella , since both regulators also participate in the regulation of flagellar gene expression .	123	We hypothesized that SlyA repression of rcsB transcription affects the motility behavior of Salmonella , since both regulators also participate in the regulation of flagellar gene expression ( 6 , 28 -- 30 ) .	4	RESULTS	Salmonella	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	rcsB	repressor	30510144	31	ver/dev	Here , we have demonstrated that the repression of rcsB by the SlyA regulator results in the modulation of RcsB-dependent genes .	138	Here , we have demonstrated that the repression of rcsB by the SlyA regulator results in the modulation of RcsB-dependent genes .	4	RESULTS	nan	1	L3	OTHER	Analysis	OTHER	Other	Level 2
SlyA	gene	rcsB	repressor	30510144	39	ver/dev	We demonstrated that overexpression of slyA resulted in decreased rcsB expression levels from both promoter mutants , suggesting that SlyA represses rcsB transcription mainly during stationary-phase .	173	We demonstrated that overexpression of slyA resulted in decreased rcsB expression levels from both promoter mutants , suggesting that SlyA represses rcsB transcription mainly during stationary phase .	5	DISCUSSION	nan	1	L2	SPEC	Analysis	OTHER	New	Level 1
SlyA	gene	rcsB	repressor	30510144	40	ver/dev	Our results led us to conclude that SlyA increases bacterial motility by repressing rcsB transcription from the PrcsB promoter .	178	Our results led us to conclude that SlyA increases bacterial motility by repressing rcsB transcription from the PrcsB promoter .	5	DISCUSSION	nan	1	L3	OTHER	Analysis	OTHER	New	Level 2
SlyA	gene	rcsB	repressor	30510144	44	ver/dev	SlyA represents one additional mechanism , since SlyA represses rcsB expression , tilting the balance toward the virulent state .	201	SlyA represents one additional mechanism by which Salmonella controls this balance through the RcsCDB system , since SlyA represses rcsB expression , tilting the balance toward the virulent state .	6	MATERIALS AND METHODS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
CRP	gene	rpoE	regulator	14553927	1	ver/dev	In addition to the autoregulation , the S. Typhimurium rpoE regulon is also likely to be regulated by negative regulation by possibly the cAMP-CRP complex .	202	In addition to the autoregulation , the S. Typhimurium rpoE regulon is also likely to be regulated by other transcription control systems , including negative regulation by CpxAR and possibly the cAMP-CRP complex .	10	3.1. IDENTI¢CATION OF PROMOTERS DIRECTING EXPRESSION OF RPOE IN S. TYPHIMURIUM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	Other	Level 1
CRP	gene	rpoE	regulator	14553927	1	ver/dev	In addition to the autoregulation , the S. Typhimurium rpoE regulon is also likely to be regulated by negative regulation by possibly the cAMP-CRP complex .	202	In addition to the autoregulation , the S. Typhimurium rpoE regulon is also likely to be regulated by other transcription control systems , including negative regulation by CpxAR and possibly the cAMP-CRP complex .	10	3.1. IDENTI¢CATION OF PROMOTERS DIRECTING EXPRESSION OF RPOE IN S. TYPHIMURIUM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	Other	Level 1
YgaA	gene	norR	activator	17024490	9	ver/dev	It was recently reported that a member of NorR , formerly known as YgaA in E. coli is responsible for the induction of the norVW operon ( encoding a Xavorubredoxin , divergently transcribed from norR ) in response to NO .	211	It was recently reported that a member of this family ( NorR , formerly known as YgaA ) in E. coli is responsible for the induction of the norVW operon ( encoding a Xavorubredoxin , divergently transcribed from norR ) in response to NO ( Hutchings et al. 2002 ; Gardner et al. 2003 ; daCosta et al. 2003 ) .	15	GENE CONTEXT ANALYSIS OF DIVERENT HMP GENES	Escherichia coli	0	L3	OTHER	Fact	OTHER	Other	Level 3
CpxR	gene	pmrC	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrC at the CpxR box-like sequences .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	pmrC	regulator	32620947	0	ver/dev	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrC at the CpxR box-like sequences .	17	Additionally , CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	2	MAIN	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	New	Level 1
