,SentenceNumber,File,SentenceNumberPerFile,NumberOfOrganism,Organisms,Mentions,OrganismSet,Sentence
0,1,1053.txt,1,0,,,,pmrG are both transcriptionally activated by PmrAB .
1,2,1735.txt,1,0,,,,"PmrA Represses Transcription of the SPI-2 ssaG Gene .
"
2,3,1735.txt,2,0,,,,"PmrA Represses ssaG Transcription Indirectly , by Hindering Expression of the ssaG Activator SsrB ."
3,4,2228.txt,1,0,,,,b-Ga-lactosidase assays _ demonstrating inhibition of s28-dependent lacZ expression by the His -- FlgM proteins ( both wild type and mutant ) in-vivo
4,5,1721.txt,1,0,,,,"IgaAmediated repression of the RcsB-YojN-RcsC system occurred at the post-translational level , as shown by chromosomal epitope tagging of the yojN genes ."
5,6,1047.txt,1,0,,,,"This result indicated that H-NS was functioning to repress csgD .
"
6,7,1047.txt,2,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"This work clearly shows that , as observed in E. coli , H-NS represses expression of csgD in Salmonella .
"
7,8,1047.txt,3,0,,,,"our earlier observations H-NS repressed expression of csgD
"
8,9,1047.txt,4,1,Salmonella,Salmonella,Salmonella,"Furthermore , we identify H-NS as a repressor of csgD in Salmonella , instead of an activator ."
9,10,2200.txt,1,0,,,,SsrBC directly activates transcription of sseJ .
10,11,1709.txt,1,0,,,,"also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region
"
11,12,1709.txt,2,0,,,,"it was suggested that H-NS represses leuO expression by interacting with an AT8 region located between LeuO binding sites AT3
"
12,13,1709.txt,3,0,,,,"it was suggested that H-NS represses leuO expression by interacting with an AT8 region located between LeuO binding sites AT7
"
13,14,1709.txt,4,0,,,,"However , the LeuO protein interacts with the LeuO binding site located downstream of leuO , making a DNA loop to counteract repression by H-NS .
"
14,15,1709.txt,5,0,,,,"Interestingly , the results indicate that H-NS is a positive regulator of STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .
"
15,16,1709.txt,6,0,,,,"the response regulator RcsB activates leuO transcription in conjunction with BglJ , counteracting H-NS repression of leuO transcription
"
16,17,1709.txt,7,0,,,,"Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions .
"
17,18,1709.txt,8,0,,,,"Because both leuO and SPI-1 are repressed by H-NS , activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions .
"
18,19,1709.txt,9,0,,,,"However , the fact that both leuO are repressed by H-NS suggests that LeuO might provide a backup mechanism for SPI-1 repression .
"
19,20,1709.txt,10,0,,,,"LeuO is a quiescent LTTR under standard laboratory conditions because leuO transcription is repressed by H-NS .
"
20,21,1709.txt,11,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig .
"
21,22,1709.txt,12,0,,,,"Such hypothetical conditions can be expected to activate leuO expression because leuO transcription is also repressed by H-NS .
"
22,23,1709.txt,13,0,,,,"The expression of leuO is repressed by H-NS , although there are some stress conditions ."
23,24,289.txt,1,0,,,,"Further , this study showed that yqhD activation was induced by direct binding of YqhC to the promoter region of the yqhD gene ."
24,25,2214.txt,1,0,,,,"Interestingly , the regulation of the stiB locus ( unlike that of stiC ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .
"
25,26,2214.txt,2,0,,,,"Interestingly , the regulation of the stiB locus ( unlike that of stiC ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts alone ."
26,27,504.txt,1,0,,,,"that HilD are each capable of independently inducing expression of the hilD genes
"
27,28,504.txt,2,0,,,,"We demonstrate that HilD are each capable of inducing expression of hilD .
"
28,29,504.txt,3,0,,,,"We wanted to determine if HilD could induce expression of hilD in the absence of the other regulators .
"
29,30,504.txt,4,0,,,,"HilD also induced expression of hilD .
"
30,31,504.txt,5,0,,,,"HilD induced expression of hilD ~ 10-to 12-fold .
"
31,32,504.txt,6,0,,,,"These data show that HilD are each capable of independently inducing expression of hilD , consistent with our model that HilD constitute a feed forward regulatory loop .
"
32,33,504.txt,7,0,,,,"We show that HilD can each independently activate expression of the hilD genes .
"
33,34,504.txt,8,0,,,,"HilD are clearly able to induce hilD transcription .
"
34,35,504.txt,9,0,,,,"HilD are all also capable of activating expression of hilD independent of each other and comprise a complex feed forward regulatory loop .
"
35,36,504.txt,10,0,,,,"not indirectly is it absolutely required for HilD to activate hilD transcription
"
36,37,504.txt,11,0,,,,"not directly is it absolutely required for HilD to activate hilD transcription
"
37,38,504.txt,12,0,,,,"This regulated induction of hilD eliminates the autoinduction of hilD expression by the HilD protein .
"
38,39,504.txt,13,0,,,,"Other features that need to be taken in account when assessing hilD transcription are the presence of an intact hilD ORF , as the HilD protein positively regulates its own expression [ 15 ] and the presence of the newly described regulatory motif hilD 3 
"
39,40,504.txt,14,0,,,,"Gre factors affect SPI-1 gene expression by modulating hilD expression The transcriptional expression of hilA is tightly modulated by three AraC activators , HilD , HilC and RtsA , which form an auto-inducing regulatory loop where each protein can activate its own expression , as well as expression of the other two regulators [ 15 ] .
"
40,41,504.txt,15,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"hilD expression from the strain complemented with HilD was significantly higher than hilD expression from both the reporter strain alone and the reporter carrying the empty vector ( Fig. 5 ) , indicating that in S. Typhi HilD positively regulates its own transcription , either directly or indirectly .
"
41,42,504.txt,16,0,,,,"Saini et al. demonstrated that the interaction of HilD with the hilD promoter is the trigger for inducing the expression of SPI1 through a stepwise increase of autoactivation .
"
42,43,504.txt,17,0,,,,Saini et al. demonstrated that the interaction of HilD with the hilD promoter is the trigger for inducing the expression of SPI1 through a stepwise increase of hilD promoter activity .
43,44,1090.txt,1,0,,,,The following studies show that PhoBR regulate hilE expression via the fimZ gene .
44,45,262.txt,1,0,,,,"also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region"
45,46,276.txt,1,0,,,,"SirA activates the virulence gene sopB in motility agar .
"
46,47,276.txt,2,0,,,,that SirA positively regulates sopB regardless of growth medium
47,48,1084.txt,1,0,,,,"that acnA expression was regulated by Fur , iron starvation
"
48,49,1084.txt,2,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"E. coli RpoS CRP SoxR FNR Fur acnA P2 P1 S. Typhimurium Expression of S. Typhimurium acnA is regulated by oxR Enhanced expression of the acnA gene in the acnB mutant suggested that PacnA was regulated .
"
49,50,1084.txt,3,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"E. coli RpoS CRP SoxR FNR Fur acnA P2 P1 S. Typhimurium Expression of S. Typhimurium acnA is regulated by ur suggested that PacnA was regulated .
"
50,51,1084.txt,4,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"E. coli RpoS CRP SoxR FNR Fur acnA P2 P1 S. Typhimurium Expression of S. Typhimurium acnA is regulated by NR suggested that PacnA was regulated .
"
51,52,1084.txt,5,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"E. coli RpoS CRP SoxR FNR Fur acnA P2 P1 S. Typhimurium Expression of S. Typhimurium acnA is regulated by RP suggested that PacnA was regulated .
"
52,53,1084.txt,6,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"However , the regulation of S. Typhimurium acnA differs from the E. coli paradigm in exhibiting relatively constant expression throughout Fur repression .
"
53,54,1084.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"However , the regulation of S. Typhimurium acnA differs from the stationary-phase induction of Furactivation observed in E. coli ."
54,55,510.txt,1,0,,,,"Moreover , the comparison of katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .
"
55,56,510.txt,2,0,,,,"Moreover , the comparison of rfaH expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .
"
56,57,510.txt,3,0,,,,"Moreover , the comparison of rfaH expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .
"
57,58,510.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"In this study , we demonstrate that RpoS also modulates rfaH promoter activity as revealed by the absence of growth-dependent regulation of an rfaH -- O antigen production in a S. typhi rpoS mutant .
"
58,59,510.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"In this study , we demonstrate that RpoS also modulates rfaH promoter activity as revealed by the absence of growth-dependent regulation of an rfaH -- lacZ-transcriptional-fusion antigen production in a S. typhi rpoS mutant .
"
59,60,510.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , we conclude that both RpoS control the rfaH promoter activity and concomitantly , the production of O-specific LPS in S. typhi .
"
60,61,510.txt,7,0,,,,"that the alternative sigma factor RpoS , a global regulator of gene expression 38 S during the transition to stationary-phase , also controls the expression of the rfaH gene
"
61,62,510.txt,8,0,,,,"that the alternative sigma factor RpoS , a global regulator of gene expression 38 S during the transition to stationary-phase , also controls the expression of the rfaH gene
"
62,63,510.txt,9,2,Chlorobaculum macestae;Mycoplasma iners,strain M;strain M,Chlorobaculum macestae;Mycoplasma iners,"Role of RpoS in O antigen production pSM103 This study To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed strain M103 .
"
63,64,510.txt,10,2,Chlorobaculum macestae;Mycoplasma iners,strain M;strain M,Chlorobaculum macestae;Mycoplasma iners,"Role of RpoS in the growth phase-dependent regulation of rfaH To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed strain M103 .
"
64,65,510.txt,11,2,Chlorobaculum macestae;Mycoplasma iners,strain M;strain M,Chlorobaculum macestae;Mycoplasma iners,"Role of RpoS in the growth phase-dependent regulation of rfaH To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed strain M103 .
"
65,66,510.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Role of RpoS in O antigen production pSM103 This study To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed an isogenic derivative of S. typhi Ty2 .
"
66,67,510.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Role of RpoS in the growth phase-dependent regulation of rfaH To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed an isogenic derivative of S. typhi Ty2 .
"
67,68,510.txt,14,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Role of RpoS in the growth phase-dependent regulation of rfaH To investigate whether RpoS played any role in the growth phase-dependent regulation of rfaH , we constructed an isogenic derivative of S. typhi Ty2 .
"
68,69,510.txt,15,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .
"
69,70,510.txt,16,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"One reason for this phenomenon could be the fact that RpoS is involved in the growth-dependent regulation of rfaH transcription in S. typhi .
"
70,71,510.txt,17,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .
"
71,72,510.txt,18,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Mol Bittner M , Valvano MA & Contreras I RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .
"
72,73,510.txt,19,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,RpoS are involved in the growth-dependent regulation of rfaH transcription in Salmonella enterica serovar Typhi .
73,74,538.txt,1,0,,,,"Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB-and RcsA-dependent colanic acid capsule synthesis cps operon .
"
74,75,538.txt,2,0,,,,"Both an rcsB single mutant and an rcsC11 rcsB double mutant exhibited wild-type virulence ( Table 1 ; Fig. 1 ) , indicating that the attenuated phenotype of the rcsC11 mutant is entirely dependent on RcsB-regulated genes and ruling out cross-talk of the mutant RcsC11 protein to other two-component systems as responsible for attenuation .
"
75,76,538.txt,3,1,Salmonella,Salmonella,Salmonella,"of the RcsC/YojN/RcsB regulatory system due to the rcsC11 allele in the sensor RcsC renders Salmonella avirulent , and that inactivation of the response regulator gene rcsB restores full virulence to the rcsC11 mutant , indicative that its attenuated phenotype results from aberrant expression of RcsB-regulated genes .
"
76,77,538.txt,4,0,,,,"We did not observe a decrease in Δ in a wza yjb rcsB mutant beyond what is observed in the rcsB mutant , suggesting that no additional RcsB-regulated factors are required for PMF maintenance ( see Fig ."
77,78,1912.txt,1,0,,,,"RpoS-and OxyR-independent induction of HPI catalase at identification of rpoS mutations in common laboratory strains .
"
78,79,1912.txt,2,0,,,,"Visick , J.E. , and Clarke , S. RpoS-and OxyR-independent induction of HPI catalase at identification of rpoS mutations in common laboratory strains .
"
79,80,1912.txt,3,0,,,,"RpoS-and OxyR-independent induction of HPI catalase at identification of rpoS mutations in common laboratory strains .
"
80,81,1912.txt,4,0,,,,RpoS-and OxyR-independent induction of HPI catalase at identification of rpoS mutations in common laboratory strains .
81,82,1906.txt,1,0,,,,"In addition , FliA was found to induce expression of the primary invasin gene invA ."
82,83,1537.txt,1,0,,,,"the pstS mutation activates PhoBR signaling
"
83,84,1537.txt,2,0,,,,"pstS induces the PhoBR two-component system
"
84,85,1537.txt,3,0,,,,pstS induces the PhoBR two-component system
85,86,1251.txt,1,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
86,87,1251.txt,2,0,,,,"yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .
"
87,88,1251.txt,3,0,,,,"gnd is the final gene in the rfb locus involved in LPS biosynthesis ( 34 ) and is located upstream of pmrE , a PmrA-regulated gene shown to be necessary for PM resistance and wild-type virulence ( 17 ) ."
88,89,909.txt,1,0,,,,"Figure 4A shows that CadC degradation is coupled to induction of cadA transcription .
"
89,90,909.txt,2,0,,,,"These results indicate that the immediate induction of cadA mRNA following stress is correlated with rapid cleavage of CadC .
"
90,91,909.txt,3,0,,,,"CadC degradation is coupled to transcriptional induction of cadA .
"
91,92,909.txt,4,0,,,,"Therefore , we reasoned that acid stress-induced proteolysis of CadC might be a posttranslational control mechanism for activating membrane-bound CadC because the induction of cadA transcription is accompanied by proteolysis of CadC ."
92,93,1245.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium SL1344,SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344,"repression of fis transcription To investigate whether RpoS affected the level of transcription of the activity of the fis promoter in the SL1344 rpoS mutant was monitored during the growth of the culture .
"
93,94,1245.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium SL1344,SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344,"repression of fis transcription To investigate whether RpoS affected the level of transcription of fis in the SL1344 rpoS mutant was monitored during the growth of the culture .
"
94,95,1245.txt,3,0,,,,"Our data indicate that the presence of the RpoS sigma factor correlates with repression of the fis gene .
"
95,96,1245.txt,4,0,,,,"As it is unlikely that RpoS represses the fis promoter directly , repression may involve an indirect negative effect .
"
96,97,1245.txt,5,0,,,,"By reducing the number of RpoDcontaining holoenzymes , RpoS may downregulate that of the fis gene ."
97,98,1523.txt,1,3,Escherichia coli;Dioscorea trifida;Dioscorea trifida;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Name;name;S. typhimurium;typhimurium,Dioscorea trifida;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"pmrH ( the first gene of an operon that contains the genes pmrHFIJKLM ; Table 1 ) is the only known PmrAB-regulated gene for which the PmrA motif is conserved in all genome Table 1 ( Continued ) m ¬ 0.753257 CAAAATATC AATTTAAT Other yafC/STM0275 STM0256 ; Ortholog of E. coli putative transcriptional regulator LysR-type ( AAC73313 .1 ) ; Blast hit to putative transcriptional regulator , LysR family ; intergenic shared STM0275 ( drug efflux protein ) distributions Name : name of the gene in the S. typhimurium genome ( ) ."
98,99,2002.txt,1,4,unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .
"
99,100,2002.txt,2,4,unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Xu S , Zou X , Sheng X et al Expression of fljB : z66 on a linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .
"
100,101,2002.txt,3,4,unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;salmonella;salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Xu S , Zou X , Sheng X et al Expression of fljB : z66 on a novel linear plasmid of salmonella enterica serovar Typhi is regulated by OmpR .
"
101,102,2002.txt,4,0,,,,"To investigate the mechanism underlying the expressional regulation of fljB : z66 , gene deletion mutants of OmpR were constructed in this study .
"
102,103,2002.txt,5,1,Salmonella,Salmonella,Salmonella,"that OmpR regulates the expression of fljB have been identified in secretion of FljB : z66 in different osmotic Salmonella by screening with the corresponding antisera .
"
103,104,2002.txt,6,1,Salmonella,Salmonella,Salmonella,"that OmpR regulates the expression of fljB have been identified in expression of FljB : z66 in different osmotic Salmonella by screening with the corresponding antisera .
"
104,105,2002.txt,7,4,unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Xu S , Zou X , Sheng X et al Expression of fljB : z66 on a novel linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .
"
105,106,2002.txt,8,4,unidentified plasmid;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,Expression of fljB : z66 on a novel linear plasmid of Salmonella enterica serovar Typhi is regulated by OmpR .
106,107,921.txt,1,0,,,,"the control of the DnaA binding to oriC can be related with the partial reestablishment of the replication asynchrony _ observed at every dam mutant
"
107,108,921.txt,2,0,,,,the control of the DnaA binding to oriC in-vitro _ observed at every dam mutant
108,109,935.txt,1,0,,,,"YdcR Directly Binds to the Promoter Region of the srfN Gene -- Like other transcriptional regulators of the GntR family , YdcR also has an HTH DNA-binding domain .
"
109,110,935.txt,2,2,Cornu aspersum;Cantareus apertus;Cornu aspersum;Cantareus apertus,helix;helix;helix;helix,Cornu aspersum;Cantareus apertus,"YdcR Directly Binds to the Promoter Region of the srfN Gene -- Like other transcriptional regulators of the GntR family , YdcR also has an N-terminal helix-turn-helix DNA-binding domain ."
110,111,1279.txt,1,0,,,,"Furthermore , STM2585 are regulated by the master regulators of the SsrB regulon .
"
111,112,1279.txt,2,0,,,,"Furthermore , STM2585 are regulated by the master regulators of the SsrB regulon ."
112,113,2016.txt,1,0,,,,LexA _ regulated because their induction is prevented by a recA mutation
113,114,1292.txt,1,2,Felis catus;unidentified,CAT;not shown,Felis catus;unidentified,"As we expected , no regulation of ompC by LeuO was observed since no differences in CAT activity were detected in the presence or absence of LeuO ( data not shown ) ."
114,115,706.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both the malT in E. coli is stimulated by H-NS ."
115,116,712.txt,1,0,,,,"Notably , EMSAs revealed that H-NS DNA binding to hilA was also enhanced by the addition of HhaR14A/R17A , although this mutant was Fig. 7B .
"
116,117,712.txt,2,0,,,,"Notably , EMSAs revealed that H-NS DNA binding to hilA was also enhanced by the addition of HhaR14A/R17A , although this mutant was completely defective for gene silencing in-vivo ."
117,118,1286.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"Research A Proteomic Analysis Reveals Differential S - Regulation of katN Locus by YncC in Salmonella r , and Françoise Norel § Norel § ¶ ‡ The stationary-phase s controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Esch .
"
118,119,1286.txt,2,0,,,,"The results reveal differential regulation of katN locus by YncC in these two closely related bacteria .
"
119,120,1286.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"A proteomic analysis reveals differential regulation of katN locus by YncC in Escherichia coli K-12 .
"
120,121,1286.txt,4,1,Salmonella,Salmonella,Salmonella,A proteomic analysis reveals differential regulation of katN locus by YncC in Salmonella .
121,122,1443.txt,1,0,,,,Our results showed that both FnrD154A bound to the lpxO promoter in a dose-dependent fashion .
122,123,29.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Previous studies have shown that H-NS contribute to hlyE expression when E. coli is grown on a solid medium .
"
123,124,29.txt,2,0,,,,"Thus , we concluded that H-NS all contribute towards the regulation of hlyE expression .
"
124,125,29.txt,3,0,,,,"Thus , it is expected that H-NS mutants increase hlyE transcription via RpoS ."
125,126,1325.txt,1,0,,,,ant does not appear to be regulated by LexA
126,127,869.txt,1,0,,,,"On the other hand , STM4264 expression could not downregulate CsgD in the STM1703 mutant .
"
127,128,869.txt,2,0,,,,STM4264 inhibit CsgD function .
128,129,1331.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by the repressor of the myo-inositol utilization genes in S. Typhimurium ."
129,130,1457.txt,1,0,,,,"Thus , it was concluded that the Fur -- Fe complex mediates repression of acnA expression ."
130,131,2176.txt,1,1,Escherichia coli,E. coli,Escherichia coli,the OxyR repressor for hemi-methylated GATC sites has been shown to regulate phase variation in the E. coli agn43 gene .
131,132,15.txt,1,0,,,,"Finally , the LuxS-PhoA fusion protein under control of the luxS promoter was subcloned as a blunt ."
132,133,1319.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .
"
133,134,1319.txt,2,0,,,,"A novel NsrR-regulated gene designated STM1808 has been identified , along with hmp , hcp-hcr , yeaR-yoaG , ygbA and ytfE .
"
134,135,1319.txt,3,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in hcp , ygbA , ytfE , STM1808 and yeaR ( Experimental Procedures ) .
"
135,136,1319.txt,4,1,Salmonella,Salmonella,Salmonella,"These data confirm previous findings with regard to hmp , and additionally demonstrate that the NsrR-regulated ytfE and STM1808 genes contribute to Salmonella virulence .
"
136,137,1319.txt,5,1,Mus sp.,mice,Mus sp.,"We have identified a novel NsrR-regulated gene designated STM1808 , and demonstrated a role for specific NsrR-regulated genes in promoting growth during nitrosative-stress in-vitro ( hmp , STM1808 , ygbA and hcp ) and during systemic infection of mice in-vivo ( hmp , STM1808 , ytfE ) .
"
137,138,1319.txt,6,1,Salmonella,Salmonella,Salmonella,STM1808 and ytfE can be added to hmp as NsrR-regulated loci that contribute to Salmonella virulence ( Fig. 6 ) .
138,139,855.txt,1,0,,,,"The rpoS mutation resulted in a two-to threefoldhigher level of induction of stiB during P starvation during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus ."
139,140,699.txt,1,0,,,,"Upon induction of the mutant phoP with arabinose in a PhoP2 background , activation of pagD peaked at 4 h .
"
140,141,699.txt,2,0,,,,"Upon induction of the mutant phoP with arabinose in a PhoP2 background , activation of pagD was observed within minutes ."
141,142,841.txt,1,0,,,,"spiC is regulated by both OmpR A two-component regulatory system regulates a two-component regulatory system We are aware of two previous reports of regulation of one two-component system by another .
"
142,143,841.txt,2,0,,,,spiC is regulated by both OmpR A two-component regulatory system regulates a two-component regulatory system We are aware of two previous reports of regulation of one two-component system by another .
143,144,2162.txt,1,0,,,,"In support of this , transcription from the P5flhDC promoter was slightly reduced upon rcsB overexpression , although we detected no binding of the RcsB-RflM complex to a promoter fragment ."
144,145,1480.txt,1,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s;Salmonella,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Overnight cultures of wild-type S. Typhimurium 14028s , isogenic rpoE mutant TF951 : : rpoE rpoE is required for Salmonella resistanced to anti-microbial peptides 791 were induced for 1 h in 0.2 % arabinose before treatment with 5 mg ml-1 Crp4 for 60 min respectively .
"
145,146,1480.txt,2,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s;Salmonella,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Overnight cultures of wild-type S. Typhimurium 14028s , isogenic rpoE mutant TF951 : : rpoE rpoE is required for Salmonella resistanced to anti-microbial peptides 791 were induced for 1 h in 0.2 % arabinose before treatment with 5 mg ml-1 Crp4 for 90 min respectively .
"
146,147,1480.txt,3,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s;Salmonella,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Overnight cultures of wild-type S. Typhimurium 14028s , the : : rpoE rpoE is required for Salmonella resistanced to anti-microbial peptides 791 were induced for 1 h in 0.2 % arabinose before treatment with 5 mg ml-1 Crp4 for 60 min respectively .
"
147,148,1480.txt,4,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s;Salmonella,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Overnight cultures of wild-type S. Typhimurium 14028s , the : : rpoE rpoE is required for Salmonella resistanced to anti-microbial peptides 791 were induced for 1 h in 0.2 % arabinose before treatment with 5 mg ml-1 Crp4 for 90 min respectively .
"
148,149,1480.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The rpoE mutant S. Typhimurium strain has enhanced susceptibility to Crp4 .
"
149,150,1480.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of rpoE Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between fdhD .
"
150,151,1480.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,Crp4 induce expression of rpoE Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between sE .
151,152,114.txt,1,0,,,,The FlhC levels were determined by immunoblotting analysis at various times after flhC transcription was induced by 50 µM IPTG .
152,153,2189.txt,1,0,,,,"CsrA also activates transcription of csrB , possibly through indirect regulation of a transcription factor .
"
153,154,2189.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Romeo , the RNA binding protein CsrA activates csrB transcription in Escherichia coli .
"
154,155,2189.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,Regulatory interactions of Csr components : the RNA binding protein CsrA activates csrB transcription in Escherichia coli .
155,156,672.txt,1,0,,,,"macB transcript levels are elevated in 12 h postinfection , consistent with potential rapid inactivation of PhoP .
"
156,157,672.txt,2,0,,,,"macB transcript levels are elevated in 8 h postinfection , consistent with potential rapid inactivation of PhoP .
"
157,158,672.txt,3,0,,,,"macB transcript levels are elevated in 4 h postinfection , consistent with potential rapid inactivation of PhoP ."
158,159,666.txt,1,1,unidentified,unknown,unidentified,"However , given that the Fnr regulators can efficiently control feoB mRNA levels in response to different levels of iron , the reason remains unknown .
"
159,160,666.txt,2,1,unidentified,unknown,unidentified,"However , given that the Fnr regulators can efficiently control feoB mRNA levels in response to different levels of oxygen , the reason remains unknown ."
160,161,100.txt,1,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon were regulated by RcsB independently of the presence of RflM .
"
161,162,100.txt,2,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to csgD were regulated by RcsB independently of the presence of RflM .
"
162,163,100.txt,3,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to dps were regulated by RcsB independently of the presence of RflM .
"
163,164,100.txt,4,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to wzzB were regulated by RcsB independently of the presence of RflM ."
164,165,1494.txt,1,1,Salmonella,Salmonella,Salmonella,"RflM functions as a transcriptional repressor in the autogenous control of the Salmonella Flagellar master operon flhDC .
"
165,166,1494.txt,2,1,Salmonella,Salmonella,Salmonella,"RflM functions as a transcriptional repressor in the autogenous control of the Salmonella Flagellar master operon flhDC .
"
166,167,1494.txt,3,1,Salmonella,salmonella,Salmonella,"Hughes , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .
"
167,168,1494.txt,4,1,Salmonella,salmonella,Salmonella,"M. , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .
"
168,169,1494.txt,5,1,Salmonella,salmonella,Salmonella,"Erhardt , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .
"
169,170,1494.txt,6,1,Salmonella,salmonella,Salmonella,"H.M. , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .
"
170,171,1494.txt,7,1,Salmonella,salmonella,Salmonella,"Singer , K.T. RflM functions as a transcriptional repressor in the autogenous control of the salmonella flagellar master operon flhDC .
"
171,172,1494.txt,8,1,Salmonella,Salmonella,Salmonella,"RflM functions as a transcriptional repressor in the autogenous control of the Salmonella flagellar master operon flhDC .
"
172,173,1494.txt,9,0,,,,"We propose that RflM stabilizes binding of unphosphorylated RcsB to the flhDC promoter in absence of environmental cues .
"
173,174,1494.txt,10,0,,,,"We determined which flhDC promoter is regulated via RflM using luxCDABE fusions to flhDC promoter mutants -LRB- Fig. 4C -RRB- .
"
174,175,1494.txt,11,0,,,,"In the present study , we elucidated the mode-of-action of RflM in regulation of flhDC .
"
175,176,1494.txt,12,1,Salmonella,Salmonella,Salmonella,"Hughes , K.T. RflM functions as a transcriptional repressor on the autogenous control of the Salmonella flagellar master operon flhDC .
"
176,177,1494.txt,13,1,Salmonella,Salmonella,Salmonella,RflM functions as a transcriptional repressor in the autogenous control of the Salmonella flagellar master operon flhDC .
177,178,128.txt,1,0,,,,"In accordance with the RNA-seq analysis , suggesting that sopD is downregulated by SlyA .
"
178,179,128.txt,2,0,,,,"Our results showed that at 3 h post-infection only , sopD were negatively regulated by SlyA , with DslyA expression increased two-and five-times , respectively ."
179,180,896.txt,1,1,Salmonella,Salmonella,Salmonella,"a regulator of the LysR family , was found to be a positive effector of the ompS1 gene in Salmonella ."
180,181,882.txt,1,1,Salmonella,Salmonella,Salmonella,"Lrp is a positive regulator of the expression of type 1 fimbriae in Salmonella through direct interaction with the fimZ promoter region .
"
181,182,882.txt,2,2,Salmonella;unidentified plasmid;unidentified plasmid,Salmonella;plasmid;plasmid,Salmonella;unidentified plasmid,"Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) .
"
182,183,882.txt,3,0,,,,"The Lrp directly binds the fimZ promoter
"
183,184,882.txt,4,0,,,,EMSA was used to test the binding of Lrp at indicated concentrations to 6 ′ - FAM-labeled fimZ promoter .
184,185,1127.txt,1,0,,,,"Under low osmolality , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
185,186,1127.txt,2,0,,,,"Under acidic pH , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn ."
186,187,1641.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , zwf .
"
187,188,1641.txt,2,0,,,,"SoxS protein , activates sodA , zwf ."
188,189,1899.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Studies with the glnA promoter of S. typhimurium have shown that NtrC bound at the enhancer , located between 2140 , interacts directly with s54 holoenzyme by means of DNA loop formation .
"
189,190,1899.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Studies with the glnA promoter of S. typhimurium have shown that NtrC bound at the enhancer , located between 2108 , interacts directly with s54 holoenzyme by means of DNA loop formation .
"
190,191,1899.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus musculus,S. Typhimurium;Typhimurium;mouse,Mus musculus;Salmonella enterica subsp. enterica serovar Typhimurium,"NtrC-dependent transcription of target genes ( Table 1 ) allows the cell to assimilate low levels of ammonia and utilize alternative nitrogen sources in nutrient-limited environments ; NtrC-regulated glnA ( glutamine synthetase ) and glnHQ ( glutamine transport ) together contribute to S. Typhimurium virulence in a mouse model and increased survival in macrophages ( Klose and Mekalanos , 1997 ) ."
191,192,1655.txt,1,0,,,,"CueR directly stimulates the transcription of copA .
"
192,193,1655.txt,2,0,,,,"Expression of copA is induced by copper ions , in a CueR-dependent manner .
"
193,194,1655.txt,3,0,,,,"CueR _ activating copA expression in response to gold
"
194,195,1655.txt,4,0,,,,CueR _ activating copA expression in response to gold
195,196,1133.txt,1,2,Escherichia coli;unidentified plasmid,E. coli;plasmid,Escherichia coli;unidentified plasmid,"However , low pH does not seem to produce sufficient levels of active RstA in E. coli because repression of csgD transcription occurred only upon overexpression of the RstA protein from a plasmid .
"
196,197,1133.txt,2,2,Escherichia coli;unidentified plasmid,E. coli;plasmid,Escherichia coli;unidentified plasmid,"However , low pH does not seem to produce sufficient levels of i.e. in E. coli because repression of csgD transcription occurred only upon overexpression of the RstA protein from a plasmid ."
197,198,1669.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Cooperative interaction between Cra in the regulation of the cydAB operon of Escherichia coli .
"
198,199,1669.txt,2,0,,,,"Cra is known to bind to at least one nonconsensus binding site within the cydAB promoter .
"
199,200,1669.txt,3,0,,,,"For example , Cra binds to a nonconsensus site in the cydAB promoter region .
"
200,201,1669.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,Cooperative interaction between Cra in the regulation of the cydAB operon of Escherichia coli .
201,202,470.txt,1,0,,,,"Secreted effectors encoded outside SPI-2 Several effectors contain a conserved N-terminal translocation motif DNA sequence analysis of the chromosomal region surrounding the PhoP-activated gene pagJ led to the identi-fication of a gene encoding a 700-amino-acid protein that was designated SspH1 ( Miao et al. , 1999 ) ."
202,203,316.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified,S. typhimurium;typhimurium;not shown,unidentified;Salmonella enterica subsp. enterica serovar Typhimurium,"These results suggest that Fis from S. typhimurium influences the expression of cspH by binding to its promoter , although a direct interaction between the cspH promoter was not shown in this study .
"
203,204,316.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified,S. typhimurium;typhimurium;not shown,unidentified;Salmonella enterica subsp. enterica serovar Typhimurium,"These results suggest that Fis from S. typhimurium influences the expression of cspH by binding to its promoter , although a direct interaction between Fis was not shown in this study .
"
204,205,316.txt,3,0,,,,"However , based on these results we could not conclude that Fis directly interacts with the cspH promoter , since this might also be due to the pleio-tropic effect of Fis , coordinating the expression of a large set of genes both by direct control at the level of transcription initiation ."
205,206,1682.txt,1,0,,,,"Importantly , Hha has been shown to bind to the hilA promoter .
"
206,207,1682.txt,2,0,,,,"The hilA promoter is directly controlled by Hha .
"
207,208,1682.txt,3,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"Nevertheless , Hha was able to bind to the S. enterica hilA promoter with high affinity .
"
208,209,1682.txt,4,0,,,,"In spite of the fact that several reports have shown that Hha influences hilA expression , information is not yet available .
"
209,210,1682.txt,5,0,,,,Hha mutants with a diminished positively charged surface can no longer regulate hilA .
210,211,1696.txt,1,0,,,,other SoxR/S _ regulated genes like sodA
211,212,302.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"Expression of AcrAB is controlled by AcrR can also be plasmid-In this study , mutations in the QRDR of parE and in the regu ¬ 62 60 This study 60 This study 60 2 ."
212,213,464.txt,1,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Wang , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
213,214,464.txt,2,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Wang , Y. , Cen , X.F. , Zhao , G.P. , , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
214,215,464.txt,3,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Wang , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
215,216,464.txt,4,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"G.P. , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
216,217,464.txt,5,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Zhao , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
217,218,464.txt,6,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"X.F. , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
218,219,464.txt,7,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Cen , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
219,220,464.txt,8,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Y. , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB .
"
220,221,464.txt,9,1,Streptomyces coelicolor,Streptomyces coelicolor,Streptomyces coelicolor,"Wang , J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB ."
221,222,1866.txt,1,0,,,,"While CsgD is suggested to activate biosynthesis of curli fimbriae directly by binding to the promoter of the csgBA operon , activation of cellulose biosynthesis by CsgD is indirect .
"
222,223,1866.txt,2,0,,,,"Therefore , in the next step the level of the CsgD protein , the proposed transcriptional activator of the csgBA promoter was investigated .
"
223,224,1866.txt,3,0,,,,"csgBA is positively regulated by the global regulator CsgD
"
224,225,1866.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .
"
225,226,1866.txt,5,0,,,,"CsgD positively regulates the transcription of the csgBA operon .
"
226,227,1866.txt,6,0,,,,"In this study , we dem-onstrated for the first time that CsgD activates transcription of the promoter regions of csgBA ."
227,228,1872.txt,1,0,,,,This raised the possibility that the yqjA and/or yqjB genes might be regulated by the PhoP protein .
228,229,458.txt,1,0,,,,"Strikingly , ugtL , is also regulated by SsrB , ."
229,230,1873.txt,1,0,,,,"The gene pmrD is transcriptionally activated by the PhoPQ system .
"
230,231,1873.txt,2,0,,,,"PhoPQ activates the expression of pmrD .
"
231,232,1873.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"PhoPQ activates pmrD in both E. coli
"
232,233,1873.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"PhoPQ activates pmrD in both S. Typhimurium
"
233,234,1873.txt,5,0,,,,"Upon activation , PhoPQ increases the transcription of pmrD .
"
234,235,1873.txt,6,0,,,,"Under limitation , the PhoPQ system induces pmrD expression .
"
235,236,1873.txt,7,0,,,,"Under Mg2 , the PhoPQ system induces pmrD expression .
"
236,237,1873.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , the PhoPQ TCS indirectly activates the PmrAB TCS via PhoP-activated pmrD expression ."
237,238,459.txt,1,0,,,,It appears that csrA is necessary to regulate the activity of UvrY .
238,239,1867.txt,1,0,,,,"In the present study , the expression from lac fusion was retained after disruption in Fig. 2A in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
239,240,1867.txt,2,0,,,,"In the present study , the expression from the hilA was retained after disruption in Fig. 2A in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
240,241,1867.txt,3,0,,,,"In the present study , the expression from lac fusion was retained after disruption in hilD in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
241,242,1867.txt,4,0,,,,"In the present study , the expression from lac fusion was retained after disruption in hilC in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
242,243,1867.txt,5,0,,,,"In the present study , the expression from the hilA was retained after disruption in hilD in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
243,244,1867.txt,6,0,,,,"In the present study , the expression from the hilA was retained after disruption in hilC in the lon , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants ."
244,245,303.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Although CpxR also regulates transcription of acrD , cpxR deletion strains is critically required for S. Typhimurium resistance to Na2WO4 .
"
245,246,303.txt,2,0,,,,"Although CpxR also regulates transcription of acrD , cpxR deletion strains do not possess a tungstate-sensitive phenotype ."
246,247,1697.txt,1,0,,,,"In vivo analyses indicate that LeuO activates hilE transcription .
"
247,248,1697.txt,2,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the occurrence of autogenous activation of hilD transcription .
"
248,249,1697.txt,3,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .
"
249,250,1697.txt,4,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in accordance with two well known facts .
"
250,251,1697.txt,5,0,,,,"that LeuO may activate hilE expression
"
251,252,1697.txt,6,0,,,,"that LeuO may activate hilE expression
"
252,253,1697.txt,7,1,Salmonella,Salmonella,Salmonella,"To test whether LeuO is an activator of a hilE : : lacZ translational fusion was constructed on the Salmonella chromosome .
"
253,254,1697.txt,8,1,Salmonella,Salmonella,Salmonella,"To test whether LeuO is an activator of hilE expression : : lacZ translational fusion was constructed on the Salmonella chromosome .
"
254,255,1697.txt,9,0,,,,"that LeuO might activate hilE transcription
"
255,256,1697.txt,10,0,,,,"LeuO activates transcription of hilE
"
256,257,1697.txt,11,0,,,,"that the transcriptional regulator LeuO directly activates transcription of hilE
"
257,258,1697.txt,12,0,,,,"The LysR-type regulator LeuO has been shown to activate hilE transcription to repress HilD activity .
"
258,259,1697.txt,13,0,,,,the major one involves the induction of hilE transcription by LeuO
259,260,465.txt,1,0,,,,"In contrast , inactivation of just the hupB gene correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures ."
260,261,471.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , previous studies have determined that NsrR negatively regulates the expression of the hcp genes ."
261,262,1683.txt,1,0,,,,"Thus OmpR/EnvZ , seem to convert pH decreases into the regulation of different virulence-factors while the primary role of rpoS appears to be protection against acid stress itself ."
262,263,317.txt,1,0,,,,fliT inhibit FlhD4C2 function at a posttranscriptional level
263,264,1668.txt,1,0,,,,"PmrA-regulated loci identified included dgoA and yibD and demonstrated 500-and 2,500-fold activation by PmrA , respectively .
"
264,265,1668.txt,2,0,,,,"The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A .
"
265,266,1668.txt,3,0,,,,"The PmrA-regulated gene mutants JSG897 ( yibD ) and JSG899 ( dgoA ) were also analyzed for sensitivity to PM by MIC assay .
"
266,267,1668.txt,4,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
267,268,1668.txt,5,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
268,269,1668.txt,6,0,,,,"For further characterization of the PmrA-regulated gene mutants , the promoter regions of yibD and dgoA were analyzed for the presence of a putative PmrA-binding site , which was defined by the occurrence of the consensus binding sequence for PmrA , YTTAAK-N5-YTTAAK ( 1 ) .
"
269,270,1668.txt,7,0,,,,"yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .
"
270,271,1668.txt,8,0,,,,"JSG897 and JSG899 , with mutations in PmrA-regulated genes yibD and dgoA , respectively , also still possessed Ara4N modification of lipid-A in similar amounts to the parental PmrAc strain .
"
271,272,1668.txt,9,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"PmrA-regulated gene mutants JSG1525 ( yibD ) and JSG1526 ( dgoA ) were as virulent as wild-type Salmonella serovar Typhimurium , so the genes interrupted have no essential role in the infection process ( Table 4 ) .
"
272,273,1668.txt,10,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Mus sp.,Salmonella;Typhimurium;mice;mice,Mus sp.;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"All PMs mutants identified in this study demonstrated a defect in virulence compared to wild-type Salmonella serovar Typhimurium when administered orally to mice , while the PmrA-regulated gene ( yibD and dgoA ) mutants showed normal virulence in mice .
"
273,274,1668.txt,11,0,,,,"While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) .
"
274,275,1668.txt,12,0,,,,"A strong match to the consensus PmrA-binding site was identified upstream of yibD , indicating direct regulation by PmrA .
"
275,276,1668.txt,13,0,,,,"To determine whether PmrA can bind directly to promoter fragments of PmrA-regulated loci that lack the published PmrA consensus binding site , gel mobility-shift assays were performed to compare the ability of purified PmrA to bind the promoters of yibD and dgoR-KAT [ 34 ] .
"
276,277,1668.txt,14,0,,,,"PmrA was able to bind the yibD promoter .
"
277,278,1668.txt,15,0,,,,"We also made double mutants deleted in additional PmrA-regulated genes or operons ( i.e. ugd , yibD , and the pbgPE operon ) ."
278,279,1654.txt,1,0,,,,"In this study , we demonstrate that SsrB directly stimulates transcription of sifB by binding upstream of their respective promoters ."
279,280,1132.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Nitric oxide , nitrite , and Fnr regulation of hmp gene expression in Escherichia coli K-12 ."
280,281,1126.txt,1,0,,,,"FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgI by introduction of a null mutation in J. Bacteriol .
"
281,282,1126.txt,2,0,,,,"FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgI by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .
"
282,283,1126.txt,3,0,,,,"Like all genes , mutations in any of flgI genes result in FlgM-dependent inhibition of s28 activity ."
283,284,1898.txt,1,0,,,,the nirB promoter _ known to be activated by Fnr under anaerobic conditions as found in the intestinal environment or intracellularly
284,285,1640.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Felis catus,SL1344;SL1344;cat,Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .
285,286,883.txt,1,0,,,,"Additionally , sigD , a gene not directly regulated by HilD , was included in the binding reactions as an internal negative control ."