CpxR	gene	pmrC	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the pmrC promoters .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	pmrC	regulator	32620947	10	ver/dev	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the pmrC promoters .	92	These results further confirm that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the phoPQ , pmrC , pmrD and pmrH promoters or indirectly regulating pmrAB and mgrB through other regulators .	10	CPXR BINDS DIRECTLY TO THE PROMOTERS OF CRRGS PHOPQ, PMRC, PMRH AND PMRD AT THE CPXR BOX-LIKE SITES	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	New	Level 1
CpxR	gene	pmrC	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrC at the CpxR box-like sequences .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrC	regulator	32620947	17	ver/dev	This study demonstrates for the first time -LRB- to the best of our knowledge -RRB- that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of pmrC at the CpxR box-like sequences .	204	This study demonstrates for the first time ( to the best of our knowledge ) that CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ , pmrC , pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB .	12	CONCLUSIONS	Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Analysis	OTHER	Other	Level 1
CpxR	gene	pmrC	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of CRRGs , binding directly to pmrC .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
CpxR	gene	pmrC	regulator	34202800	18	ver/dev	Zhai et al. showed that in S. Typhimurium , CpxR regulate transcription of colistin resistance-related genes , binding directly to pmrC .	376	Zhai et al. [ 119 ] showed that in S. Typhimurium , the AcrAB-TolC efflux pump and CpxR regulate transcription of colistin resistance-related genes ( CRRGs ) , binding directly to the phoPQ , pmrC , pmrH , and pmrD promoters of box-type CpxR sequences , or indirectly to pmrAB and mgrB .	9	3.3.1. THE PHOP-PHOQ SYSTEM	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L3	OTHER	Other	OTHER	New	Level 2
Sigma28	gene	flgM	activator	9765212	1	att	Mutations in the carboxy-terminal half of FlgM disrupt anti-s factor activity To better understand the mechanism by which FlgM prevents s28-dependent transcription , we isolated flgM mutants defective in this activity ( Hughes et al. 1993 ; Daughdrill et al. 1997 ) .	55	Mutations in the carboxy-terminal half of FlgM disrupt anti-s factor activity To better understand the mechanism by which FlgM prevents s28-dependent transcription , we isolated flgM mutants defective in this activity ( Hughes et al. 1993 ; Daughdrill et al. 1997 ) .	3	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgM	activator	9765212	11	att	S. typhimurium mutants expressing FlgM * proteins with only a 4 - to10-fold higher Kd for the interaction with s28 could be easily distinguished from their flgM + parent strain on the basis of s28-dependent gene expression ( Daughdrill et al. 1997 ) .	274	S. typhimurium mutants expressing FlgM * proteins with only a 4 - to10-fold higher Kd for the interaction with s28 could be easily distinguished from their flgM + parent strain on the basis of s28-dependent gene expression ( Daughdrill et al. 1997 ) .	6	HIS–S28 CORE RNAP 4.8 3.9 800	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L1	SPEC	Other	OTHER	Other	Level 1
Sigma28	gene	flgM	activator	9765212	12	att	TH3920 is deleted for the flgM locus , and contains a transcriptional-fusion of lacZ to the fliC gene , which serves as a reporter for s28-dependent transcription .	328	TH3920 is deleted for the flgM locus , and contains a transcriptional fusion of lacZ to the fliC gene , which serves as a reporter for s28-dependent transcription .	9	PLASMID CONSTRUCTIONS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgM	activator	9765212	4	att	In vivo assays of b-galactosidase expression from s28-dependent promoters in the presence of the flgM * alleles were consistent with the results of the in-vitro transciption assays ; strains expressing the mutant FlgM * L66S and FlgM * I82T proteins had threeand six-fold higher levels of b-galactosidase activity , respectively , compared with isogenic flgM + strains ( data not shown ) .	63	In vivo assays of b-galactosidase expression from s28-dependent promoters in the presence of the flgM * alleles were consistent with the results of the in vitro transciption assays ; strains expressing the mutant FlgM * L66S and FlgM * I82T proteins had threeand six-fold higher levels of b-galactosidase activity , respectively , compared with isogenic flgM + strains ( data not shown ) .	3	RESULTS	unidentified	1	L3	OTHER	Analysis	NEG	Other	Level 1