286,287,129.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Although CpxR also regulates transcription of mdtA , cpxR deletion strains is critically required for S. Typhimurium resistance to Na2WO4 .
"
287,288,129.txt,2,0,,,,"Although CpxR also regulates transcription of mdtA , cpxR deletion strains do not possess a tungstate-sensitive phenotype ."
288,289,897.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Transcriptional regulation of flhD by QseBC ( FliA ) in enterohaemorrhagic Escherichia coli .
289,290,667.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"L.A. Cummings , W.D. Wilkerson , T. Bergsbaken , B.T. Cookson , In vivo , fliC expression by Salmonella enterica serovar Typhimurium is eterogeneous , regulated by ClpX , Mol ."
290,291,1495.txt,1,0,,,,"These results suggest that CpxR represses hilA by affecting the autoregulation of HilD .
"
291,292,1495.txt,2,0,,,,our results _ indicating that CpxR represses the HilD-dependent expression of hilA
292,293,101.txt,1,0,,,,"PhoPQ-regulated genes include lpxO , whose product results in the addition of 2-hydroxymyristate to the 3 = position of lipid-A ( A ) ; pagL , whose product results in deacylation at the 3 = position of lipid-A ( B ) ; and pagP , whose product results in the addition of a palmitate chain to the 2 = position of lipid-A ( C ) .
"
293,294,101.txt,2,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; sdiA , a regulator of quorum-sensing and virulence ( Ahmer et al. 1998 ; Volf et al. 2002 ) ; permeases of oligopeptides , such as oppF and oppB ( Goodell and Higgins 1987 ; Orchard and Goodrich-Blair 2004 ) ; and several genes involved in drug resistance , such as emrE and nudF .
"
294,295,101.txt,3,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; a regulator of virulence ; permeases of oligopeptides .
"
295,296,101.txt,4,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; a regulator of quorum-sensing ; permeases of oligopeptides ."
296,297,2188.txt,1,0,,,,The hilA promoter is directly controlled by RtsAB .
297,298,115.txt,1,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"To investigate whether z66 is regulated by FlhDC like other biphasic S. enterica mutants were affected by the osmotic environment , an ompR mutant was also prepared ."
298,299,1481.txt,1,0,,,,"the positive regulator IHF could indicate that loss of RpoS , but not of IHF , ensures a significant repression of the spvR gene in the intracellular environment of fibroblasts"
299,300,673.txt,1,0,,,,"Barchiesi J , Castelli ME , Soncini FC et al. mgtA expression is induced by Rob overexpression ."
300,301,840.txt,1,0,,,,"As described previously , the microarray data showed repression of the PmrAB-regulated pmrF gene ."
301,302,698.txt,1,0,,,,"These observations support the model that Lrp acts as a conjugation activator by promoting traJ transcription , whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis .
"
302,303,698.txt,2,0,,,,"This result suggested that Lrp activates the transcription of traJ .
"
303,304,698.txt,3,0,,,,"The concomitant observation that the tra operon remains repressed in TraJ-background is also relevant , as it suggests that Lrp activates the tra operon indirectly by enhancing traJ transcription .
"
304,305,698.txt,4,0,,,,"The concomitant observation that the tra operon remains repressed in an Lrp is also relevant , as it suggests that Lrp activates the tra operon indirectly by enhancing traJ transcription ."
305,306,2163.txt,1,0,,,,"The distal half of this motif is very similar to the consensus sequence previously defined for a subset of PhoP-regulated genes that contain a promoter pattern known as architecture I ( 48 ) , whereas the other half of the motif is not conserved in slrP .
"
306,307,2163.txt,2,0,,,,"that PhoP can directly bind to the promoter region of slrP
"
307,308,2163.txt,3,0,,,,"Direct regulation of slrP expression by PhoP .
"
308,309,2163.txt,4,0,,,,"The level of expression of the lac fusions indicated that these fragments contained the motifs necessary for PhoP regulation of slrP .
"
309,310,2163.txt,5,0,,,,"As seen in Fig. 7B , PhoP was able to bind to the promoters of slrP .
"
310,311,2163.txt,6,0,,,,"FIG 7 PhoP binds to the promoter of slrP .
"
311,312,2163.txt,7,0,,,,"slot blot-based experiments _ showing binding of PhoP to DNA fragments containing the promoter region of slrP
"
312,313,2163.txt,8,0,,,,"Similarly , the expression of slrP , also encoding an effector protein , is controlled by the response regulator PhoP in SPI-2-inducing conditions32 ."
313,314,2177.txt,1,0,,,,"The two-component regulatory SirA/BarA function through HilD , thus inducing invF ."
314,315,854.txt,1,0,,,,"Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) ."
315,316,1318.txt,1,0,,,,"In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 25 ± 11 after ( Fig. .
"
316,317,1318.txt,2,0,,,,"In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 25 ± 11 after r 24 .
"
317,318,1318.txt,3,0,,,,"In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 after ( Fig. .
"
318,319,1318.txt,4,0,,,,"In contrast , when MAE121 ( STM3388 : : Km ) was compared with UMR1 , a higher CsgD expression was observed at 10 h , while downregulation of CsgD was 37 ± 3 % after growth for 16 after r 24 ."
319,320,14.txt,1,2,Salmonella;Salmonella;unidentified,Sal-monella;monella;not shown,unidentified;Salmonella,"However , LeuO could increase transcriptional activity in N-minimal-medium , as overexpression of the leuO gene resulted in a 2-fold induction of casA transcription compared to an absence of overexpression in the wild-type Sal-monella strain -LRB- data not shown -RRB- .
"
320,321,14.txt,2,2,Salmonella;Salmonella;unidentified,Sal-monella;monella;not shown,unidentified;Salmonella,"However , LeuO could increase transcriptional activity in N-minimal-medium , as overexpression of the leuO gene resulted in a 2-fold induction of casA transcription compared to an absence of overexpression in the wild-type Sal-monella strain -LRB- data not shown -RRB- .
"
321,322,14.txt,3,0,,,,"Results Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the absence of LeuO .
"
322,323,14.txt,4,0,,,,"Results Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the presence ."
323,324,1330.txt,1,0,,,,"Furthermore , we demonstrate that SoxS mediate repression of rob by binding to its promoter region .
"
324,325,1330.txt,2,0,,,,"rob is negatively regulated by SoxS The transcript levels of rob in the DsoxS strains were repressed after treatment with NaOCl as in the wild type .
"
325,326,1330.txt,3,0,,,,"rob is negatively regulated by SoxS The transcript levels of rob in the DmarA strains were repressed after treatment with NaOCl as in the wild type .
"
326,327,1330.txt,4,0,,,,"This confirms our previous results that repression of rob in the must have been due to overexpression of SoxS .
"
327,328,1330.txt,5,0,,,,"The results above suggest that SoxS could mediate together a repression of rob in response to NaOCl .
"
328,329,1330.txt,6,1,Escherichia coli,E. coli,Escherichia coli,other studies _ performed in E. coli where rob was shown to be negatively regulated by both SoxS by a direct interaction with its promoter region
329,330,1456.txt,1,0,,,,"Transcription of selected PhoPQ-regulated genes , hmpA and rpoD was determined by standard PCR using the synthesized cDNAs and the primers listed in table S4 ."
330,331,1442.txt,1,0,,,,"Taken together , these results show that CpxR represses the autoregulation of ssrB located in SPI-2 ."
331,332,868.txt,1,0,,,,"On the one hand , ugd expression is promoted in low Mg2 + in a process that requires the Mg2 + - responsive PhoP -- PhoQ two-component system , the PhoP-regulated shunt protein PmrD and the PmrA -- PmrB two-component system ( Kox et al. , 2000 ) .
"
332,333,868.txt,2,0,,,,"The PhoP -- PhoQ -- PmrA -- PmrB pathway of ugd activation in macrophages may be the same as that taking 2 + place in low Mg , where the PhoP -- PhoQ system activates the PmrA -- PmrB system via the PhoP-regulated protein PmrD ( Fig. 1 ; Kox et al. , 2000 ) .
"
333,334,868.txt,3,0,,,,"Boxed region indicates what was previously known about the regulation of ugd transcription by the PhoP -- PmrA -- PmrB systems before the studies .
"
334,335,868.txt,4,0,,,,"Boxed region indicates what was previously known about the regulation of ugd transcription by the PhoP -- PhoQ -- PmrB systems before the studies .
"
335,336,868.txt,5,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"For example , the ugd promoter of Salmonella ( Fig. 1B ) , but not of Escherichia coli , harbors a PhoP box that is located much further upstream from an RNA polymerase binding site than in other PhoP-regulated promoters ( Table 3 ) .
"
336,337,868.txt,6,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
337,338,868.txt,7,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
338,339,868.txt,8,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .
"
339,340,868.txt,9,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .
"
340,341,868.txt,10,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
341,342,868.txt,11,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .
"
342,343,868.txt,12,1,Salmonella,Salmonella,Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
343,344,868.txt,13,1,Salmonella,Salmonella,Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- ."
344,345,1324.txt,1,1,Salmonella,Salmonella,Salmonella,"Inactivation of rpoN does not affect sensitivity to protamine In Salmonella , PmrA-and PhoP-regulated covalent modifications reduce the overall net negative charge of the lipopo-lysaccharide ."
345,346,28.txt,1,3,Escherichia coli;Dioscorea trifida;Dioscorea trifida;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Name;name;S. typhimurium;typhimurium,Dioscorea trifida;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"pmrH ( the first gene of an operon that contains the genes pmrHFIJKLM ; Table 1 ) is the only known PmrAB-regulated gene for which the PmrA motif is conserved in all genome Table 1 ( Continued ) m ¬ 0.753257 CAAAATATC AATTTAAT Other yafC/STM0275 STM0256 ; Ortholog of E. coli putative transcriptional regulator LysR-type ( AAC73313 .1 ) ; Blast hit to putative transcriptional regulator , LysR family ; intergenic shared STM0275 ( drug efflux protein ) distributions Name : name of the gene in the S. typhimurium genome ( ) .
"
346,347,28.txt,2,0,,,,"However , Lee et al. [ 21 ] demonstrated that the loss of pmrC and the pmrHFIJKLM operon ( also called the pbg operon ) resulted in PM resistance equal to that of a pmrA mutant strain , suggesting a limited role for PmrAB-regulated core modification in PM resistance .
"
347,348,28.txt,3,0,,,,The pmrHFIJKLM operon is directly regulated by PmrAB .
348,349,1287.txt,1,0,,,,Deletion of either hilC in this experiment did not block regulation by either HilE .
349,350,713.txt,1,0,,,,"From the data , it is apparent that both OmpR activate the transcriptional-fusions to spiC ."
350,351,707.txt,1,1,Salmonella,Salmonella,Salmonella,"ChbR bound to the region upstream of the chiP gene in Salmonella at the sequence .
"
351,352,707.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"no binding of ChbR to the chiP upstream region of E. coli was detected ( D )
"
352,353,707.txt,3,1,Escherichia coli,E. coli,Escherichia coli,no binding of ChbR to the chiP upstream region of E. coli was detected ( Fig. 2C )
353,354,1293.txt,1,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of orgA remains unaffected .
"
354,355,1293.txt,2,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgK remains unaffected .
"
355,356,1293.txt,3,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgH remains unaffected .
"
356,357,1293.txt,4,0,,,,"In addition , HilD directly activate sipA in non-HilA dependent manner ."
357,358,1278.txt,1,0,,,,"To investigate the mechanism underlying the expressional regulation of fljB : z66 , gene deletion mutants of FlhDC were constructed in this study .
"
358,359,1278.txt,2,0,,,,"To investigate whether fljB is regulated by FlhDC like other biphasic S. fliA mutants were affected by the osmotic environment , an ompR mutant was also prepared .
"
359,360,1278.txt,3,0,,,,"To investigate whether fljB is regulated by FlhDC like other biphasic S. flhDC mutants were affected by the osmotic environment , an ompR mutant was also prepared .
"
360,361,1278.txt,4,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"To investigate whether fljB is regulated by FlhDC like other biphasic S. enterica mutants were affected by the osmotic environment , an ompR mutant was also prepared ."
361,362,934.txt,1,0,,,,"Additional experiments , showed that NsrR-binding plays a major role in the induction of hcr operon ."
362,363,2017.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the RpoS-activated promoter Px1 is the primary driver of topA transcription during stationary-phase , and it may compete with and repress the exponential-growth promoter P4 ( Qi et al. , 1997 ) ."
363,364,2003.txt,1,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , psiF are regulated by the alternative sigma factor RpoS ."
364,365,920.txt,1,0,,,,"We therefore hypothesized that the signals from PhoBR two-component regulators are processed through FimZ , leading to the repression of hilA .
"
365,366,920.txt,2,0,,,,"We therefore hypothesized that the signals from the PhoPQ are processed through FimZ , leading to the repression of hilA ."
366,367,1244.txt,1,0,,,,HU regulates rpoS translation .
367,368,908.txt,1,0,,,,YdiV indirectly represses fliZ transcription through FlhD4C2
368,369,1522.txt,1,4,Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Felis catus;Clostridium aminobutyricum,Typhimurium;E. coli;cat;Clostridium aminobutyricum,Felis catus;Clostridium aminobutyricum;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Apart from the PhoP/PhoQ-regulated ugd ( pagA ) gene , which in serovar Typhimurium has been demonstrated to be transcriptionally active inside macrophages and to be necessary for growth in a low-magnesium environment ( 1 , 19 , 20 ) , two genes were identified with homology to the E. coli tdh gene and the cat2 gene in Clostridium aminobutyricum ."
369,370,1536.txt,1,0,,,,"Because transcription elongation into the mgtA coding region is controlled by the Mg2 + - responding mgtA leader RNA higher levels of PhoP-P are produced only when levels drop below a certain threshold .
"
370,371,1536.txt,2,0,,,,"Because transcription elongation into the mgtA coding region is controlled by the Mg2 + - responding mgtA leader RNA higher levels of PhoP-P are produced only when cytoplasmic Mg2 drop below a certain threshold .
"
371,372,1536.txt,3,0,,,,"Because transcription elongation into the mgtA coding region is controlled by the Mg2 + - responding the resulting higher levels of PhoP-P are produced only when levels drop below a certain threshold .
"
372,373,1536.txt,4,0,,,,"Because transcription elongation into the mgtA coding region is controlled by the Mg2 + - responding the resulting higher levels of PhoP-P are produced only when cytoplasmic Mg2 drop below a certain threshold .
"
373,374,1536.txt,5,0,,,,"Because transcription elongation into the mgtA coding region is controlled by the Mg2 + - responding the MgtA protein higher levels of PhoP-P are produced only when levels drop below a certain threshold .
"
374,375,1536.txt,6,0,,,,Because transcription elongation into the mgtA coding region is controlled by the Mg2 + - responding the MgtA protein higher levels of PhoP-P are produced only when cytoplasmic Mg2 drop below a certain threshold .
375,376,1250.txt,1,0,,,,Direct regulation of kgtP genes by SlyA in response to ROS .
376,377,1907.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
377,378,539.txt,1,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
378,379,539.txt,2,0,,,,"b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .
"
379,380,539.txt,3,0,,,,"D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .
"
380,381,539.txt,4,0,,,,"To examine the effects of the PhoQ-T48X mutations on the entire PhoP/PhoQ signaling pathway in-vivo , we measured the expression of mgtA ( a PhoP-activated gene that encodes a Mg2 transporter ) by measuring the-ga-lactosidase activity of the mgtA : : lacZ-transcriptional-fusion ( 18 ) .
"
381,382,539.txt,5,0,,,,"To examine the effects of the PhoQ-T48X mutations on the entire PhoP/PhoQ signaling pathway in-vivo , we measured the expression of mgtA ( a PhoP-activated gene that encodes a Mg2 transporter ) by measuring the-ga-lactosidase activity of the mgtA : : lacZ-transcriptional-fusion ( 18 ) .
"
382,383,539.txt,6,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
383,384,539.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"Indeed , experiments carried out with the PhoP-activated mgtA promoter of Escherichia coli demonstrated the critical role that certain PhoP box nucleotides play in mgtA expression and that the purified PhoP protein and RNA polymerase were sufficient to promote mgtA transcription in-vitro ( 13 ) .
"
384,385,539.txt,8,0,,,,"We first examined the effect of the C-terminal His tag on PhoQ activity in-vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ-transcriptional-fusion [ 15 ] .
"
385,386,539.txt,9,0,,,,"We first examined the effect of the C-terminal His tag on PhoQ activity in-vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ-transcriptional-fusion [ 15 ] .
"
386,387,539.txt,10,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .
"
387,388,539.txt,11,0,,,,"$ , PhoP ; # , PhoP ~ P ; & , PhoPHis ; % , PhoPHis ~ P. Response ( RU DNA binding of PhoP proteins by SPR A BIAcore biosensor was used to examine , in real-time , the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .
"
388,389,539.txt,12,0,,,,"The mRNA lev - encoded products are produced in the correct els of the PhoP-activated mgtA , phoP , pmrD , locales , at the required amounts and for the ap - and mig-14 genes increased after the shift to low propriate extents of time .
"
389,390,539.txt,13,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;mice,Salmonella enterica;Mus sp.;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Inactivation of the phoP or levels of the PhoP-activated genes increased , phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2 + virulent for mice and unable to proliferate within ( except for the mgtA gene , which reached the phagocytic cells ( 4-6 ) .
"
390,391,539.txt,14,0,,,,"Recently , it has been shown that high-level expression of the Rob protein , results in the induction of the mgtA gene from a PhoP-independent promoter .
"
391,392,539.txt,15,0,,,,"As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .
"
392,393,539.txt,16,0,,,,"This behavior reflects : first , that the PhoP-activated regulator RstA is necessary for transcription of feoB but not of mgtA in mildly acidic pH ( Choi , et al. , 2009 ) .
"
393,394,539.txt,17,0,,,,"Moreover , deletion of the mgtA gene did not decrease the levels of PhoP-activated mRNAs in a strain with a PhoQ variant that is blind to periplasmic Mg2 + ( Fig. 4 ) .
"
394,395,539.txt,18,0,,,,"Distinct temporal expression of PhoP-activated genes in response to mildly acidic pH and low Mg2 + he MgtA protein is necessary for full transcription of a subset of PhoP-activated genes hen the PhoQ inducing signal is low Mg2 + T w Wild-type and mgtA strains had similar pagC and pagK mRNA levels at 2 h post induction ( Fig. 2A ) ( i.e. , ratio of wild-type/mgtA of 1 ) .
"
395,396,539.txt,19,0,,,,"Therefore , the mgtA requirement for normal expression of a subset of PhoP-activated genes does not result from inefficient transcription of the autoregulated phoP gene ( Soncini et al. , 1995 ) in the mgtA mutant ( Fig .
"
396,397,539.txt,20,0,,,,"Therefore , the mgtA requirement for normal expression of a subset of PhoP-activated genes does not result from inefficient transcription of the autoregulated phoP gene ( Soncini et al. , 1995 ) in the mgtA mutant ( Fig .
"
397,398,539.txt,21,0,,,,"MgtA 
"
398,399,539.txt,22,0,,,,"If MgtA exerts its regulatory function by removing Mg2 + away from PhoQ , deletion of the mgtA gene should not affect expression of PhoP-activated genes in a strain lacking the phoQ gene .
"
399,400,539.txt,23,0,,,,"19 additional genes _ known to be directly activated by the PhoP protein in mgtA strains following a 4 h incubation in 10 μM Mg
"
400,401,539.txt,24,0,,,,"19 additional genes _ known to be directly activated by the PhoP protein in mgtA strains following a 4 h incubation in 10 μM Mg
"
401,402,539.txt,25,0,,,,"A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .
"
402,403,539.txt,26,0,,,,"The PhoP-activated mgtA gene specifies a Mg2 + transporter that enhances PhoP-P levels by transporting Mg2 + away from the periplasm , where it acts as an inhibitory signal for PhoQ ( 16 ) .
"
403,404,539.txt,27,0,,,,"This regulatory architecture defines a two-tier structure among PhoP-activated genes based on whether they require mgtA for maximal expression ( 16 ) .
"
404,405,539.txt,28,1,unidentified,unknown,unidentified,"The PhoP-activated genes most dependent on the MgtA protein specify proteins of unknown function and , like the mgtA gene , are not required for virulence in an animal ( 19 -- 21 ) .
"
405,406,539.txt,29,1,Salmonella,Salmonella,Salmonella,"This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 
"
406,407,539.txt,30,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,Transcription of the PhoP-activated phoP and mgtA genes was higher in wild-type S. enterica than in strains expressing the cadAB genes constitutively when the inducing condition was acidic pH ( Fig. 6C and D ) .
407,408,1913.txt,1,0,,,,"InvF activates expression of sopB .
"
408,409,1913.txt,2,0,,,,Our RNA-seq data show strong upregulation of sopB by InvF ( see of RcsB .
409,410,277.txt,1,0,,,,"Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .
"
410,411,277.txt,2,0,,,,"We also identified AraC-regulated genes that are transcribed due to read-through of inefficient Rho-independent terminators ( ygeA and polB ) .
"
411,412,277.txt,3,0,,,,ygeA are positively regulated by AraC due to partial read-through of Rho-independent terminators .
412,413,511.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"With regard to transcriptional regulation of thefru operon , the results summarized here and previously , as well as unpublished results -LRB- Cao and Saier -RRB- suggest that the fru regulon in S. typhimurium is complex ; that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru -LRB- Cao and Saier , unpublished results -RRB- ; that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; that it may be regulated at the transcriptional level by two or more distinct mechanisms -LRB- possibly involving two distinct inducers , fructose-i-phos-phate and fructose -RRB- which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation ."
413,414,1085.txt,1,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .
"
414,415,1085.txt,2,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .
"
415,416,1085.txt,3,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .
"
416,417,1085.txt,4,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL .
417,418,1091.txt,1,0,,,,"-RRB- b-galactosidase Activity b-galactosidase Activit SirA induction of invF requires HilD Previous evidence suggested that SirA required the HilC/HilD/RtsA binding sites in the hilA promoter to induce expression of hilA .
"
418,419,1091.txt,2,0,,,,-RRB- b-galactosidase Activity b-galactosidase Activit SirA induction of hilA requires HilD Previous evidence suggested that SirA required the HilC/HilD/RtsA binding sites in the hilA promoter to induce expression of hilA .
419,420,505.txt,1,0,,,,"PmrE/PmrF operon is involved in lipid-A and core glycosylation The PhoP-regulated locus , pmrCAB , mediates the addition of aminoarabinose and ethanolamine to lipid-A and the changes in core polysaccharide structure [ 26 , 38 , 39 ] ."
420,421,263.txt,1,0,,,,"These observations support the model that Lrp acts as a conjugation activator by promoting traJ transcription , whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis ."
421,422,2215.txt,1,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"E. coli MprA proteins activate expression of hlyE , thereby conferring a hemolytic phenotype on E. coli ."
422,423,288.txt,1,0,,,,"Mutation of the tolB locus resulted in induction of the RcsB regulon , we examined cps expression in tolB isogenic strains ."
423,424,1708.txt,1,1,Salmonella,Salmonella,Salmonella,"We recently identified a number of new Salmonella PmrA-regulated genes , including one locus with homology to both lpt-3 and lptA of N. meningitidis ( 34 ) ."
424,425,2201.txt,1,0,,,,"To find the conserved DNA-binding motifs for each group of orthologous RhaR regulators , we used initial training sets of genes that are co-localized with rhaR orthologs ( putative operons containing at least one candidate L-Rha utilization gene and that are located in the vicinity of a maximum ten genes from a rhaR gene ) , and then we updated each set by the most likely RhaRregulated genes confirmed by the comparative genomics tests as well as functional considerations ( i.e. , involvement of candidate target genes in the L-Rha utilization pathway ) ."
425,426,1720.txt,1,0,,,,"Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC .
"
426,427,1720.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in SCV of macrophages .
"
427,428,1720.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in the Salmonellacontaining vacuole of macrophages .
"
428,429,1720.txt,4,0,,,,"Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC , leading to cytoplasmic acidification ."
429,430,2229.txt,1,0,,,,The MetR protein acts as an activator for the transcription of metF .
430,431,1046.txt,1,1,Salmonella,Salmonella,Salmonella,"As OmpR also controls the expression of the acid-induced virulence operon ssrAB , acid shock induction of ompR was examined to gain insight into how Salmonella links virulence with survival at extreme acid-pH .
"
431,432,1046.txt,2,0,,,,"In this paper , we examine the details of ompR induction by the potential roles of alternative OmpR phosphodonors in acid tolerance .
"
432,433,1046.txt,3,0,,,,"OmpR _ serving as an activator of ompR transcription during P1 , transcript
"
433,434,1046.txt,4,0,,,,"OmpR _ serving as an activator of ompR transcription during the P2
"
434,435,1046.txt,5,0,,,,"OmpR _ serving as an activator of ompR transcription during acid shock
"
435,436,1046.txt,6,0,,,,"A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR -LRB- as indicated -RRB- for 2 h at room temperature .
"
436,437,1046.txt,7,0,,,,"A. Western blot analysis of OmpR was used to examine the effect of hns on the acid shock induction of ompR .
"
437,438,1046.txt,8,1,Salmonella,Salmonella,Salmonella,"As OmpR also controls the expression of the acid-induced virulence operon ssrAB , acid shock induction of ompR was examined to gain insight into how Salmonella links virulence with survival at extreme acid-pH .
"
438,439,1046.txt,9,0,,,,"In this paper , we examine the details of ompR induction by the potential roles of alternative OmpR phosphodonors in acid tolerance .
"
439,440,1046.txt,10,0,,,,"OmpR _ serving as an activator of ompR transcription during P1 , transcript
"
440,441,1046.txt,11,0,,,,"OmpR _ serving as an activator of ompR transcription during the P2
"
441,442,1046.txt,12,0,,,,"OmpR _ serving as an activator of ompR transcription during acid shock
"
442,443,1046.txt,13,0,,,,"A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR -LRB- as indicated -RRB- for 2 h at room temperature .
"
443,444,1046.txt,14,0,,,,"A. Western blot analysis of OmpR was used to examine the effect of hns on the acid shock induction of ompR .
"
444,445,1046.txt,15,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"CadC interacts directly with OmpR Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter ( Bang et al. , 2002 ) , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter or RNA polymerase ."
445,446,1052.txt,1,0,,,,LacI whose expression is under the control of the araC PBAD system
446,447,1734.txt,1,3,Escherichia coli;Dioscorea trifida;Dioscorea trifida;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Name;name;S. typhimurium;typhimurium,Dioscorea trifida;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"pmrH ( the first gene of an operon that contains the genes pmrHFIJKLM ; Table 1 ) is the only known PmrAB-regulated gene for which the PmrA motif is conserved in all genome Table 1 ( Continued ) m ¬ 0.753257 CAAAATATC AATTTAAT Other yafC/STM0275 STM0256 ; Ortholog of E. coli putative transcriptional regulator LysR-type ( AAC73313 .1 ) ; Blast hit to putative transcriptional regulator , LysR family ; intergenic shared STM0275 ( drug efflux protein ) distributions Name : name of the gene in the S. typhimurium genome ( ) ."
447,448,1044.txt,1,0,,,,"These results agree well with those for the proU operon when H-NS binds within the proV operon .
"
448,449,1044.txt,2,0,,,,"the H-NS-regulated proU operon where H-NS binds to downstream-regul-atory element within the proV structural gene
"
449,450,1044.txt,3,0,,,,"the H-NS-regulated proU operon where H-NS binds to the DRE within the proV structural gene
"
450,451,1044.txt,4,0,,,,"four H-NS _ regulated proV
"
451,452,1044.txt,5,0,,,,"the hemX gene were used as negative control regions , respectively , as H-NS binds to the proV promoter .
"
452,453,1044.txt,6,0,,,,"the hemX gene were used as positive control regions , respectively , as H-NS binds to the proV promoter .
"
453,454,1044.txt,7,0,,,,"The proV promoter were used as negative control regions , respectively , as H-NS binds to the proV promoter .
"
454,455,1044.txt,8,0,,,,"The proV promoter were used as positive control regions , respectively , as H-NS binds to the proV promoter ."
455,456,1722.txt,1,0,,,,"To test if the HTH DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of binding to the flhDC promoter , we analyzed the function of a RflM mutant .
"
456,457,1722.txt,2,0,,,,"To test if the HTH DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC to the flhDC promoter , we analyzed the function of a RflM mutant .
"
457,458,1722.txt,3,2,Cornu aspersum;Cantareus apertus;Cornu aspersum;Cantareus apertus,helix;helix;helix;helix,Cornu aspersum;Cantareus apertus,"To test if the helix-turn-helix DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of binding to the flhDC promoter , we analyzed the function of a RflM mutant .
"
458,459,1722.txt,4,2,Cornu aspersum;Cantareus apertus;Cornu aspersum;Cantareus apertus,helix;helix;helix;helix,Cornu aspersum;Cantareus apertus,"To test if the helix-turn-helix DNA-binding domain of RflM is required for RcsB/RflM-dependent repression of flhDC to the flhDC promoter , we analyzed the function of a RflM mutant ."
459,460,1736.txt,1,0,,,,"When , finally , the RpoS-controlled stationary-phase of growth is reached , arcA is suppressed in an RpoS-dependent fashion ."
460,461,1050.txt,1,0,,,,"moreover , we demonstrate that CpxR-P negatively affects the stability of HilD and thus decreases the expression of HilD-target genes hilA , located in SPI-1 ."
461,462,1078.txt,1,0,,,,63 PhoPQ-regulated PhoPQ-regulated pagO sopD 0 ?
462,463,2217.txt,1,0,,,,"the mdtA expression is directly regulated by binding of BaeR at the promoter region
"
463,464,2217.txt,2,0,,,,"the mdtA expression is directly regulated by binding of BaeR at the promoter region
"
464,465,2217.txt,3,0,,,,"Moreover , we show that both members of this system conWrmed that His 250 from BaeS are required , even though BaeR binds speciWcally to the mdtA promoter with more aYnity ."
465,466,2203.txt,1,0,,,,"Hha , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated ."
466,467,1087.txt,1,1,Triportheus paranensis,tetRA,Triportheus paranensis,"To confirm that the observed changes in Pclass2 activity are a result of the modulation of FlhD4C2 autoregulation by FliT , we replaced the flhDC promoter with tetRA ) .
"
467,468,1087.txt,2,1,Triportheus paranensis,tetRA,Triportheus paranensis,"To confirm that the observed changes in Pclass2 activity are a result of the modulation of FlhD4C2 autoregulation by FliT , we replaced the flhDC promoter with the tetRA element from Tn10 ( PflhDC : ) .
"
468,469,1087.txt,3,0,,,,"Our data suggest that under certain environmental conditions a basal level of FlhD4C2 activity is maintained via a balance between external regulation of flhDC expression through , for example , FliT inhibition of FlhD4C2 .
"
469,470,1087.txt,4,0,,,,"The class 1 operon flhDC produces the multimeric master regulator of flagellar synthesis , FlhD4C2 ."
470,471,513.txt,1,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"From the data in Fig. 3 , it is apparent that inactivation of the ChbR repressor completely prevents residual chiP induction by chitobiose in ΔchiX background in E. coli as it does in Salmonella .
"
471,472,513.txt,2,0,,,,"Activation of chbBCA expression by ChbR is essential to relieve ChiX repression of chiP .
"
472,473,513.txt,3,0,,,,"In the presence of chitobiose -LRB- induced -RRB- , ChbR bound to the product of the action of the ChbG enzyme , probably monoacetylated Chb6P sequesters the ChiX sRNA so relieving the translational repression of chiP .
"
473,474,513.txt,4,0,,,,"In the presence of chitobiose -LRB- induced -RRB- , ChbR bound to its inducing signal sequesters the ChiX sRNA so relieving the translational repression of chiP ."
474,475,275.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) ."
475,476,1939.txt,1,0,,,,"Interestingly , both regulons are controlled by the argR repressor , while the biosynthesis genes of the other amino-acids are controlled by the transcription factors Lrp .
"
476,477,1939.txt,2,0,,,,"Interestingly , both regulons are controlled by the argR repressor , while the biosynthesis genes of the other amino-acids are controlled by the transcription factors Lrp ."
477,478,261.txt,1,0,,,,"Hence , binding of IHF to the ptsG promoters is unspecific , which is in line with previous data reporting that IHF binds DNA with lower affinity also in sequence-independent manner ."
478,479,507.txt,1,1,Escherichia coli,E. coli,Escherichia coli,Role of multiple CytR binding sites on induction at the E. coli udp promoter .
479,480,1093.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
480,481,249.txt,1,0,,,,"Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA-P mediated regulation of rcsB ."
481,482,1905.txt,1,0,,,,"kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .
"
482,483,1905.txt,2,0,,,,"kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .
"
483,484,1905.txt,3,0,,,,"kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .
"
484,485,1905.txt,4,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .
"
485,486,1905.txt,5,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .
"
486,487,1905.txt,6,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators ."
487,488,1911.txt,1,0,,,,These results imply that Lrp-mediated regulation of invF gene expression affects expression of the SPI-1 effectors .
488,489,1520.txt,1,0,,,,"These observations indicate that the proposed Lrp-mediated repression of the ilvGp2 promoter is not responsible for the defects , since leucine in general did not allow-growth recovery of the relA strains on M9/17 medium ."
489,490,2029.txt,1,0,,,,"that a RcsB-RflM protein complex coordinately represses flhDC transcription
"
490,491,2029.txt,2,0,,,,"a stable RcsB-RflM protein complex is able to efficiently repress flhDC transcription
"
491,492,2029.txt,3,0,,,,"We next analyzed the mode of action of the RcsB-RflM complex in repression of flhDC gene transcription .
"
492,493,2029.txt,4,0,,,,"DNA-binding domain of RflM is indispensable to mediate repression of flhDC by the RcsB-RflM complex .
"
493,494,2029.txt,5,0,,,,the P1flhDC promoter _ resulting in high affinity binding of a RcsB-RflM heterodimer and repression of flhDC operon transcription
494,495,1246.txt,1,0,,,,"Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .
"
495,496,1246.txt,2,0,,,,"In light of the role for SPI-2 in adaptation to the macrophage , it was interesting to observe that the macrophage-induced genes mig-3 and mig-14 , and a number of PhoP-PhoQ-activated genes also showed a dependency on Fis ( Table 3 ) .
"
496,497,1246.txt,3,0,,,,"RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) ."
497,498,1252.txt,1,1,Triportheus paranensis,tetRA,Triportheus paranensis,"To test the hypothesis that FliZ may operate through FliT , we compared tetRA background to control for flhDC autoregulation -LRB- Fig. 4B -RRB- .
"
498,499,1252.txt,2,0,,,,"One possibility is that FliZ regulates flhDC transcription .
"
499,500,1252.txt,3,1,Xenorhabdus nematophila,Xenorhabdus nematophila,Xenorhabdus nematophila,"In the related insect pathogen Xenorhabdus nematophila , FliZ was recently shown to bind to the flhDC promoter .
"
500,501,1252.txt,4,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Likewise , our data show that FliZ is not a transcriptional regulator of the flhDC operon in S. enterica serovar Typhimurium , whereas it is in X. nematophila ."
501,502,1534.txt,1,0,,,,"kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .
"
502,503,1534.txt,2,0,,,,"kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .
"
503,504,1534.txt,3,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .
"
504,505,1534.txt,4,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators ."
505,506,2015.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Contents lists available at ScienceDirect Microbiological Research journal homepage : www.elsevier.com/locate/micres FimY of Salmonella enterica serovar Typhimurium functions as a DNA-binding protein and binds the fimZ promoter Ke-Chuan Wang a , Yuan-Hsun Hsu a , b , Yi-Ning Huang c , Jiunn-Horng Lin c , d , Kuang-Sheng c , ∗ Yeh a Graduate Institute of Medical Sciences , College of Medicine , Taipei Medical University , 250 Wu-Hsing Street , Taipei 11031 , Taiwan b Department of Microbiology and Immunology , School of Medicine , College of Medicine , Taipei Medical University , 250 Wu-Hsing Street , Taipei 11031 , Taiwan c Department of Veterinary Medicine , School of Veterinary Medicine , College of Bioresources and Agriculture , National Taiwan University , 1 Roosevelt Road , Section 4 , Taipei 10617 , Taiwan d Division of Animal Medicine , Animal Technology Institute Taiwan , Chunan , Miaoli 35053 , Taiwan i n f o a r t i c l e a b s t r a c t Salmonella enterica serovar Typhimurium produces type 1 fimbriae with binding specificity to mannose residues ."
506,507,936.txt,1,1,Salmonella,Salmonella,Salmonella,"Expression of hmpA is repressed by Fur in Salmonella , making it responsive The SOS response Free radicals are potent inducers of bacterial SOS responses in-vitro ."
507,508,922.txt,1,0,,,,Our investigations indicate that DksA does not appear to contribute to hmp transcription
508,509,1508.txt,1,0,,,,"It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .
"
509,510,1508.txt,2,0,,,,It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .
510,511,2001.txt,1,0,,,,"HilA , is believed to directly activate expression from the invF promoters in SPI1 .
"
511,512,2001.txt,2,0,,,,"HilA activates the expression of the regulatory gene invF , the first gene of the large SPI1 inv ± spa ± sip gene cluster .
"
512,513,2001.txt,3,0,,,,"HilA may activate invF , by interacting * Author for correspondence .
"
513,514,2001.txt,4,0,,,,"HilA is a member of the ToxR/OmpR-like family of transcriptional regulatory proteins and is required for induction of the SPI-1 prg operon , and is also required for optimal expression of invF .
"
514,515,2001.txt,5,0,,,,"The straight , solid-headed arrows show that HilA protein directly activates the expression of invF .
"
515,516,2001.txt,6,0,,,,"In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .
"
516,517,2001.txt,7,0,,,,"In this scheme , activation of invF transcription by HilD and HilC leads to co-transcriptional activation of the downstream sip genes , as has been shown for HilA-activated transcription from the invF promoter ( Darwin and Miller , 1999a ; Eichelberg et al. , 1999 ; Lostroh and Lee , 2000 ) .
"
517,518,2001.txt,8,0,,,,"We considered that HilD and HilC might also bind upstream of invF and directly activate transcription from the HilA-activated invF promoter .
"
518,519,2001.txt,9,0,,,,"We considered that HilD and HilC might also bind upstream of invF and directly activate transcription from the HilA-activated invF promoter .
"
519,520,2001.txt,10,2,unidentified plasmid;Prairie vole hantavirus,plasmid;pVV,Prairie vole hantavirus;unidentified plasmid,"We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .
"
520,521,2001.txt,11,2,unidentified plasmid;Prairie vole hantavirus,plasmid;pVV,Prairie vole hantavirus;unidentified plasmid,"We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .
"
521,522,2001.txt,12,0,,,,"HilA activates invF .
"
522,523,2001.txt,13,0,,,,"By binding upstream of invF , HilA directly activates expression of the invF operons that encode the components of the TTS apparatus .
"
523,524,2001.txt,14,0,,,,"HilC do not activate invF expression from the HilA-dependent invF promoter Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .
"
524,525,2001.txt,15,0,,,,"HilC do not activate invF expression from the HilA-dependent invF promoter Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .
"
525,526,2001.txt,16,0,,,,"HilD do not activate invF expression from the HilA-dependent invF promoter Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .
"
526,527,2001.txt,17,0,,,,"HilD do not activate invF expression from the HilA-dependent invF promoter Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .
"
527,528,2001.txt,18,0,,,,"HilA activates transcription of invF from a start site .
"
528,529,2001.txt,19,0,,,,"HilA activates invF .
"
529,530,2001.txt,20,0,,,,"HilA activates invF operon expression by binding to the invF promoter .
"
530,531,2001.txt,21,0,,,,"HilA activates invF operon expression by binding to the invF promoter .
"
531,532,2001.txt,22,0,,,,"Apparently , HilA activates the expression of invF .
"
532,533,2001.txt,23,0,,,,"invF genes where the HilA transcriptional regulator induces invF -LRB- as well genes -RRB-
"
533,534,2001.txt,24,0,,,,"Moreover , HilA indirectly regulates the expression of secreted proteins by activating the transcription of the SPI-1 invF gene .
"
534,535,2001.txt,25,0,,,,"HilA in the invasion pathway independently activate the expression of invF .
"
535,536,2001.txt,26,0,,,,"These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C .
"
536,537,2001.txt,27,0,,,,"One of the operons directly activated by HilA contains invF gene .
"
537,538,2001.txt,28,0,,,,"By binding upstream of invF , HilA directly activates the expression of invF .
"
538,539,2001.txt,29,0,,,,"By binding upstream of invF , HilA directly activates the expression of invF .
"
539,540,2001.txt,30,0,,,,"invF is positively regulated by HilD through HilA
"
540,541,2001.txt,31,0,,,,"As HilA is a transcriptional activator of invF , the ΔhilA strain provides a measure of uninduced invF expression ."
541,542,711.txt,1,0,,,,PhoP/Q controls the expression of pagC .
542,543,1285.txt,1,0,,,,"HilD do not seem to regulate expression of hilD .
"
543,544,1285.txt,2,0,,,,"These results indicate that Lon is involved in the autoregulation of hilD transcription by modulating amounts of HilD .
"
544,545,1285.txt,3,0,,,,"This work demonstrates the regulation of hilD by HilD .
"
545,546,1285.txt,4,0,,,,"Of these regulators , HilD can be considered as the most important single regulator of PhilA since the hilD knockout strain shows nearly basal levels of HilA under inducing conditions .
"
546,547,1285.txt,5,0,,,,"Transcription of hilD is under the control of an autogenous , positive feedback loop by the HilD product ( Ellermeier et al. 2005 ; Slauc Figure 3 .
"
547,548,1285.txt,6,0,,,,"Transcription of hilD is under the control of an autogenous , positive feedback loop by the HilD product ( Ellermeier et al. 2005 ; Ellermeier Figure 3 .
"
548,549,1285.txt,7,0,,,,"Interestingly , hilD mRNA levels have been found to be dependent upon Dam activity , thus suggesting posttranscriptional control of HilD expression .
"
549,550,1285.txt,8,0,,,,"Interestingly , hilD mRNA levels have been found to be dependent upon DNA adenine methylation activity , thus suggesting posttranscriptional control of HilD expression .
"
550,551,1285.txt,9,0,,,,"HilD also directly controls the expression of the SPI-1 genes hilD .
"
551,552,1285.txt,10,0,,,,"The evidence that L-arabinose regulates SPI-1 expression through HilD suggested that hilD expression itself might be controlled by L-arabinose .
"
552,553,1285.txt,11,1,Iris germanica;Iris germanica,FLAG;FLAG,Iris germanica,"CpxR Represses hilD and thus Indirectly Affects HilD-regulated Genes Several global regulators control the expression of the SPI-1 genes by directly affecting the expression , activity or concentration of FLAG-tagged gene , was analyzed by Western blotting using monoclonal anti-FLAG or polyclonal anti-SseB antibodies .
"
553,554,1285.txt,12,0,,,,"The C-terminal domain of RNAPa has been shown to be important for transcription of HilD-regulated genes in-vivo , as the mutation of leucine 289 to phenylalanine within this domain fails to induced hilA expression , similarly to a hilD null mutant ( Boddicker et al. , 2003 ) .
"
554,555,1285.txt,13,0,,,,"The control of HilD by Pat was through post-transcriptional mechanisms , moderately repressing hilD translation while significantly reducing HilD stability .
"
555,556,1285.txt,14,0,,,,"Thus , although HilD is capable of auto-regulation , the results could not be due to the loss of this regulatory protein controlling its own expres ¬ Pat post-transcriptionally regulates HilD The regulation of hilD is complex ; hilD is also regulated by the transcriptional regulators HilC and RtsA , which constitute a feed-forward circuit to control the downstream SPI1 regulator Hil .
"
556,557,1285.txt,15,0,,,,"Thus , although HilD is capable of auto-regulation , the results could not be due to the loss of this regulatory protein controlling its own expres ¬ Pat post-transcriptionally regulates HilD The regulation of hilD is complex ; hilD regulates itsel .
"
557,558,1285.txt,16,0,,,,"Because the extent of the regulatory effect was only 1.5 fold , we tested whether the IscR‐mediated regulation of hilD had any effect on the expression of downstream HilD‐regulated genes .
"
558,559,1285.txt,17,0,,,,"Indeed , we showed that apo‐IscR , which prevails in an iscU mutant , down‐regulates the expression of the master regulator hilD and thereby of several downstream HilD‐regulated genes .
"
559,560,1285.txt,18,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
560,561,1285.txt,19,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
561,562,1285.txt,20,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
562,563,1285.txt,21,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
563,564,1285.txt,22,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
564,565,1285.txt,23,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
565,566,1285.txt,24,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
566,567,1285.txt,25,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
567,568,1285.txt,26,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
568,569,1285.txt,27,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
569,570,1285.txt,28,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
570,571,1285.txt,29,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
571,572,1285.txt,30,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
572,573,1285.txt,31,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
573,574,1285.txt,32,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
574,575,1285.txt,33,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
575,576,1285.txt,34,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
576,577,1285.txt,35,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
577,578,1285.txt,36,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
578,579,1285.txt,37,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
579,580,1285.txt,38,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
580,581,1285.txt,39,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
581,582,1285.txt,40,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
582,583,1285.txt,41,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
583,584,1285.txt,42,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
584,585,1285.txt,43,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
585,586,1285.txt,44,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
586,587,1285.txt,45,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
587,588,1285.txt,46,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
588,589,1285.txt,47,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
589,590,1285.txt,48,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
590,591,1285.txt,49,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the grant D0480901 , UR Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
591,592,1285.txt,50,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
592,593,1285.txt,51,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
593,594,1285.txt,52,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
594,595,1285.txt,53,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
595,596,1285.txt,54,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
596,597,1285.txt,55,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
597,598,1285.txt,56,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
598,599,1285.txt,57,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
599,600,1285.txt,58,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
600,601,1285.txt,59,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
601,602,1285.txt,60,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
602,603,1285.txt,61,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
603,604,1285.txt,62,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
604,605,1285.txt,63,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
605,606,1285.txt,64,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
606,607,1285.txt,65,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
607,608,1285.txt,66,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
608,609,1285.txt,67,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
609,610,1285.txt,68,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
610,611,1285.txt,69,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
611,612,1285.txt,70,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
612,613,1285.txt,71,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
613,614,1285.txt,72,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
614,615,1285.txt,73,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
615,616,1285.txt,74,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
616,617,1285.txt,75,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
617,618,1285.txt,76,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
618,619,1285.txt,77,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
619,620,1285.txt,78,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
620,621,1285.txt,79,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
621,622,1285.txt,80,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
622,623,1285.txt,81,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"activity of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
623,624,1285.txt,82,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
624,625,1285.txt,83,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
625,626,1285.txt,84,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
626,627,1285.txt,85,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
627,628,1285.txt,86,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
628,629,1285.txt,87,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
629,630,1285.txt,88,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
630,631,1285.txt,89,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
631,632,1285.txt,90,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
632,633,1285.txt,91,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
633,634,1285.txt,92,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
634,635,1285.txt,93,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
635,636,1285.txt,94,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
636,637,1285.txt,95,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
637,638,1285.txt,96,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
638,639,1285.txt,97,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by grants BIO2010-15417 and AGL2013-45339-R , CB , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
639,640,1285.txt,98,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
640,641,1285.txt,99,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
641,642,1285.txt,100,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
642,643,1285.txt,101,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
643,644,1285.txt,102,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
644,645,1285.txt,103,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
645,646,1285.txt,104,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
646,647,1285.txt,105,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , grant 2014SGR1260 , CB , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
647,648,1285.txt,106,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
648,649,1285.txt,107,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
649,650,1285.txt,108,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
650,651,1285.txt,109,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , grant 2012/ACUP/00048 , CB , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
651,652,1285.txt,110,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
652,653,1285.txt,111,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Engineering Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
653,654,1285.txt,112,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , d Ce Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
654,655,1285.txt,113,3,Salmonella;Salmonella enterica;Salmonella;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of HilD are tightly Funding : This work was supported by Competitiveness , the Catalonian government , the RecerCaixa program , the Swedish Research Council Natural Sciences Abstract Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar 1 Departament de Genètica , Microbiologia i Estadıstica , Universitat de Barcelona , Barcelona , Spain , 2 Department of Microbiology , , Tum Biology , Karolinska Institutet , Stockholm , Sweden The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated proce .
"
655,656,1285.txt,114,0,,,,"https://doi.org/10.1371/journal.ppat.1006312.g004 The 3 
"
656,657,1285.txt,115,0,,,,"https://doi.org/10.1371/journal.ppat.1006312.g004 The 3 
"
657,658,1285.txt,116,0,,,,"https://doi.org/10.1371/journal.ppat.1006312.g004 The 3 
"
658,659,1285.txt,117,0,,,,"HilD is the dominant regulator of the system , as a hilD mutant had almost no hilA expression , whereas deletion of either rtsA decreased hilA expression less significantly .
"
659,660,1285.txt,118,0,,,,"HilD is the dominant regulator of the system , as a hilD mutant had almost no hilA expression , whereas deletion of either hilC decreased hilA expression less significantly .
"
660,661,1285.txt,119,0,,,,"Although the actual mechanism is known in only a few cases , we have shown that regulation is primarily through either translation of the hilD message or control of HilD protein activity ."
661,662,1291.txt,1,0,,,,"Activation of tolC gene transcription is achieved through the direct binding of a positive regulator of the AraC/XylS family , to the operator regions of these genes ."
662,663,705.txt,1,0,,,,"The genes slrP and dsbA are also induced by HilD independently of InvF .
"
663,664,705.txt,2,0,,,,"The genes slrP and dsbA are also induced by HilD independently of both HilA .
"
664,665,705.txt,3,0,,,,"In this context , slrP is induced by overexpression of HilD independently of the central SPI1 regulator HilA , with RtsA ."
665,666,739.txt,1,0,,,,SseJ Activation by RhoA in HeLa Cells Is Critical for Enzymatic Activity -- Six sseJ mutant genes were generated based upon information regarding the SseJ-RhoA binding surface .
666,667,1454.txt,1,0,,,,"PhoP binds to the promoter region of pagC .
"
667,668,1454.txt,2,1,Salmonella,Salmonella,Salmonella,"The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .
"
668,669,1454.txt,3,0,,,,"mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .
"
669,670,1454.txt,4,0,,,,"The pagC genes appear to be regulated by both PhoP , by a mechanism .
"
670,671,1454.txt,5,0,,,,"pagC were used as controls for PhoP-and SsrB-dependent expression , respectively .
"
671,672,1454.txt,6,0,,,,"Two StpA-repressed PhoP-dependent genes _ bound by pagC
"
672,673,1454.txt,7,0,,,,"pagC genes are regulated by a similar mechanism , involving the response regulator of the PhoP/PhoQ two-component system .
"
673,674,1454.txt,8,0,,,,"pagC genes are regulated by a similar mechanism , involving the response regulator of the PhoP/PhoQ two-component system .
"
674,675,1454.txt,9,0,,,,"pagC genes are regulated by a similar mechanism , involving PhoP .
"
675,676,1454.txt,10,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .
"
676,677,1454.txt,11,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .
"
677,678,1454.txt,12,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , pagC were selected to evaluate the role of Pat in the regulation of PhoP activity ."
678,679,1332.txt,1,0,,,,"Instead , as MntR has been shown to work as a repressor , MntR may exert its effect by repressing the expression of a repressor of cdtB expression .
"
679,680,1332.txt,2,0,,,,"Instead , as MntR has been shown to work as a repressor , MntR may exert its effect by repressing the expression of a repressor of cdtB expression ."
680,681,1326.txt,1,0,,,,SirA _ activated by crp genes
681,682,2149.txt,1,0,,,,"To investigate if SPI4 belongs to prg , we analyzed the expression of siiA : : luc under PhoPQ-inducing conditions , i.e. , during-growth in PCN P , minimal-medium with limiting amounts of inorganic-phosphate and acidic pH. These culture conditions result in activation of PhoPQ-activated genes and repression of prg ."
682,683,1440.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Interestingly , mgrB is a PhoP-regulated gene that has been found to mediate feedback in this system , since deletion of this gene results in a potent increase in PhoP-regulated transcription in E. coli .
"
683,684,1440.txt,2,3,Escherichia coli;Salmonella;Salmonella;Yersinia pestis,E. coli;S. enterica;enterica;Yersinia pestis,Yersinia pestis;Escherichia coli;Salmonella,"In addition , overexpression of mgrB decreases PhoP-regulated transcription in E. coli , S. enterica , and Yersinia pestis ( 47 ) ."
684,685,2161.txt,1,0,,,,The failure of mntH : : lacZ-fusions to be induced by paraquat is consistent with the absence of a SoxS promoter element .
685,686,1468.txt,1,0,,,,"CRP control of porin expression A facilitates target recognition mutational analyses show that the ompX recognition site in CyaR is strongly conserved Identification of sRNA targets
"
686,687,1468.txt,2,0,,,,CRP control of porin expression A facilitates target recognition Our phylogenetic show that the ompX recognition site in CyaR is strongly conserved Identification of sRNA targets
687,688,842.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid .
"
688,689,842.txt,2,1,unidentified plasmid,plasmid,unidentified plasmid,"To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in an isogenic fliZ mutant constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid .
"
689,690,842.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"To better understand the putative role of FliZ as a positive regulator of flagellar gene expression , we measured gene expression from a subset of flagellar promoters in the wild type constitutively expressing fliZ from the PLtetO-1 promoter on a plasmid .
"
690,691,842.txt,4,0,,,,FliA-dependent activation of FlgM ensures an effectiv `` off 
691,692,16.txt,1,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
692,693,856.txt,1,0,,,,"On the other hand , the FimY-FimZ complex might also bind the fimZ promoters to regulate these genes ."
693,694,2175.txt,1,0,,,,"Furthermore , STM1330 are regulated by SlyA ."
694,695,103.txt,1,0,,,,"S1 ) and that the ssrB promoter mutation had no effect on the expression of the PmrA-activated pmrC gene ( Fig. 5C ) .
"
695,696,103.txt,2,0,,,,a posttranslational activator of PmrA represses ssrB transcription
696,697,1497.txt,1,0,,,,"The FlhD2C2 showed residual activity in initiating fliA transcription , so a small fraction of the complex is probably activated by a DnaK chaperone-independent pathway ."
697,698,665.txt,1,0,,,,It is known that prgH is under the regulation of PhoP .
698,699,671.txt,1,0,,,,"InvF production indirectly increases transcription of the sipA genes
"
699,700,671.txt,2,0,,,,"InvF production directly increases transcription of the sipA genes
"
700,701,671.txt,3,0,,,,"InvF production indirectly increases transcription of the sipA genes
"
701,702,671.txt,4,0,,,,"InvF production directly increases transcription of the sipA genes
"
702,703,671.txt,5,0,,,,"InvF positively regulates effector proteins within sipA and located outside -LRB- sopE -RRB- with the help of chaperone SicA .
"
703,704,671.txt,6,0,,,,"InvF positively regulates effector proteins within sipA and located outside -LRB- sopD -RRB- with the help of chaperone SicA .
"
704,705,671.txt,7,0,,,,InvF positively regulates effector proteins within sipA and located outside -LRB- sopB -RRB- with the help of chaperone SicA .
705,706,1483.txt,1,0,,,,HilD do not seem to regulate expression of prgH .
706,707,117.txt,1,0,,,,"As shown in Fig. 5 , OxyR was able to bind to a DNA fragment corresponding to the coding region of the katG gene .
"
707,708,117.txt,2,0,,,,"As shown in Fig. 5 , OxyR was able to bind to both promoter regions corresponding to the coding region of the katG gene ."
708,709,881.txt,1,1,Salmonella,Salmonella,Salmonella,ZupT determines changes in intracellular zinc concentration of Lack Previous studies have shown that zinT are coregulated by Zur and that ZinT accumulation is strongly induced by EDTA and repressed by zinc .23 The addition of 0.5 μM ZnSO4 to the culture medium causes the complete abrogation of ZinT accumulation in a wild type Salmonella strai
709,710,659.txt,1,0,,,,"However , despite the fact that the deletion of stpA did not affect s38 protein levels at LEP , our data showed that rpoS mRNA levels were significantly lower in the absence of StpA -LRB- in strain JH3003 -RRB- at LEP compared with Table S1 , Fig. 7C .
"
710,711,659.txt,2,0,,,,"However , despite the fact that the deletion of stpA did not affect s38 protein levels at LEP , our data showed that rpoS mRNA levels were significantly lower in the absence of StpA -LRB- in strain JH3003 -RRB- at LEP compared with wild type .
"
711,712,659.txt,3,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
712,713,659.txt,4,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
713,714,659.txt,5,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
714,715,659.txt,6,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
715,716,659.txt,7,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
716,717,659.txt,8,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
717,718,659.txt,9,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
718,719,659.txt,10,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
719,720,659.txt,11,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
720,721,659.txt,12,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
721,722,659.txt,13,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
722,723,659.txt,14,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
723,724,659.txt,15,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
724,725,659.txt,16,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
725,726,659.txt,17,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
726,727,659.txt,18,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
727,728,659.txt,19,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,StpA in S. Typhimurium was recently proposed to repress the rpoS regulon during exponential-growth
728,729,895.txt,1,0,,,,"Like STM1344 , STM1697 suppresses the transcription of class 3 flagella regulon genes by binding to a component of the master regulator of the flagella regulon FlhD4C2 .
"
729,730,895.txt,2,0,,,,"Like STM1344 , STM1697 suppresses the transcription of class 3 flagella regulon genes by binding to a component of the master regulator of the flagella regulon FlhD4C2 .
"
730,731,895.txt,3,0,,,,"Like STM1344 , STM1697 suppresses the transcription of class 2 flagella regulon genes by binding to a component of the master regulator of the flagella regulon FlhD4C2 .
"
731,732,895.txt,4,0,,,,"Like STM1344 , STM1697 suppresses the transcription of class 2 flagella regulon genes by binding to a component of the master regulator of the flagella regulon FlhD4C2 .
"
732,733,895.txt,5,0,,,,"In this work , we characterize a molecular mechanism for how STM1697 affects invasion through interaction with the master regulator of the flagella regulon FlhD4C2 .
"
733,734,895.txt,6,0,,,,"Schematic diagram _ illustrating the interplay between STM1697 in the regulation of FlhD4C2 functionality
"
734,735,895.txt,7,0,,,,"STM1697 suppress the functionality of the master regulator of the flagella regulatory cascade , FlhD4C2 .
"
735,736,895.txt,8,0,,,,"The right figure presents the model of the STM16972FlhD4C2 hetero-hexamer The binding of STM1697 to FlhD4C2 restrains RNA poly - merase recruitment Previous studies showed that class II flagellar genes are only transcribed by 70-containing RNA polymerase in the presence of the FlhD4C2 complex .
"
736,737,895.txt,9,0,,,,The binding of STM1697 to FlhD4C2 restrains RNAP recruitment .
737,738,1130.txt,1,0,,,,"However , at 30 ∞ C , SdiA activates srgE regardless of the presence of AHLs .
"
738,739,1130.txt,2,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"In response to AHLs , SdiA activates two Salmonella-specific loci , srgE
"
739,740,1130.txt,3,1,Salmonella,Salmonella,Salmonella,"In response to AHL under laboratory conditions , Salmonella SdiA activates the expression of the chromosomally encoded srgE gene .
"
740,741,1130.txt,4,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,Typhimu;Salmonella;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SdiA upregulates two loci in S. Typhimu-rium , resistance to complement killing operon , located on the Salmonella virulence plasmid , and srgE -LRB- sdiA-regulated gene -RRB- , a horizontally acquired gene located on the chromosome .
"
741,742,1130.txt,5,0,,,,"as was the case for sdiA , suggesting that there was sufficient SdiA to activate srgE"
742,743,1656.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The AcrR protein is known in E. coli to repress transcription of the acrAB operon .
"
743,744,1656.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"In S. enterica , AcrR represses expression of acrAB .
"
744,745,1656.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , AcrR represses expression of acrAB .
"
745,746,1656.txt,4,0,,,,"AcrR repress the expression of acrAB .
"
746,747,1656.txt,5,0,,,,"AcrR are repressors of acrAB .
"
747,748,1656.txt,6,0,,,,AcrR represses the expression of acrAB locally .
748,749,1642.txt,1,0,,,,a clpP mutation results in increased concentrations of RpoS
749,750,1124.txt,1,0,,,,Most of these genes were induced at a higher level in the RpoS-mutant background with mgtC .
750,751,498.txt,1,0,,,,Analysis of flhDC expression in Y. enterocolitica revealed a role of OmpR/EnvZ in the positive control of the flagellar operon .
751,752,1118.txt,1,0,,,,"The regulation of YgaE to ompC seems more obvious than ompF due to the more abundant expression of ompC than ompF .
"
752,753,1118.txt,2,0,,,,"whether the regulation of YgaE to ompC is direct
"
753,754,1118.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,This result suggested that YgaE does not influence the growth of S. Typhi by the regulation of ompC .
754,755,467.txt,1,0,,,,"STM2123 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools ."
755,756,1695.txt,1,0,,,,"Hha , is one of repressors of hilA transcription .
"
756,757,1695.txt,2,0,,,,"Positive regulators include HilD , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
757,758,1695.txt,3,0,,,,"Positive regulators include CsrB , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
758,759,1695.txt,4,0,,,,"Positive regulators include FadD , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
759,760,1695.txt,5,0,,,,"Positive regulators include EnvZ/OmpR , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
760,761,1695.txt,6,0,,,,"Positive regulators include FliZ , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
761,762,1695.txt,7,0,,,,"Positive regulators include BarA/SirA , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
762,763,1695.txt,8,0,,,,"Positive regulators include Fis , HU , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
763,764,1695.txt,9,0,,,,"Positive regulators include some nucleoid binding proteins , while the nucleoid binding proteins Hha and H-NS are negatively regulating hilA transcription .
"
764,765,1695.txt,10,0,,,,"Fahlen et al. have shown that the histonelike protein Hha acts as a repressor of hilA .
"
765,766,1695.txt,11,0,,,,"In exponential phase cells , the results provided evidence that Hha repress hilA expression .
"
766,767,1695.txt,12,0,,,,"Our work shows that Hha repress hilA under account for SPI1 gene silencing .
"
767,768,1695.txt,13,0,,,,"Our work shows that Hha repress hilA under a set of physiological conditions .
"
768,769,1695.txt,14,0,,,,Our work shows that Hha repress hilA under a set of well-defined environmental .
769,770,301.txt,1,0,,,,"In contrast , entB expression in the yggX gshA strain was decreased by deferoxamine , indicating the presence of more iron-bound Fur ."
770,771,1859.txt,1,0,,,,The promoters of gatR are negatively regulated by GatR .
771,772,315.txt,1,0,,,,We note that two previous studies provided strong evidence that flhD is not regulated by HilA .
772,773,1681.txt,1,0,,,,"In addition , genetic and biochemical data showed that the RpoA subunit of RNA polymerase ( RNAP ) participates in the HilD/HilC-induced activation of the hilA promoter ( 5 , 35 ) ."
773,774,473.txt,1,0,,,,"For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated .
"
774,775,473.txt,2,1,Salmonella,Salmonella,Salmonella,"Interestingly , when Salmonella was grown in low Mg2 + to induce PhoP-activated transcription , multiple short transcripts were detected with a radiolabeled DNA probe corresponding to the mgtCBR leader region ( 22 ) ."
775,776,1871.txt,1,0,,,,"The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A .
"
776,777,1871.txt,2,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
777,778,1871.txt,3,0,,,,"yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .
"
778,779,1871.txt,4,0,,,,"While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) ."
779,780,1865.txt,1,0,,,,"If the effect of Cra were direct , Cra would bind to more nonconsensus sites within the iscR region .
"
780,781,1865.txt,2,0,,,,"If the effect of Cra were direct , Cra would bind to one nonconsensus sites within the iscR region .
"
781,782,1865.txt,3,0,,,,"To determine whether Cra could bind to the iscR promoter region , EMSAs were performed with purified Cra protein .
"
782,783,1865.txt,4,0,,,,"Indeed , Cra bound to the iscR promoter region , albeit with relatively low affinity .
"
783,784,1865.txt,5,0,,,,"The weak binding of Cra to the iscR promoter was not surprising given the lack of a consensus sequence .
"
784,785,1865.txt,6,0,,,,Cra binds to the iscR promoter region in-vitro .
785,786,329.txt,1,0,,,,"Thus , one explanation for the transcription we observe following overexpression of slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins ."
786,787,328.txt,1,0,,,,"Moreover , dps are repressed by the Fe-responsive regulator Fur and induced under conditions of Fe limitation , whereas ftnA are maximally expressed when Fe is abundant .
"
787,788,328.txt,2,0,,,,"Moreover , dps are repressed by the Fe-responsive regulator Fur and induced under conditions of Fe limitation , whereas bfr are maximally expressed when Fe is abundant .
"
788,789,328.txt,3,0,,,,"These data suggest that dps are negatively regulated by Fur in Fe-rich-medium .
"
789,790,328.txt,4,0,,,,"Whether Fur represses dps by indirect mechanisms remains to be determined .
"
790,791,328.txt,5,0,,,,"Whether Fur represses dps by direct mechanisms remains to be determined .
"
791,792,328.txt,6,0,,,,"hence are expressed under iron-replete conditions consistent with iron storage/detoxification roles , while dps are negatively regulated by Fur"
792,793,1864.txt,1,1,Salmonella,Salmonella,Salmonella,"Inactivation of rpoN does not affect sensitivity to protamine In Salmonella , PmrA-and PhoP-regulated covalent modifications reduce the overall net negative charge of the lipopo-lysaccharide ."
793,794,1870.txt,1,0,,,,"A ∆ sopB muta , was also able to activate RhoG ."
794,795,1680.txt,1,0,,,,"To further this finding , prgH , a PhoPQ-repressed gene carried on pathogenicity island I and involved in the formation of the type III secretion system ( TTSS ) apparatus ( 2 ) , was tested for its role in the enhanced biofilm formation on gallstones observed in the phoP-null mutant ."
795,796,314.txt,1,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; sdiA , a regulator of quorum-sensing and virulence ( Ahmer et al. 1998 ; Volf et al. 2002 ) ; permeases of oligopeptides , such as oppF and oppB ( Goodell and Higgins 1987 ; Orchard and Goodrich-Blair 2004 ) ; and several genes involved in drug resistance , such as emrE and nudF ."
796,797,1858.txt,1,0,,,,"Under these growth-conditions , taiA and clyA expression was similar to that of pagC , a PhoPQ-activated gene ."
797,798,472.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"LeuO is known to activate bglJ in E. coli while RcsB-BglJ heterodimers activate leuO transcription .
"
798,799,472.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Schnetz , K. RcsB-BglJ activates the Escherichia coli leuO gene .
"
799,800,472.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , , K. RcsB-BglJ activates the Escherichia coli leuO gene .
"
800,801,472.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Schnetz , K. RcsB-BglJ activates the Escherichia coli leuO gene .
"
801,802,472.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"Stratmann , T. , Pul , U. , Wurm , R. , Wagner , R. , , K. RcsB-BglJ activates the Escherichia coli leuO gene .
"
802,803,472.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,RcsB-BglJ activates the Escherichia coli leuO gene .
803,804,466.txt,1,0,,,,"FlhC regulation by FliZ support our fliC transcription timecourse .
"
804,805,466.txt,2,0,,,,T s of fliC expression is inverted in the absence of FliZ su en e c h T le layers of heterogeneity shape the fliC expression census ltip u M We hypothesized that modulating production of FliZ would reveal the extent to which fliC expression can be controlled by these two regulators .
805,806,300.txt,1,0,,,,"Our results show that CpxR , induces the transcription of the clpX encoding the ClpXP protease ."
806,807,1694.txt,1,0,,,,SsrBC directly activates transcription of sifB .
807,808,1119.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi;Typhi-murium,Salmonella enterica subsp. enterica serovar Typhimurium,"Interestingly , slyA of S. Typhi-murium has been shown to be induced via the PhoP/PhoQ two-component system following internalization of the bacteria by macrophages .
"
808,809,1119.txt,2,0,,,,"the PhoP/PhoQ 2-com-ponent system activates slyA transcription by sensing Mg2
"
809,810,1119.txt,3,0,,,,Transcription of the slyA locus is activated by the PhoP/PhoQ 2-component system .
810,811,499.txt,1,0,,,,"H-NS controls transcriptional repression of pagC , by acting on the up-52 fragment
"
811,812,499.txt,2,0,,,,Multiple studies have shown that expression of pagC is strongly repressed by H-NS
812,813,1643.txt,1,0,,,,"The double hns hha-mutant showed the highest b-galactosidase activities at low-temperature , indicating that Hha enhances H-NS-mediated hilA silen-cing .
"
813,814,1643.txt,2,0,,,,"The double hns hha-mutant showed the highest b-galactosidase activities at both low-osmolarity , indicating that Hha enhances H-NS-mediated hilA silen-cing .
"
814,815,1643.txt,3,0,,,,The Hha protein enhances the silencing effect of H-NS on hilA .
815,816,1125.txt,1,0,,,,"marA transcription is repressed by MarR .
"
816,817,1125.txt,2,0,,,,"marA transcription is de-repressed by compounds , probably through their binding to MarR .
"
817,818,1125.txt,3,0,,,,"marA transcription is de-repressed by plumbagin , probably through their binding to MarR .
"
818,819,1125.txt,4,0,,,,"marA transcription is de-repressed by dinitrophenol , probably through their binding to MarR .
"
819,820,1125.txt,5,0,,,,"marA transcription is de-repressed by benzoate , probably through their binding to MarR .
"
820,821,1125.txt,6,0,,,,"marA transcription is de-repressed by salicylate , probably through their binding to MarR ."
821,822,1131.txt,1,0,,,,The PhoP/PhoQ and PhoR/PhoB two-component regulatory systems have been shown to repress the expression of hilA by controlling expression of hilE .
822,823,1657.txt,1,0,,,,"FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgA by introduction of a null mutation in J. Bacteriol .
"
823,824,1657.txt,2,0,,,,"FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgA by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .
"
824,825,1657.txt,3,0,,,,"Like all genes , mutations in any of the flgA result in FlgM-dependent inhibition of s28 activity ."
825,826,894.txt,1,0,,,,"I. PhoP activates ranscription of pmrAB .
"
826,827,894.txt,2,0,,,,"I. PhoP activates ranscription of pmrAB .
"
827,828,894.txt,3,0,,,,"I. PhoP activates ranscription of pmrAB .
"
828,829,894.txt,4,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .
"
829,830,894.txt,5,0,,,,"I. PhoP activates ranscription of pmrAB .
"
830,831,894.txt,6,0,,,,"I. PhoP activates ranscription of pmrAB .
"
831,832,894.txt,7,0,,,,I. PhoP activates ranscription of pmrAB .
832,833,658.txt,1,0,,,,"InvF also activate transcription of sopE , found elsewhere on the chromosome .
"
833,834,658.txt,2,0,,,,"InvF induces the expression of sopE -LSB- 14e16 -RSB- .
"
834,835,658.txt,3,0,,,,InvF activates expression of sopE .
835,836,880.txt,1,2,Phaeoacremonium santali;Salmonella;Salmonella,a 28;S. enterica;enterica,Phaeoacremonium santali;Salmonella,"Two proteins also have a 28 % identity to a 130 aa central portion of STM4509 , a modulator of HilA expression , the master regulator of pathogenicity island 1 type III secretion system in S. enterica ."
836,837,670.txt,1,0,,,,We first examined the effect of the C-terminal His tag on PhoQ activity in-vivo by measuring the expression of mgtA ( a PhoP-activated gene that encodes an Mg2 + transporter ) through the β-galactosidase activity of an mgtA : : lacZ-transcriptional-fusion [ 15 ] .
837,838,116.txt,1,0,,,,hilA transcription in turn activates the transcription of the InvF transcriptional regulator
838,839,1482.txt,1,0,,,,ygaE _ coregulated by RpoS
839,840,1496.txt,1,1,unidentified,unknown,unidentified,"The last gene in the rck operon , is a regulator of the AraC-family of transcription factors whose target genes are unknown ."
840,841,102.txt,1,0,,,,"Effect of lrp mutations on the expression of traJ transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of the regulatory genes traJ and finP .
"
841,842,102.txt,2,0,,,,"Effect of lrp mutations on the expression of finP transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of the regulatory genes traJ and finP .
"
842,843,102.txt,3,0,,,,"Effect of lrp mutations on the expression of tra transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of the regulatory genes traJ and finP .
"
843,844,102.txt,4,0,,,,"Effect of lrp mutations on the expression of traJ transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of the first gene of the tra operon , .
"
844,845,102.txt,5,0,,,,"Effect of lrp mutations on the expression of traJ transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of traY , .
"
845,846,102.txt,6,0,,,,"Effect of lrp mutations on the expression of finP transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of the first gene of the tra operon , .
"
846,847,102.txt,7,0,,,,"Effect of lrp mutations on the expression of finP transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of traY , .
"
847,848,102.txt,8,0,,,,"Effect of lrp mutations on the expression of tra transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of the first gene of the tra operon , .
"
848,849,102.txt,9,0,,,,"Effect of lrp mutations on the expression of tra transcriptional units To identify the promoter regulated by Lrp in the transfer regulon of pSLT , we investigated the effect of lrp mutations on the expression of traY , .
"
849,850,102.txt,10,0,,,,"that Lrp could bind to the lrp regulatory region in the absence of amino-acids
"
850,851,102.txt,11,1,Escherichia coli,E. coli,Escherichia coli,"It has been shown previously that leucine does not alter the binding of Lrp to the regulatory region of the E. coli lrp gene .
"
851,852,102.txt,12,0,,,,"The modifications to the patterns of hypersensitivity seen in the lrp regulatory region in the presence and absence of leucine are consistent with an adjustment to the Lrp -- DNA contacts due to the influence of the amino-acid on Lrp protein structure .
"
852,853,102.txt,13,0,,,,"The modifications to the patterns of protection seen in the lrp regulatory region in the presence and absence of leucine are consistent with an adjustment to the Lrp -- DNA contacts due to the influence of the amino-acid on Lrp protein structure .
"
853,854,102.txt,14,0,,,,"The effect of adding leucine is not to remodel it so that the negative influence of the Lrp protein on lrp promoter function is attenuated .
"
854,855,102.txt,15,0,,,,"The effect of adding leucine is not to abolish DNA interaction so that the negative influence of the Lrp protein on lrp promoter function is attenuated .
"
855,856,102.txt,16,0,,,,"The effect of adding leucine is not to abolish Lrp so that the negative influence of the Lrp protein on lrp promoter function is attenuated .
"
856,857,102.txt,17,0,,,,"( A ) The mRNA levels of Lrp-regulated genes in chromosome lrp mutants .
"
857,858,102.txt,18,0,,,,"The chromosome K36Q , K36R , of Lrp-regulated genes in chromosome lrp mutants ."
858,859,664.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
859,860,857.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli .
"
860,861,857.txt,2,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
861,862,857.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli .
862,863,17.txt,1,0,,,,"For example , transcription of the fliAZ operon in X. nemato-phila is FlhD4C2 dependent , whereas the equivalent fliAZY operon is under independent control of both Pclass2 ."
863,864,2174.txt,1,0,,,,"Among the 38 genes , osmB were previously reported to be regulated by RpoS ."
864,865,1469.txt,1,0,,,,"STM3611 , as a class III flagellar gene , is indirectly regulated by STM1697 via FliA ."
865,866,2160.txt,1,0,,,,"The TviA protein interacts in conjunction with the RcsB regulator protein at the promoter upstream of tviA to control the transcription of tviB -LRB- encoding an enzyme similar to GDP-mannose dehydrogenase involved a 2 , no agglutination ; 1/2 , weak agglutination ; 111 , strong agglutination ; 1111 , very strong agglutination ."
866,867,843.txt,1,0,,,,"There is a much closer correspondence between the effects of IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU , as are the genes .
"
867,868,843.txt,2,0,,,,"There is a much closer correspondence between the effects of HU among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either HU , as are the genes ."
868,869,1327.txt,1,0,,,,"Previous work from our laboratory demonstrated that PhoP also regulates mig-14 .
"
869,870,1327.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,SL1344;14028s,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .
"
870,871,1327.txt,3,1,Salmonella,Salmonella,Salmonella,"The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .
"
871,872,1327.txt,4,0,,,,"mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .
"
872,873,1327.txt,5,0,,,,"The mig-14 genes appear to be regulated by both PhoP , by a mechanism .
"
873,874,1327.txt,6,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
874,875,1441.txt,1,0,,,,"In vitro binding of IHF to the hilA regulatory region To further test the hypothesis that IHF interferes with H-NS-mediated silencing of hilA , we performed competitive EMSAs between IHF on the hilA promoter region .
"
875,876,1441.txt,2,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihB mutant alleles on hilA expression in cells growing in LB-medium suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
876,877,1441.txt,3,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihB mutant alleles on hilA expression in cells entering the stationary-phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
877,878,1441.txt,4,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihB mutant alleles on hilA expression in cells entering the gel-shift data suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
878,879,1441.txt,5,0,,,,"EMSA experiments suggest that binding of IHF to the hilA regulatory region might abolish the silencing of such a promoter region .
"
879,880,1441.txt,6,0,,,,EMSA experiments suggest that binding of IHF to the hilA regulatory region might abolish H-NS binding .
880,881,2148.txt,1,0,,,,"SoxS _ regulated , including acnA"
881,882,1455.txt,1,0,,,,"These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the prgs prgHIJK .
"
882,883,1455.txt,2,0,,,,These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the PhoP-repressed genes prgHIJK .
883,884,1333.txt,1,0,,,,"invF encodes an AraC-like transcriptional regulator of additional SPI-1 invasion genes
"
884,885,1333.txt,2,0,,,,"Within SPI-1 , HilA controls invF , which encodes a transcriptional regulator of the AraC family ."
885,886,738.txt,1,0,,,,"Activated OxyR induces sufA ahpCF .
"
886,887,738.txt,2,0,,,,Activated OxyR induces sufA lipids .
887,888,704.txt,1,0,,,,"In addition to these conditions , hilA is repressed by PhoP/PhoQ .
"
888,889,704.txt,2,0,,,,"PhoP/PhoQ is activated by low cation concentrations , implying that hilA is repressed by these conditions .
"
889,890,704.txt,3,0,,,,"Since the PhoP/PhoQ system represses hilA expression , it can be speculated that either virK are regulated by PhoP/PhoQ in an opposite way or VirK negatively influences hilA expression .
"
890,891,704.txt,4,0,,,,"Since the PhoP/PhoQ system represses hilA expression , it can be speculated that either both hilA are regulated by PhoP/PhoQ in an opposite way or VirK negatively influences hilA expression ."
891,892,1290.txt,1,0,,,,the yjbEFGH operon are regulated by the RcsA-RcsB heterodimer .
892,893,1284.txt,1,0,,,,other SoxR/S _ regulated genes like fumC
893,894,710.txt,1,1,unidentified,unidentified,unidentified,"Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) .
"
894,895,710.txt,2,1,unidentified,unidentified,unidentified,"Mutations in a previously unidentified PhoP-activated gene lead to increased hilA expression .
"
895,896,710.txt,3,0,,,,"The response regulator PhoP represses hilA and the prg ( PhoP-repressed genes ) genes ( Pegues et al. , 1995 ; Bajaj et al. , 1996 ) , whereas transcription of PhoP-activated genes ( pag ) required for survival within macrophages is activated ( Miller et al. , 1989 ; Belden and Miller , 1994 ) ."
896,897,923.txt,1,0,,,,"On the other hand , STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a post-transcriptional level .
"
897,898,923.txt,2,0,,,,"On the other hand , STM3388 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional level .
"
898,899,923.txt,3,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"For curli production in S. enterica , STM3388 activate CsgD , while four Citation Cowles KN , Willis DK , Engel TN , Jones JB , Barak JD .
"
899,900,923.txt,4,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"For cellulose production in S. enterica , STM3388 activate CsgD , while four Citation Cowles KN , Willis DK , Engel TN , Jones JB , Barak JD ."
900,901,2000.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"The S. Typhimurium ferritins are differentially regulated Previous studies in E. coli have shown that Fur positively regulates ftnA expression under Fe-replete conditions .
"
901,902,2000.txt,2,0,,,,"Thus , ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .
"
902,903,2000.txt,3,0,,,,"Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .
"
903,904,2000.txt,4,0,,,,"Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA .
"
904,905,2000.txt,5,0,,,,"In the case of the iron-storage protein ferritin , FtnA , gene expression is induced by Fur with an extended Fur binding site -LRB- containing five tandem Fur boxes -RRB- located upstream of the ftnA promoter ."
905,906,1509.txt,1,0,,,,pagJ are known to be regulated by SlyA
906,907,2014.txt,1,0,,,,"plasmids _ expressing HhaR17A under control of the native hha promoter
"
907,908,2014.txt,2,0,,,,"plasmids _ expressing HhaR17A under control of the native hha promoter
"
908,909,2014.txt,3,0,,,,plasmids _ expressing HhaR17A under control of the native hha promoter
909,910,937.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"It has also been reported that the Escherichia coli Fur is a positive regulator of sodB gene expression , although the precise mechanism ... .
"
910,911,937.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Fur positive regulation of iron superoxide dismutase in Escherichia coli : functional analysis of the sodB promoter .
"
911,912,937.txt,3,1,Salmonella,Salmonella,Salmonella,"Fur activation of SPI1 is not mediated through the Fur-regulated small RNAs RfrA and RfrB , which are the Salmonella ortholog and paralog of RyhB that control expression of sodB .
"
912,913,937.txt,4,0,,,,"Known `` Fur-activated 
"
913,914,937.txt,5,0,,,,"both of which contribute to Fur regulation of sodB
"
914,915,937.txt,6,0,,,,"both of which contribute to Fur regulation of sodB
"
915,916,937.txt,7,0,,,,"Fur regulation of sodB are mechanistically different .
"
916,917,937.txt,8,0,,,,"Consequently , if Fur acts as a simple repressor of the factor , as it does with ryhB controlling sodB , then the Fur binding site must be far from consensus , leading to weak binding of Fur under normal laboratory conditions ; overproduction of Fur leads to further repression .
"
917,918,937.txt,9,1,Escherichia coli,Escherichia coli,Escherichia coli,"Fur positive regulation of iron superoxide dismutase in Escherichia coli : functional analysis of the sodB promoter .
"
918,919,937.txt,10,0,,,,"each _ being able to contribute to the positive regulation of the iron-superoxide dismutase gene sodB by Fur
"
919,920,937.txt,11,0,,,,"This can be illustrated by the reciprocal regulation of sodB , encoding sodA , encoding the manganese-superoxide dismutase by Fe - Fur .
"
920,921,937.txt,12,0,,,,"This can be illustrated by the reciprocal regulation of sodB , encoding the iron-superoxide dismutase , encoding the manganese-superoxide dismutase by Fe - Fur .
"
921,922,937.txt,13,1,Escherichia coli,Escherichia coli,Escherichia coli,"S. Dubrac , D. Touati , Fur positive regulation of iron superoxide dismutase in Escherichia coli : functional analysis of the sodB promoter , J. Bacteriol .
"
922,923,937.txt,14,1,Escherichia coli,Escherichia coli,Escherichia coli,"Fur positive regulation of iron superoxide dismutase in Escherichia coli : functional analysis of the sodB promoter .
"
923,924,937.txt,15,1,Escherichia coli,Escherichia coli,Escherichia coli,Fur positive regulation of iron superoxide dismutase in Escherichia coli : functional analysis of the sodB promoter .
924,925,1253.txt,1,0,,,,"However , it seems unlikely that acid induction of ompR results from changes in phosphorylation levels , as ompR remains acid inducible in a mutant containing a constitutively active yet nonphosphorylated OmpRD55E .
"
925,926,1253.txt,2,0,,,,"However , it seems unlikely that acid induction of ompR results from changes in phosphorylation levels , as ompR remains acid inducible in a mutant containing a constitutively active yet nonphosphorylated OmpRD55E ."
926,927,1535.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
927,928,2028.txt,1,0,,,,"Of hha sigma-28 , pagD , hha encodes a noted global repressor of virulence genes .
"
928,929,2028.txt,2,0,,,,"Of hha sigma-28 , hype , hha encodes a noted global repressor of virulence genes .
"
929,930,2028.txt,3,0,,,,"Of hha sigma-28 , bigA , hha encodes a noted global repressor of virulence genes .
"
930,931,2028.txt,4,0,,,,"Of hha sigma-28 , ychP , hha encodes a noted global repressor of virulence genes ."
931,932,1521.txt,1,0,,,,"If the protein of interest dimerizes , the LexADBD binds to its cognate sulA promoter , repressing the expression of a transcriptionally linked lacZ gene ."