Sigma28	gene	flgM	activator	9765570	6	att	FlgM inhibits s28-depen-dent transcription , and 80 % of flgM gene transcription is from a s28-dependent , class 3 promoter .	548	FlgM inhibits s28-depen-dent transcription , and 80 % of flgM gene transcription is from a s28-dependent , class 3 promoter .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
Sigma28	gene	flgM	activator	9765570	7	att	Accumulation of FlgM inhibits s28-dependent transcription , including that directed by the class 3 promoter for the flgM gene .	550	Accumulation of FlgM inhibits s28-dependent transcription , including that directed by the class 3 promoter for the flgM gene .	11	DISCUSSION	nan	1	L3	OTHER	Other	OTHER	New	Level 2
RcsB	gene	rcsA	activator	12519186	49	ver/dev	The rcsA dependence of the tolB-promoted activation of Fig. 2B places this RcsB-regulated gene in the first group .	137	The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .	6	DEFINING THE CIS-ACTING SEQUENCES REQUIRED FOR UGD TRANSCRIPTION	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	activator	27558204	0	ver/dev	To better characterize the contribution of RcsB to persistence within tomatoes , rcsA genes were deleted	53	To better characterize the contribution of RcsA and RcsB to persistence within tomatoes , rcsA and rcsB genes were deleted and the abilities of the corresponding mutants to multiply in red and green tomatoes were tested ( strains and pri-mers used to construct them are listed in Supporting Information Tables S1 and S2 ) .	7	SALMONELLA RCSA AND RCSB GENES ARE INVOLVED IN PERSISTENCE WITHIN TOMATOES	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
RcsB	gene	rcsA	activator	28588134	2	ver/dev	Although our initial experiments focused on phenotypes dependent on RcsA , some residual capsule synthesis can be observed in rcsA mutant strains as a result of capsular operon activation by the RcsB homodimer .	158	Although our initial experiments focused on phenotypes dependent on RcsA , some residual capsule synthesis can be observed in rcsA mutant strains as a result of capsular operon activation by the RcsB homodimer ( 14 ) .	3	RESULTS	nan	1	L2	OTHER	Other	OTHER	Other	Level 1
RcsB	gene	rcsA	activator	33751923	21	ver/dev	When phosphorylated , RcsB binds RcsA to activate expression of rcsA .	645	When phosphorylated , RcsB binds RcsA to activate expression of several genes , such as osmB , osmC , bdm , ftsZ , rprA , wza , and rcsA .	25	RCSBCD	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	dinP	activator	21102598	0	ver/dev	the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes include dinP	78	DNA damage created by quinolone antibiotics has been shown to be sufficient to stimulate umuC transcription and the SOS response .4,5 The initial response to DNA damage is the reduction in LexA protein levels and induction of LexA repressed genes , which include lexA , umuDC and dinP .2,3 ( In Escherichia .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	nan	1	L3	OTHER	Other	OTHER	New	Level 2
LexA	gene	dinP	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
LexA	gene	dinP	activator	21102598	1	ver/dev	coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .	79	coli , dinB and dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic that induces double-stranded breaks in DNA in a DNA gyrase-dependent manner .9 In E.coli , the expression of sbmC is induced by DNA-damaging agents , possesses a quasicanonical LexA box and much like umuDC , the expression of sbmC is RecA and LexA dependent .9 Thus , upregulation of umuD , lexA , dinP and sbmC by all nine FQs is likely LexA dependent .	8	RESULTS IDENTIFICATION OF FQ-RESPONSIVE PROMOTERS	Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium	1	L2	SPEC	Analysis	NEG	Other	Level 1
NagC	TU	glmUS	regulator	24450479	8	ver/dev	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in nagEBACD , glmUS , chbBCARFG , fimB , although the galP gene is controlled via a single operator with high affinity .	68	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli ( nagEBACD , glmUS , chbBCARFG , fimB ) , although the galP gene is controlled via a single operator with high affinity ( El Qaidi et al. , 2009 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2
NagC	TU	glmUS	regulator	24450479	8	ver/dev	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in nagEBACD , glmUS , chbBCARFG , fimB , although the galP gene is controlled via a single operator with high affinity .	68	Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli ( nagEBACD , glmUS , chbBCARFG , fimB ) , although the galP gene is controlled via a single operator with high affinity ( El Qaidi et al. , 2009 ) .	4	RESULTS	nan	1	L3	OTHER	Other	OTHER	Other	Level 2