932,933,1247.txt,1,0,,,,"The PmrA training set consisted of the promoter regions of three known PmrAB-regulated genes ( ugd [ 7,15,17 ] , pmrH [ 7,14,17,19 ] and pmrC [ 2,14 ] ) for which the binding of the PmrA protein to the promoter regions was verified by DNA footprint analysis [ 14,15 ] .
"
933,934,1247.txt,2,0,,,,"However , Lee et al. [ 21 ] demonstrated that the loss of pmrC and the pmrHFIJKLM operon ( also called the pbg operon ) resulted in PM resistance equal to that of a pmrA mutant strain , suggesting a limited role for PmrAB-regulated core modification in PM resistance .
"
934,935,1247.txt,3,0,,,,"PmrAB-regulated genes include pmrHFIJKL , whose product results in the addition of aminoarabinose to the 1 and 4 = phosphates of lipid-A ( D ) ; pmrC , whose product results in the addition of phosphoethanolamine to the 1 and 4 = phosphates of lipid-A ( E ) ; cptA , whose product results in the addition of phosphoethanolamine to the LPS core ( F ) ; pmrG , whose product results in the addition of phosphate to heptose present in the LPS core ( G ) ; and cld , whose product results in an O-antigen chain length determinant ( H ) ."
935,936,1910.txt,1,0,,,,"Studies of bacteria have , to date , revealed that hilA expression is regulated by a complex array of HU ."
936,937,1904.txt,1,0,,,,"Transcription of the fis gene in CSH50 Fis protein expression is controlled by a post-transcriptional mechanism .
"
937,938,1904.txt,2,0,,,,"Transcription of the fis gene in CSH50 Fis protein expression is controlled at the level of fis transcription .
"
938,939,1904.txt,3,0,,,,"The influence of low oxygen tension on expression of the Fis protein was shown to be a manifestation of its impact on the activity of the fis gene promoter .
"
939,940,1904.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella,S. Typhi;Typhi;S. enterica;enterica,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,the fis expression in S. Typhi _ suggesting that Fis is also regulated by its level in S. enterica
940,941,248.txt,1,0,,,,"In the context of mgtA , the RNA-mediated control of transcription elongation by cytoplasmic Mg2 + complements the tight control of transcription initiation by extracytoplasmic Mg2 + facilitated by the PhoP/Q two-component system .
"
941,942,248.txt,2,0,,,,"In the context of mgtA , the RNA-mediated control of transcription elongation by cytoplasmic Mg2 + complements the tight control of transcription initiation by extracytoplasmic Mg2 + facilitated by the PhoP/Q two-component system ."
942,943,260.txt,1,0,,,,"In contrast , inactivation of just the hupB gene correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures .
"
943,944,260.txt,2,0,,,,"Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level .
"
944,945,260.txt,3,0,,,,"Here , inactivation of hupA resulted in the downregulation of many RpoS-dependent genes while the hupB mutation caused the same genes to be expressed at a higher level ."
945,946,1092.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
946,947,506.txt,1,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB may come into play ."
947,948,512.txt,1,0,,,,These data indicate that CRP represses expression of parC .
948,949,1086.txt,1,0,,,,"In addition , we provide evidence that ArcA directly downregulates ompD expression under H2O2-mediated stress .
"
949,950,1086.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,The experimental evidence indicates that ArcA is a transcriptional repressor of the S. Typhimurium ompD gene .
950,951,1938.txt,1,0,,,,"Activation of feoB transcription by the RstA protein is necessary for repression of iron-responsive genes .
"
951,952,1938.txt,2,0,,,,"To investigate further whether the Fe transporter FeoB is necessary for repression of iron-responsive genes by the RstA protein , we constructed a strain with a deletion of the feoB gene .
"
952,953,1938.txt,3,0,,,,"The feoB deletion prevented the RstA-promoted repression of transcription levels of Fig. 3B .
"
953,954,1938.txt,4,0,,,,"Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels ."
954,955,274.txt,1,0,,,,"Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB-medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .
"
955,956,274.txt,2,0,,,,"We next compared the mRNA levels of fhuF between the feoA promoter mutant strains found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain .
"
956,957,274.txt,3,0,,,,We next compared the mRNA levels of fhuF between the wild-type promoter mutant strains found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain .
957,958,2202.txt,1,0,,,,"For example , hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .
"
958,959,2202.txt,2,0,,,,"However , HilD is auto-regulated , which could explain the observed downregulation of hilD in the DfliZ mutant during planktonic growth ."
959,960,1079.txt,1,0,,,,"Among them , fimA are shown to be activated by Lrp ."
960,961,2216.txt,1,0,,,,"The SpvR protein functions as a transcriptional activator for the spvA promoter
"
961,962,2216.txt,2,0,,,,"Therefore , we determined whether the SpvR protein from serovar Arizona was able to activate transcription from the spvA promoter of serovar Dublin .
"
962,963,2216.txt,3,0,,,,We also demonstrated that the serovar Arizona SpvR protein is a functional activator of the spvA promoter .
963,964,1737.txt,1,0,,,,"In the case of PmrA/B regulation , the response regulator PhoP activates pmrD .
"
964,965,1737.txt,2,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
965,966,1737.txt,3,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"However , the E. coli pmrD gene was induced in low Mg2 in a phoP-dependent manner , like other members of the E. coli PhoP regulon .
"
966,967,1737.txt,4,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"However , the E. coli pmrD gene was induced in low Mg2 in Fig. 5A , like other members of the E. coli PhoP regulon .
"
967,968,1737.txt,5,0,,,,"The mRNA lev - encoded products are produced in the correct els of the PhoP-activated mgtA , phoP , pmrD , locales , at the required amounts and for the ap - and mig-14 genes increased after the shift to low propriate extents of time .
"
968,969,1737.txt,6,0,,,,"As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .
"
969,970,1737.txt,7,0,,,,"otes time-dependent resistance to polymyxin B MgtA prom The PhoP-activated pmrD and ugtL genes encode products mediating the chemical modification of negatively charged residues in the lipopolysaccharide ( LPS ) , thereby conferring resistance to the cationic peptide antibiotic polymyxin B ( Kox et al. , 2000 ; Shi et al. , 2004 ) .
"
970,971,1737.txt,8,0,,,,"A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .
"
971,972,1737.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , the PhoPQ TCS indirectly activates the PmrAB TCS via PhoP-activated pmrD expression ( Kox et al. , 2000 ) ."
972,973,1051.txt,1,0,,,,"The isogenic phoP tolC strain showed intermediate permeability , as expected from the fact that some of the PhoPQ-regulated modification reactions , especially the palmitoylation of lipid-A , occur in the wild-type strain to a considerable extent ( 21 ) ."
973,974,1045.txt,1,0,,,,"The two-component regulatory OmpR/EnvZ function through HilD , thus inducing invF ."
974,975,1723.txt,1,1,unidentified,not shown,unidentified,"Using the aTc-inducible expression system , we observed that FliZ is unable to increase the activity of Pclass2 promoters in the flhDC mutant -LRB- results not shown -RRB- .
"
975,976,1723.txt,2,0,,,,"FliZ is responsible for increased levels of FlhC protein independent of flhDC transcription .
"
976,977,1723.txt,3,0,,,,"HilD therefore represents a potential growth-phase specific mechanism by which FliZ could upregulate flhDC transcription coordinately with SPI-1 genes .
"
977,978,1723.txt,4,0,,,,"FliZ is needed for eficient induction of the Spi-1 system via post-translational activation of the Spi-1 regulatory protein HilD , which in turn activates flhDC gene transcription .
"
978,979,1723.txt,5,0,,,,"The flagellar regulator FliZ is a post-transcriptional activator of flhDC that positively regulates SPI1 by activating the hilD-rtsAB cascade .
"
979,980,1723.txt,6,1,unidentified,unknown,unidentified,FliZ increases flhDC synthesis through an unknown mechanism .
980,981,2212.txt,1,0,,,,"These results show that HilD positively controls the expression of the phoH genes , independently of InvF .
"
981,982,2212.txt,2,0,,,,"These results show that HilD positively controls the expression of the phoH genes , independently of HilA .
"
982,983,2212.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"HilD induces the expression of phoH , in the absence of other Salmonella-specific regulators .
"
983,984,2212.txt,4,0,,,,"Thus , HilD positively regulates the expression of the phoH genes , and positively .
"
984,985,2212.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD positively regulates phoH in S. Typhimurium .
"
985,986,2212.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"HilD induces the expression of phoH , in E. coli MC4100 ."
986,987,1069.txt,1,0,,,,"In low-Mg2 + environment -LRB- extracytoplasmic Mg2 + -RRB- , the PhoPQ two-component systems directly activates mgtA transcription ."
987,988,2206.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Here we report that YgaE is a repressor of ompC in S. Typhi ; it can be partially explained why the expression of ompC is not up-regulated under hyperosmotic-stress .
"
988,989,2206.txt,2,0,,,,"The repression of YgaE to ompC means less pathways for antibiotics .
"
989,990,2206.txt,3,0,,,,"The repression of YgaE to ompC means less pathways for nutrition .
"
990,991,2206.txt,4,0,,,,"One explanation for these phenomena is the repression of YgaE to ompC occurs only in the very early stage of hyperosmotic-stress as an emergency approach to protect the bacteria .
"
991,992,2206.txt,5,0,,,,"As time goes by , other mechanisms are involved in the process of handling the hyperosmotic-stress , the repression of YgaE to ompC relieves .
"
992,993,2206.txt,6,0,,,,the expressions of ompC were obviously repressed by YgaE at the early stage
993,994,1727.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Sequence analysis and regulation of the htrA gene of Escherichia coli : a s-32 independent mechanism of heat-inducible transcription .
994,995,1041.txt,1,0,,,,"In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145-and 9.5-fold compared with H-NSWT levels ."
995,996,1055.txt,1,0,,,,this effect was reflected by induction of cspB and proteins ( CspE ) in response to preadaptation to cold-stress
996,997,1733.txt,1,1,unidentified plasmid,Plasmid,unidentified plasmid,"Plasmid-encoded HilD overcomes the Fis effect on hilA The hilD locus encodes an AraC-like activator of hilA expression .
"
997,998,1733.txt,2,0,,,,"AraC-like transcriptional activators activate hilA transcription by binding upstream of the hilA promoter DNA
"
998,999,1733.txt,3,0,,,,"AraC-like transcriptional activators activate hilA transcription by binding upstream of the hilA promoter DNA
"
999,1000,1733.txt,4,0,,,,"AraC-like transcriptional activators activate hilA transcription by binding upstream of the hilA promoter DNA
"
1000,1001,1733.txt,5,0,,,,"AraC-like transcriptional activators activate hilA transcription by binding upstream of the hilA promoter DNA
"
1001,1002,1733.txt,6,0,,,,"AraC-like transcriptional activators activate hilA transcription by binding upstream of the hilA promoter DNA
"
1002,1003,1733.txt,7,0,,,,"AraC-like transcriptional activators activate hilA transcription by binding upstream of the hilA promoter DNA
"
1003,1004,1733.txt,8,0,,,,"three AraC family members can independently activate hilA
"
1004,1005,1733.txt,9,0,,,,"three AraC family members can independently activate hilA
"
1005,1006,1733.txt,10,0,,,,"three AraC family members can independently activate hilA
"
1006,1007,1733.txt,11,0,,,,"The AraC-like transcriptional regulator HilD , positively regulates the expression of the SPI-1 genes in a cascade fashion , mainly by directly inducing the expression of hilA ."
1007,1008,1900.txt,1,1,Salmonella,Salmonella,Salmonella,"It was reported that hlyE could be activated by SlyA , an important regulator of virulence genes in Salmonella ."
1008,1009,258.txt,1,1,Salmonella,Salmonella,Salmonella,DISCUSSION A MntR-independent Mechanism _ Contributing to Mn2-re-sponsive mntH Transcription in Salmonella
1009,1010,1914.txt,1,0,,,,a galF transcript is regulated by RtsB
1010,1011,270.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Interplay between global regulators of Escherichia coli : effect of H-NS on the transcription of the gene osmC .
"
1011,1012,270.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Gutierrez , C. Interplay between global regulators of Escherichia coli : effect of H-NS on transcription of the gene osmC ."
1012,1013,1082.txt,1,0,,,,"To our knowledge , the influence of CpxR on the mRNA levels of soxS genes has not been demonstrated ."
1013,1014,516.txt,1,0,,,,"Because PhoP/PhoQ regulates more than 40 genes , additional PhoP/PhoQ-activated genes , including pmrD and pagD , were examined to determine if bile specifically regulated pagC , or if it has a general effect on PhoP/PhoQ-regulated genes .
"
1014,1015,516.txt,2,0,,,,"The results establish that other PhoP/PhoQ-regulated genes were unaffected by the presence of bile ( as exemplified by pagD and pmrD , Fig. 2 ) , suggesting that pagC is specifically affected by bile ."
1015,1016,502.txt,1,0,,,,The simplest hypothesis is that SirA represses the master regulator of the flagellar regulon flhDC gene fusions .
1016,1017,1096.txt,1,0,,,,"In Fig. 3A , addition of 100 nM SsrBC results in a 5-fold induction of a 140-nt sifA transcript compared with the absence of SsrBC .
"
1017,1018,1096.txt,2,0,,,,SsrBC directly activates transcription of sifA .
1018,1019,264.txt,1,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
1019,1020,1928.txt,1,0,,,,A reduction in flgM mRNA translation would relieve inhibition of s28 .
1020,1021,933.txt,1,1,Salmonella,Salmonellae,Salmonella,"siiF , were induced much more than two-fold in the RpoS-mutant than in the wild type Salmonellae ."
1021,1022,2010.txt,1,0,,,,"Our data suggest that under certain environmental conditions a basal level of FlhD4C2 activity is maintained via a balance between external regulation of flhDC expression through , for example , FliT inhibition of FlhD4C2 ."
1022,1023,1519.txt,1,0,,,,"Another ` Fur-activated 
"
1023,1024,1519.txt,2,0,,,,"the small regulatory RNA ryhB is responsible for the Fur-mediated regulation of several genes relevant to this study
"
1024,1025,1519.txt,3,0,,,,"The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure .
"
1025,1026,1519.txt,4,0,,,,"Thus , ryhB transcription is dependent on regulation by the Fur protein in response to iron availability ."
1026,1027,2004.txt,1,1,Salmonella,Salmonellae,Salmonella,"pduF , were induced much more than two-fold in the RpoS-mutant than in the wild type Salmonellae ."
1027,1028,927.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Microarray analysis of chemostat-cultured E. coli cells demonstrated that the RpoS-controlled mdtABC operon is upregulated in response to zinc excess ( Lee et al. , 2005 ) ."
1028,1029,1243.txt,1,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in STM1808 ."
1029,1030,1525.txt,1,0,,,,"SoxRS-regulated expression and genetic analysis of the yggX gene of Esch-erichia coli .
"
1030,1031,1525.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"SoxRS-regulated expression and genetic analysis of the yggX gene of Escherichia coli .
"
1031,1032,1525.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,SoxRS-regulated expression and genetic analysis of the yggX gene of Escherichia coli .
1032,1033,2038.txt,1,0,,,,"Positive regulation by CsgD is indicated by solid lines because putative CsgD binding sites have been found upstream from the csgB promoters .
"
1033,1034,2038.txt,2,0,,,,"Indeed , it has been suggested , although it has never been shown , that CsgD binds to conserved 11-bp sequences upstream of the csgB promoters , activating transcription of these genes .
"
1034,1035,2038.txt,3,0,,,,"In vitro , unphosphorylated CsgD binds directly to the promoter region of csgB .
"
1035,1036,2038.txt,4,0,,,,"To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgB , coding for curli fimbria production , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .
"
1036,1037,2038.txt,5,0,,,,"To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in absence of CsgD in both cya genetic backgrounds .
"
1037,1038,2038.txt,6,0,,,,"To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in absence of CsgD in both wt genetic backgrounds .
"
1038,1039,2038.txt,7,0,,,,"To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in presence of CsgD in both cya genetic backgrounds .
"
1039,1040,2038.txt,8,0,,,,"To further corroborate the CsgD involvement in the cAMP-mediated control of the expression of biofilm , the csgB expression was monitored in presence of CsgD in both wt genetic backgrounds ."
1040,1041,1531.txt,1,0,,,,"HilC positively regulate sprB , most likely cotrans-criptionally with hilC itself , since sprB are cotranscribed -LRB- see Fig .
"
1041,1042,1531.txt,2,0,,,,"HilC positively regulate sprB , most likely cotrans-criptionally with hilC itself , since hilC are cotranscribed -LRB- see Fig ."
1042,1043,1257.txt,1,0,,,,"In the presence of Mn , MntR represses the expression of mntH , through direct binding of specific sites within the promoter regions of these genes .
"
1043,1044,1257.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Hantke , K. Dual repression by Fe - Mn - MntR of the mntH gene , encoding an NRAMP-like Mn transporter in Escherichia coli .
"
1044,1045,1257.txt,3,0,,,,"Mn2 can bind to MntR to facilitate its binding to the mntH promoter via 5-TTT-GCCTTAAGGAAAC-3 , resulting in repression of mntH transcription .
"
1045,1046,1257.txt,4,0,,,,"Mn2 can bind to MntR to facilitate its binding to the mntH promoter via a palindromic sequence , resulting in repression of mntH transcription .
"
1046,1047,1257.txt,5,0,,,,"a different palindromic sequence _ termed MntR-box , 5-AAACATAGCAAAGGCTATGTTT-3 , thus implementing repression of mntH transcription
"
1047,1048,1257.txt,6,0,,,,"a different palindromic sequence _ termed MntR-box , 5-AAACATAGCAAAGGCTATGTTT-3 , thus implementing repression of mntH transcription
"
1048,1049,1257.txt,7,0,,,,"18 -RRB- was substituted with i.e. stemR -LSB- mut -RSB- , this MntR-independent regulation was eliminated because mntH transcription could no longer be repressed by Mn2 .
"
1049,1050,1257.txt,8,0,,,,"18 -RRB- was substituted with an alternative sequence , this MntR-independent regulation was eliminated because mntH transcription could no longer be repressed by Mn2 ."
1050,1051,728.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
1051,1052,714.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
1052,1053,714.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
1053,1054,1280.txt,1,0,,,,"Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by opening ATG for translation , depending on the above-mentioned critical concentration .
"
1054,1055,1280.txt,2,0,,,,"Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by opening the RBS , depending on the above-mentioned critical concentration .
"
1055,1056,1280.txt,3,0,,,,"Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by blocking ATG for translation , depending on the above-mentioned critical concentration .
"
1056,1057,1280.txt,4,0,,,,"Looking at the 50UTR region of avrA , it is very likely that the CsrA action takes place at the upstream untranslated region of the mRNA itself , maybe by binding to the GGA motif on 25 NT of 50UTR region proximal to the first ATG of the avrA open reading frame , or by blocking the RBS , depending on the above-mentioned critical concentration .
"
1057,1058,1280.txt,5,0,,,,"it is suggested here that the CsrA protein can directly regulate the avrA mRNA
"
1058,1059,1280.txt,6,0,,,,"It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA destabilising the avrA mRNA provides a extremely sensitive means to alter virulence gene expression in response to environmental conditions .
"
1059,1060,1280.txt,7,0,,,,"It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA destabilising the avrA mRNA provides a rapid means to alter virulence gene expression in response to environmental conditions .
"
1060,1061,1280.txt,8,0,,,,"It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA stabilising the avrA mRNA provides a extremely sensitive means to alter virulence gene expression in response to environmental conditions .
"
1061,1062,1280.txt,9,0,,,,It can be suggested therefore that any post-transcrip-tional regulation by the cooperative action of CsrA stabilising the avrA mRNA provides a rapid means to alter virulence gene expression in response to environmental conditions .
1062,1063,1294.txt,1,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .
"
1063,1064,1294.txt,2,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .
"
1064,1065,1294.txt,3,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .
"
1065,1066,1294.txt,4,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .
"
1066,1067,1294.txt,5,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad .
"
1067,1068,1294.txt,6,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .
"
1068,1069,1294.txt,7,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .
"
1069,1070,1294.txt,8,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .
"
1070,1071,1294.txt,9,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .
"
1071,1072,1294.txt,10,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad ."
1072,1073,700.txt,1,0,,,,"The presence of CoCl2 increases expression of the Furregulated gene entB .
"
1073,1074,700.txt,2,0,,,,"Growth in the presence of cobalt resulted in derepression of the Fur-regulated gene entB , a phenotype that could be reversed by the addition of iron , cysteine , or glutathione to the growth medium or by anoxic growth .
"
1074,1075,700.txt,3,0,,,,"Mutant strains are sensitive to hydrogen-peroxide and superoxide , deregulate the expression of the Fur-regulated gene entB , and fail to grow on succinate medium .
"
1075,1076,700.txt,4,0,,,,"The status of labile iron can be monitored via expression of the Fur-regulated gene entB .
"
1076,1077,700.txt,5,0,,,,"Regardless of the explanation , these results appear at odds with previous studies , which established that cells exposed to Co contain less iron and reported up-regulation of Fur-controlled entB and fhuF also directly destabilize particularly labile Fe -- S clusters such as those present on Fe -- S scaffolds ."
1077,1078,847.txt,1,0,,,,SlyA is also involved in the regulation of virK
1078,1079,2164.txt,1,0,,,,"Activation of the acrAB operon is achieved through the direct binding of a positive regulator of the AraC/XylS family , to the operator regions of these genes ."
1079,1080,1479.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"C.F. OmpR are positive regulation of tppB of Salmonella typhimurium .
"
1080,1081,1479.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Gibson MM , Ellis EM , Graeme-Cook KA et al OmpR are pleiotropic regulatory proteins : positive regulation of tppB of Salmonella typhimurium .
"
1081,1082,1479.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,OmpR are positive regulation of tppB of Salmonella typhimurium .
1082,1083,2170.txt,1,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .
"
1083,1084,2170.txt,2,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( examples include mgtBC ) .
"
1084,1085,2170.txt,3,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag include mgtBC ) ."
1085,1086,13.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ."
1086,1087,853.txt,1,1,Escherichia coli,E : coli,Escherichia coli,"InvF are sufficient to activate transcription of sicA ± lacZYA in E : coli CC118lpir .
"
1087,1088,853.txt,2,0,,,,"InvF activates a promoter upstream of sicA , causing additional expression of sicAsipBCDA .
"
1088,1089,853.txt,3,0,,,,"Our RNA-seq data show strong upregulation of sicA by InvF ( see of RcsB .
"
1089,1090,853.txt,4,0,,,,"As the sicA promoter has the longest relaxation time for SPI-1 , induction of sic/sip by InvF represents a key commitment step to the associated burden of producing effector proteins .
"
1090,1091,853.txt,5,0,,,,"As the sicA promoter has the longest relaxation time for SPI-1 , induction of sic/sip by InvF represents a key commitment step to virulence ."
1091,1092,1337.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RamA confers MDR in Salmonella Typhimurium via increased expression of acrB .
"
1092,1093,1337.txt,2,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .
"
1093,1094,1337.txt,3,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .
"
1094,1095,1337.txt,4,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .
"
1095,1096,1337.txt,5,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .
"
1096,1097,1337.txt,6,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB .
"
1097,1098,1337.txt,7,1,Salmonella;Salmonella;Salmonella,Sal-monella;monella;enterica,Salmonella,RamA confers multidrug resistance in Sal-monella enterica via increased expression of acrB .
1098,1099,1451.txt,1,0,,,,"Analysis of hns expression has indicated that the two gene products are capable of both cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .
"
1099,1100,1451.txt,2,0,,,,"Analysis of hns expression has indicated that the two gene products are capable of both negative autogenous control ; that is , StpA levels are significantly increased in an hns mutant background .
"
1100,1101,1451.txt,3,0,,,,"Analysis of stpA expression has indicated that the two gene products are capable of both cross-regulation ; that is , StpA levels are significantly increased in an hns mutant background .
"
1101,1102,1451.txt,4,0,,,,"Analysis of stpA expression has indicated that the two gene products are capable of both negative autogenous control ; that is , StpA levels are significantly increased in an hns mutant background .
"
1102,1103,1451.txt,5,0,,,,"However , as the expression of lacZ pRO310 fusion was still partially repressed in mutant , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .
"
1103,1104,1451.txt,6,1,Salmonella,Salmonella,Salmonella,"However , as the expression of lacZ pRO310 fusion was still partially repressed in a Salmonella hns , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .
"
1104,1105,1451.txt,7,0,,,,"However , as the expression of the ompS1 was still partially repressed in mutant , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background .
"
1105,1106,1451.txt,8,1,Salmonella,Salmonella,Salmonella,"However , as the expression of the ompS1 was still partially repressed in a Salmonella hns , the possibility of StpA also acting as a repressor was explored as StpA is increased in a mutant hns background ."
1106,1107,2158.txt,1,0,,,,"Taken together , these results indicate that PmrA functions as a negative regulator of ssaG .
"
1107,1108,2158.txt,2,0,,,,"In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator or by furthering expression of an ssaG repressor .
"
1108,1109,2158.txt,3,0,,,,"Second , chromatin immunoprecipitation experiments revealed that an HA-tagged PmrA bound to the ssaG promoter ."
1109,1110,1445.txt,1,1,unidentified,unknown,unidentified,"The last gene in srgC , is a regulator of the AraC-family of transcription factors whose target genes are unknown .
"
1110,1111,1445.txt,2,0,,,,"The last two ORFs of srgC , encode a transcriptional regulator of the AraC family respectively ."
1111,1112,1323.txt,1,0,,,,narH are positively regulated by SlyA
1112,1113,884.txt,1,0,,,,conditions under which either ssrB was repressed by OmpR
1113,1114,890.txt,1,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihfA mutant alleles on hilA expression in cells growing in LB-medium suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
1114,1115,890.txt,2,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihfA mutant alleles on hilA expression in cells entering the stationary-phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
1115,1116,890.txt,3,0,,,,IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihfA mutant alleles on hilA expression in cells entering the gel-shift data suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
1116,1117,648.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
1117,1118,660.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1118,1119,660.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1119,1120,660.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Hengge-Aronis , R. The LysR-like regulator LeuO n Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1120,1121,660.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1121,1122,660.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"Hengge-Aronis , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1122,1123,660.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"Klauck , E. , Bohringer , J. , , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1123,1124,660.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"Hengge-Aronis , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1124,1125,660.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,"Klauck , E. , Bohringer , J. , , R. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1125,1126,660.txt,9,1,Escherichia coli,Escherichia coli,Escherichia coli,"The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
"
1126,1127,660.txt,10,1,Escherichia coli,Escherichia coli,Escherichia coli,The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA .
1127,1128,106.txt,1,0,,,,Besides the putative ` rck operon 
1128,1129,1492.txt,1,0,,,,four H-NS _ regulated ssrA
1129,1130,1486.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,Putative regulation by the global regulators RcsB was evaluated by generating three isogenic S. Typhi deletion mutants of argR .
1130,1131,112.txt,1,0,,,,FimYZ regulates the fimA .
1131,1132,674.txt,1,1,Escherichia coli,E. coli,Escherichia coli,Examination of the sequence revealed that SoxS binds with high affinity in a manner characteristic of class I promoters in the zwf promoters of E. coli .
1132,1133,1109.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY .
"
1133,1134,1109.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;typhimu,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"FimZ binds the Salmonella typhimu-rium fimA promoter region and may regulate its own expression with FimY .
"
1134,1135,1109.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhimu,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"FimZ binds the Salmonella Typhimu-rium fimA promoter region and may regulate its own expression with FimY .
"
1135,1136,1109.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"[ 40 ] K. Yeh , J.K. Tinker , S. Clegg , FimZ binds the Salmonella typhimurium fimA promoter region and may regulate its own expression with FimY , Microbiol ."
1136,1137,489.txt,1,0,,,,"SsrBc was found to bind in a concentration-dependent manner to the ssrA promoter -LRB- Fig .
"
1137,1138,489.txt,2,0,,,,"In the absence of O2 , however , NO did not affect the binding of SsrBc to ssrA .
"
1138,1139,489.txt,3,0,,,,An SsrBc C203D variant failed to bind to the ssrA promoter .
1139,1140,1653.txt,1,0,,,,"In the present study , the expression from lac fusion was retained after disruption in hilC in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
1140,1141,1653.txt,2,0,,,,"In the present study , the expression from the hilA was retained after disruption in hilC in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
1141,1142,1653.txt,3,0,,,,"that RtsA are each capable of independently inducing expression of the hilC genes
"
1142,1143,1653.txt,4,0,,,,"We demonstrate that RtsA are each capable of inducing expression of hilC .
"
1143,1144,1653.txt,5,0,,,,"We had previously demonstrated that RtsA increased expression of hilC .
"
1144,1145,1653.txt,6,0,,,,"We wanted to determine if RtsA could induce expression of hilC in the absence of the other regulators .
"
1145,1146,1653.txt,7,0,,,,"RtsA also induced expression of hilC .
"
1146,1147,1653.txt,8,0,,,,"RtsA induced expression of hilC approximately threeto fourfold .
"
1147,1148,1653.txt,9,0,,,,"These data show that RtsA are each capable of independently inducing expression of hilC , consistent with our model that RtsA constitute a feed forward regulatory loop .
"
1148,1149,1653.txt,10,0,,,,"We show that RtsA can each independently activate expression of the hilC genes .
"
1149,1150,1653.txt,11,0,,,,RtsA are all also capable of activating expression of hilC independent of each other and comprise a complex feed forward regulatory loop .
1150,1151,1135.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"Research A Proteomic Analysis Reveals Differential S - Regulation of the Dependent yciGFE Locus by YncC in Salmonella r , and Françoise Norel § Norel § ¶ ‡ The stationary-phase s controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Esch .
"
1151,1152,1135.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"Our results indicate that differences between E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by YncC in these two enterobacteria .
"
1152,1153,1135.txt,3,1,Salmonella,Salmonella,Salmonella,"Our results indicate that differences between Salmonella , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by YncC in these two enterobacteria .
"
1153,1154,1135.txt,4,0,,,,"The results reveal differential regulation of the yciGFE locus by YncC in these two closely related bacteria .
"
1154,1155,1135.txt,5,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"It is remarkable that in E. coli K-12 , regulation of yciGFE by YncC are intimately linked , whereas in Salmonella , YncC directly activates transcription
"
1155,1156,1135.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"A proteomic analysis reveals differential regulation of the S-dependent yciGFE locus by YncC in Escherichia coli K-12 .
"
1156,1157,1135.txt,7,1,Salmonella,Salmonella,Salmonella,A proteomic analysis reveals differential regulation of the S-dependent yciGFE locus by YncC in Salmonella .
1157,1158,1121.txt,1,0,,,,OmpR Directly Represses cadC/BA compared the transcriptome of the ompR null .
1158,1159,1647.txt,1,0,,,,"The observation that phoPQ and pmrAB mutants showed an increased susceptibility to colistin and polymyxin B , in the presence of eDNA , indicated a role for PhoPQ/PmrAB-regulated phenotypes in resistance to membrane acting antimicrobial peptides , likely through the aminoarabinose modification of LPS via the pmr operon ."
1159,1160,1874.txt,1,0,,,,"Like marRAB , tolC are positively regulated by SoxS .
"
1160,1161,1874.txt,2,0,,,,"8 -- 13 _ shown that SoxS , play a role in antimicrobial resistance by activating tolC"
1161,1162,338.txt,1,1,Salmonella virus P22,P22,Salmonella virus P22,"Furthermore , increasing the level of DgoR by providing the corresponding gene on pFPV-dgoR was able to abolish induction of dgoT : : MudK by P22 wt , but had no obvious effect on phage infection per se .
"
1162,1163,338.txt,2,2,unidentified plasmid;Salmonella virus P22,plasmid;P22,Salmonella virus P22;unidentified plasmid,"Furthermore , increasing the level of DgoR by providing the corresponding gene on a multicopy plasmid was able to abolish induction of dgoT : : MudK by P22 wt , but had no obvious effect on phage infection per se ."
1163,1164,1860.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons involved in bio-film formation , EPS production
"
1164,1165,1860.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons involved in bio-film formation , transport production
"
1165,1166,1860.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons involved in bio-film formation , virulence production
"
1166,1167,1860.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of lpfE genes
"
1167,1168,1860.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of fimA genes
"
1168,1169,1860.txt,6,0,,,,"CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under stressrelated conditions .
"
1169,1170,1860.txt,7,0,,,,"CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under low-temperature .
"
1170,1171,1860.txt,8,0,,,,"CsgD acts as a positive transcriptional regulator for both operons , csgBAC and csgDEFG , and initiates transcription under low-osmolarity ."
1171,1172,1848.txt,1,1,Salmonella,Salmonella,Salmonella,"Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are low in ions found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .
"
1172,1173,1848.txt,2,1,Salmonella,Salmonella,Salmonella,"Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are low in Mg2 found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .
"
1173,1174,1848.txt,3,1,Salmonella,Salmonella,Salmonella,"Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are acidic in ions found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .
"
1174,1175,1848.txt,4,1,Salmonella,Salmonella,Salmonella,"Such conditions may occur when the patho-gen invades host cells as in-vivo measurements suggest that Salmonella-containing vacuoles are acidic in Mg2 found that , in contrast to the PhoPQ repression effect , RpoS stimulates the expression of flagella as reduced amounts of flagellin were found in an rpoS : : kan mutant .
"
1175,1176,1848.txt,5,0,,,,"In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .
"
1176,1177,1848.txt,6,0,,,,"In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .
"
1177,1178,1848.txt,7,0,,,,"In all those studies , it has been shown that induction of bioluminescence can accurately report induction of the rpoS regulon and thus , induction of RpoS .
"
1178,1179,1848.txt,8,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"In E. coli , the genes overlap with those of the RpoS regulon although induction of rpoS itself is not enough for the increased acid resistance observed since rpoS did not protect E. coli from subsequent exposure to pH 3 .
"
1179,1180,1848.txt,9,0,,,,"Presumably , the posttranscriptional mechanisms responsible for regulation of RpoS protein expression were sufficiently robust to withstand our attempts at overwhelming them through ectopic transcriptional upregulation of the rpoS gene .
"
1180,1181,1848.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"However , rpoS might also contribute to the virulence of this serotype because RpoS − strains of S. Typhi are less cytotoxic than RpoS + strai
"
1181,1182,1848.txt,11,0,,,,"H-NS-deficient mutants strongly increased RpoS due to enhanced rpoS translation .
"
1182,1183,1848.txt,12,0,,,,"At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L Fig. 4A .
"
1183,1184,1848.txt,13,0,,,,"At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L NaCl LB broth .
"
1184,1185,1848.txt,14,0,,,,"At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt Fig. 4A .
"
1185,1186,1848.txt,15,0,,,,"At exponential phase , when RpoS level should be very low in strain , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt NaCl LB broth .
"
1186,1187,1848.txt,16,0,,,,"At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L Fig. 4A .
"
1187,1188,1848.txt,17,0,,,,"At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in 0.3 mol/L NaCl LB broth .
"
1188,1189,1848.txt,18,0,,,,"At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt Fig. 4A .
"
1189,1190,1848.txt,19,0,,,,"At exponential phase , when RpoS level should be very low in an rpoS , only a general increase of about 20 % was observed in the b-galactosidase activity of rpoS : : Apr strains grown either in no salt NaCl LB broth .
"
1190,1191,1848.txt,20,0,,,,"Figure 4 ( A ) Static biofilm formation of eight targeted gene Transcriptomic comparison of biofilm and planktonic-cells showed that rpoS was highly expressed in both populations , and that several RpoS-activated genes showed biofilm-specific patterns of expression .
"
1191,1192,1848.txt,21,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"9 100 90 8 80 70 7 6 The rpoS alleles determine the salt-inducible VBNC state in Salmonella enterica 60 50 5 4 40 30 Osmotic stress reduced the amount of RpoS protein in the three strains during the induction of the VBNC state .
"
1192,1193,1848.txt,22,4,Salmonella;Salmonella enterica;Salmonella;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2,Salmonella;Salmonella enterica;enterica;LT2;LT2,Salmonella enterica;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella,"9 100 90 8 80 70 7 6 The rpoS alleles determine the salt-inducible VBNC state in Salmonella enterica 60 50 5 4 40 30 Osmotic stress reduced the amount of RpoS protein in LT2 during the induction of the VBNC state .
"
1193,1194,1848.txt,23,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"9 100 90 8 80 70 7 6 The rpoS alleles determine the salt-inducible VBNC state in Salmonella enterica 60 50 5 4 40 30 Osmotic stress reduced the amount of RpoS protein in S. Oranienburg Sa99004 during the induction of the VBNC state .
"
1194,1195,1848.txt,24,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"9 100 90 8 80 70 7 6 The rpoS alleles determine the salt-inducible VBNC state in Salmonella enterica 60 50 5 4 40 30 Osmotic stress reduced the amount of RpoS protein in S. Dublin KDX1 during the induction of the VBNC state .
"
1195,1196,1848.txt,25,4,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2,S. Typhimurium;Typhimurium;strain LT2;LT2;LT2,Salmonella enterica;Lopadostoma turgidum;Salmonella enterica subsp. enterica serovar Typhimurium LT2;Salmonella enterica subsp. enterica serovar Typhimurium,"In this study , we investigated effect of rpoS disruption and expression on intracellular levels of RpoS during induction of VBNC state , using S. Typhimurium strain LT2 .
"
1196,1197,1848.txt,26,0,,,,"In this study , we investigated effect of rpoS disruption and expression on intracellular levels of RpoS during induction of VBNC state , using S. Dublin .
"
1197,1198,1848.txt,27,0,,,,"In this study , we investigated effect of rpoS disruption and expression on intracellular levels of RpoS during induction of VBNC state , using S. Oranienburg .
"
1198,1199,1848.txt,28,0,,,,"Intracellular levels of RpoS protein during the induction of 0 1 2 3 4 5 6 7 day rpoS + , log10CFU/mL rpoS + , viability ΔrpoS , viability ΔrpoS , log10CFU/mL Fig. 5 .
"
1199,1200,1848.txt,29,0,,,,"Intracellular levels of RpoS protein during the induction of 0 1 2 3 4 5 6 7 8 9 Incubation time rpoS + , log10CFU/mL rpoS + , viability ΔrpoS , viability ΔrpoS , log10CFU/mL Fig. 5 .
"
1200,1201,1848.txt,30,0,,,,"To further distinguish between the contribution of RpoS to rdar morphotype expression , we compared the phenotype of an arcZ mutant with an rpoS mutant in the MAE52 strain background .
"
1201,1202,1848.txt,31,0,,,,"This tolerance appeared to be reflected in the upregulation of rpoS of the RpoS regulon .
"
1202,1203,1848.txt,32,0,,,,"Cell lysates were isolated from strains while in exponential phase prior to measuring the length of their lag Length of lag phase during osmotic-stress was To further investigate the potential contribution of RpoS to growth during hyperosmotic-stress , a rpoS deletion mutant was generated , M-09DrpoS .
"
1203,1204,1848.txt,33,0,,,,"Cell lysates were isolated from strains while in stationary phase prior to measuring the length of their lag Length of lag phase during osmotic-stress was To further investigate the potential contribution of RpoS to growth during hyperosmotic-stress , a rpoS deletion mutant was generated , M-09DrpoS .
"
1204,1205,1848.txt,34,0,,,,"The rpoS mutation resulted in a two-to threefoldhigher level of induction of a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus ."
1205,1206,1690.txt,1,1,Salmonella,Salmonella,Salmonella,5 The Salmonella endogenous promoter for pepT is regulated by CRP .
1206,1207,304.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
1207,1208,462.txt,1,0,,,,"Therefore , SoxS is proposed to bind to the upstream region of acrA .
"
1208,1209,462.txt,2,0,,,,This suggests that SoxS competitively bind to the upstream region of acrA .
1209,1210,476.txt,1,0,,,,"Altogether , these observations suggested that the residual chiP induction by chitobiose in the ΔchiX background is unlikely to be due to direct activation by ChbR at the chiP promoter .
"
1210,1211,476.txt,2,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"From the data in Fig. 3 , it is apparent that inactivation of the ChbR repressor completely prevents residual chiP induction by chitobiose in ΔchiX background in E. coli as it does in Salmonella .
"
1211,1212,476.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"Given that the E. coli sequence lacks the ChbR binding site and shows no binding to the purified protein in-vitro , these findings suggest that the ChbR requirement for the residual induction of chiP by chitobiose is independent of ChbR binding to the chiP promoter region .
"
1212,1213,476.txt,4,1,Salmonella;Salmonella;Salmonella,Sal-monella;monella;Salmonella,Salmonella,"Final proof that the ChbR binding site at − 180 in Sal-monella is not implicated in chitobiose induction of chiP came from replacing the ChbR binding site in Salmonella with h 11 -- lacZ fusion construct on the chromosome .
"
1213,1214,476.txt,5,0,,,,"Intriguingly , while footprint analysis confirmed such binding , we obtained no evidence for a ChbR involvement in chiP induction other than its indirect role as activator of chbBCARFG transcription .
"
1214,1215,476.txt,6,1,Salmonella,Salmonella,Salmonella,"Furthermore , replacement of the ChbR binding site in the Salmonella chiP promoter region with the sequence did not affect chiP induction by chitobiose to any significant extent .
"
1215,1216,476.txt,7,0,,,,Activation of chbBCA expression by ChbR is essential to relieve ChiX repression of chiP .
1216,1217,310.txt,1,0,,,,"Activated OxyR induces katE , dps ahpCF .
"
1217,1218,310.txt,2,0,,,,"Activated OxyR induces katE , dps lipids .
"
1218,1219,310.txt,3,0,,,,"Activated OxyR induces katE , DNA-protection ahpCF .
"
1219,1220,310.txt,4,0,,,,"Activated OxyR induces katE , DNA-protection lipids ."
1220,1221,1684.txt,1,0,,,,"Based on available literature data , the FNR-regulated pepT gene promoter was chosen as a starting point for our investigations .16 pepT is transcribed from two promoters .
"
1221,1222,1684.txt,2,1,Salmonella,Salmonella,Salmonella,5 The Salmonella endogenous promoter for pepT is regulated by Fnr .
1222,1223,477.txt,1,0,,,,"IgaAmediated repression of the RcsB-YojN-RcsC system occurred at the post-translational level , as shown by chromosomal epitope tagging of the rcsB genes ."
1223,1224,1685.txt,1,0,,,,"Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter .
"
1224,1225,1685.txt,2,0,,,,Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter .
1225,1226,311.txt,1,0,,,,"However , when SirA is overproduced in a barA mutant there is strong stimulation of invasion gene expression ."
1226,1227,305.txt,1,0,,,,"csgBA is positively regulated by the global regulator CsgD
"
1227,1228,305.txt,2,0,,,,"First , we show that unphosphorylated CsgD binds to the promoter regions of its target genes csgBA and adrA and stimulates their transcription in-vitro .
"
1228,1229,305.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to adrA promoter regions In S. Typhimurium the expression of csgBA is positively regulated by the transcriptional regulator CsgD .
"
1229,1230,305.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to the csgBA In S. Typhimurium the expression of adrA is positively regulated by the transcriptional regulator CsgD .
"
1230,1231,305.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to the csgBA In S. Typhimurium the expression of csgBA is positively regulated by the transcriptional regulator CsgD .
"
1231,1232,305.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to the csgBA In S. Typhimurium the expression of csgBA is positively regulated by the transcriptional regulator CsgD .
"
1232,1233,305.txt,7,0,,,,"In order to demonstrate the direct binding of CsgD to the csgBA promoter regions we performed EMSA with purified CsgD-His6 tagged protein ( Fig .
"
1233,1234,305.txt,8,0,,,,"In order to demonstrate the direct binding of CsgD to the csgBA promoter regions we performed electrophoretic-mobility-shift assays with purified CsgD-His6 tagged protein ( Fig .
"
1234,1235,305.txt,9,0,,,,"Since CsgD is highly integrated into the c-di-GMP signalling network , we investigated whether c-di-GMP affects the binding of CsgD-His6 to the csgBA .
"
1235,1236,305.txt,10,0,,,,"Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the csgBA promoter fragments , compared with Fig. 5A .
"
1236,1237,305.txt,11,0,,,,"Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the csgBA promoter fragments , compared with CsgD alone .
"
1237,1238,305.txt,12,0,,,,"Since the binding of CsgD to the csgBA is altered in the presence of the phosphodonor AcP , we investigated whether CsgD can be phosphorylated in-vitro .
"
1238,1239,305.txt,13,0,,,,"However , we discovered that c-di-GMP , is not required for binding of CsgD to the csgBA promoters .
"
1239,1240,305.txt,14,0,,,,"However , we discovered that an integral part of the regulatory network , is not required for binding of CsgD to the csgBA promoters .
"
1240,1241,305.txt,15,0,,,,"CsgD directly binds to the csgBA upstream promoter region and positively regulates the expression of cellulose biosynthesis by activating expression of adrA , encoding a diguanylate cyclase ."
1241,1242,1691.txt,1,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
1242,1243,1691.txt,2,0,,,,"Together with a bioinformatic analysis of other Enterobacteriaceae species , these data identify a conserved AraC regulon that includes 7 previously described AraC-regulated genes ( araB , araA , araD , araE , araF , araG , and araH ) as well as three novel targets identified in this work ( ytfQ , araT , and araU ) ."
1243,1244,1849.txt,1,0,,,,"The FlhDC-regulated ycgR and yhjH genes ( Ko and Park , 2000 ) were also strongly repressed ( 0.08-and 0.18-fold at 45 min respectively ; Table 8 ) ."
1244,1245,463.txt,1,0,,,,"that Fur represses crl transcription
"
1245,1246,463.txt,2,0,,,,"that Fur represses crl transcription
"
1246,1247,463.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"crl transcription in E. coli W3110 is repressed by Fur -LRB- by 100-fold -RRB- -LRB- by more than 10-fold -RRB- .
"
1247,1248,463.txt,4,0,,,,These results suggested that crl transcription is not repressed by Fur in ATCC 14028 .
1248,1249,1861.txt,1,0,,,,"J Antimicrob Chemother 2013 ; 1551 -- 1557 doi : 10.1093 / jac/dkt069 Advance Access publication 14 March 2013 Genetic inactivation of acrAB of efflux induces expression of L. J. V. Piddock1 Infection , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK , Tel : +44 -121 -- 414-6966 ; Fax : +44-121-414-6819 ; E-mail : l.j.v.piddock@bham.ac.uk Objectives : The transcriptional activator RamA regulates production of the multidrug resistance efflux AcrAB .
"
1249,1250,1861.txt,2,0,,,,"J Antimicrob Chemother 2013 ; 68 : 10.1093 / jac/dkt069 Advance Access publication 14 March 2013 Genetic inactivation of acrAB of efflux induces expression of L. J. V. Piddock1 Infection , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK , Tel : +44 -121 -- 414-6966 ; Fax : +44-121-414-6819 ; E-mail : l.j.v.piddock@bham.ac.uk Objectives : The transcriptional activator RamA regulates production of the multidrug resistance efflux AcrAB ."
1250,1251,339.txt,1,0,,,,"the former _ being regulated by a promoter located upstream of the pstS gene regulated by PhoB
"
1251,1252,339.txt,2,0,,,,the former _ being regulated by a promoter located upstream of the pstS gene regulated by PhoB
1252,1253,1875.txt,1,0,,,,"Constitutive expression of phoP also results in attenuated virulence and decreased survival in macrophages , suggesting that the ability to switch between repression of PhoPQ during infection is important ."
1253,1254,1120.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Anaerobic regulation of the Escherichia coli dmsABC operon requires the molyb-date-responsive regulator ModE .
1254,1255,1646.txt,1,0,,,,"The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure ."
1255,1256,1652.txt,1,3,Salmonella;Escherichia coli;unidentified plasmid,Salmonella;E. coli;plasmid,Escherichia coli;Salmonella;unidentified plasmid,"Therefore , this enzyme activity would be another determinant for the RstAcontrolled iron response in Salmonella and also a reason that expression of the E. coli feoB gene from plasmid results in equally enhanced Fe ( II ) uptake in cells grown aerobically or anaerobically ( 12 ) .
"
1256,1257,1652.txt,2,0,,,,"This result was correlated with regulation of the feoB gene in response to RstA activation : in the wild-type strain , iron decreased feoB transcription whereas RstA expression highly increased it .
"
1257,1258,1652.txt,3,0,,,,"This result was correlated with regulation of the feoB gene in response to iron activation : in the wild-type strain , iron decreased feoB transcription whereas RstA expression highly increased it ."
1258,1259,1134.txt,1,0,,,,"These results revealed a reciprocal regulatory relationship between IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfB .
"
1259,1260,1134.txt,2,0,,,,These results revealed a reciprocal regulatory relationship between HU at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfB .
1260,1261,488.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1261,1262,488.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1262,1263,488.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1263,1264,488.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1264,1265,488.txt,5,0,,,,"Expression of acrAB-tolC is regulated by AcrR .
"
1265,1266,488.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1266,1267,488.txt,7,1,Salmonella,Salmonella,Salmonella,"Other regulators of AcrR did not contrib-ute to acrAB induction by indole in Salmonella .
"
1267,1268,488.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1268,1269,488.txt,9,1,Escherichia coli,Escherichia coli,Escherichia coli,"D. Ma , M. Alberti , C. Lynch , H. Nikaido , J.E. Hearst , The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals , Mol .
"
1269,1270,488.txt,10,0,,,,"Furthermore , a local repres-6 -- 10 sor , AcrR , has been identified to play a role in the regulation of acrAB genes .
"
1270,1271,488.txt,11,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1271,1272,488.txt,12,1,Escherichia coli,Escherichia coli,Escherichia coli,"The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals .
"
1272,1273,488.txt,13,1,Salmonella,Salmonella,Salmonella,"For example , acrAB transcription in Salmonella is controlled by AcrR , ."
1273,1274,1108.txt,1,0,,,,"SsrBC Stimulates Transcription of sifA in Vitro in the Absence of Additional Factors -- To determine whether SsrB could directly activate transcription , we used purified SsrBC in an in-vitro-transcription assay ."
1274,1275,113.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
1275,1276,1487.txt,1,0,,,,"Since swarming motility in both cysB and cysE is restored by the inclusion of cysteine in the swarm medium , a CysB-regulated gene outside of the cysteine biosynthetic genes is not the reason that these strains are incapable of swarming on standard swarm medium ."
1276,1277,675.txt,1,0,,,,"The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure ."
1277,1278,661.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"In response to AHLs , SdiA activates two Salmonella-specific loci , the rck operon
"
1278,1279,661.txt,2,1,Salmonella,Salmonella,Salmonella,"In response to AHL under laboratory conditions , Salmonella SdiA activates the expression of the rck operon .
"
1279,1280,661.txt,3,1,Salmonella,Salmonella,Salmonella,"In Salmonella , rck is induced by SdiA .
"
1280,1281,661.txt,4,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,Typhimu;Salmonella;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SdiA upregulates two loci in S. Typhimu-rium , the rck operon , located on the Salmonella virulence plasmid , and srgE -LRB- sdiA-regulated gene -RRB- , a horizontally acquired gene located on the chromosome .
"
1281,1282,661.txt,5,0,,,,"In response to AHLs , SdiA increases the expression of the rck operon .
"
1282,1283,661.txt,6,0,,,,"SdiA increases the expression of the rck operon .
"
1283,1284,661.txt,7,0,,,,"In this study , we first confirmed that the transcriptional regulation of rck by SdiA resulted in an increase of Rck protein expression .
"
1284,1285,661.txt,8,0,,,,"SdiA positively regulates two loci in the rck operon .
"
1285,1286,661.txt,9,1,Salmonella,Salmonella,Salmonella,SdiA in Salmonella activates expression of the rck operon .
1286,1287,1493.txt,1,0,,,,"In addition , DsrA may fall into Group I sRNAs , as it directly stimulates translation of rpoS mRNA , whereas it interferes with the expression of H-NS , which -- by repressing the expression of the flhDC repressor HdfR -- acts as an indirect activator of FlhDC expression ."
1287,1288,107.txt,1,1,hybrid,hybrid,hybrid,"Efforts in our laboratory to demonstrate binding of purified HilE protein to the hilA promoter have failed , however , recent work demonstrated that the HilE protein interacts with HilD , using a bacterial two-hybrid assay .
"
1288,1289,107.txt,2,0,,,,"colleagues have identified HilE as a negative regulator of hilA transcription .
"
1289,1290,107.txt,3,0,,,,"Jones have identified HilE as a negative regulator of hilA transcription .
"
1290,1291,107.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , a hilA was regulated by HilE only when HilD protein was present .
"
1291,1292,107.txt,5,0,,,,"Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE .
"
1292,1293,107.txt,6,0,,,,"Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE .
"
1293,1294,107.txt,7,0,,,,"To determine the effects of HilE on the regulation of hilA via PhoPQ , we conducted a-galactosidase assay .
"
1294,1295,107.txt,8,0,,,,"To determine the effects of HilE on the regulation of hilA via PhoPQ , we conducted lacZY expression .
"
1295,1296,107.txt,9,1,hybrid,hybrid,hybrid,Fahlen et al. identified HilE as a negative regulator of hilA transcription provided bacterial two-hybrid data .
1296,1297,649.txt,1,0,,,,"RamA binds to the upstream region of acrA .
"
1297,1298,649.txt,2,0,,,,"acrA binds RamA
"
1298,1299,649.txt,3,0,,,,This suggests that RamA competitively bind to the upstream region of acrA .
1299,1300,891.txt,1,0,,,,"Thus , we concluded that FNR all contribute towards the regulation of hlyE expression .
"
1300,1301,891.txt,2,0,,,,"that during anaerobic-growth in liquid cultures in the absence of glucose , FNR is the major regulator of hlyE expression
"
1301,1302,891.txt,3,0,,,,"In summary , the data suggest that FNR are positive regulators of hlyE expression in liquid culture in response to glucose-starvation , respectively .
"
1302,1303,891.txt,4,0,,,,"In summary , the data suggest that FNR are positive regulators of hlyE expression in liquid culture in response to oxygen , respectively .
"
1303,1304,891.txt,5,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
1304,1305,891.txt,6,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
1305,1306,891.txt,7,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
1306,1307,891.txt,8,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
1307,1308,891.txt,9,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
1308,1309,891.txt,10,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter ."
1309,1310,885.txt,1,0,,,,"For genes , we found two genes , ydhI are negatively regulated by SlyA ."
1310,1311,1444.txt,1,0,,,,"HN-S is a negative regulator of ompR expression A previous report demonstrated that CRP affected ompR expression .
"
1311,1312,1444.txt,2,0,,,,HN-S is a negative regulator of ompR expression A previous report demonstrated that CRP affected ompR expression .
1312,1313,1322.txt,1,0,,,,"These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cAMP and cAMP-receptor-protein -LRB- CRP -RRB- .
"
1313,1314,1322.txt,2,0,,,,These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cyclic AMP and cAMP-receptor-protein -LRB- CRP -RRB- .
1314,1315,1336.txt,1,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Our finding that CpxR can influence the susceptibility of S. enterica serovar Typhimurium to β-lactam in both △ acrB backgrou also supports the second suggestion .
"
1315,1316,1336.txt,2,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Our finding that CpxR can influence the susceptibility of S. enterica serovar Typhimurium to aminoglycosides in both △ acrB backgrou also supports the second suggestion .
1316,1317,2159.txt,1,0,,,,"The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , mutation of the putative RcsB binding site in the ugd promoter abolished tolB-promoted ugd transcription .
"
1317,1318,2159.txt,2,0,,,,"The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , Fig. 2B abolished tolB-promoted ugd transcription .
"
1318,1319,2159.txt,3,0,,,,"The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , yojN genes abolished tolB-promoted ugd transcription .
"
1319,1320,2159.txt,4,0,,,,"The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , rcsC genes abolished tolB-promoted ugd transcription .
"
1320,1321,2159.txt,5,0,,,,"The tolB mutationpromoted activation is mediated by the RcsA protein because inactivation of the rcsA , rcsB genes abolished tolB-promoted ugd transcription ."
1321,1322,1450.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) ."
1322,1323,2171.txt,1,0,,,,"The coding sequence of the coding sequence of the arcA gene in SE8743 were identical , suggesting that the difference in resistance to RNI/ROI maybe due to the activity of genes regulated by ArcA .
"
1323,1324,2171.txt,2,0,,,,"The coding sequence of the arcA gene in SE2472 were identical , suggesting that the difference in resistance to RNI/ROI maybe due to the activity of genes regulated by ArcA .
"
1324,1325,2171.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To obtain a global view of ArcA-controlled biological processes , we classified proteins with altered expression levels in S. Typhimurium arcA cells into Clusters of Orthologous Groups ( COGs ) ( Table I ) ."
1325,1326,1478.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for anaerobic induction of hyaB in Salmonella typhimurium .
"
1326,1327,1478.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for acid-pH induction of hyaB in Salmonella typhimurium ."
1327,1328,852.txt,1,0,,,,"Direct regulation of sopE2 genes by SlyA in response to ROS .
"
1328,1329,852.txt,2,0,,,,"Our results showed that at 3 h post-infection only , sopE2 were negatively regulated by SlyA , with DslyA expression increased two-and five-times , respectively ."
1329,1330,12.txt,1,0,,,,marR controls the production of MarA in response to environmental signals .
1330,1331,846.txt,1,2,Lateolabrax japonicus;Escherichia coli,Suzuki;Escherichia coli,Escherichia coli;Lateolabrax japonicus,"T. Suzuki , C. Ueguchi , T. Mizuno , H-NS regulates OmpF expression through micF antisense RNA in Escherichia coli , J. Bacteriol ."
1331,1332,2165.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) .
"
1332,1333,2165.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"H-NS-dependent repression of clyA in the E. coli K-12 STy strains YMZ19 ( clyA hns ) ( shaded bars ) _ carrying different constructs
"
1333,1334,2165.txt,3,0,,,,"H-NS-dependent repression of clyA hns .
"
1334,1335,2165.txt,4,0,,,,"H-NS-dependent repression of clyA hns _ carrying different constructs
"
1335,1336,2165.txt,5,0,,,,"Expression of STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .
"
1336,1337,2165.txt,6,0,,,,"SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sseJ loci .
"
1337,1338,2165.txt,7,0,,,,"SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sifB .
"
1338,1339,2165.txt,8,0,,,,"SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA .
"
1339,1340,2165.txt,9,0,,,,The overexpression of H-NS repressed SPI-2 gene expression -LRB- comparing `` rpoE hns uninduced 
1340,1341,701.txt,1,1,Salmonella,Salmonella,Salmonella,"sseJ ( Figure 2 ) was further analyzed because although PmrAB-regulated genes have been implicated in animal virulence [ 2 ] , no direct link between SPI-2 ( Salmonella pathogenicity island 2 ) gene regulation and PmrAB has been demonstrated yet .
"
1341,1342,701.txt,2,0,,,,We predicted the PmrAB-dependent regulation of four additional targets : sseJ .
1342,1343,1295.txt,1,0,,,,Expression of hilA is coordinately controlled by the HilD/HilC/RtsA complex
1343,1344,1281.txt,1,0,,,,"Thus , SsrBC directly regulates transcription of sifB by binding upstream of the respective promoters ."
1344,1345,715.txt,1,1,Salmonella,Salmonella,Salmonella,"Osborne et al. [ 27 ] recently reported that srfN , an ancestral PhoP-regulated gene , acquired an SsrB-regula-tory module during Salmonella "
1345,1346,729.txt,1,1,Pasteurella multocida,Pasteurella multocida,Pasteurella multocida,"In agreement with this possibility , it has been recently demonstrated that the fur gene of Pasteurella multocida , is positively regulated by the cAMP-CRP complex .
"
1346,1347,729.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the basal expression of the cAMP-regulated S. typhimurium pepE gene , was analysed .
"
1347,1348,729.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"To ascertain whether transcription of other cAMP-CRP-dependent promoters is affected in the fur mutant , the induction of the E. coli lac operon , was analysed ."
1348,1349,1530.txt,1,1,synthetic construct,Primer,synthetic construct,"Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM ."
1349,1350,2039.txt,1,1,Felis catus,cat,Felis catus,"the expression of the hilD-cat fusion _ revealing that CpxR represses hilD
"
1350,1351,2039.txt,2,0,,,,"CpxR could directly repress the transcription of hilD .
"
1351,1352,2039.txt,3,0,,,,"our results _ indicating that CpxR represses the HilD-dependent expression of hilD
"
1352,1353,2039.txt,4,0,,,,FIGURE 4 CpxR represses the autoregulation of hilD .
1353,1354,1256.txt,1,0,,,,It has been demonstrated that expression of the pbgPE operon -LRB- also called pmrHFIJKLM operon -RRB- are induced by PmrAB activation .
1354,1355,1242.txt,1,0,,,,"DksA , plays a role in regulating hfq gene expression"
1355,1356,1524.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , ansB is positively coregulated by Fnr ."
1356,1357,2005.txt,1,0,,,,Beside unspecific effects this could be due to indirect repression of hilD via RcsB/RflM as described before .
1357,1358,926.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
1358,1359,932.txt,1,0,,,,"This insertion is upstream of the kinase domain ; it appears to cause tetrathionate-independent induction of the ttrBCA operon via TtrR , since expression requires OxrA protein .
"
1359,1360,932.txt,2,0,,,,"This insertion is upstream of the kinase domain ; it appears to cause tetrathionate-independent induction of the ttrBCA operon via TtrR , since expression requires anaerobic conditions ."
1360,1361,1518.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
1361,1362,2011.txt,1,0,,,,The gene pmrD is transcriptionally repressed by the PmrAB system .
1362,1363,1097.txt,1,0,,,,"Although H-NS reduces the transcription of more than 100 genes , it also is shown to be a negative regulator for rpoS translation .
"
1363,1364,1097.txt,2,0,,,,"H-NS binds directly to rpoS mRNA to enhance cleavage of the mRNA .
"
1364,1365,1097.txt,3,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1365,1366,1097.txt,4,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1366,1367,1097.txt,5,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1367,1368,1097.txt,6,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1368,1369,1097.txt,7,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1369,1370,1097.txt,8,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1370,1371,1097.txt,9,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1371,1372,1097.txt,10,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"sRNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1372,1373,1097.txt,11,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1373,1374,1097.txt,12,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1374,1375,1097.txt,13,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1375,1376,1097.txt,14,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs RprA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1376,1377,1097.txt,15,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1377,1378,1097.txt,16,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes turnover of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth .
"
1378,1379,1097.txt,17,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of rss at various stages throughout the exponential phase of growth .
"
1379,1380,1097.txt,18,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"The small RNAs DsrA have a greater role in the control of E. coli rpoS expression compared to Salmonella , whereas the H-NS paralog StpA promotes proteolysis of σS indirectly through the repression of the antiadapter protein encoding gene ira at various stages throughout the exponential phase of growth ."
1380,1381,503.txt,1,0,,,,"Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) ."
1381,1382,1929.txt,1,0,,,,"the transcriptional results showed that LeuO positively induced assT at different points of the growth curve
"
1382,1383,1929.txt,2,0,,,,"A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for the dsbL-dsbI transcriptional units in the absence of cloned leuO SPI-2 .
"
1383,1384,1929.txt,3,0,,,,"A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for assT transcriptional units in the absence of cloned leuO SPI-2 .
"
1384,1385,1929.txt,4,0,,,,"A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for the dsbL-dsbI transcriptional units in a leuO background , in N-minimal-medium SPI-2 .
"
1385,1386,1929.txt,5,0,,,,"A LeuO-dependent promoter is necessary for induction of the complete assT-dsbL-dsbI operon in rich-medium , whereas transcriptional start sites were determined for assT transcriptional units in a leuO background , in N-minimal-medium SPI-2 .
"
1386,1387,1929.txt,6,0,,,,"Because LeuO still activates assT , although at 25 % of the wild-type levels , we analyzed , by footprinting of a DNA fragment lacking II sites , whether there are other LeuO-binding sites in this region .
"
1387,1388,1929.txt,7,0,,,,"Because LeuO still activates assT , although at 25 % of the wild-type levels , we analyzed , by footprinting of a DNA fragment lacking both LBS I sites , whether there are other LeuO-binding sites in this region .
"
1388,1389,1929.txt,8,1,unidentified,not shown,unidentified,"The data indicate that assT is induced in N-minimal-medium in the absence of LeuO , since the same activity was observed in all of the constructions in a leuO isogenic background -LRB- data not shown -RRB- .
"
1389,1390,1929.txt,9,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In a subsequent study to pursue more targets in Salmonella Typhi , LeuO was found to also positively regulate assT ."
1390,1391,265.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , five transcription factors have been implicated : hmp transcription is repressed by FNR .
"
1391,1392,265.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , five transcription factors have been implicated : hmp transcription is repressed by FNR ."
1392,1393,271.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .
"
1393,1394,271.txt,2,1,unidentified,not shown,unidentified,"On the other hand , neither Ca2 + nor Co2 + , K + , Ni2 + , Zn2 + , Mn2 + , Cu2 + , Ga3 + or Ru3 + ( at concentrations of up to 1 mM ) could induce PmrA-activated genes ( Wosten et al. , 2000 ) or kill the DpmrC ugd pmrG triple mutant ( data not shown ) .
"
1394,1395,271.txt,3,0,,,,"Inactivation of the PmrA-activated genes mediating the modification of the two lipid-A phosphates and the Hep ( II ) phosphate in the core region resulted in a strain ( i.e. the DpmrC ugd pmrG triple mutant ) that was as susceptible to Fe ( III ) as the DpmrAB mutant ( Table 1 ) and that bound more iron than the wild-type strain ( Fig. 1B ) .
"
1395,1396,271.txt,4,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
1396,1397,271.txt,5,0,,,,"Furthermore , a strain deleted for of all three pmrC , ugd and pmrG genes and harbouring the pmrA505 allele , which encodes a PmrA protein that promotes transcription of PmrA-activated genes even under noninducing conditions ( Kox et al. , 2000 ) , was as susceptible to Fe ( III ) as the DpmrAB mutant ( Table 1 ) ."
1397,1398,517.txt,1,1,unidentified,unknown,unidentified,"Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .
"
1398,1399,517.txt,2,1,unidentified,unknown,unidentified,"Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .
"
1399,1400,517.txt,3,1,unidentified,unknown,unidentified,"Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .
"
1400,1401,517.txt,4,1,unidentified,unknown,unidentified,"Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .
"
1401,1402,517.txt,5,1,unidentified,unknown,unidentified,"Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .
"
1402,1403,517.txt,6,1,unidentified,unknown,unidentified,"Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM0834 was unknown .
"
1403,1404,517.txt,7,0,,,,This analysis demonstrated that neither STM0834 was regulated by PmrA .
1404,1405,1083.txt,1,4,Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Felis catus;Clostridium aminobutyricum,Typhimurium;E. coli;cat;Clostridium aminobutyricum,Felis catus;Clostridium aminobutyricum;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Apart from the PhoP/PhoQ-regulated ugd ( pagA ) gene , which in serovar Typhimurium has been demonstrated to be transcriptionally active inside macrophages and to be necessary for growth in a low-magnesium environment ( 1 , 19 , 20 ) , two genes were identified with homology to the E. coli tdh gene and the cat2 gene in Clostridium aminobutyricum ."
1405,1406,1915.txt,1,0,,,,"PhoP/PhoQ is activated by low cation concentrations , implying that hilA is repressed by these conditions ."
1406,1407,259.txt,1,0,,,,"P1 is an RpoS-regulated gearbox promoter located 407 bp upstream of the acnA start codon and is responsible for stationary-phase induction of acnA expression .
"
1407,1408,259.txt,2,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli RpoS CRP SoxR FNR Fur acnA P2 P1 S. Typhimurium Expression of S. Typhimurium acnA is regulated by oxR Enhanced expression of the acnA gene in the acnB mutant suggested that PacnA was regulated .
1408,1409,1901.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcription of micF is controlled by SoxS ."
1409,1410,1054.txt,1,0,,,,29 pagC survival pagD pagK PhoPQ-regulated 0 ?
1410,1411,1732.txt,1,0,,,,"To our knowledge , the influence of CpxR on the mRNA levels of marA genes has not been demonstrated ."
1411,1412,1726.txt,1,0,,,,The negative effect of StpA on s38 levels at MEP does not occur during LEP as StpA-dependent control of s38 stability is probably compensated at the rpoS mRNA level .
1412,1413,1040.txt,1,1,synthetic construct,primer,synthetic construct,"Among the SPI-5 genes , primer-extension analysis revealed that sopB were induced at entry into the stationary-phase under standard growt conditions independently of RpoS ."
1413,1414,1068.txt,1,0,,,,"kdgM -LRB- encoding oligogalacturonate-specific porin -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators .
"
1414,1415,1068.txt,2,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators ."
1415,1416,2207.txt,1,0,,,,the mechanism _ resulting in regulation of csgD expression by MltE
1416,1417,2213.txt,1,0,,,,polB are positively regulated by arabinose due to partial read-through of Rho-independent terminators .
1417,1418,2205.txt,1,0,,,,"Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .
"
1418,1419,2205.txt,2,0,,,,"Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .
"
1419,1420,2205.txt,3,0,,,,"Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .
"
1420,1421,2205.txt,4,0,,,,"Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .
"
1421,1422,2205.txt,5,0,,,,"Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM1827 .
"
1422,1423,2205.txt,6,0,,,,"Indirect regulation of biofilm formation by STM1697 The EAL domain protein STM3611 , a c-di-GMP phosphodiesterase , is one of the negative regulators of CsgD expression ."
1423,1424,298.txt,1,0,,,,"The PhoBR two-component regulatory system also represses expression of hilA in response to its normal signal , low extracellular Pi ."
1424,1425,1718.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) ."
1425,1426,2211.txt,1,0,,,,"RtsA in particular , also activate , independent of the effector gene slrP , encoding the periplasmic disulphide bond isomerase .
"
1426,1427,2211.txt,2,0,,,,"The genes slrP and dsbA are also induced by RtsA independently of InvF .
"
1427,1428,2211.txt,3,0,,,,"The genes slrP and dsbA are also induced by RtsA independently of both HilA .
"
1428,1429,2211.txt,4,0,,,,"In this context , slrP is induced by overexpression of RtsA independently of the central SPI1 regulator HilA , with RtsA .
"
1429,1430,2211.txt,5,0,,,,"In this context , slrP is induced by overexpression of RtsA independently of the central SPI1 regulator HilA , with RtsA .
"
1430,1431,2211.txt,6,0,,,,"In this context , slrP is induced by overexpression of HilD independently of the central SPI1 regulator HilA , with RtsA .
"
1431,1432,2211.txt,7,0,,,,"In this context , slrP is induced by overexpression of HilC independently of the central SPI1 regulator HilA , with RtsA ."
1432,1433,1730.txt,1,0,,,,"When Fe -- Fur is bound to fur box , gene transcription is prevented .
"
1433,1434,1730.txt,2,0,,,,"Consequently , a global study of the iron modulon will provide insight into the extent and nature of Fur-regulated gene expression and may offer clues to the acid-sensitive nature of fur mutants .
"
1434,1435,1730.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimu,Salmonella enterica subsp. enterica serovar Typhimurium,"In view of the disparate regulation of the S. Typhimu-rium Fe storage proteins by Fur , the virulence of a fur mutant was also examined .
"
1435,1436,1730.txt,4,0,,,,"Since many of the genes are regulated by the global transcriptional iron regulator Fur , real-time RT-PCR was also performed for the fur gene ; a significant , 2.5-fold reduction in gene expression was observed in the wild-type strain .
"
1436,1437,1730.txt,5,0,,,,"The fur gene , an important regulator of the Fur operon revealed a significant increase in transcription .
"
1437,1438,1730.txt,6,1,unidentified plasmid,plasmid,unidentified plasmid,"Accession Log2 geometric p-value mean fold change Gene Definition/function/gene product Pathogenicity island hilD SPI-1 regulator a spaP SPI-1 surface presentation of antigens sprB SPI-1 transcriptional regulator ssaL SPI-2 secretion system apparatus protein AE008831 6.95 AE008832 1.90 2.13 E 07 0.0033 AE008831 1.99 0.0033 AE008761 1.63 0.0012 Virulence-associated fur Regulator of the Fur possibly oxygen-radicals mig5 Macrophage-inducible , a putative carbonic anhydrase , found on virulence plasmid 5.55 E 05 AE008728 2.23 Fig. 1 .
"
1438,1439,1730.txt,7,0,,,,"Accession Log2 geometric p-value mean fold change Gene Definition/function/gene product Pathogenicity island hilD SPI-1 regulator a spaP SPI-1 surface presentation of antigens sprB SPI-1 transcriptional regulator ssaL SPI-2 secretion system apparatus protein AE008831 6.95 AE008832 1.90 2.13 E 07 0.0033 AE008831 1.99 0.0033 AE008761 1.63 0.0012 Virulence-associated fur Regulator of the Fur a regulon
"
1439,1440,1730.txt,8,0,,,,"A fur mutant is unable to grow on succinate as a sole carbon source due to a lack of positive regulation of the genes cycle by Fur .
"
1440,1441,1730.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,Putative regulation by Fur was evaluated by generating three isogenic S. Typhi deletion mutants of fur .
1441,1442,2239.txt,1,0,,,,"Furthermore , electrophoretic-mobility-shift assays showed that both H-NS bind to the ssrAB region containing the repressing sequences .
"
1442,1443,2239.txt,2,0,,,,"the mechanism by which H-NS regulate the expression of ssrAB for the first time that HilD is able to displace H-NS from one of its target genes
"
1443,1444,2239.txt,3,0,,,,"Our data from the expression analysis showed that H-NS regulate the expression of ssrAB mainly by acting on the 119/336 regions , respectively .
"
1444,1445,2239.txt,4,0,,,,"Our data from the expression analysis showed that H-NS regulate the expression of ssrAB mainly by acting on the 55/240 regions , respectively .
"
1445,1446,2239.txt,5,0,,,,"To further dissect ated regulation of ssrAB , we analyzed the interaction of H-NS to different segments of the 302/478 region by EMSAs .
"
1446,1447,2239.txt,6,0,,,,"To further dissect ated regulation of ssrAB , we analyzed the interaction of H-NS to different segments of the 302/478 region by electro-phoretic mobility-shift assays .
"
1447,1448,2239.txt,7,0,,,,"H-NS bind to the same regions of ssrAB .
"
1448,1449,2239.txt,8,0,,,,"DISCUSSION In this study , we elucidated the mechanism by which H-NS regulate the expression of ssrAB .
"
1449,1450,2239.txt,9,0,,,,"Furthermore , we showed that H-NS binds to the region 111 to 287 of ssrAB .
"
1450,1451,2239.txt,10,0,,,,"Furthermore , our EMSAs revealed that H-NS binds to at least two different sites along the 111/287 region of ssrAB .
"
1451,1452,2239.txt,11,0,,,,"the model in which H-NS represses the expression of ssrAB initially by binding by forming a nucleoprotein filament on the promoter
"
1452,1453,2239.txt,12,0,,,,The regions _ required for the regulation of ssrAB by H-NS
1453,1454,1056.txt,1,0,,,,"Thus , it is possible that AraC regulates transcription from the site within sseD under conditions ."
1454,1455,1042.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
1455,1456,1724.txt,1,0,,,,"The 210 and 235 regions of the putative RpoS-regulated promoter of yciG ( yciGp1 ) are underlined .
"
1456,1457,1724.txt,2,0,,,,"yciF was initially identified by a screen for RpoSregulated genes and a putative RpoS-dependent promoter has been located upstream of yciG [ 39 ] .
"
1457,1458,1724.txt,3,0,,,,"Because yciF was identified in a screen for RpoSregulated genes , we examined transcription of yciG : : luc with and without RpoS to determine if activation of yciGFE-katN by bile was dependent upon RpoS ."
1458,1459,1917.txt,1,0,,,,"Hence , binding of IHF to the lacZ promoters is unspecific , which is in line with previous data reporting that IHF binds DNA with lower affinity also in sequence-independent manner ."
1459,1460,529.txt,1,0,,,,Control of ssrB expression also includes activation by additional TCS PhoP/PhoQ and EnvZ/OmpR .
1460,1461,1903.txt,1,0,,,,"Thus , it is possible that RtsA can regulate the expression of ssrAB ."
1461,1462,267.txt,1,0,,,,"SprB , regulates the expression of sptP ."
1462,1463,501.txt,1,0,,,,"The Transcription Regulatory Function of LeuO Protein As part of the promoter relay mechanism , the expression of leuO is closely regulated at the chromosome site .
"
1463,1464,501.txt,2,0,,,,"For the leuO locus , LeuO-mediated regulation involves the binding of the protein to the promoter region .
"
1464,1465,501.txt,3,0,,,,"LeuO are involved in regulation of leuO .
"
1465,1466,501.txt,4,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"To study LeuO-dependent regulation of SPI-1 in S. enterica serovar Typhimurium , transcription of the leuO gene was freed from H-NS repression by introducing a T-POP element upstream of leuO ( Fig ."
1466,1467,1095.txt,1,0,,,,"However , repression of hilA by oleate is evident in the absence of FadR ."
1467,1468,1081.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Two-stage control of the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS gene .
"
1468,1469,1081.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Two-stage control of the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene .
"
1469,1470,1081.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,Two-stage control of the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS gene .
1470,1471,515.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) ."
1471,1472,273.txt,1,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"However , in contrast to E. coli , S. Typhimurium acnA was activated , by Fur .
"
1472,1473,273.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"However , the regulation of S. Typhimurium acnA differs from the stationary-phase induction of Furactivation observed in E. coli ."
1473,1474,924.txt,1,1,Salmonella,Salmonella,Salmonella,"Altogether , these results show that bapA , like csgAB , is regulated by CsgD , which plays a central role in biofilm formation in Salmonella strains .
"
1474,1475,924.txt,2,2,Salmonella;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Enteritidis;S. Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Interestingly , the gene bapA and genes of the capsule operons , which are regulated by CsgD in S. enterica serovar Enteritidis strains ( Latasa et al. , 2005 ; Gibson et al. , 2006 ) were not found to be CsgD-regulated in S. Typhimurium under the experimental conditions ."
1475,1476,1268.txt,1,0,,,,"As expected for a PhoP-activated gene , there was no slyA transcription when bacteria were grown under PhoP-repress-ing conditions ( i.e. 10 mM Mg2 ) , regardless of the presence of a functional phoP gene ( Fig. 4A ) .
"
1476,1477,1268.txt,2,1,synthetic construct,primer,synthetic construct,Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by PhoP because the mRNA level of transcripts is reduced significantly in the slyA mutants grown in low-Mg2 conditions -LRB- Fig .
1477,1478,2007.txt,1,0,,,,"Therefore , the LysR regulator LtrR is implicated in the regulation of envZ ."
1478,1479,2013.txt,1,0,,,,"Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .
"
1479,1480,2013.txt,2,0,,,,"Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .
"
1480,1481,2013.txt,3,0,,,,"Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM0459 , AsnC family transcriptional regulator .
"
1481,1482,2013.txt,4,0,,,,"Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; thymidine phosphorylase .
"
1482,1483,2013.txt,5,0,,,,"Six genes were shown to be activated by PmrA : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 ."
1483,1484,930.txt,1,0,,,,"Although MarA can act as an activator or repressor depending on the gene it is regulating , the repression of acrR allows expression of acrAB .
"
1484,1485,930.txt,2,0,,,,"Although MarA can act as an activator or repressor depending on the orientation of the mar box , the repression of acrR allows expression of acrAB ."
1485,1486,918.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS stabilization where PhoPQ participates by serving as a transcriptional activator of the iraP gene in S. Typhimurium
"
1486,1487,918.txt,2,0,,,,PhoPQ is specifically by increasing the transcription of iraP
1487,1488,1254.txt,1,0,,,,"Activation of dgkA gene is ensured by the two-basic regulator BasR , combining dgkA function of phospholipid ."
1488,1489,1532.txt,1,0,,,,"SsrBC Stimulates Transcription of sifB in Vitro in the Absence of Additional Factors -- To determine whether SsrB could directly activate transcription , we used purified SsrBC in an in-vitro-transcription assay ."
1489,1490,1526.txt,1,0,,,,fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of fliA by OmpR .
1490,1491,1240.txt,1,0,,,,"Schneiders T. , Levy S.B. MarA-mediated transcriptional repression of the rob promoter .
"
1491,1492,1240.txt,2,0,,,,"In agreement with these results , the molecular mechanism of repression of rob by MarA was shown to be due to steric hindrance at the level of the promoter region .
"
1492,1493,1240.txt,3,0,,,,"Furthermore , we demonstrate that MarA mediate repression of rob by binding to its promoter region .
"
1493,1494,1240.txt,4,0,,,,"rob is negatively regulated by MarA The transcript levels of rob in the DsoxS strains were repressed after treatment with NaOCl as in the wild type .
"
1494,1495,1240.txt,5,0,,,,"rob is negatively regulated by MarA The transcript levels of rob in the DmarA strains were repressed after treatment with NaOCl as in the wild type .
"
1495,1496,1240.txt,6,0,,,,"This confirms our previous results that repression of rob in the must have been due to overexpression of MarA .
"
1496,1497,1240.txt,7,0,,,,"The results above suggest that MarA could mediate together a repression of rob in response to NaOCl .
"
1497,1498,1240.txt,8,0,,,,"mean ± SD NaOC _ supporting our hypothesis of a repression of rob by both MarA and Sox
"
1498,1499,1240.txt,9,1,Escherichia coli,E. coli,Escherichia coli,"other studies _ performed in E. coli where rob was shown to be negatively regulated by both MarA by a direct interaction with its promoter region
"
1499,1500,1240.txt,10,0,,,,"the expression of rob is repressed by the transcription factors MarA
"
1500,1501,1240.txt,11,0,,,,"J Biol Chem 277:30463 -- 30468 Schneiders T , Levy SB MarA-mediated transcriptional repression of the rob promoter ."
1501,1502,1297.txt,1,0,,,,"Since one of our models proposes that Fur represses a repressor of HilD , we performed random mutagenesis of a strain with a fur deletion .
"
1502,1503,1297.txt,2,0,,,,"For example , hilD expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .
"
1503,1504,1297.txt,3,0,,,,"For example , rtsA expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .
"
1504,1505,1297.txt,4,0,,,,"For example , hilA expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes ."
1505,1506,703.txt,1,0,,,,"Besides the mgtA gene , only 2 of these 13 overlapping operons were directly regulated by the PhoPQ two-component system organisms .
"
1506,1507,703.txt,2,0,,,,"Besides the mgtA gene , only 2 of these 13 overlapping operons were directly regulated by the PhoPQ two-component system in .
"
1507,1508,703.txt,3,0,,,,"Superimposed on the regulation of transcription initiation by the PhoPQ system , the mgtA gene is subject to an additional control mechanism .
"
1508,1509,703.txt,4,1,Glyptocephalus cynoglossus,witch,Glyptocephalus cynoglossus,"The result that the expression of the mgtA-lacZ fusion is essentially insensitive to the Mg2 concentration in the ribos-witch mutants is unexpected , because the initiation of transcription at the mgtA promoter would be predicted to be subject to residual control by this cation via the PhoPQ system ."
1509,1510,717.txt,1,0,,,,four H-NS _ regulated yciG
1510,1511,1283.txt,1,0,,,,"Both the phoN mutant induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : a phoN Fig. 4A , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
1511,1512,1283.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Both the S. Typhimurium wild type induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : a phoN Fig. 4A , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
1512,1513,1283.txt,3,0,,,,"Both the phoN mutant induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : a phoN SW681 , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
1513,1514,1283.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Both the S. Typhimurium wild type induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : a phoN SW681 , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion ."
1514,1515,688.txt,1,0,,,,"These loci represent PmrA-activated genes , like those identified in this study , that are regulated by PmrA at the transcriptional level and that do contain ( yibD ) or do not contain ( dgoRKAT ) the consensus binding site ( within a 200 bp region upstream of the translational start ) binding of PmrA to dgop1 , PmrA was incubated with dgop1 and specific or non-specific cold ( unlabeled ) competitors .
"
1515,1516,688.txt,2,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .
"
1516,1517,688.txt,3,0,,,,"The PmrA-activated yibD and dgoA genes are dispensable for resistance to polymyxin B and Fe ( III ) ( Tamayo et al. , 2002 ) ."
1517,1518,10.txt,1,0,,,,"Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) ."
1518,1519,850.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
1519,1520,850.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
1520,1521,2173.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Regulation of expression of the ethanol dehydrogenase gene ( adhE ) in Escherichia coli by catabolite repressor activator protein Cra .
1521,1522,2167.txt,1,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .
"
1522,1523,2167.txt,2,0,,,,"These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the prgs prgHIJK .
"
1523,1524,2167.txt,3,0,,,,These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- repression of the PhoP-repressed genes prgHIJK .
1524,1525,1308.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To circumvent this issue and facilitate the examination of YdcRregulated srfN transcription in-vitro , we further introduced a YdcR-expressing plasmid into the ydcR strain , whose expression is under the control of arabinose .
"
1525,1526,1308.txt,2,0,,,,"Furthermore , we found evidence that YdcR directly control its expression on the transcriptional level by binding to the promoter region of the srfN gene .
"
1526,1527,1308.txt,3,0,,,,"Futhermore,-galactosidase assays were used to establish the transcriptional control of the srfN gene by YdcR .
"
1527,1528,1308.txt,4,0,,,,"Taken together , these results indicate that YdcR controls the expression of the srfN gene at the transcriptional level .
"
1528,1529,1308.txt,5,0,,,,"First , we used qRT-PCR to measure the transcript levels of srfN and found the regulation of YdcR on the expression of SrfN indeed occurs on the transcriptional level .
"
1529,1530,1308.txt,6,1,Salmonella;Salmonella,Sal-monella;monella,Salmonella,Further-galactosidase assays of Sal-monella strains also confirmed that YdcR can mediate transcriptional regulation of srfN in bacteria .
1530,1531,844.txt,1,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK ."
1531,1532,1320.txt,1,1,Terfezia albida,to 15,Terfezia albida,"Compared with the wild type , the expression levels of the pmrH gene in the mutants with reduced susceptibility were increased 2-to 15-fold , showing that the pmrB mutations changed the regulation of the PmrA-PmrB-dependent genes ."
1532,1533,1446.txt,1,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,HU has been reported to regulate narH positively in E. coli whereas hupA acts negatively on narH transcription in Salmonella -LRB- Supplementary Fig .
1533,1534,1452.txt,1,0,,,,"7 min 25 min hilD AraC-family SPI1 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of ( groEL , groES , grpE , SEN1800 and ht encoding heat-shock proteins .
"
1534,1535,1452.txt,2,0,,,,"7 min 25 min hilD AraC-family transcriptional regulator 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of ( groEL , groES , grpE , SEN1800 and ht encoding heat-shock proteins ."
1535,1536,1334.txt,1,0,,,,"7 min 25 min hilD AraC-family SPI1 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of f gen encoding heat-shock proteins .
"
1536,1537,1334.txt,2,0,,,,7 min 25 min hilD AraC-family transcriptional regulator 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of f gen encoding heat-shock proteins .
1537,1538,38.txt,1,0,,,,"that HilC are each capable of independently inducing expression of the hilD genes
"
1538,1539,38.txt,2,0,,,,"We demonstrate that HilC are each capable of inducing expression of hilD .
"
1539,1540,38.txt,3,0,,,,"We wanted to determine if HilC could induce expression of hilD in the absence of the other regulators .
"
1540,1541,38.txt,4,0,,,,"HilC also induced expression of hilD .
"
1541,1542,38.txt,5,0,,,,"HilC induced expression of hilD ~ 10-to 12-fold .
"
1542,1543,38.txt,6,0,,,,"These data show that HilC are each capable of independently inducing expression of hilD , consistent with our model that HilC constitute a feed forward regulatory loop .
"
1543,1544,38.txt,7,0,,,,"We show that HilC can each independently activate expression of the hilD genes .
"
1544,1545,38.txt,8,0,,,,"HilC are clearly able to induce hilD transcription .
"
1545,1546,38.txt,9,0,,,,"HilC are all also capable of activating expression of hilD independent of each other and comprise a complex feed forward regulatory loop .
"
1546,1547,38.txt,10,0,,,,"HilC is known to independently activate hilD transcription
"
1547,1548,38.txt,11,0,,,,Figure 5A shows that hilD transcription was induced by both HilC in the hilD background .
1548,1549,878.txt,1,0,,,,"FimW inhibition of type 1 fimbrial production may be mediated by repression of the promoter activity of fimY .
"
1549,1550,878.txt,2,0,,,,FimW inhibition of type 1 fimbrial production may be mediated by repression of the promoter activity of fimY .
1550,1551,893.txt,1,0,,,,"We found induction of the OxyR-dependent trxC gene .
"
1551,1552,893.txt,2,0,,,,induction of the OxyR-dependent trxC gene _ encoding thioredoxin-2
1552,1553,139.txt,1,0,,,,"However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig ."
1553,1554,887.txt,1,0,,,,"For example , sopB seem to be regulated directly by InvF through modulation of invF expression .
"
1554,1555,887.txt,2,0,,,,sopB is known to be controlled by the SPI-1 regulator InvF
1555,1556,677.txt,1,0,,,,Direct regulation of glpA genes by SlyA in response to ROS .
1556,1557,1485.txt,1,0,,,,"The response regulator PhoP was found to play a key role in the repression of tlpA in conjunction with two other regulators , TlpA itself .
"
1557,1558,1485.txt,2,0,,,,"The response regulator PhoP was found to play a key role in the repression of tlpA in conjunction with two other regulators , RpoS itself .
"
1558,1559,1485.txt,3,0,,,,"Consistent with that , a putative PhoP binding motif was identified in the upstream region of tlpA , suggesting that PhoP may directly repress tlpA expression .
"
1559,1560,1485.txt,4,0,,,,"The presence of a PhoP binding sequence in the promoter region would indicate that the repression of tlpA by PhoP is direct ; however , further studies are needed in order to confirm this ."
1560,1561,111.txt,1,0,,,,"Other genes varied in prevalence , including trhH ( encoding pilus assembly protein ) , sirA ( two-component system with barA ) , pagK ( PhoPQ-activated protein ) , and sseK1 ( encoding putative-secreted effector protein ) .
"
1561,1562,111.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Paratyphi,S. Typhimurium;Typhimurium;Paratyphi,Salmonella enterica subsp. enterica serovar Paratyphi;Salmonella enterica subsp. enterica serovar Typhimurium,"In contrast to S. Typhimurium and S. Paratyphi B dT , no pagK ( encoding a PhoPQ-activated protein ) was detected , but stkC was present .
"
1562,1563,111.txt,3,0,,,,"Furthermore , PAT DE4 was positive for the outer membrane receptor gene instead of but no signal was obtained for the islet genes htrE ( probable porin/fimbrial assembly protein ) , sopD2 ( secreted effector protein ) , srfJ ( putative virulence factor , activated by transcription factor SsrB ) and sseK2 ( translocated effector protein SSEK2 by type III secretion system ) while pagK ( PhoPQ-activated protein ) was present only in this array type ."
1563,1564,2198.txt,1,0,,,,The mgtCB operon is regulated by the PhoP .
1564,1565,105.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
1565,1566,105.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
1566,1567,1491.txt,1,0,,,,"HilD , regulates the expression of phoH .
"
1567,1568,1491.txt,2,0,,,,"that HilD directly controls the expression of the phoH genes
"
1568,1569,1491.txt,3,0,,,,"HilD binds to the regulatory regions of phoH .
"
1569,1570,1491.txt,4,0,,,,"To further define whether the HilD-mediated regulation of phoH is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .
"
1570,1571,1491.txt,5,0,,,,"To further define whether the HilD-mediated regulation of phoH is direct , we analyzed the interaction of HilD with the regulatory region of these genes .
"
1571,1572,1491.txt,6,0,,,,"Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the phoH genes .
"
1572,1573,1491.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,S. Typhimurium;S. Typhimurium SL1344;Typhimurium;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium,"In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : phoH .
"
1573,1574,1491.txt,8,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of phoH .
"
1574,1575,1491.txt,9,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of phoH .
"
1575,1576,1491.txt,10,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of phoH .
"
1576,1577,1491.txt,11,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of phoH .
"
1577,1578,1491.txt,12,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of phoH .
"
1578,1579,1491.txt,13,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of phoH .
"
1579,1580,1491.txt,14,2,Felis catus;Escherichia coli,cat;E. coli,Felis catus;Escherichia coli,"Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of phoH .
"
1580,1581,1491.txt,15,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of phoH .
"
1581,1582,1491.txt,16,2,Felis catus;Salmonella;Salmonella,cat;Salmonella;Salmonella-specific,Felis catus;Salmonella,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of phoH .
"
1582,1583,1491.txt,17,0,,,,"Thus , HilD directly regulates the expression of the phoH genes , and positively .
"
1583,1584,1491.txt,18,0,,,,HilD binds to the regulatory region of phoH .
1584,1585,663.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential-growth and a decrease in expression during stationary-phase ( Xu and Johnson , 1995 ) .
"
1585,1586,663.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,SL1344;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344,"proP and other Intraperitoneal LD50 5 , 25 , 25 4 10 3 10 7 SL1344 SL1344 fis : : kan Fis-regulated promoters have been found to have both low-affinity and high-affinity Fis binding sites ."
1586,1587,1678.txt,1,0,,,,"Thus , SsrBC directly regulates transcription of sseJ by binding upstream of the respective promoters ."
1587,1588,1644.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of fimA genes
"
1588,1589,1644.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of fimA genes"
1589,1590,1122.txt,1,1,Salmonella,Salmonella,Salmonella,"By 120 min , the PmrA-dependent lipid-A modifications were wild-type Salmonella and expressed lower amounts of pbgP transcript than Figures 6B .
"
1590,1591,1122.txt,2,1,Salmonella,Salmonella,Salmonella,"By 120 min , the PmrA-dependent lipid-A modifications were wild-type Salmonella and expressed lower amounts of pbgP transcript than the ugd mutant .
"
1591,1592,1122.txt,3,1,Salmonella,Salmonella,Salmonella,"By 120 min , the PmrA-dependent lipid-A modifications were visible Salmonella and expressed lower amounts of pbgP transcript than Figures 6B .
"
1592,1593,1122.txt,4,1,Salmonella,Salmonella,Salmonella,"By 120 min , the PmrA-dependent lipid-A modifications were visible Salmonella and expressed lower amounts of pbgP transcript than the ugd mutant ."
1593,1594,1136.txt,1,0,,,,"Interestingly , both regulons are controlled by the argR repressor , while the biosynthesis genes of the other amino-acids are controlled by TrpR .
"
1594,1595,1136.txt,2,0,,,,"Interestingly , both regulons are controlled by the argR repressor , while the biosynthesis genes of the other amino-acids are controlled by TrpR ."
1595,1596,1650.txt,1,0,,,,"The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .
"
1596,1597,1650.txt,2,0,,,,"Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB-and RcsA-dependent colanic acid capsule synthesis cps operon .
"
1597,1598,1650.txt,3,0,,,,"Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB-and RcsA-dependent colanic acid capsule synthesis cps operon .
"
1598,1599,1650.txt,4,0,,,,"These results indicate that constitutive expression and/or inhibition of RcsB-regulated genes inhibits phagocytosis , possibly resulting from capsule overproduction , and reduces bacterial replication within macrophages in a mechanism that requires genes in addition to rcsA and cps .
"
1599,1600,1650.txt,5,0,,,,"The regulatory gene rcsA are responsible , in part , for the virulence attenuation of the rcsC11 mutant Genes under the control of the RcsB protein can be divided into two groups ."
1600,1601,1888.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"StpA repressed ompS1 expression in a mutant hns background H-NS negatively regulates ompS1 expression in both S. Typhimurium .
"
1601,1602,1888.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,StpA repressed ompS1 expression in a mutant hns background H-NS negatively regulates ompS1 expression in both S. Typhi .
1602,1603,1863.txt,1,0,,,,hilA expression in the hha strain increased 181-fold compared with H-NSWT levels .
1603,1604,449.txt,1,0,,,,"In the absence-of-arabinose , AraC represses transcription of araBAD by forming a repression loop .
"
1604,1605,449.txt,2,0,,,,"Although arabinose-dependent repression by AraC has not been observed before , there are clear parallels with arabinose-de-pendent activation of araBAD transcription .
"
1605,1606,449.txt,3,0,,,,"Thus , arabinose-dependent repression of ydeNM by AraC would use the same mechanism as arabinose-dependent activation of araBAD ."
1606,1607,1877.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To investigate the contribution of the ClpXP protease to the virulence of serovar Typhimurium we initially cloned the clpP operon from the pathogenic strain serovar Typhimurium x3306
"
1607,1608,1877.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To measure the contribution of the ClpXP protease in serovar Typhimurium virulence , we determined the abilities of serovar Typhimurium clpP : Cm , clpP : clpX .
"
1608,1609,1877.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To measure the contribution of the ClpXP protease in serovar Typhimurium virulence , we determined the abilities of serovar Typhimurium clpP : Cm , clpP : Km .
"
1609,1610,1877.txt,4,0,,,,"Levels of FlhC , in the ClpXP protease-depleted mutant Our previous study showed that the level of bgalactosidase activity in cells was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpP .
"
1610,1611,1877.txt,5,0,,,,"Levels of FlhD , in the ClpXP protease-depleted mutant Our previous study showed that the level of bgalactosidase activity in cells was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpP .
"
1611,1612,1877.txt,6,0,,,,"Levels of master regulators , in the ClpXP protease-depleted mutant Our previous study showed that the level of bgalactosidase activity in cells was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpP ."
1612,1613,313.txt,1,0,,,,"Of note , it seems unlikely that the increased degradation of HilD is mediated by changes in protease expression or activity , as the expression of lon is not increased by bile treatment ."
1613,1614,1687.txt,1,3,Salmonella;Salmonella enterica;Salmonella;unidentified,Salmonella;Salmonella enterica;enterica;unknown,Salmonella enterica;unidentified;Salmonella,"In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary-phase ( 4 ) ."
1614,1615,475.txt,1,0,,,,"HilE negatively regulates hilA transcription .
"
1615,1616,475.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimu,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimu-rium invasive phenotype .
"
1616,1617,475.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of Salmonella enterica serovar Typhimurium invasive phenotype .
"
1617,1618,475.txt,4,0,,,,"HilD _ suggesting that HilE represses expression of hilA by inhib-iting the activity of HilD
"
1618,1619,475.txt,5,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1619,1620,475.txt,6,1,hybrid,hybrid,hybrid,"HilE has been shown via two-hybrid studies to interact with HilD , suggesting that HilE represses hilA by directly preventing HilD function .
"
1620,1621,475.txt,7,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1621,1622,475.txt,8,0,,,,"Positive regulators include HilD , while HilE are negatively regulating hilA transcription .
"
1622,1623,475.txt,9,0,,,,"Positive regulators include CsrB , while HilE are negatively regulating hilA transcription .
"
1623,1624,475.txt,10,0,,,,"Positive regulators include FadD , while HilE are negatively regulating hilA transcription .
"
1624,1625,475.txt,11,0,,,,"Positive regulators include EnvZ/OmpR , while HilE are negatively regulating hilA transcription .
"
1625,1626,475.txt,12,0,,,,"Positive regulators include FliZ , while HilE are negatively regulating hilA transcription .
"
1626,1627,475.txt,13,0,,,,"Positive regulators include BarA/SirA , while HilE are negatively regulating hilA transcription .
"
1627,1628,475.txt,14,0,,,,"Positive regulators include Fis , HU , while HilE are negatively regulating hilA transcription .
"
1628,1629,475.txt,15,0,,,,"Positive regulators include some nucleoid binding proteins , while HilE are negatively regulating hilA transcription .
"
1629,1630,475.txt,16,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1630,1631,475.txt,17,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"2003 HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1631,1632,475.txt,18,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1632,1633,475.txt,19,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1633,1634,475.txt,20,1,hybrid,hybrid,hybrid,"We have shown by two-hybrid analysis that HilE interacts with HilD to repress hilA transcription .
"
1634,1635,475.txt,21,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1635,1636,475.txt,22,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1636,1637,475.txt,23,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1637,1638,475.txt,24,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1638,1639,475.txt,25,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1639,1640,475.txt,26,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Baxter , M. A. , Fahlen , T. F. , Wilson , R. L. & Jones , B. D. HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
"
1640,1641,475.txt,27,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,HilE negatively regulates hilA transcription and expression of the Salmonella enterica serovar Typhimurium invasive phenotype .
1641,1642,461.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .
"
1642,1643,461.txt,2,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in hcp , ygbA , ytfE , STM1808 and yeaR ( Experimental Procedures ) ."
1643,1644,1693.txt,1,0,,,,Among these RpoS-induced genes the dinB gene encoding the trans-lesion DNA polymerase Pol IV can be found ( Layton and Foster 2003 ) .
1644,1645,307.txt,1,0,,,,"The promoter of the purHD operon , is repressed by the PurR protein ."
1645,1646,460.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
1646,1647,306.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
1647,1648,1692.txt,1,1,Escherichia virus 186,coliphage 186,Escherichia virus 186,"All three phage genomes included a homologue of the tum gene of coliphage 186 , which encodes a LexA-repressed cI antirepressor .
"
1648,1649,1692.txt,2,0,,,,"Control region of Fels-2 tum gene includes a LexA-repressed promoter .
"
1649,1650,1692.txt,3,0,,,,"The tum homologue of Fels-2 was responsible for lexA lethality and had a LexA-repressed promoter .
"
1650,1651,1692.txt,4,0,,,,LexA protein represses the phage tum
1651,1652,1686.txt,1,0,,,,"slyA is positively regulated by HilD
"
1652,1653,1686.txt,2,0,,,,slyA is positively regulated by HilD
1653,1654,312.txt,1,0,,,,"Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with wild-type MAE52 , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant -LRB- Fig. 3C ; Fig .
"
1654,1655,312.txt,2,0,,,,"Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with S2 , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant -LRB- Fig. 3C ; Fig .
"
1655,1656,312.txt,3,0,,,,"Unexpectedly , the rpoS mutant of MAE52 showed higher CsgD levels compared with Figs. 3C , probably an indirect effect due to the lack of cellulose expression .36 CsgD was downregulated by 52 % after 16 h in the hfq rpoS double mutant in comparison with the rpoS single mutant -LRB- Fig. 3C ; Fig ."
1656,1657,474.txt,1,0,,,,"Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- S -RSB- cluster is reversibly inactivated by NO .
"
1657,1658,474.txt,2,0,,,,"Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- Fe is reversibly inactivated by NO .
"
1658,1659,474.txt,3,0,,,,"genes _ involved in nitrosative-stress protection under the control of NsrR ( hmpA , , ygbA , hcp , yeaR-yoaG )"
1659,1660,1876.txt,1,0,,,,"The region occupied by SlyA covers the 35 promoter elements , thus by binding at these sites SlyA denies RNA polymerase access to the promoter , thereby repressing slyA expression .
"
1660,1661,1876.txt,2,0,,,,"The region occupied by SlyA covers the 10 promoter elements , thus by binding at these sites SlyA denies RNA polymerase access to the promoter , thereby repressing slyA expression .
"
1661,1662,1876.txt,3,0,,,,"The size and location of the relatedness of the DNA sequences within the region indicated that at least five SlyA dimers bind at PslyA to repress slyA expression .
"
1662,1663,1876.txt,4,0,,,,The size and location of the region of protection indicated that at least five SlyA dimers bind at PslyA to repress slyA expression .
1663,1664,1862.txt,1,0,,,,"Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) .
"
1664,1665,1862.txt,2,1,unidentified,unknown,unidentified,"However , given that the Fur regulators can efficiently control feoB mRNA levels in response to different levels of iron , the reason remains unknown .
"
1665,1666,1862.txt,3,1,unidentified,unknown,unidentified,"However , given that the Fur regulators can efficiently control feoB mRNA levels in response to different levels of oxygen , the reason remains unknown ."
1666,1667,448.txt,1,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) ."
1667,1668,1137.txt,1,0,,,,"This is consistent with RNA-seq analysis results , where , in the presence of NaOCl , glpA expression in WT showed a log2 fold-change of 3.6 compared to the mutant , suggesting that glpA is upregulated by SlyA .
"
1668,1669,1137.txt,2,0,,,,These results suggest that SlyA upregulates the glpA gene .
1669,1670,1889.txt,1,0,,,,Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in def mutant with a concomitant 50-fold reduction in deletion rate .
1670,1671,1651.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium virK is positively regulated by PhoP/PhoQ .
1671,1672,1645.txt,1,0,,,,"the response regulator CsgD in turn regulates the transcription of adrA
"
1672,1673,1645.txt,2,0,,,,"In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 : : csgD ] , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of its own promoter , which exclusively activates cellulose A C Arabinose 0.1 % Glucose 0.1 % 3934 3934BADstm2689 B 3934BADstm2689 3934 3934 ara gluc ∆ stm2689 205 kD Fig. 3 .
"
1673,1674,1645.txt,3,0,,,,"In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring : csgD , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of of its own prom .
"
1674,1675,1645.txt,4,0,,,,"In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of of its own prom .
"
1675,1676,1645.txt,5,1,Salmonella,Salmonella,Salmonella,"Altogether , these results show that bapA , like adrA , is regulated by CsgD , which plays a central role in biofilm formation in Salmonella strains .
"
1676,1677,1645.txt,6,0,,,,"Positive regulation by CsgD is indicated by solid lines because putative CsgD binding sites have been found upstream from the adrA promoters .
"
1677,1678,1645.txt,7,0,,,,"CsgD controls the expression of adrA .
"
1678,1679,1645.txt,8,0,,,,"Indeed , it has been suggested , although it has never been shown , that CsgD binds to conserved 11-bp sequences upstream of the adrA promoters , activating transcription of these genes .
"
1679,1680,1645.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to adrA promoter regions In S. Typhimurium the expression of adrA is positively regulated by the transcriptional regulator CsgD .
"
1680,1681,1645.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to adrA promoter regions In S. Typhimurium the expression of adrA is positively regulated by the transcriptional regulator CsgD .
"
1681,1682,1645.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to adrA promoter regions In S. Typhimurium the expression of csgBA is positively regulated by the transcriptional regulator CsgD .
"
1682,1683,1645.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Results CsgD binds directly to the csgBA In S. Typhimurium the expression of adrA is positively regulated by the transcriptional regulator CsgD .
"
1683,1684,1645.txt,13,0,,,,"In order to demonstrate the direct binding of CsgD to the adrA promoter regions we performed EMSA with purified CsgD-His6 tagged protein ( Fig .
"
1684,1685,1645.txt,14,0,,,,"In order to demonstrate the direct binding of CsgD to the adrA promoter regions we performed electrophoretic-mobility-shift assays with purified CsgD-His6 tagged protein ( Fig .
"
1685,1686,1645.txt,15,0,,,,"Since CsgD is highly integrated into the c-di-GMP signalling network , we investigated whether c-di-GMP affects the binding of CsgD-His6 to adrA promoter region .
"
1686,1687,1645.txt,16,0,,,,"To investigate the binding of CsgD to the adrA promoter region , a 257 bp 32P-labelled fragment from bp -222 to +35 was subjected to Fig. 2E .
"
1687,1688,1645.txt,17,0,,,,"To investigate the binding of CsgD to the adrA promoter region , a 257 bp 32P-labelled fragment from bp -222 to +35 was subjected to DNase I footprint analysis .
"
1688,1689,1645.txt,18,0,,,,"Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA , compared with Fig. 5A .
"
1689,1690,1645.txt,19,0,,,,"Pre-incubation of CsgD-His6 with 10 mM AcP led to a decreased binding of CsgD to the adrA , compared with CsgD alone .
"
1690,1691,1645.txt,20,0,,,,"Since the binding of CsgD to the adrA promoter regions is altered in the presence of the phosphodonor AcP , we investigated whether CsgD can be phosphorylated in-vitro .
"
1691,1692,1645.txt,21,0,,,,"However , we discovered that c-di-GMP , is not required for binding of CsgD to the adrA promoters .
"
1692,1693,1645.txt,22,0,,,,"However , we discovered that an integral part of the regulatory network , is not required for binding of CsgD to the adrA promoters .
"
1693,1694,1645.txt,23,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene involved in bio-film formation , EPS production
"
1694,1695,1645.txt,24,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene involved in bio-film formation , transport production
"
1695,1696,1645.txt,25,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene involved in bio-film formation , virulence production
"
1696,1697,1645.txt,26,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of lpfE genes
"
1697,1698,1645.txt,27,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of fimA genes
"
1698,1699,1645.txt,28,1,Vibrio cholerae,Vibrio cholerae,Vibrio cholerae,"In contrast to the CsgD homolog in Vibrio cholerae , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .
"
1699,1700,1645.txt,29,0,,,,"In contrast to VpsT , CsgD does not bind c-di-GMP as CsgD-mediated transcriptional activation of adrA is unaffected by c-di-GMP in-vitro .
"
1700,1701,1645.txt,30,0,,,,"To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgB , coding for adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids .
"
1701,1702,1645.txt,31,0,,,,"To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD , coding for adrA , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids ."
1702,1703,1123.txt,1,0,,,,"In S. Tm , cib expression is negatively regulated in a Fur - dependent way .
"
1703,1704,1123.txt,2,1,Dipturus trachyderma,ray,Dipturus trachyderma,"In S. Tm , cib expression is negatively regulated in a Fur - locus for x-ray sensitivity A .
"
1704,1705,1123.txt,3,0,,,,"In S. Tm , cib expression is negatively regulated in a Fur - LexA ."
1705,1706,1679.txt,1,0,,,,"Recent work by Lee et al. revealed that the expression of ssrAB itself is regulated by OmpR ± Env .
"
1706,1707,1679.txt,2,1,Salmonella,Salmonella,Salmonella,"As OmpR also controls the expression of the acid-induced virulence operon ssrAB , acid shock induction of ompR was examined to gain insight into how Salmonella links virulence with survival at extreme acid-pH .
"
1707,1708,1679.txt,3,0,,,,"Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .
"
1708,1709,1679.txt,4,1,Salmonella,Salmonella,Salmonella,"As OmpR also controls the expression of the acid-induced virulence operon ssrAB , acid shock induction of ompR was examined to gain insight into how Salmonella links virulence with survival at extreme acid-pH .
"
1709,1710,1679.txt,5,0,,,,"Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .
"
1710,1711,1679.txt,6,0,,,,"turn _ regulated by the OmpR -- EnvZ two-component system , by direct binding of OmpR to the ssrAB promoter
"
1711,1712,1679.txt,7,0,,,,"turn _ regulated by the OmpR -- EnvZ two-component system , by direct binding of OmpR to the ssrAB promoter
"
1712,1713,1679.txt,8,0,,,,"OmpR binds directly to the ssrAB promoter .
"
1713,1714,1679.txt,9,0,,,,"These results indicate that other than ssrAB , is not a result of direct binding of OmpR to their promoters .
"
1714,1715,1679.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR is also known to interact with the endogenous two-component regulator of SPI-2 , ssrAB in S. Typhimurium .
"
1715,1716,1679.txt,11,0,,,,"OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrB proteins .
"
1716,1717,1679.txt,12,0,,,,"OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA proteins .
"
1717,1718,1679.txt,13,0,,,,"The expression of the SsrA-SsrB two-component system is regulated by the OmpR-EnvZ two-component system by OmpR binding directly to the ssrAB promoter .
"
1718,1719,1679.txt,14,0,,,,"Since OmpR binds to the 83/6 region , it is possible that the sequence is involved in the positive regulation of ssrAB by OmpR .
"
1719,1720,1679.txt,15,0,,,,"To determine how OmpR to regulate the expression of ssrAB in response to different growth-conditions is a matter of future studies .
"
1720,1721,1679.txt,16,0,,,,To determine how OmpR to regulate the expression of ssrAB in response to different growth-conditions is a matter of our current .
1721,1722,1490.txt,1,0,,,,RpoS ( as ) was found to be required for N starvation induction of stiA .
1722,1723,104.txt,1,1,unidentified,not shown,unidentified,"P-galac-tosidase activities were determined in a constitutively derepressed crp mutant background in order to quantitate promoter activities independent of regulation by CAMP-CRP -LRB- the results were unaffected by addition of CAMP-data not shown -RRB- .
"
1723,1724,104.txt,2,0,,,,"Therefore , overproduction of cAMP by crp mutants must be the indirect consequence of a defect in CRP-mediated regulation of adenylate cyclase activity rather thancya expression , a conclusion .
"
1724,1725,104.txt,3,0,,,,"Therefore , overproduction of cAMP by crp mutants must be the direct consequence of a defect in CRP-mediated regulation of adenylate cyclase activity rather thancya expression , a conclusion .
"
1725,1726,104.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Mechanism of the down-regulation of cAMP-receptor-protein by glucose in Escherichia coli : role of autoregulation of the crp gene .
"
1726,1727,104.txt,5,1,Salmonella,Salmonella,Salmonella,"One possible route would be regulation of crp by SdsR , for CRP-deficient Salmonella display altered susceptibility to antibiotic challenge ."
1727,1728,2199.txt,1,0,,,,"Downstream of oafA , but within the same horizontal acquisition , is the site of a second SsrB-regulated fusion ( srfE ) , within an msgA ( macrophage survival gene ) 29 homologue ( P 10 ; Fig. 2 ) ."
1728,1729,662.txt,1,0,,,,"3.7 PhoPQ represses transcription of the class 3 flagellar gene fliC whereas RpoS mildly induces it Assembly of the bacterial flagellum requires the expression of nearly 50 genes .
"
1729,1730,662.txt,2,0,,,,"Further analysis indicated that PhoPQ also negatively regulates class fliC as the level of ten-fold repression in transcription .
"
1730,1731,662.txt,3,0,,,,Further analysis indicated that PhoPQ also negatively regulates class fliC as the level of transcription .
1731,1732,676.txt,1,0,,,,"However , our data also show that both deletion of cpxA of CpxR slightly repress the expression of the SPI-1 genes in the absence of the Lon protease , suggesting an additional minor Lon-independent mechanism for the repression of the SPI-1 genes by CpxR-P ."
1732,1733,110.txt,1,0,,,,narJ are positively regulated by SlyA
1733,1734,1484.txt,1,0,,,,"Since the lethality was not relieved by mutations by inactivation of RcsA , it can be concluded that cps genes do not participate in yrfF lethality ."
1734,1735,138.txt,1,0,,,,"63 PhoPQ-regulated PhoPQ-regulated pagO sopD 0 ?
"
1735,1736,138.txt,2,0,,,,To the functional category related to the `` cell envelope 
1736,1737,886.txt,1,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , have been associated with increased acrB .
"
1737,1738,886.txt,2,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , MarA , have been associated with increased acrB .
"
1738,1739,886.txt,3,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , SoxS , have been associated with increased acrB .
"
1739,1740,886.txt,4,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , RamA , have been associated with increased acrB ."
1740,1741,892.txt,1,0,,,,"Results from DNase-I-protection assays provide direct evidence that SsrB binds at ssrA , although the binding sites lie within the .
"
1741,1742,892.txt,2,0,,,,"In addition , the SsrB regulator also directly binds and autoregulates the ssrA promoters to activate their expression .
"
1742,1743,892.txt,3,1,Salmonella,Salmonella,Salmonella,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we examined biofilm formation of Salmonella strains possessing H867Q mutations in ssrA ( Kenney unpublished ) .
"
1743,1744,892.txt,4,1,Salmonella,Salmonella,Salmonella,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we examined biofilm formation of Salmonella strains possessing H867Q mutations in ssrA ( Walthers unpublished ) .
"
1744,1745,892.txt,5,1,Salmonella,Salmonella,Salmonella,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we examined biofilm formation of Salmonella strains possessing D739A mutations in ssrA ( Kenney unpublished ) .
"
1745,1746,892.txt,6,1,Salmonella,Salmonella,Salmonella,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we examined biofilm formation of Salmonella strains possessing D739A mutations in ssrA ( Walthers unpublished ) .
"
1746,1747,892.txt,7,1,Salmonella,Salmonella,Salmonella,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we examined biofilm formation of Salmonella strains possessing H405Q mutations in ssrA ( Kenney unpublished ) .
"
1747,1748,892.txt,8,1,Salmonella,Salmonella,Salmonella,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we examined biofilm formation of Salmonella strains possessing H405Q mutations in ssrA ( Walthers unpublished ) .
"
1748,1749,892.txt,9,0,,,,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we compared them to ssrA ."
1749,1750,1453.txt,1,0,,,,"The modifications include the PhoP/PhoQ-regulated expression of pagP , which is involved in the acylation at position 2 of the proximal unit of lipid-A ( Bishop , 2005 ) , and the PmrA/PmrB-controlled expression of the factors required for the addition of 4-amino-4-deoxy-L-arabinose ( L-Ara4N ) and phosphoethanolamine ( pEtN ) to phosphate groups of the lipid-A ( Groisman et al. , 1997 ; Gunn et al. , 2000 ; Lee et al. , 2004 ) ."
1750,1751,879.txt,1,1,Mus sp.,mice,Mus sp.,"Mutants in pmrE or pmrF , two PmrA-activated loci , lack Ara4N modification to lipid-A and demonstrate reduced virulence when administered orally to mice ( 19 ) .
"
1751,1752,879.txt,2,0,,,,"A drop of extracellular ion concentration from the millimolar to micromolar range can also promote PmrA-mediated upregulation of the pmrF operon .
"
1752,1753,879.txt,3,3,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.,S. enterica;enterica;Typhimurium;mice,Mus sp.;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Additionally , previously identified PmrA-activated genes , such as pmrE and pmrF that affect Ara4N biosynthesis , have been shown to play a role in virulence of S. enterica serovar Typhimurium in mice [ 7,14 ] .
"
1753,1754,879.txt,4,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .
"
1754,1755,879.txt,5,0,,,,"The PmrA-activated pbgPE operon [ also referred to as arn ( Breazeale et al. , 2003 ) and pmrF ( Gunn et al. , 1998 ) ] consists of seven genes ."
1755,1756,39.txt,1,0,,,,There was no evidence of SsrB binding at ssaR .
1756,1757,1335.txt,1,0,,,,"B. Troxell , M.L. Sikes , R.C. Fink , A. Vazquez-Torres , J. Jones-Carson , H.M. Hassan , Fur egatively regulates hns ."
1757,1758,1321.txt,1,0,,,,"slyA _ controlled by PhoP/PhoQ regulatory systems , to promote intracellular bacterial survival in the phagosome
"
1758,1759,1321.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,Analysis of the transcriptome of the S. typhimurium slyA mutant revealed that many slyA-dependent genes are also controlled by the magnesium-sensing PhoP/PhoQ regulatory system .
1759,1760,1447.txt,1,0,,,,"To better characterize the contribution of RcsA to persistence within tomatoes , rcsB genes were deleted"
1760,1761,2166.txt,1,0,,,,"RtsB negatively regulates flhDC
"
1761,1762,2166.txt,2,0,,,,"RtsB negatively regulates flhDC
"
1762,1763,2166.txt,3,0,,,,"RtsB negatively regulates expression of flhDC .
"
1763,1764,2166.txt,4,0,,,,"RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon .
"
1764,1765,2166.txt,5,0,,,,"In turn , RtsB represses the flhDC promoter ."
1765,1766,845.txt,1,1,unidentified,not shown,unidentified,The unique pattern of expression of sseJ was also found not to be attributable to coordinate regulation by PhoPQ ( not shown ) .
1766,1767,1309.txt,1,0,,,,"Intracellular induction of HA-tagged PipB expression is not detected for an SsrB mutant ( ssrB : : kan ) .
"
1767,1768,1309.txt,2,0,,,,"SsrB , in turn , activates ssrB .
"
1768,1769,1309.txt,3,0,,,,"SsrB , in turn , activates ssrB .
"
1769,1770,1309.txt,4,0,,,,"These results demonstrated that SsrB is necessary to activate the ssrB promoter even in the absence of PmrA repression .
"
1770,1771,1309.txt,5,0,,,,"Because the putative 19-bp Fur box is located only 5 bp because Fur binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .
"
1771,1772,1309.txt,6,0,,,,"Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site on Fig. 4A binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .
"
1772,1773,1309.txt,7,0,,,,"Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site on the ssrB promoter binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter ."
1773,1774,851.txt,1,0,,,,"hilA are negatively regulated by SlyA
"
1774,1775,851.txt,2,0,,,,Direct regulation of hilA genes by SlyA in response to ROS .
1775,1776,11.txt,1,0,,,,"CRP together with AraC , which is active only in the presence of i.e. the secondary signal , bind to the araBAD promoter
"
1776,1777,11.txt,2,0,,,,"CRP together with AraC , which is active only in the presence of L-arabinose , bind to the araBAD promoter"
1777,1778,689.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli flagellar motility is negatively regulated by RcsB binding to the RcsAB box of the promoter of the flagellar master regulator flhDC .
"
1778,1779,689.txt,2,0,,,,"RcsB is a previously described negative regulator of flhDC
"
1779,1780,689.txt,3,0,,,,"We determined which flhDC promoter is regulated via RcsB using luxCDABE fusions to flhDC promoter mutants -LRB- Fig. 4C -RRB- .
"
1780,1781,689.txt,4,0,,,,"gyrA was not shifted , indicating specific binding of RcsB to the flhDC promoter .
"
1781,1782,689.txt,5,0,,,,"A control DNA fragment was not shifted , indicating specific binding of RcsB to the flhDC promoter .
"
1782,1783,689.txt,6,0,,,,"A. Dose response curve of the binding of gray and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using MST .
"
1783,1784,689.txt,7,0,,,,"A. Dose response curve of the binding of gray and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis .
"
1784,1785,689.txt,8,0,,,,"A. Dose response curve of the binding of RcsB protein and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using MST .
"
1785,1786,689.txt,9,0,,,,"A. Dose response curve of the binding of RcsB protein and His6-SUMO-RflM/RcsB complex ( black ) to the RcsB/RflM binding site of the flhDC promoter determined using microscale thermophoresis .
"
1786,1787,689.txt,10,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC Discussion Regulation of flagellar synthesis is controlled by the RcsCDB phosphorelay system in both S. enterica serovar Typhimurium .
"
1787,1788,689.txt,11,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC Discussion Regulation of flagellar synthesis is controlled by the RcsCDB phosphorelay system in both S. enterica serovar Typhimurium .
"
1788,1789,689.txt,12,1,Escherichia coli,E. coli,Escherichia coli,"In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC Discussion Regulation of flagellar synthesis is controlled by the RcsCDB phosphorelay system in both E. coli .
"
1789,1790,689.txt,13,1,Escherichia coli,E. coli,Escherichia coli,"In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC Discussion Regulation of flagellar synthesis is controlled by the RcsCDB phosphorelay system in both E. coli .
"
1790,1791,689.txt,14,1,Salmonella,Salmonella,Salmonella,"In Salmonella , however , RcsB-mediated regulation of the flagellar master operon flhDC has been described to be independent from RcsA .
"
1791,1792,689.txt,15,0,,,,"In the present study , we elucidated the mode-of-action of RcsB in regulation of flhDC .
"
1792,1793,689.txt,16,0,,,,"the P1flhDC promoter _ resulting in high affinity binding of a RcsB-RflM heterodimer and repression of flhDC operon transcription
"
1793,1794,689.txt,17,0,,,,"Phosphorylated RcsB is able to bind as homodimer with low affinity to the RcsB box in the flhDC promoter region .
"
1794,1795,689.txt,18,0,,,,RcsB also regulate cell motility by interacting with the flhDC promoter .
1795,1796,2172.txt,1,0,,,,"It is tempting to speculate that SsrB activates oafA within macrophages , via the inversion system , to trigger a protective LPS conformational change ."
1796,1797,1282.txt,1,0,,,,"Then , phosphorylated PhoP binds to the promoter of the mgtCBR operon ."
1797,1798,716.txt,1,0,,,,"The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiB , has been characterized .
"
1798,1799,716.txt,2,0,,,,"In contrast , RpoS was found to be required for the negative regulation of stiB during logarithmic phase .
"
1799,1800,716.txt,3,0,,,,"In contrast , RpoS was found to be required for the negative regulation of stiB during C starvation-induced stationary-phase .
"
1800,1801,716.txt,4,0,,,,"In contrast , RpoS was found to be required for the negative regulation of stiB during P starvation-induced stationary-phase .
"
1801,1802,716.txt,5,0,,,,"RpoS functions in the negative regulation of stiB .
"
1802,1803,716.txt,6,0,,,,"The rpoS mutation resulted in a two-to threefoldhigher level of induction of a fiveto sixfold-higher level of induction during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .
"
1803,1804,716.txt,7,0,,,,"The rpoS mutation resulted in a two-to threefoldhigher level of induction of stiB during P starvation during C starvation , suggesting that RpoS is involved in the negative regulation of the stiB locus .
"
1804,1805,716.txt,8,0,,,,"The fact that RpoS is an alternative a factor suggests that rpoS controls the expression of a negative regulator of stiB .
"
1805,1806,716.txt,9,0,,,,"Since stiB are regulated by RpoS , we wanted to examine the combined effects of sti mutations on starvation survival .
"
1806,1807,716.txt,10,0,,,,"Since stiB are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .
"
1807,1808,716.txt,11,0,,,,"Role of the alternative a factor RpoS , or a 
"
1808,1809,716.txt,12,0,,,,"On the basis of the fact that stiB are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .
"
1809,1810,716.txt,13,0,,,,"On the basis of the fact that stiB are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA are not induced and/or because stiB is overexpressed in an rpoS mutant ."
1810,1811,702.txt,1,0,,,,the sodA gene is negatively regulated by FNR44
1811,1812,1296.txt,1,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
1812,1813,1296.txt,2,0,,,,"phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .
"
1813,1814,1296.txt,3,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .
"
1814,1815,1296.txt,4,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .
"
1815,1816,1296.txt,5,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .
"
1816,1817,1296.txt,6,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .
"
1817,1818,1296.txt,7,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnB .
"
1818,1819,1296.txt,8,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnB .
"
1819,1820,1296.txt,9,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrH .
"
1820,1821,1296.txt,10,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP1 .
"
1821,1822,1296.txt,11,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrH .
"
1822,1823,1296.txt,12,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP1 .
"
1823,1824,1296.txt,13,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnC .
"
1824,1825,1296.txt,14,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnC .
"
1825,1826,1296.txt,15,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrF .
"
1826,1827,1296.txt,16,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP2 .
"
1827,1828,1296.txt,17,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrF .
"
1828,1829,1296.txt,18,0,,,,"slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP2 .
"
1829,1830,1296.txt,19,0,,,,"As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .
"
1830,1831,1296.txt,20,0,,,,"Two additional PhoP-activated genes , slyB and phoN , were used as positive and negative controls , respectively , since previous experiments have shown direct interaction of PhoP with the promoter of slyB but not with the promoter of phoN ( 50 ) .
"
1831,1832,1296.txt,21,0,,,,"A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) ."
1832,1833,1527.txt,1,0,,,,YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 .
1833,1834,1241.txt,1,0,,,,"However , mutations in neither galR did not affect repression by NagC ."
1834,1835,1255.txt,1,0,,,,"One possible reason for the detrimental effects of bfr overexpression in strains carrying an intact Fur repressor is titration of the Fur-repressed small RNA RyhB by bfr mRNA .
"
1835,1836,1255.txt,2,0,,,,"One possible reason for the detrimental effects of bfr overexpression in strains carrying an intact Fur repressor is titration of the Fur-repressed small RNA RyhB by bfr mRNA .
"
1836,1837,1255.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .
"
1837,1838,1255.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA ."
1838,1839,919.txt,1,0,,,,CspA is involved in the cold-shock response by stimulating the transcription of the cold-shock-inducible promoters of gyrA .
1839,1840,1533.txt,1,0,,,,"This study shows that flhE is transcribed as part of an flhBAE flagellar operon , under the control of the flagellar master regulator FlhD2C2 ."
1840,1841,2012.txt,1,0,,,,"aspA , are activated by CRP-cAMP in Table S1 .
"
1841,1842,2012.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"aspA , are activated by CRP-cAMP in E. coli ."
1842,1843,931.txt,1,0,,,,"The constitutive phoP gene was placed under the control of an arabinose-inducible promoter to examine the kinetics of PhoP-activated gene induction and the resultant modifications of LPS .
"
1843,1844,931.txt,2,1,unidentified,unknown,unidentified,"We placed the constitutive phoP gene under the control of an arabinose-inducible promoter and used this to determine the kinetics of activation of several pag genes as well as the modification of lipid-A with 2-hydroxymyristate , which can be added as a result of activation of an unknown PhoP-activated gene ( s ) .
"
1844,1845,931.txt,3,0,,,,"To identify genes necessary for bile resistance , MudJ transposon mutagenesis was performed on a strain containing a phoP mutation that results in constitutive expression of PhoP-activated genes .
"
1845,1846,931.txt,4,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
1846,1847,931.txt,5,0,,,,"D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .
"
1847,1848,931.txt,6,0,,,,"As expected for a PhoP-activated gene , there was no slyA transcription when bacteria were grown under PhoP-repress-ing conditions ( i.e. 10 mM Mg2 ) , regardless of the presence of a functional phoP gene ( Fig. 4A ) .
"
1848,1849,931.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,SL1344;14028s,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .
"
1849,1850,931.txt,8,0,,,,"The mRNA lev - encoded products are produced in the correct els of the PhoP-activated mgtA , phoP , pmrD , locales , at the required amounts and for the ap - and mig-14 genes increased after the shift to low propriate extents of time .
"
1850,1851,931.txt,9,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;mice,Salmonella enterica;Mus sp.;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Inactivation of the phoP or levels of the PhoP-activated genes increased , phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2 + virulent for mice and unable to proliferate within ( except for the mgtA gene , which reached the phagocytic cells ( 4-6 ) .
"
1851,1852,931.txt,10,0,,,,"RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .
"
1852,1853,931.txt,11,1,synthetic construct,primer,synthetic construct,"Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by PhoP because the mRNA level of transcripts is reduced significantly in the phoP mutants grown in low-Mg2 conditions -LRB- Fig .
"
1853,1854,931.txt,12,0,,,,"phoP and slyB are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification and CAMP resistance , we identified Udg , EptA , ArnA ( also named PbgP3 or PmrI ) , ArnB ( PbgP1 or PmrH ) , and ArnC ( PbgP2 or PmrF ) .
"
1854,1855,931.txt,13,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .
"
1855,1856,931.txt,14,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .
"
1856,1857,931.txt,15,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PmrI -RRB- .
"
1857,1858,931.txt,16,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified Udg , EptA , ArnA -LRB- also named PbgP3 -RRB- .
"
1858,1859,931.txt,17,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnB .
"
1859,1860,931.txt,18,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnB .
"
1860,1861,931.txt,19,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrH .
"
1861,1862,931.txt,20,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP1 .
"
1862,1863,931.txt,21,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrH .
"
1863,1864,931.txt,22,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP1 .
"
1864,1865,931.txt,23,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified ArnC .
"
1865,1866,931.txt,24,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified ArnC .
"
1866,1867,931.txt,25,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PmrF .
"
1867,1868,931.txt,26,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for CAMP resistance , we identified PbgP2 .
"
1868,1869,931.txt,27,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PmrF .
"
1869,1870,931.txt,28,0,,,,"phoP are the most conserved genes in PhoP regulons across the Enterobacteriaceae family , and SlyB can decrease PhoP protein activity .27 SlyA can enhance the overall transcription of PhoP-activated loci .22 IraP is transcriptionally activated by PhoP to stabilize another regulator RpoS .28 For the proteins in the group for LPS modification , we identified PbgP2 .
"
1870,1871,931.txt,29,0,,,,"As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .
"
1871,1872,931.txt,30,0,,,,"Therefore , the mgtA requirement for normal expression of a subset of PhoP-activated genes does not result from inefficient transcription of the autoregulated phoP gene ( Soncini et al. , 1995 ) in the mgtA mutant ( Fig .
"
1872,1873,931.txt,31,0,,,,"Given that PhoQ is essential to activate the wild-type PhoP protein ( Chamnongpol and Groisman , 2000 ) , we used a strain harboring the phoP * allele , which specifies a PhoP variant that displays enhanced autophosphorylation from acetyl phosphate in-vitro and in-vivo ( Chamnongpol and Groisman , 2000 ) , and thus , can promote transcription of PhoP-activated genes in the absence of PhoQ .
"
1873,1874,931.txt,32,0,,,,"A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) .
"
1874,1875,931.txt,33,0,,,,"These effects are not specific to the phoP gene because they were also observed with the PhoP-activated mgtC gene ( Fig. 2B ) .
"
1875,1876,931.txt,34,1,Salmonella;Salmonella;Salmonella;Salmonella;Salmonella;Salmonella,S. enterica;enterica;S. enterica;enterica;S. enterica;enterica,Salmonella,"A S. enterica strain expressing PhoQ ( N67D , E112D ) from its normal chromosomal location induced the PhoP-activated phoP gene like the isogenic strain with the wild-type S. enterica phoQ gene ( Fig. 3A ) ; this result argues that these periplasmic residues are not essential for the response to acidic pH. The PhoQ proteins from both S. enterica and S. bongori harbor a histidine residue at position 157 .
"
1876,1877,931.txt,35,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,Transcription of the PhoP-activated phoP and mgtA genes was higher in wild-type S. enterica than in strains expressing the cadAB genes constitutively when the inducing condition was acidic pH ( Fig. 6C and D ) .
1877,1878,1269.txt,1,0,,,,"This result was dependent on RstA-activated feoAB transcription because Fe ( II ) uptake in the feoA promoter mutant strain reached wild-type levels upon RstA expression ( Fig. 3A ) .
"
1878,1879,1269.txt,2,0,,,,"We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .
"
1879,1880,1269.txt,3,0,,,,"The RstA protein maintained wild-type levels of the Fur protein but exceptionally activated transcription of the feoAB operon directly to the feoA promoter .
"
1880,1881,1269.txt,4,0,,,,"In sum , our experiments dem-onstrated that the RstA protein activates transcription of the feoAB operon via its direct binding to the feoA promoter .
"
1881,1882,1269.txt,5,0,,,,The labeled wild-type feoA promoter was incubated with increasing concentrations of the RstA protein .
1882,1883,925.txt,1,0,,,,"However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .
"
1883,1884,925.txt,2,0,,,,"To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .
"
1884,1885,925.txt,3,0,,,,"The levels of uvrB mRNA were increased 3.5-to 6-fold in both strains as compared to a lexA1 strain ( Figure S1 a ) , implying that LexA-regulated genes were expressed as normal in the multiple polymerase mutant ."
1885,1886,2006.txt,1,0,,,,"mcpC , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .
"
1886,1887,2006.txt,2,0,,,,"mcpC , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop ."
1887,1888,514.txt,1,0,,,,"As FliT is thought to prevent FlhD4C2 from inhibiting its own expression , we hypothesize that reduced fliT expression reduces flhDC expression ."
1888,1889,1080.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The presence of a putative sequence to which the cAMP-CRP complex binds in the E. coli fur promoter has been suggested on the basis of computational analysis .
"
1889,1890,1080.txt,2,1,Pasteurella multocida,Pasteurella multocida,Pasteurella multocida,"In agreement with this possibility , it has been recently demonstrated that the fur gene of Pasteurella multocida , is positively regulated by the cAMP-CRP complex ."
1890,1891,272.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"For example , in E. coli , IHF has been shown to regulate envZ operon ."
1891,1892,266.txt,1,0,,,,"Known regulators of the AcrAB -- TolC efflux pump include the AraC/XylS-type regulatory genes marA -- 15 16,17 rob ."
1892,1893,1094.txt,1,0,,,,"Motility retardation of all fragments except gatB , revealed specific binding of cAMP-CRP-His6 to PgatR .
"
1893,1894,1094.txt,2,0,,,,"Motility retardation of all fragments except gatB , revealed specific binding of cAMP-CRP-His6 to PgatZ .
"
1894,1895,1094.txt,3,0,,,,"Motility retardation of all fragments except gatB , revealed specific binding of cAMP-CRP-His6 to PgatY ."
1895,1896,500.txt,1,0,,,,"Our results suggested that FimY may function as a DNA-binding protein to activate fimZ .
"
1896,1897,500.txt,2,0,,,,FimY was previously reported to activate fimZ
1897,1898,528.txt,1,0,,,,"In addition , the global flagellar regulator flhD was also found to be repressed by Fur-5 , although not selected with the applied cutoff ."
1898,1899,1902.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"However , another report indicated that the nucleoid protein H-NS , was a negative regulator of E. coli ompC .
"
1899,1900,1902.txt,2,0,,,,"We suspected that H-NS might regulate ompC indirectly , at least in part , by controlling ompR .
"
1900,1901,1902.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"However , another report indicated that the nucleoid protein H-NS , was a negative regulator of E. coli ompC .
"
1901,1902,1902.txt,4,0,,,,"We suspected that H-NS might regulate ompC indirectly , at least in part , by controlling ompR ."
1902,1903,1916.txt,1,0,,,,"This paper is available on line at http://www.jbc.org 9083 PhoP-activated gene pagP ( 29 ) .
"
1903,1904,1916.txt,2,0,,,,"The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .
"
1904,1905,1916.txt,3,0,,,,"Thus , we investigated the role of the PhoP-activated pagP and pgtE genes , because they had been implicated in resistance to the alpha-helical peptide C18G ( Guo et al. , 1998 ; Guina et al. , 2000 ) .
"
1905,1906,1916.txt,4,0,,,,"Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .
"
1906,1907,1916.txt,5,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] ."
1907,1908,1043.txt,1,0,,,,"To investigate the mechanism underlying the expressional regulation of fljB : z66 , gene deletion mutants of the regulators FliA were constructed in this study .
"
1908,1909,1043.txt,2,0,,,,"To investigate whether fljB is regulated by FliA like other biphasic S. fliA mutants were affected by the osmotic environment , an ompR mutant was also prepared .
"
1909,1910,1043.txt,3,0,,,,"To investigate whether fljB is regulated by FliA like other biphasic S. flhDC mutants were affected by the osmotic environment , an ompR mutant was also prepared .
"
1910,1911,1043.txt,4,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"To investigate whether fljB is regulated by FliA like other biphasic S. enterica mutants were affected by the osmotic environment , an ompR mutant was also prepared ."
1911,1912,1725.txt,1,0,,,,"To better characterize the contribution of RcsB to persistence within tomatoes , rcsA genes were deleted"
1912,1913,2238.txt,1,0,,,,"SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression of the spvABCD operon .
"
1913,1914,2238.txt,2,1,unidentified plasmid,plasmid,unidentified plasmid,"SpvR positively regulates the plasmid-encoded spvABCD operon
"
1914,1915,2238.txt,3,0,,,,"Furthermore , RpoS appears essential for SpvR-assisted induction of the spvABCD genes .
"
1915,1916,2238.txt,4,0,,,,SpvR induces the expression of the spvABCD operon .
1916,1917,1731.txt,1,0,,,,"The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure ."
1917,1918,1057.txt,1,0,,,,"Therefore , we compared the transcription of HilD-regulated genes in eK297R and eWT in the lon deletion background , which excludes the effect of protein stability , and found that the messenger RNA levels of HilD-regulated genes in eK297R increased dramatically compared with these in eWT ( Figure 3D ) , indicating that K297R mimicking deacetylation can effectively activate HilD-regulated genes by increasing its DNA-binding affiffinity in the lon mutant background in-vivo .
"
1918,1919,1057.txt,2,0,,,,"Therefore , we compared the transcription of HilD-regulated genes in eK297R and eWT in the lon deletion background , which excludes the effect of protein stability , and found that the messenger RNA levels of HilD-regulated genes in eK297R increased dramatically compared with these in eWT ( Figure 3D ) , indicating that K297R mimicking deacetylation can effectively activate HilD-regulated genes by increasing its DNA-binding affiffinity in the lon mutant background in-vivo ."
1919,1920,2210.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression Matías 2 , Guido C M .
"
1920,1921,2210.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella,S. Typhi;Typhi;S. enterica;enterica,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhi , the expression of hlyE is under the control of the transcriptional regulatory protein PhoP , a master regulator of intracellular survival of S. enterica .
"
1921,1922,2210.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella,S. Typhi;Typhi;S. enterica;enterica,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhi , the expression of hlyE is under the control of the transcriptional regulatory protein PhoP , a master regulator of intracellular survival of S. enterica ."
1922,1923,1719.txt,1,1,Terfezia albida,to 15,Terfezia albida,"Compared with the wild type , the expression levels of the pmrH gene in the mutants with reduced susceptibility were increased 2-to 15-fold , showing that the pmrA mutations changed the regulation of the PmrA-PmrB-dependent genes ."
1923,1924,299.txt,1,0,,,,"It has been reported that the PhoP protein , a response regulator of the PhoP/PhoQ two-component system , directly activates transcription of the rstA gene ."
1924,1925,2204.txt,1,0,,,,"Fur negatively regulates hns .
"
1925,1926,2204.txt,2,0,,,,"Fur negatively regulates hns .
"
1926,1927,2204.txt,3,0,,,,"Fur negatively regulates hns .
"
1927,1928,2204.txt,4,0,,,,"Fur negatively regulates hns .
"
1928,1929,2204.txt,5,0,,,,"Fur negatively regulates hns .
"
1929,1930,2204.txt,6,0,,,,"Fur negatively regulates hns .
"
1930,1931,2204.txt,7,0,,,,"Fur negatively regulates hns .
"
1931,1932,2204.txt,8,0,,,,"Fur negatively regulates hns .
"
1932,1933,2204.txt,9,0,,,,Fur negatively regulates hns .
1933,1934,1756.txt,1,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
1934,1935,1756.txt,2,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .
"
1935,1936,1756.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The ugtL gene was first identified as part of a Salmonella-specific DNA region harbouring the PhoP-activated pcgL gene , which encodes a D-Ala-D-Ala dipeptidase ( Hilbert et al. , 1999 ) .
"
1936,1937,1756.txt,4,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] ."
1937,1938,1030.txt,1,0,,,,HilA binds the promoter of ssaH
1938,1939,1024.txt,1,0,,,,"Previous studies have shown that CpxR-P activates the expression of the cpxRA operon .
"
1939,1940,1024.txt,2,0,,,,CpxR is in agreement with previous studies indicating that CpxR-P induces the expression of the cpxRA operon
1940,1941,1742.txt,1,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .
"
1941,1942,1742.txt,2,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .
"
1942,1943,1742.txt,3,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .
"
1943,1944,1742.txt,4,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .
"
1944,1945,1742.txt,5,0,,,,"STM1344 is the most upstream component , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad .
"
1945,1946,1742.txt,6,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , O .
"
1946,1947,1742.txt,7,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , U. Römlin .
"
1947,1948,1742.txt,8,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , T. Romeo .
"
1948,1949,1742.txt,9,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , A. Lamprokostopoulou .
"
1949,1950,1742.txt,10,0,,,,"STM1344 is an integral part of the sessility-motility switch , as the expression of STM1344 is directly repressed by the binding of the carbon storage regulator CsrA , a sessility-motility switcher , to the STM1344 mRNA -LRB- K. Jonas , A. N. Edwards , I. Ahmad ."
1950,1951,2263.txt,1,0,,,,"Notably , we observed significantly higher transcript levels of these genes in the ydcI cells compared with the WT , indicating their transcriptional repression by YdcI ."
1951,1952,598.txt,1,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
1952,1953,1018.txt,1,0,,,,The promoters of gatY are negatively regulated by GatR .
1953,1954,2277.txt,1,0,,,,"However , regulation of hilA by osmolarity is much more incremental than regulation by PhoPQ is predicted to be .
"
1954,1955,2277.txt,2,0,,,,"However , regulation of hilA by osmolarity is much more incremental than regulation by PhoPQ is predicted to be .
"
1955,1956,2277.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In this work , we have studied how PhoPQ , HilE , together to regulate the S. Typhimurium SPI-1 transcriptional activator hilA ."
1956,1957,201.txt,1,0,,,,Data _ suggesting that PhoP represses SPI1 by activating hilE expression
1957,1958,1795.txt,1,0,,,,"In the presence of Mn , MntR represses the expression of sitABCD , through direct binding of specific sites within the promoter regions of these genes .
"
1958,1959,1795.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Slauch , J.M. Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
"
1959,1960,1795.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Ikeda , J.S. , Janakiraman , A. , Kehres , D.G. , Maguire , M.E. , Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
"
1960,1961,1795.txt,4,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
"
1961,1962,1795.txt,5,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
"
1962,1963,1795.txt,6,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
"
1963,1964,1795.txt,7,0,,,,"Both mntH and sitABCD are under the control of MntR
"
1964,1965,1795.txt,8,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
"
1965,1966,1795.txt,9,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Slauch , J. M. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1966,1967,1795.txt,10,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"M. E. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1967,1968,1795.txt,11,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Maguire Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1968,1969,1795.txt,12,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"D. G. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1969,1970,1795.txt,13,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Kehres Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1970,1971,1795.txt,14,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"A. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1971,1972,1795.txt,15,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Janakiraman Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1972,1973,1795.txt,16,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"J. S. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1973,1974,1795.txt,17,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Ikeda Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by MntR .
"
1974,1975,1795.txt,18,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR .
1975,1976,567.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Mlc is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli .
1976,1977,573.txt,1,0,,,,"Furthermore , PAT DE4 was positive for the outer membrane receptor gene instead of but no signal was obtained for the islet genes htrE ( probable porin/fimbrial assembly protein ) , sopD2 ( secreted effector protein ) , srfJ ( putative virulence factor , activated by transcription factor SsrB ) and sseK2 ( translocated effector protein SSEK2 by type III secretion system ) while pagK ( PhoPQ-activated protein ) was present only in this array type ."
1977,1978,2288.txt,1,0,,,,"A supershift for HilD-Myc was only observed in the presence of the anti-Myc antibody , not in the presence of the anti-HA antibody , indicating that HilD-Myc is bound to the invF promoter ."
1978,1979,1781.txt,1,0,,,,"The OmpR/EnvZ two-component regulatory system regulates ompC in response to changes in osmolarity .
"
1979,1980,1781.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhi , the OmpR/EnvZ system is involved in the regulation of the ompC , where both OmpF are expressed as abundant outer-mem-brane proteins as in E. coli .
"
1980,1981,1781.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhi , the OmpR/EnvZ system is involved in the regulation of the ompC , where both OmpC are expressed as abundant outer-mem-brane proteins as in E. coli ."
1981,1982,215.txt,1,0,,,,"Mu transposition in the region from ybjP to artP -LRB- underlined -RRB- was not influenced by IPTG addition , whereas ParBP1 expression with IPTG reduced transposition 100-fold in the region from cbiM to cbiN ."
1982,1983,1959.txt,1,0,,,,"When system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter .
"
1983,1984,1959.txt,2,1,Salmonella,Salmonella,Salmonella,"When the Salmonella PmrA PmrB is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein binds to the pmrD promoter .
"
1984,1985,1959.txt,3,0,,,,the pmrD promoter harbors binding sites for both PmrA proteins
1985,1986,1971.txt,1,1,Salmonella,Salmonella,Salmonella,Other regulators of SdiA did not contrib-ute to acrAB induction by indole in Salmonella .
1986,1987,229.txt,1,0,,,,"As suggested by our previous study , establishing the Mg2-responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the slyA mutants in low-Mg2 conditions .
"
1987,1988,229.txt,2,0,,,,"As suggested by our previous study , establishing the Mg2-responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the slyA mutants in PhoP-activating conditions .
"
1988,1989,229.txt,3,0,,,,"Thus , one explanation for the transcription we observe following overexpression of slyA may be that both SlyA and SsrB counteract binding of both H-NS and YdgD/Hha in this A+T rich SPI-2 region ."
1989,1990,1965.txt,1,0,,,,"he RpoS-dependent genes osmY were found to be strongly upregulated by DOC in exponential cultures .
"
1990,1991,1965.txt,2,0,,,,"As expected , the level of expression of osmY was significantly lower in the absence of osmY : : GFP induction by DOC was very modest in the RpoS mutant 2 .
"
1991,1992,1965.txt,3,0,,,,"As expected , the level of expression of osmY was significantly lower in the absence of RpoS : : GFP induction by DOC was very modest in the RpoS mutant 2 .
"
1992,1993,1965.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"Recently , reports on E. coli have also implicated integration host factor in the RpoS-dependent stationary-phase induction of osmY .
"
1993,1994,1965.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"Recently , reports on E. coli have also implicated Lrp host factor in the RpoS-dependent stationary-phase induction of osmY ."
1994,1995,1232.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"PagP is an outer membrane palmitoyl transferase The S. typhimurium PhoP/PhoQ-regulated gene pagP is required for the synthesis of hepta-acylated lipid-A by the addition of palmitate to the 2 position N-linked 3-hydroxymyristate on the proximal glucosamine of lipid-A .
"
1995,1996,1232.txt,2,0,,,,"The modifications include the PhoP/PhoQ-regulated expression of pagP , which is involved in the acylation at position 2 of the proximal unit of lipid-A ( Bishop , 2005 ) , and the PmrA/PmrB-controlled expression of the factors required for the addition of 4-amino-4-deoxy-L-arabinose ( L-Ara4N ) and phosphoethanolamine ( pEtN ) to phosphate groups of the lipid-A ( Groisman et al. , 1997 ; Gunn et al. , 2000 ; Lee et al. , 2004 ) ."
1996,1997,1554.txt,1,0,,,,"The lacZ promoter fragment was used as positive control for CRP binding , as described elsewhere ."
1997,1998,2049.txt,1,0,,,,"A third PhoP-PhoQ-regulated gene is pgtE , which encodes an outer membrane protease that can cleave-helical AMPs ( 19 ) .
"
1998,1999,2049.txt,2,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
1999,2000,1540.txt,1,0,,,,"STM3611 , as a class III flagellar gene , is indirectly regulated by STM1344 via FliA ."
2000,2001,1226.txt,1,2,unidentified plasmid;Plasmid F,plasmid;plasmid F,Plasmid F;unidentified plasmid,"To further test the idea that LexA regulates the Fels-2 tum promoter , we placed this promoter region adjacent to the lacZ gene on plasmid F 128 .
"
2001,2002,1226.txt,2,0,,,,"LexA-dependent control of a Fels-2 tum : : Cam 168.2 180.3 a Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked Gifsy-2 .
"
2002,2003,1226.txt,3,0,,,,"LexA-dependent control of a Fels-2 tum : : Cam 168.2 180.3 a Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked Gifsy-1 .
"
2003,2004,1226.txt,4,0,,,,"LexA-dependent control of a Fels-2 tum : : Cam 168.2 180.3 a Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked prophages Fels-2 .
"
2004,2005,1226.txt,5,0,,,,"LexA-dependent control of a Fels-2 tum : : Cam 168.2 180.3 a Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked Gifsy-2 .
"
2005,2006,1226.txt,6,0,,,,"LexA-dependent control of a Fels-2 tum : : Cam 168.2 180.3 a Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked Gifsy-1 .
"
2006,2007,1226.txt,7,0,,,,"LexA-dependent control of a Fels-2 tum : : Cam 168.2 180.3 a Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked prophages Fels-2 .
"
2007,2008,1226.txt,8,1,Nitrolancea hollandica,Strain LB,Nitrolancea hollandica,"LexA-dependent control of a Fels-2 tum : : lac fusiona - lac strains Relevant genotype Strain LB mitomycin C LB TT23764 recA lexA 3.6 95.2 TT23765 lexA41 : Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked Gifsy-2 .
"
2008,2009,1226.txt,9,1,Nitrolancea hollandica,Strain LB,Nitrolancea hollandica,"LexA-dependent control of a Fels-2 tum : : lac fusiona - lac strains Relevant genotype Strain LB mitomycin C LB TT23764 recA lexA 3.6 95.2 TT23765 lexA41 : Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked Gifsy-1 .
"
2009,2010,1226.txt,10,1,Nitrolancea hollandica,Strain LB,Nitrolancea hollandica,"LexA-dependent control of a Fels-2 tum : : lac fusiona - lac strains Relevant genotype Strain LB mitomycin C LB TT23764 recA lexA 3.6 95.2 TT23765 lexA41 : Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked prophages Fels-2 .
"
2010,2011,1226.txt,11,1,Nitrolancea hollandica,Strain LB,Nitrolancea hollandica,"LexA-dependent control of a Fels-2 tum : : lac fusiona - lac strains Relevant genotype Strain LB mitomycin C LB TT23764 recA lexA 3.6 95.2 TT23765 lexA41 : Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked Gifsy-2 .
"
2011,2012,1226.txt,12,1,Nitrolancea hollandica,Strain LB,Nitrolancea hollandica,"LexA-dependent control of a Fels-2 tum : : lac fusiona - lac strains Relevant genotype Strain LB mitomycin C LB TT23764 recA lexA 3.6 95.2 TT23765 lexA41 : Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked Gifsy-1 .
"
2012,2013,1226.txt,13,1,Nitrolancea hollandica,Strain LB,Nitrolancea hollandica,"LexA-dependent control of a Fels-2 tum : : lac fusiona - lac strains Relevant genotype Strain LB mitomycin C LB TT23764 recA lexA 3.6 95.2 TT23765 lexA41 : Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked prophages Fels-2 .
"
2013,2014,1226.txt,14,0,,,,"LexA-dependent control of a Fels-2 tum : : lac fusiona - Galactosidase activity in F 128-Fels-2 tum : : Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked Gifsy-2 .
"
2014,2015,1226.txt,15,0,,,,"LexA-dependent control of a Fels-2 tum : : lac fusiona - Galactosidase activity in F 128-Fels-2 tum : : Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked Gifsy-1 .
"
2015,2016,1226.txt,16,0,,,,"LexA-dependent control of a Fels-2 tum : : lac fusiona - Galactosidase activity in F 128-Fels-2 tum : : Both strains contained the proB1567 : : sulA46 : : Spc insertions and lacked prophages Fels-2 .
"
2016,2017,1226.txt,17,0,,,,"LexA-dependent control of a Fels-2 tum : : lac fusiona - Galactosidase activity in F 128-Fels-2 tum : : Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked Gifsy-2 .
"
2017,2018,1226.txt,18,0,,,,"LexA-dependent control of a Fels-2 tum : : lac fusiona - Galactosidase activity in F 128-Fels-2 tum : : Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked Gifsy-1 .
"
2018,2019,1226.txt,19,0,,,,LexA-dependent control of a Fels-2 tum : : lac fusiona - Galactosidase activity in F 128-Fels-2 tum : : Both strains contained the proB1567 : : Tn10 : : Spc insertions and lacked prophages Fels-2 .
2019,2020,942.txt,1,0,,,,"The RstA protein controlled iron-responsive genes through the Fur-Fe protein because deletion of the fur gene abrogated RstA-mediated repression of these genes .
"
2020,2021,942.txt,2,0,,,,The regulatory effect of the RstA protein occurred through the Fur protein because the RstA protein failed to repress transcription of the iron-regu-lated genes in a fur deletion strain .
2021,2022,2061.txt,1,0,,,,"RtsA in particular , also activate , independent of dsbA , encoding the periplasmic disulphide bond isomerase .
"
2022,2023,2061.txt,2,0,,,,"The genes slrP and dsbA are also induced by RtsA independently of InvF .
"
2023,2024,2061.txt,3,0,,,,The genes slrP and dsbA are also induced by RtsA independently of both HilA .
2024,2025,1568.txt,1,0,,,,"Because PhoP/PhoQ regulates more than 40 genes , additional PhoP/PhoQ-activated genes , including pmrD and pagD , were examined to determine if bile specifically regulated pagC , or if it has a general effect on PhoP/PhoQ-regulated genes ."
2025,2026,2075.txt,1,0,,,,"Despite its low expression level in our in-vitro conditions , the sseJ fusion showed a clear PmrAB-dependent induction by excess .
"
2026,2027,2075.txt,2,0,,,,"Despite its low expression level in our in-vitro conditions , the sseJ fusion showed a clear PmrAB-dependent induction by Fe3 ."
2027,2028,956.txt,1,0,,,,This tolerance appeared to be reflected in the upregulation of rpoH of the RpoS regulon .
2028,2029,765.txt,1,0,,,,"To demonstrate the interaction of CRP with gat promoters by EMSA , CRP-His6 was added in increasing concentrations to the 300-bp fragments located upstream of gatB ."
2029,2030,1597.txt,1,0,,,,"Previously , we have determined that the cse1 promoter is repressed by the global regulators H-NS and LRP whereas LeuO participates in its positive regulation ; also , it can be expressed independently of LeuO in N-MM ."
2030,2031,1583.txt,1,0,,,,"To define the role of SoxS in the regulation of ompW expression , we constructed transcriptional-fusions .
"
2031,2032,1583.txt,2,0,,,,"SoxS binds to the regulatory region of the ompW gene The transcriptional-fusions showed that SoxS is a genetic element .
"
2032,2033,1583.txt,3,0,,,,"Binding of purified SoxS to the ompW promoter strongly suggests that the PQ-and SoxS-mediated activation of ompW is the result of a direct interaction between the promoter and SoxS .
"
2033,2034,1583.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,SoxS regulates the expression of the S. Typhimurium ompW gene .
2034,2035,771.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of CD11c dendritic cells in the lamina .
"
2035,2036,771.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the RcsB regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes dendritic cells in the lamina .
"
2036,2037,771.txt,3,0,,,,RcsB interacts with TviA to bind to the tviA promoter to activate the Vi antigen expression .
2037,2038,759.txt,1,0,,,,"Repression of ompF by MarA is thought to occur indirectly through its activation of micF .
"
2038,2039,759.txt,2,1,Escherichia coli,E. coli,Escherichia coli,Studies in E. coli indicate that MarA indirectly represses ompF .
2039,2040,981.txt,1,0,,,,These results show for the first time induction of dksA expression suggest that DksA regulates the expression of virulence-factors .
2040,2041,995.txt,1,1,Salmonella,Salmonella,Salmonella,"Partial transcriptional regulation of the lpxO gene by and PhoP in Salmonella .
"
2041,2042,995.txt,2,0,,,,"The PhoP-regulated genes described and the modifications their products mediate are : pagP , palmitoyl transferase ; lpxO , formation of 2-hydroxy myristate ; pagL , 3-O-deacylase ."
2042,2043,1346.txt,1,0,,,,"( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain ."
2043,2044,1420.txt,1,0,,,,"The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P .
"
2044,2045,1420.txt,2,0,,,,The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P .
2045,2046,2129.txt,1,0,,,,"Therefore , the observation that FlhD4C2 bound to a coding region of fliC is not that surprising ."
2046,2047,1434.txt,1,0,,,,"while transcription of acrAB is activated by bile , this activation is independent of marRAB , as well as Rob , RpoS or PhoP -- PhoQ
"
2047,2048,1434.txt,2,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. typhimurium;typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Bile-mediated activation of the mar operon occurs independently of Rob Rob , a known activator of marRAB in E. coli , was examined for its role in bile activation of the mar operon in S. typhimurium .
"
2048,2049,1434.txt,3,0,,,,Rob activate marRAB transcription .
2049,2050,1352.txt,1,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihB mutant alleles on hilA expression in cells growing in LB-medium suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
2050,2051,1352.txt,2,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihfA mutant alleles on hilA expression in cells growing in LB-medium suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
2051,2052,1352.txt,3,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihB mutant alleles on hilA expression in cells entering the stationary-phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
2052,2053,1352.txt,4,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihfA mutant alleles on hilA expression in cells entering the stationary-phase , the effect on hilA transcription of the H-NS antagonist in double ihf hns mutants suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
2053,2054,1352.txt,5,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihB mutant alleles on hilA expression in cells entering the gel-shift data suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
2054,2055,1352.txt,6,0,,,,"IHF alleviates H-NS-mediated repression of hilA transcription The effect of ihfA mutant alleles on hilA expression in cells entering the gel-shift data suggest that the IHF protein functions as a transcriptional regulator of the hilA gene .
"
2055,2056,1352.txt,7,0,,,,"The increase in the degree of stimulation in the presence of H-NS indicates that in-vitro , IHF can alleviate H-NS-mediated repression of hilA transcription .
"
2056,2057,1352.txt,8,0,,,,"In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145-and 9.5-fold compared with H-NSWT levels .
"
2057,2058,1352.txt,9,0,,,,How HilD counteracts the H-NS-mediated repression of hilA
2058,2059,76.txt,1,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"Thus , the ppGpp-dependent induction of RpoS-dependent genes , would be spoT dependent during P starvation and relA dependent during C starvation .
"
2059,2060,76.txt,2,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"Thus , the ppGpp-dependent induction of RpoS , would be spoT dependent during P starvation and relA dependent during C starvation ."
2060,2061,836.txt,1,0,,,,Two StpA-repressed PhoP-dependent genes _ bound by pagC
2061,2062,2115.txt,1,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .
"
2062,2063,2115.txt,2,0,,,,These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- mgtBC .
2063,2064,188.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhi 129-0238 also activated RpoSmediated stress responses , with upregulation of otsAB , spoVR , yeaG , katE , sodC , osmY , in line with previous findings .
"
2064,2065,188.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhi 129-0238 also activated RpoSmediated stress responses , with upregulation of otsAB , spoVR , yeaG , katE , sodC , ecnB , in line with previous findings .
"
2065,2066,188.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhi 129-0238 also activated RpoSmediated stress responses , with upregulation of otsAB , spoVR , yeaG , katE , sodC , poxB , in line with previous findings .
"
2066,2067,188.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhimurium 14028 also activated RpoSmediated stress responses , with upregulation of otsAB , spoVR , yeaG , katE , sodC , osmY , in line with previous findings .
"
2067,2068,188.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhimurium 14028 also activated RpoSmediated stress responses , with upregulation of otsAB , spoVR , yeaG , katE , sodC , ecnB , in line with previous findings .
"
2068,2069,188.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhimurium 14028 also activated RpoSmediated stress responses , with upregulation of otsAB , spoVR , yeaG , katE , sodC , poxB , in line with previous findings ."
2069,2070,1408.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] ."
2070,2071,2101.txt,1,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; sdiA , a regulator of quorum-sensing and virulence ( Ahmer et al. 1998 ; Volf et al. 2002 ) ; permeases of oligopeptides , such as oppF and oppB ( Goodell and Higgins 1987 ; Orchard and Goodrich-Blair 2004 ) ; and several genes involved in drug resistance , such as emrE and nudF ."
2071,2072,62.txt,1,0,,,,"Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadB .
"
2072,2073,62.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in SCV of macrophages .
"
2073,2074,62.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in the Salmonellacontaining vacuole of macrophages .
"
2074,2075,62.txt,4,0,,,,"Activated OmpR then represses the cadC/BA operon by directly binding to both cadB promo-ters , leading to cytoplasmic acidification ."
2075,2076,822.txt,1,0,,,,"We reasoned that because Crl participates in the negative regulation by S , a crl mutant should display a competitive advantage over the wild-type strain .
"
2076,2077,822.txt,2,0,,,,"The finding that the crl mutant had an advantage over the wild-type strain for fitness in stationary-phase indicated that Crl contributes to negative regulation by S .
"
2077,2078,822.txt,3,0,,,,The finding that the crl mutant had an advantage over the wild-type strain for growth-on-succinate in stationary-phase indicated that Crl contributes to negative regulation by S .
2078,2079,89.txt,1,0,,,,"If the protein of interest dimerizes , the LexADBD binds to its cognate sulA promoter , repressing the expression of a transcriptionally linked lacZ gene ."
2079,2080,1385.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , SirA also directly activates the horizontally acquired regulatory genes hilC .
"
2080,2081,1385.txt,2,0,,,,"In contrast , the presence of a hilD mutation completely blocked SirA induction of hilC .
"
2081,2082,1385.txt,3,0,,,,"Our data suggest that SirA induces expression of hilC via HilD .
"
2082,2083,1385.txt,4,0,,,,"In support of our model , we demonstrate that SirA induction of hilC requires the presence of HilD .
"
2083,2084,1385.txt,5,0,,,,"SirA does this by directly activating hilC regulatory genes .
"
2084,2085,1385.txt,6,0,,,,"SirA controls these genes by directly activating hilC regulatory genes .
"
2085,2086,1385.txt,7,0,,,,"On the basis of these data , the authors concluded that SirA activates the system by direct action on hilC .
"
2086,2087,1385.txt,8,0,,,,"SirA , positively regulates hilC .
"
2087,2088,1385.txt,9,0,,,,"SirA positively controls the transcription of hilC .
"
2088,2089,1385.txt,10,0,,,,"SirA , positively regulates the transcription of hilC ."
2089,2090,611.txt,1,0,,,,"Group III is represented by OmrA/B , which by binding directly to flhDC and csgD mRNA [ 62,75 ] , can down-regulate both motility and the expression of CsgD-controlled curli fibres and cellulose ."
2090,2091,177.txt,1,0,,,,Expression of lysA is activated by LysR in the presence of diaminopimelate .
2091,2092,163.txt,1,0,,,,"In either case , HilD/C could activate invF"
2092,2093,605.txt,1,0,,,,"the oxyR gene encodes a DNA binding , transcriptional dual regulator of the LysR family"
2093,2094,1391.txt,1,0,,,,"also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuABCD leucine biosynthetic operon , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region"
2094,2095,639.txt,1,0,,,,"Although argT is controlled by nitrogen status through a sN-dependent promoter , there are no nearby binding sites for the general nitrogen control protein NtrC .
"
2095,2096,639.txt,2,0,,,,"Although argT is controlled by nitrogen status through a sN-dependent promoter , there are no nearby binding sites for the general nitrogen control protein NtrC ."
2096,2097,1622.txt,1,0,,,,"PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid-A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase ."
2097,2098,1144.txt,1,0,,,,"As shown in Fig. 1 ( a , b ) , we found a sequence homologous to the RcsB-binding site present in other well-characterized RcsB-regulated genes , located 272 nt upstream from the previously described dps +1 transcription site ( Mouslim & Groisman , 2003 ; Yoo et al. , 2007 ) .
"
2098,2099,1144.txt,2,0,,,,"Taken together , our results confirm that RcsB promotes dps expression by directly binding to the promoter region of dps .
"
2099,2100,1144.txt,3,0,,,,"To determine which of the RcsB phosphorylation pathway is involved in the control of dps expression , levels of b-galactosidase : : lacZYA was determined in tolB P double rcsB mutants .
"
2100,2101,1144.txt,4,0,,,,"To determine which of the RcsB phosphorylation pathway is involved in the control of dps expression , levels of b-galactosidase : : lacZYA was determined in tolB rcsB , tolB PrcsDB .
"
2101,2102,1144.txt,5,0,,,,"Although Yoo et al. reported that dps expression is induced during the stationary-phase by the Fur regulator , our results demonstrated that this gene is also regulated by RcsB ."
2102,2103,1150.txt,1,0,,,,"However , the sirA knock-out does not lead to a complete loss in HilD levels since HilD is regulated by HilE , EnvZ/OmpRr , etc. ."
2103,2104,1636.txt,1,0,,,,"YdgT , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated ."
2104,2105,1178.txt,1,0,,,,"We also found that H-NS represses acrEF .
"
2105,2106,1178.txt,2,0,,,,"A recent study has shown that acrEF is repressed by H-NS ,36 whereas acrAB is not repressed .
"
2106,2107,1178.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"K. Nishino , M. Hayashi-Nishino , A. Yamaguchi , H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multi-drug efflux genes acrEF , Antimicrob ."
2107,2108,1839.txt,1,0,,,,sefR encodes an AraC-like regulator of sef gene expression
2108,2109,375.txt,1,0,,,,"Because PhoP/PhoQ regulates more than 40 genes , additional PhoP/PhoQ-activated genes , including pmrD and pagD , were examined to determine if bile specifically regulated pagC , or if it has a general effect on PhoP/PhoQ-regulated genes .
"
2109,2110,375.txt,2,0,,,,"The results establish that other PhoP/PhoQ-regulated genes were unaffected by the presence of bile ( as exemplified by pagD and pmrD , Fig. 2 ) , suggesting that pagC is specifically affected by bile ."
2110,2111,413.txt,1,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"To investigate whether z66 is regulated by FliA like other biphasic S. enterica mutants were affected by the osmotic environment , an ompR mutant was also prepared ."
2111,2112,1187.txt,1,0,,,,"STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM3611 , required for the downregulation of CsgD expression .
"
2112,2113,1187.txt,2,0,,,,"YdiV also indirectly contributes to the activation of CsgD mediated biofilm formation through inhibition of the c-di-GMP phosphodiesterase STM3611 .
"
2113,2114,1187.txt,3,0,,,,STM3611 inhibit CsgD function .
2114,2115,1193.txt,1,0,,,,"The fliZ mutation did not have a significant effect on the sirA expression , indicating that FliZ control of the hilA expression is not mediated by transcriptional activation of the sirA gene .
"
2115,2116,1193.txt,2,0,,,,These results suggest that FliZ may directly regulate the hilA transcription .
2116,2117,407.txt,1,0,,,,"of coloniesa unique insertions Function fimW 18 Inhibitor of type 1 fimbria regulator FimZ Outer membrane protein ; passive diffusion of filament biosynthesis chaperone Basal body protein ; stability of MotAB complexes of MS ring Secreted effector ; colocalizes with host .
"
2117,2118,407.txt,2,0,,,,"of coloniesa unique insertions Function fimW 18 Inhibitor of type 1 fimbria regulator FimZ Outer membrane protein ; passive diffusion of biosynthesis membrane protein Flagellar cytoplasmic anchor MS ring protein Flagellar biosynthesis sigma factor Rod/hook ; stability of MotAB complexes of MS ring Secreted effector ; colocalizes with host .
"
2118,2119,407.txt,3,0,,,,"of coloniesa unique insertions Function fimW 18 Inhibitor of type 1 fimbria regulator FimZ Outer membrane protein ; passive diffusion of ions , hydrophilic solutes Flagellar export apparatus ; stability of MotAB complexes of MS ring Secreted effector ; colocalizes with host ."
2119,2120,361.txt,1,0,,,,"Although not significantly enriched within the set of directly PhoPQ-regulated genes , the functional class related to pathogenicity and virulence also contained potential PhoPQ-dependent targets ( pagC , mgtC , virK , and STM0306 ) ."
2120,2121,1805.txt,1,0,,,,CspA is involved in the cold-shock response by stimulating the transcription of the cold-shock-inducible promoters of hns .
2121,2122,349.txt,1,0,,,,"Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .
"
2122,2123,349.txt,2,0,,,,"We also identified AraC-regulated genes that are transcribed due to read-through of inefficient Rho-independent terminators ( ygeA and polB ) .
"
2123,2124,349.txt,3,1,unidentified,unidentified,unidentified,"It is possible that some or all of the novel AraC-regulated genes have as-yet-unidentified connections to arabinose metabolism , although this seems especially unlikely for polB , which encodes a well-characterized DNA polymerase .
"
2124,2125,349.txt,4,0,,,,"polB are positively regulated by AraC due to partial read-through of Rho-independent terminators .
"
2125,2126,349.txt,5,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"We did not detect regulation of polB by AraC in S. enterica .
"
2126,2127,349.txt,6,0,,,,"Hence , polB regulation by AraC may be widely conserved ."
2127,2128,1811.txt,1,2,Salmonella;Mus sp.,Salmonella;mice,Mus sp.;Salmonella,We considered the possibility of the SsrB-repressed sciS being such a gene because its inactivation was reported to increase Salmonella virulence in BALB/c mice infected orally ( 4 ) .
2128,2129,1810.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Moreover , RcsB regulates yddX in E. coli ."
2129,2130,348.txt,1,0,,,,"overall expression was a ¡ ected to the same extent as seen in the rpoS mutant leading to the conclusion that SlyA is also not a main regulator of dsb
"
2130,2131,348.txt,2,1,Salmonella,Salmonella,Salmonella,"Recent studies with Salmonella rpoS expression suggest that conditions encountered within host cells may partially resemble stationary-phase ( 20 ) ; however , the patterns of SlyA-regulated proteins were significantly different in stationary-phase and during infection of macrophages ."
2131,2132,1804.txt,1,0,,,,"The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA , which was confirmed by yeast agglutination assay ."
2132,2133,406.txt,1,1,Salmonella,Salmonella,Salmonella,"To test the possibility that the effect of the tdcA mutation was increased under inducing conditions for PhoP-activated genes , Salmonella cultures were shifted from N minimal-medium containing a repressing Mg concentration ( 2 mM ) to that contain-2 + ing an activating Mg concentrations ( 50 μM ) ( Fig. 5B ) ."
2133,2134,1192.txt,1,0,,,,"Like marRAB , tolC are positively regulated by SoxS ."
2134,2135,360.txt,1,0,,,,"The expression of hilA , the key regulator of SPI-1 gene expression , is negatively affected by PhoP-PhoQ ."
2135,2136,374.txt,1,0,,,,"Notably , during-growth-on-glucose , less Acs is made because Crp can not fully activate acs expression when cAMP levels are low .
"
2136,2137,374.txt,2,0,,,,"Notably , during-growth-on-glucose , less Acs is made because Crp can not fully activate acs expression when cyclic AMP levels are low .
"
2137,2138,374.txt,3,0,,,,"Notably , CRP activates acs ."
2138,2139,1838.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"STM3216 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI4-encoded genes , and repressed by SsrB .
"
2139,2140,1838.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"STM3216 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-associated genes , and repressed by SsrB .
"
2140,2141,1838.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"STM3216 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-encoded genes , and repressed by SsrB ."
2141,2142,1186.txt,1,0,,,,"Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .
"
2142,2143,1186.txt,2,0,,,,"In addition , the lack of consensus PmrA-binding sites in the promoters of STM4568 suggested that these genes may be indirectly activated by PmrA ."
2143,2144,412.txt,1,0,,,,"This is in contrast to what has been observed for sodB regulation ; overproduction of Fur had little if any effect on sodB expression , presumably because Fur repression of rfrB is essentially complete in these conditions .
"
2144,2145,412.txt,2,0,,,,"This is in contrast to what has been observed for sodB regulation ; overproduction of Fur had little if any effect on sodB expression , presumably because Fur repression of rfrA is essentially complete in these conditions .
"
2145,2146,412.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , expression of sodB is activated by Fur via repression of the small RNA RyhB ."
2146,2147,1179.txt,1,0,,,,"Recent studies indicate that HilA binds to specific sequences in the invF promoters .
"
2147,2148,1179.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"By placing invF encoding the secretion machinery under direct control of HilA , S. typhimurium ensures that secreted the secretion apparatus are produced simultaneously .
"
2148,2149,1179.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"By placing invF encoding the secretion machinery under direct control of HilA , S. typhimurium ensures that secreted effectors are produced simultaneously .
"
2149,2150,1179.txt,4,0,,,,"Fis affects expression of invF : : Tn5lacZY in the absence of HilA Current models for the regulation of invasion genes suggest that there is a HilA-independent pathway to invF expression .
"
2150,2151,1179.txt,5,0,,,,"These results indicate that Fis is also involved in the regulation of invF expression in a HilA-independent manner .
"
2151,2152,1179.txt,6,0,,,,"It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilC to activate invF .
"
2152,2153,1179.txt,7,0,,,,"It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilC to bind upstream of .
"
2153,2154,1179.txt,8,0,,,,"It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD to activate invF .
"
2154,2155,1179.txt,9,0,,,,"It will be interesting to determine how the binding of HilA upstream of invF affects the ability of HilD to bind upstream of .
"
2155,2156,1179.txt,10,0,,,,"HilA activates invF operon expression by binding to the invF promoter .
"
2156,2157,1179.txt,11,0,,,,"Transcription of invF is primarily regulated by HilA
"
2157,2158,1179.txt,12,0,,,,"Dam-dependent regulation of invF was still observed in HilA
"
2158,2159,1179.txt,13,0,,,,"The invF gene is regulated by the HilA protein .
"
2159,2160,1179.txt,14,0,,,,"Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .
"
2160,2161,1179.txt,15,0,,,,"Additionally , HilA can bind to specific sequences in the promoter of invF , a transcriptional regulator ."
2161,2162,1151.txt,1,0,,,,"The ORF of malS is regulated by MalT , the activator of the maltose system in E. col ."
2162,2163,1637.txt,1,1,Salmonella,Salmonella,Salmonella,"A number of fusions to genes in known virulence regulons such as sodA ( manganese superoxide dismutase ) , pagJ ( a PhoPQ-activated gene ) and ssaE ( in Salmonella patho-genicity island 2 , SPI2 ) were identified ."
2163,2164,1623.txt,1,0,,,,"Under conditions of low-osmolarity , the transcription of iagA is negatively controlled by the RcsB regulator , acting in concert with the TviA protein ."
2164,2165,1145.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
2165,2166,638.txt,1,0,,,,the PinvF probe in EMSA _ supporting the notion that expression of invF is indirectly regulated by IscR
2166,2167,162.txt,1,0,,,,"For example , the apparent activation of flagellar genes by H-NS most likely occurs by a repressor of the flagellar regulators flhDC .
"
2167,2168,162.txt,2,0,,,,"H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly .
"
2168,2169,162.txt,3,0,,,,"H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly ."
2169,2170,1390.txt,1,0,,,,"The SlyA Proteins Bind to the ugtL Promoter -- We conducted gel shift assays .
"
2170,2171,1390.txt,2,0,,,,The SlyA Proteins Bind to the ugtL Promoter -- We conducted a 536-bp DNA fragment .
2171,2172,604.txt,1,0,,,,"a 1.1 1.1 a membran , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant
"
2172,2173,604.txt,2,0,,,,"a 1.1 1.1 a a rbsA 1.1 ABC superfamily -LRB- -RRB- , -- D-ribose high-affinity transport protein ABC superfamily -LRB- -RRB- , D-ribose transport protein ABC superfamil , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant
"
2173,2174,604.txt,3,0,,,,"rbs Operon That Are Regulated by luxS = Autoinducer-2 at Mid-Log Phase a 1.1 1.1 a membran , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant
"
2174,2175,604.txt,4,0,,,,"rbs Operon That Are Regulated by luxS = Autoinducer-2 at Mid-Log Phase a 1.1 1.1 a a rbsA 1.1 ABC superfamily -LRB- -RRB- , -- D-ribose high-affinity transport protein ABC superfamily -LRB- -RRB- , D-ribose transport protein ABC superfamil , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant"
2175,2176,610.txt,1,0,,,,"Similarly , PmrA activated transcription of the dgoA locus by nearly 500-fold .
"
2176,2177,610.txt,2,0,,,,"Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .
"
2177,2178,610.txt,3,0,,,,"Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .
"
2178,2179,610.txt,4,0,,,,"The PmrA-activated yibD and dgoA genes are dispensable for resistance to polymyxin B and Fe ( III ) ( Tamayo et al. , 2002 ) ."
2179,2180,1384.txt,1,0,,,,"Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system ."
2180,2181,88.txt,1,0,,,,"To demonstrate the interaction of CRP with gat promoters by EMSA , CRP-His6 was added in increasing concentrations to the 300-bp fragments located upstream of gatY ."
2181,2182,176.txt,1,0,,,,"Two StpA-repressed PhoP-dependent genes bound by StpA , pagC and ugtL , are also directly repressed by H-NS ( Perez et al. , 2008 ) ."
2182,2183,2100.txt,1,0,,,,"While transcriptional regulation of sopA by HilA/InvF has been described in the literature , sopD regulation is less well understood ( indicated by a dashed black arrow ) ."
2183,2184,1409.txt,1,0,,,,Fnr Bind to the lpxO Promoter Region Our results indicate that Fnr have a role .
2184,2185,823.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"So , it is possible that OmpR independently regulate the expression of tviA in S. typhi at osmotic-stress .
"
2185,2186,823.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of CD11c dendritic cells in the lamina .
"
2186,2187,823.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Acquisition of the tviA gene by S. Typhi integrated the regulation of flagella into the OmpR regulons , such that flagellum expression is decreased following invasion of the intestinal mucosa , thereby avoiding detection by TLR5 present on the basolateral surface of enterocytes dendritic cells in the lamina .
"
2187,2188,823.txt,4,0,,,,"OmpR binds to the promoters of tviA to activate their transcription ; however , it negatively regulates hfq in an indirect manner .
"
2188,2189,823.txt,5,0,,,,"OmpR binds to the promoters of tviA to activate their transcription ; however , it positively regulates tviB .
"
2189,2190,823.txt,6,0,,,,": -LRB- 0123456789 OmpR also binds to the promoter of tviA to activate its transcription , and thus act as an activator of Vi antigen .
"
2190,2191,823.txt,7,0,,,,"These results indicated that the transcription of tviA was under negative control of OmpR , respectively .
"
2191,2192,823.txt,8,0,,,,"These results indicated that the transcription of tviA was under positive control of OmpR , respectively .
"
2192,2193,823.txt,9,0,,,,"Thus , OmpR only directly regulates two , i.e. , tviA , of the four genes ."
2193,2194,63.txt,1,0,,,,"Figure 5A shows that hilD transcription was induced by both Fur in the hilD background .
"
2194,2195,63.txt,2,0,,,,"There was transcriptional induction of hilD in response to Fur
"
2195,2196,63.txt,3,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2196,2197,63.txt,4,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2197,2198,63.txt,5,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2198,2199,63.txt,6,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2199,2200,63.txt,7,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2200,2201,63.txt,8,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2201,2202,63.txt,9,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2202,2203,63.txt,10,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in-vivo .
"
2203,2204,63.txt,11,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,Fur activates the expression of Salmonella enterica pathogenicity Island 1 by directly interacting with the hilD operator in-vivo .
2204,2205,837.txt,1,0,,,,The molecular mechanism for hilA repression by PhoPQ has not been characterized .
2205,2206,77.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"STM3138 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI4-encoded genes , and repressed by SsrB .
"
2206,2207,77.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"STM3138 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-associated genes , and repressed by SsrB .
"
2207,2208,77.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"STM3138 , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-encoded genes , and repressed by SsrB ."
2208,2209,189.txt,1,1,Salmonella,Salmonella,Salmonella,"The rstA gene also seems to be a member of the PhoP regulon in Salmonella because a computational approach discovered the rstA promoter features shared with a group of PhoP-regulated promoters ( 35 , 36 ) .
"
2209,2210,189.txt,2,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
2210,2211,2114.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Clarke , M.B. , and Sperandio , V. Transcriptional regulation of flhDC by FliA in enterohaemorrhagic Escherichia coli .
"
2211,2212,2114.txt,2,0,,,,"To investigate whether z66 is regulated by FliA like other biphasic S. flhDC mutants were affected by the osmotic environment , an ompR mutant was also prepared .
"
2212,2213,2114.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Clarke M , Sperandio V. Transcriptional regulation of flhDC by FliA in enterohaemorrhagic Escherichia coli .
"
2213,2214,2114.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,Transcriptional regulation of flhDC by sigma ( FliA ) in enterohaemorrhagic Escherichia coli .
2214,2215,1435.txt,1,0,,,,"Downstream of oafA , but within the same horizontal acquisition , is the site of a second SsrB-regulated fusion ( srfE ) , within an msgA ( macrophage survival gene ) 29 homologue ( P 10 ; Fig. 2 ) ."
2215,2216,1353.txt,1,0,,,,"the steady-state levels _ achieved by the strain with the wild-type phoPQ promoter after induction of the PhoP/PhoQ system
"
2216,2217,1353.txt,2,0,,,,the steady-state levels _ achieved by the strain with the wild-type phoPQ promoter after induction of the PhoP/PhoQ system
2217,2218,1347.txt,1,0,,,,"The main regulator of HilD , thereby activates flhDC transcription .
"
2218,2219,1347.txt,2,0,,,,"The main regulator of HilD , binds upstream of the flhDC P5 transcriptional start site .
"
2219,2220,1347.txt,3,0,,,,"Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV .
"
2220,2221,1347.txt,4,0,,,,"Furthermore , HilD directly controls the expression of the flhDC operon encoding FlhDC .
"
2221,2222,1347.txt,5,0,,,,"Likewise , HilD binds the flhDC promoter to activate the flagellar regulon ."
2222,2223,2128.txt,1,0,,,,"To investigate whether z66 is regulated by FliA like other biphasic S. fliA mutants were affected by the osmotic environment , an ompR mutant was also prepared .
"
2223,2224,2128.txt,2,0,,,,"These results indicate that the fliA operon itself is under the positive control of FliA .
"
2224,2225,2128.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium;S. typhimurium;typhimurium;mice;S. typhimurium;typhimurium,Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium,"In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype ."
2225,2226,1421.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Negative regulation of mutS RpoS global regulators of Escherichia coli K-12 .
"
2226,2227,1421.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Negative regulation of mutS RpoS global regulators of Escherichia coli K-12 .
"
2227,2228,1421.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Negative regulation of mutS RpoS global regulators of Escherichia coli K-12 .
"
2228,2229,1421.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,Negative regulation of mutS RpoS global regulators of Escherichia coli K-12 .
2229,2230,994.txt,1,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of orgA remains unaffected .
"
2230,2231,994.txt,2,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgK remains unaffected .
"
2231,2232,994.txt,3,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgH remains unaffected .
"
2232,2233,994.txt,4,0,,,,"In addition , HilD directly activate sipC in non-HilA dependent manner ."
2233,2234,980.txt,1,0,,,,Our recent observations indicate that SlyA exerts a direct effect by binding at ssrB .
2234,2235,758.txt,1,1,Salmonella,Salmonella,Salmonella,"We report here that StpA are the main negative regulators of ompS1 expression in Salmonella .
"
2235,2236,758.txt,2,1,Salmonella,Salmonella,Salmonella,"We report here that StpA are the main positive regulators of ompS1 expression in Salmonella .
"
2236,2237,758.txt,3,1,Salmonella,Salmonella,Salmonella,"Moreover it has been reported that StpA are the main negative regulators of ompS1 expression in Salmonella .
"
2237,2238,758.txt,4,1,Salmonella,Salmonella,Salmonella,Moreover it has been reported that StpA are the main positive regulators of ompS1 expression in Salmonella .
2238,2239,1582.txt,1,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rpoS .
"
2239,2240,1582.txt,2,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rcsC .
"
2240,2241,1582.txt,3,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : slyA .
"
2241,2242,1582.txt,4,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : phoP .
"
2242,2243,1582.txt,5,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : ssrA/B .
"
2243,2244,1582.txt,6,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : ompR .
"
2244,2245,1582.txt,7,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rpoS .
"
2245,2246,1582.txt,8,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rcsC .
"
2246,2247,1582.txt,9,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : slyA .
"
2247,2248,1582.txt,10,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : phoP .
"
2248,2249,1582.txt,11,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : ssrA/B .
"
2249,2250,1582.txt,12,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of virK is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : ompR .
"
2250,2251,1582.txt,13,0,,,,"These results indicate that both virK are regulated by PhoP .
"
2251,2252,1582.txt,14,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,SL1344;14028s,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .
"
2252,2253,1582.txt,15,1,Salmonella,Salmonella,Salmonella,"The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .
"
2253,2254,1582.txt,16,0,,,,"Inhibition on the expression was also obtained when the action of linoleic and linolenic fatty-acids were assayed using well-known PhoP-regulated genes other than virK , indicating that the effect was global on the PhoP -- PhoQ controlled regulon ( Viarengo et al. , 2013 ) .
"
2254,2255,1582.txt,17,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
2255,2256,770.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
2256,2257,764.txt,1,0,,,,"To demonstrate the interaction of CRP with gat promoters by EMSA , CRP-His6 was added in increasing concentrations to the 300-bp fragments located upstream of gatZ ."
2257,2258,1596.txt,1,0,,,,"the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes include lexA
"
2258,2259,1596.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2259,2260,1596.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2260,2261,1596.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2261,2262,1596.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2262,2263,1596.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2263,2264,1596.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2264,2265,1596.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2265,2266,1596.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2266,2267,1596.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2267,2268,1596.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2268,2269,1596.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent .
"
2269,2270,1596.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of lexA by all nine FQs is likely LexA dependent ."
2270,2271,2074.txt,1,0,,,,"Finally , rpoS is epistatic over phoPQ , reinforcing the fact that the induction of the hlyE expression under low concentration of Mg2 + depends on PhoPQ .
"
2271,2272,2074.txt,2,0,,,,It is possible that PhoPQ is participating in the increase of hlyE transcription under low Mg2 .
2272,2273,957.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"The level of expression of tviA in the ompR mutant is nearly 10-fold lower than that in the wild type strain , suggesting that the expression of tviA in S. typhi is activated by OmpR at the early stage of osmotic-stress .
"
2273,2274,957.txt,2,0,,,,"The result demonstrates that the expression of tviA is activated by OmpR .
"
2274,2275,957.txt,3,0,,,,": -LRB- 0123456789 OmpR also binds to the promoter of tviA to activate its transcription , and thus act as an activator of Vi antigen ."
2275,2276,943.txt,1,0,,,,"H-NS bound to the complete 5 = region of assT at a concentration of Fig. 8B .
"
2276,2277,943.txt,2,0,,,,H-NS bound to the complete 5 = region of assT at a concentration of 200 nM H-NS .
2277,2278,1569.txt,1,0,,,,"The two-component regulatory SirA/BarA function through HilD , thus inducing hilA ."
2278,2279,2060.txt,1,0,,,,"SprB , regulates the expression of sopE ."
2279,2280,1541.txt,1,0,,,,that CRP activates expression of acrB in stationary-phase
2280,2281,2048.txt,1,0,,,,"our fliC transcription timecourse in which FliZ increases fliC expression at later timepoints during-growth
"
2281,2282,2048.txt,2,0,,,,"our fliC transcription timecourse in which FliZ increases fliC expression at later timepoints during-growth
"
2282,2283,2048.txt,3,0,,,,"our fliC transcription timecourse in which FliZ increases fliC expression at later timepoints during-growth
"
2283,2284,2048.txt,4,0,,,,"Thus , the impact of FliZ upon the fliC census is enhanced at 5 hours compared to 2.5 hours under conditions of metered expression .
"
2284,2285,2048.txt,5,0,,,,"FliZ increases both fliC expression in the absence of ydiV .
"
2285,2286,2048.txt,6,0,,,,"cellular factors _ required for FliZ to activate fliC expression
"
2286,2287,2048.txt,7,0,,,,Cells low in activated FlhD4C2 would require more FliZ to activate fliC expression
2287,2288,1227.txt,1,0,,,,"RflM enhances binding affinity of RcsB to the flhDC target promoter DNA .
"
2288,2289,1227.txt,2,0,,,,We propose that RflM enhances target specific-ity of the RcsB-RflM complex to the binding site within the flhDC promoter independent of the phosphorylation state of RcsB .
2289,2290,1233.txt,1,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"To determine whether the PhoP/PhoQ system is activated differently in S. enterica and S. bongori , we investigated expression of the PhoP-dependent phoP gene in bacteria grown under different PhoQ-inducing conditions using a pphoP-gfp fusion given that PhoP positively autoregulates its own expression ( Soncini et al. , 1995 ) ."
2290,2291,1555.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Downregulation of the Escherichia coli guaB promoter by upstream-bound cyclic-AMP-receptor-protein .
2291,2292,1964.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SirA Orthologs Affect both Motility 43210 The sirA gene of Salmonella enterica serovar Typhimurium encodes a two-component response regulator of the FixJ family .
"
2292,2293,1964.txt,2,0,,,,"No further increase in PefA expression was apparent in a sirA csrB csrC DfimAICDHF mutant ( TS133 ) ( Figure 2C ) , thus the lack of SirA or inactivation of the SirA-regulated genes csrB and csrC produced similar effects on PefA expression ."
2293,2294,228.txt,1,1,synthetic construct,primer,synthetic construct,"Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by SlyA because the mRNA level of transcripts is reduced significantly in the slyA mutants grown in low-Mg2 conditions -LRB- Fig .
"
2294,2295,228.txt,2,0,,,,The induction of slyA transcription was also visually detected by using a SlyA-green fluorescent protein transcriptional-fusion .
2295,2296,1970.txt,1,0,,,,"The L-Ara4N-mediated negative feedback is not limited to PmrA-dependent genes specifying LPS-modifying enzymes , because mRNA levels of the PmrA-activated aroQ ( Tamayo et al. , 2005b ) , which encodes a chorismate mutase , are lower in the wild-type than in the ugd mutant at 120 min , even though these strains produce similar amounts of aroQ transcript at 20 min ( Figure S4A ) ."
2296,2297,572.txt,1,0,,,,"The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , mutation of the putative RcsB binding site in the ugd promoter abolished tolB-promoted ugd transcription .
"
2297,2298,572.txt,2,0,,,,"The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , Fig. 2B abolished tolB-promoted ugd transcription .
"
2298,2299,572.txt,3,0,,,,"The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , yojN genes abolished tolB-promoted ugd transcription .
"
2299,2300,572.txt,4,0,,,,"The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , rcsC genes abolished tolB-promoted ugd transcription .
"
2300,2301,572.txt,5,0,,,,"The tolB mutationpromoted activation is mediated by another member of the two-component family , the RcsC -- YojN -- RcsB phosphorelay because inactivation of the rcsA , rcsB genes abolished tolB-promoted ugd transcription ."
2301,2302,1958.txt,1,0,,,,"Mechanistically , HilD indirectly regulates SsrB-regulated genes by antagonizing the H-NS-mediated repression of ssrAB at stationary-phase under SPI-1 inducing conditions [ 30 ] ( see also Fig 2 ) ."
2302,2303,214.txt,1,0,,,,"( B ) - Galactosidase activity from GolS-or CueR-regulated transcriptional-fusions golB : : lacZ ( PgolB ) or copA-lacZ ( PcopA ) , respectively , on cells carrying either wild-type golS and cueR , or golSL , golSsL , or golSC111S , replacing the wild-type copy of golS , or cueRL , replacing cueR ."
2303,2304,1780.txt,1,0,,,,"We have previously shown that nlpI have opposing effects on biofilm formation at decreased growth temperatures with NlpI , respectively , suppressing biofilm formation .
"
2304,2305,1780.txt,2,0,,,,"We have previously shown that nlpI have opposing effects on biofilm formation at decreased growth temperatures with NlpI , respectively , enhancing biofilm formation ."
2305,2306,2289.txt,1,0,,,,"As InvF is a transcriptional activator of other effector proteins , tnpA indirectly represses these genes .
"
2306,2307,2289.txt,2,0,,,,"As InvF is a transcriptional activator of SPI-1 , tnpA indirectly represses these genes ."
2307,2308,1794.txt,1,0,,,,"STM1344 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis ."
2308,2309,200.txt,1,1,Escherichia coli,E. coli,Escherichia coli,Lrp negatively regulates the porin gene ompC expression in E. coli
2309,2310,566.txt,1,0,,,,"Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .
"
2310,2311,566.txt,2,0,,,,"AFM imaging revealed that unphosphorylated SsrB was able to bind to the csgD regulatory region
"
2311,2312,566.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2312,2313,566.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2313,2314,566.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2314,2315,566.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2315,2316,566.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2316,2317,566.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2317,2318,566.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2318,2319,566.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2319,2320,566.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2320,2321,566.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2321,2322,566.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2322,2323,566.txt,14,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2323,2324,566.txt,15,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2324,2325,566.txt,16,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2325,2326,566.txt,17,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2326,2327,566.txt,18,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2327,2328,566.txt,19,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2328,2329,566.txt,20,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2329,2330,566.txt,21,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
2330,2331,566.txt,22,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected SsrB differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
2331,2332,566.txt,23,1,Dipturus trachyderma,ray,Dipturus trachyderma,"Unphosphorylated SsrB binds to the csgD regulatory region SsrB is X-ray crystallography suggested that phosphorylation was required for DNA binding .
"
2332,2333,566.txt,24,0,,,,"Unphosphorylated SsrB binds to the csgD regulatory region SsrB is a NarL family member suggested that phosphorylation was required for DNA binding .
"
2333,2334,566.txt,25,0,,,,"Surprisingly , we observed binding of SsrB , D56A SsrB and SsrBc to distinct regions of the csgD regulatory region .
"
2334,2335,566.txt,26,0,,,,"Binding showed that unphosphorylated SsrB was capable of binding csgD .
"
2335,2336,566.txt,27,0,,,,"Closer examination revealed a sharp curvature at the regions where SsrB was bound to csgD .
"
2336,2337,566.txt,28,0,,,,"Thus , unphosphorylated SsrB can bind to the csgD regulatory region when it has been coated with the repressor H-NS .
"
2337,2338,566.txt,29,0,,,,complexes _ formed by the binding of SsrB and/or H-NS to the csgD regulatory region
2338,2339,1019.txt,1,0,,,,"SlyA is also involved in the regulation of mig-14
"
2339,2340,1019.txt,2,0,,,,"The mig-14 genes appear to be regulated by both SlyA , by a mechanism ."
2340,2341,2276.txt,1,0,,,,"LexA-P139A , repressed sulA"
2341,2342,2262.txt,1,0,,,,ydiV inhibit FlhD4C2 function at a posttranscriptional level
2342,2343,599.txt,1,1,synthetic construct,Primer,synthetic construct,"Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM ."
2343,2344,1025.txt,1,0,,,,"Our results indicate that only the PmrA regulator binds to the wzz promoter , inducing fepE gene expression ."
2344,2345,1743.txt,1,0,,,,"If a condition exists in which hilA is repressed while invF expression is induced through HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?
"
2345,2346,1743.txt,2,0,,,,"Loss of hns , however , does not relieve repression of hilA by oxygen -LRB- as opposed to osmolarity -RRB- and expression of hilA in an hns mutant still requires HilD under inducing -LRB- high-osmolarity , low oxygen -RRB- growth-conditions .
"
2346,2347,1743.txt,3,0,,,,"Loss of hns , however , does not relieve repression of hilA by oxygen -LRB- as opposed to osmolarity -RRB- and expression of hilA in an hns mutant still requires HilD under inducing L. C. Lee , unpublished observations .
"
2347,2348,1743.txt,4,0,,,,"Loss of hns , however , does not relieve repression of hilA by oxygen -LRB- as opposed to osmolarity -RRB- and expression of hilA in an hns mutant still requires HilD under inducing L. Schechter Lee , unpublished observations .
"
2348,2349,1743.txt,5,0,,,,"This finding suggests that HilE functions as a repressor by binding to HilD to prevent its activation of the hilA promoter .
"
2349,2350,1743.txt,6,0,,,,"For example , hilA expression are decreased by deletion of fur at the level of transcription via HilD , supporting the idea that HilD controls the transcription of these genes .
"
2350,2351,1743.txt,7,0,,,,"Transcriptional activation by HilD relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha .
"
2351,2352,1743.txt,8,0,,,,"HilD relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha .
"
2352,2353,1743.txt,9,0,,,,"Coincident with this reduction in HilD protein , hilA = was potently repressed by 9.7-fold repression .
"
2353,2354,1743.txt,10,0,,,,"Coincident with this reduction in HilD protein , hilA = was potently repressed by bile .
"
2354,2355,1743.txt,11,0,,,,"H-NS repression of hilA counteracts transcriptional activation by HilD
"
2355,2356,1743.txt,12,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including repression of hilA by preventing HilD function .
"
2356,2357,1743.txt,13,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including repression of hilA by binding to .
"
2357,2358,1743.txt,14,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2358,2359,1743.txt,15,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
2359,2360,1743.txt,16,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2360,2361,1743.txt,17,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
2361,2362,1743.txt,18,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2362,2363,1743.txt,19,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
2363,2364,1743.txt,20,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2364,2365,1743.txt,21,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
2365,2366,1743.txt,22,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2366,2367,1743.txt,23,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
2367,2368,1743.txt,24,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2368,2369,1743.txt,25,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
2369,2370,1743.txt,26,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2370,2371,1743.txt,27,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA ."
2371,2372,1757.txt,1,0,,,,"UvrY in turn activates the expression of csrB
"
2372,2373,1757.txt,2,1,Escherichia coli,E. coli,Escherichia coli,UvrY of E. coli both control the csr system by directly activating the csrB gene .
2373,2374,1031.txt,1,0,,,,"Strain FeCl3 MIC ( mM ) 3200-100-1600-100 1600-100-1600 Wild-type DpmrAB/vector DpmrAB/ppmrG DpmrAB DpmrAB rfaY DpmrC ugd pmrG DpmrC ugd pmrG rfaY Modification of the Hep ( I ) phosphate with phosphoethanolamine is not required for Fe ( III ) resistance The core region of the LPS has two phosphates : one at Hep ( II ) that is targeted by PmrG ( Fig. 2C ) , and one at Hep ( I ) that can be modified with phosphoethanolamine by the PmrA-activated cptA gene product ( Tamayo et al. , 2005 ) ."
2374,2375,1999.txt,1,1,Salmonella,Salmonella,Salmonella,"Summary The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by via the PmrA -- PmrB by low Mg2 + in a process .
"
2375,2376,1999.txt,2,1,Salmonella,Salmonella,Salmonella,"Summary The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by via the PmrA -- PmrB two-component system + in a process .
"
2376,2377,1999.txt,3,0,,,,"Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .
"
2377,2378,1999.txt,4,0,,,,"Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .
"
2378,2379,1999.txt,5,1,unidentified,not shown,unidentified,"On the other hand , neither Ca2 + nor Co2 + , K + , Ni2 + , Zn2 + , Mn2 + , Cu2 + , Ga3 + or Ru3 + ( at concentrations of up to 1 mM ) could induce PmrA-activated genes ( Wosten et al. , 2000 ) or kill the DpmrC ugd pmrG triple mutant ( data not shown ) .
"
2379,2380,1999.txt,6,0,,,,"Inactivation of the PmrA-activated genes mediating the modification of the two lipid-A phosphates and the Hep ( II ) phosphate in the core region resulted in a strain ( i.e. the DpmrC ugd pmrG triple mutant ) that was as susceptible to Fe ( III ) as the DpmrAB mutant ( Table 1 ) and that bound more iron than the wild-type strain ( Fig. 1B ) .
"
2380,2381,1999.txt,7,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
2381,2382,1999.txt,8,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
2382,2383,1999.txt,9,0,,,,"Furthermore , a strain deleted for of all three pmrC , ugd and pmrG genes and harbouring the pmrA505 allele , which encodes a PmrA protein that promotes transcription of PmrA-activated genes even under noninducing conditions ( Kox et al. , 2000 ) , was as susceptible to Fe ( III ) as the DpmrAB mutant ( Table 1 ) .
"
2383,2384,1999.txt,10,1,Salmonella,Salmonella,Salmonella,"Synthesis of Ara4N and addition to the lipid-A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .
"
2384,2385,1999.txt,11,0,,,,"This is because inactivation of lpxT hindered the generation of lipid-A singly substituted with pEtN or L-Ara4N ( Figure 3E ) , and it eliminated the increased Fe3 + association to the bacterial cell and transcription of PmrA-activated genes displayed by pmrR and ugd mutants ( Figures 4A , 4D-E and 5D-F ) .
"
2385,2386,1999.txt,12,0,,,,"To test this hypothesis , we determined the β2 galactosidase activity produced by strains harboring chromosomal lac transcriptional-fusions to the PmrA-activated pbgP operon and ugd gene .
"
2386,2387,1999.txt,13,0,,,,Deletion of the ugd gene in these mutant strains further enhanced mRNA levels of PmrA-activated genes ( Figures 5A and 5B ) .
2387,2388,1741.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To determine whether Fur regulation of tcf was specific to S. Typhi , the tcfA was transformed into S. Typhimurium .
"
2388,2389,1741.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"To determine whether Fur regulation of tcf was specific to S. Typhi , the tcfA was transformed into their isogenic fur mutants .
"
2389,2390,1741.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"To determine whether Fur regulation of tcf was specific to S. Typhi , the tcfA was transformed into E. coli K-12 ."
2390,2391,2248.txt,1,0,,,,Various ligands can occupy the `` upper 
2391,2392,1027.txt,1,0,,,,"-RRB- , narG -LRB- are positively regulated by SlyA"
2392,2393,1033.txt,1,1,Iris germanica,FLAG,Iris germanica,"Real-time PCR analysis revealed that upon RstA expression , transcriptional repression of the fhuF gene by the FLAG-tagged Fur protein was as efficient as in the strain with the wild-type Fur protein ( see Fig .
"
2393,2394,1033.txt,2,0,,,,The feoB deletion prevented the RstA-promoted repression of transcription levels of fhuF .
2394,2395,1755.txt,1,0,,,,"The effect of spermine NONOate on the PhoPQ-dependent induction of the lpxO : : lacZ-transcriptional-fusion is shown in , Miller Units , M.U. is represented as the mean6SEM of 4 -- 6 independent observations from 2 -- 3 separate experiments .
"
2395,2396,1755.txt,2,0,,,,"The effect of spermine NONOate on the PhoPQ-dependent induction of the lpxO : : lacZ-transcriptional-fusion is shown in , panel A. b-galactosidase activity is represented as the mean6SEM of 4 -- 6 independent observations from 2 -- 3 separate experiments ."
2396,2397,2274.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"E. coli strains were shown to express higher levels of flagellum genes and increased motility , possibly due to the inhibition of fliA promoters by DksA .
"
2397,2398,2274.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"E. coli strains were shown to express higher levels of che-motaxis genes and increased motility , possibly due to the inhibition of fliA promoters by DksA ."
2398,2399,1769.txt,1,0,,,,"Previously , we have determined that the cse1 promoter is repressed by the global regulators H-NS and LRP whereas LeuO participates in its positive regulation ; also , it can be expressed independently of LeuO in N-MM ."
2399,2400,2260.txt,1,0,,,,"These data showed that cAMP-CRP binds to the promoters of gatZ , ."
2400,2401,1782.txt,1,0,,,,"hilA are negatively regulated by SlyA
"
2401,2402,1782.txt,2,0,,,,"These results suggest that hilA is downregulated by SlyA .
"
2402,2403,1782.txt,3,0,,,,These results suggest that SlyA negatively regulates hilA .
2403,2404,216.txt,1,0,,,,"PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .
"
2404,2405,216.txt,2,0,,,,"Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .
"
2405,2406,216.txt,3,0,,,,"PmrA has been shown to bind pmrHFIJKLM .
"
2406,2407,216.txt,4,0,,,,"PmrA regulates the transcription of the pmrHFIJKLM operon .
"
2407,2408,216.txt,5,0,,,,"PmrA controls the expression of pmrHFIJKLM .
"
2408,2409,216.txt,6,0,,,,"After being phosphorylated by PmrB , PmrA can effectively bind to the transcriptional sites of pmrHFIJKLM ."
2409,2410,570.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates Fis to control Salmonella Typhi hlyE expression Matías 2 , Guido C M .
"
2410,2411,570.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates Fis to control Salmonella Typhi hlyE expression Matías 1 , Alejandro A Hida .
"
2411,2412,570.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates Fis to control Salmonella Typhi hlyE expression Matías , Nicolás A Villa .
"
2412,2413,570.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates Fis to control Salmonella Typhi hlyE expression Matías , Leonardo M Rodrígu .
"
2413,2414,570.txt,5,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates Fis to control Salmonella Typhi hlyE expression Matías R Jofr .
"
2414,2415,570.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Altogether , these results suggest that Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .
"
2415,2416,570.txt,7,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates Fis to control Salmonella Typhi hlyE expression .
"
2416,2417,570.txt,8,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,RpoS integrates Fis to control Salmonella Typhi hlyE expression .
2417,2418,564.txt,1,0,,,,This surprising result suggested that the spiC promoter in pCS192 is at least partially regulated by Mg2 through a PhoP-and PhoQ-independent pathway .
2418,2419,202.txt,1,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , ygaU are regulated by the alternative sigma factor RpoS ."
2419,2420,1796.txt,1,0,,,,two genes encode response regulators are regulated by SlyA yhjB
2420,2421,1966.txt,1,0,,,,"In the context of high YdiV expression , strong induction of fliZ reduced the fliC-OFF subpopulation from 76.3 % to 55.5 % .
"
2421,2422,1966.txt,2,0,,,,"In the context of high YdiV expression , strong induction of fliZ increased the fliC-HIGH subpopulation from 6.9 % to 26 % ."
2422,2423,558.txt,1,0,,,,"250 M Fig. 4A _ suggesting that DksA is not involved in the regulation of hmp transcription
"
2423,2424,558.txt,2,0,,,,"250 M the NO-donor spermine NONOate _ suggesting that DksA is not involved in the regulation of hmp transcription
"
2424,2425,558.txt,3,0,,,,"250 M Fig. 4A _ suggesting that DksA is not involved in the regulation of hmp transcription
"
2425,2426,558.txt,4,0,,,,250 M the NO-donor spermine NONOate _ suggesting that DksA is not involved in the regulation of hmp transcription
2426,2427,1972.txt,1,0,,,,The mgtC gene is transcriptionally controlled by the PhoP-PhoQ regulatory system .
2427,2428,969.txt,1,1,Salmonella,Salmonella,Salmonella,"However , the sequence , the length , , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC/McbR .
"
2428,2429,969.txt,2,1,Salmonella,Salmonella,Salmonella,"However , the position of H-NS binding regions , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC/McbR .
"
2429,2430,969.txt,3,1,Salmonella,Salmonella,Salmonella,"However , the position of the McbR/YncC , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC/McbR ."
2430,2431,1225.txt,1,0,,,,Fur also positively regulates invF .
2431,2432,1543.txt,1,0,,,,"that acnA expression was regulated by FNR , oxygen starvation"
2432,2433,1557.txt,1,0,,,,"Although SirA does not regulate csrA , this gene was also under crp/cya control .
"
2433,2434,1557.txt,2,0,,,,"However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA ."
2434,2435,1231.txt,1,0,,,,"Therefore , the slower increasing of FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of s ClpAP , HslVU and L .
"
2435,2436,1231.txt,2,0,,,,"Therefore , the slower increasing of FlhC proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of f protea ."
2436,2437,955.txt,1,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in hcp .
"
2437,2438,955.txt,2,0,,,,"Additional experiments , showed that NsrR-binding plays a major role in the induction of the hcp ."
2438,2439,1219.txt,1,0,,,,"As the predicted tnpA -- invF base-pairing interaction extends 30 nt upstrea of the HilA-dependent TSS for invF , the HilC-dependent invF transcript may be subject to even stronger repression by tnpA ."
2439,2440,2076.txt,1,0,,,,"On the one hand , in low Mg2 + , the PhoP/PhoQ two component regulatory system activates transcription initiation of the mgtCBR operon .
"
2440,2441,2076.txt,2,0,,,,"When the PhoP/PhoQ two component system is activated by low Mg transcribes mgtCBR messenger RNAs .
"
2441,2442,2076.txt,3,0,,,,"When the PhoP/PhoQ two component system is activated by low Mg binds to the promoter region of the mgtCBR operon .
"
2442,2443,2076.txt,4,0,,,,"When the PhoP/PhoQ two component 2 is activated by low Mg transcribes mgtCBR messenger RNAs .
"
2443,2444,2076.txt,5,0,,,,When the PhoP/PhoQ two component 2 is activated by low Mg binds to the promoter region of the mgtCBR operon .
2444,2445,2062.txt,1,0,,,,The binding activity of SsrBc to its ssrA cognate promoter was inhibited by 100 μM ONOO .
2445,2446,941.txt,1,0,,,,"Although the STM4264 mutant showed the highest c-di-GMP concentration , CsgD expression was lower than in the STM1703 mutant .
"
2446,2447,941.txt,2,0,,,,"STM4264 is located upstream of STM1703 , since STM1703 can complement an STM4264 defect by downregulation of CsgD versa .
"
2447,2448,941.txt,3,0,,,,"STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 , required for the downregulation of CsgD expression .
"
2448,2449,941.txt,4,0,,,,"STM1344 positively affects the expression of the major regulator of CsgD , through the downregulation of the expression of the phosphodiesterases STM1703 and STM3611 .
"
2449,2450,941.txt,5,0,,,,"STM1703 inhibit CsgD function .
"
2450,2451,941.txt,6,0,,,,"During growth on low salt agar plates , STM1703 is the major inhibitor of CsgD , while the other three PDEs play more minor roles ."
2451,2452,799.txt,1,0,,,,"Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .
"
2452,2453,799.txt,2,0,,,,"Other known PmrA-activated genes were not present , including pmrE ( ugd ) , other genes of the pmrHFIJKLM operon , dgoA [ 34 ] , or the more recently identified PmrA-activated genes found by in silico analyses [ 35 ] .
"
2453,2454,799.txt,3,0,,,,"PmrA mediates induction of pmrHFIJKLM .
"
2454,2455,799.txt,4,1,Salmonella,Salmonella,Salmonella,"Synthesis of Ara4N and addition to the lipid-A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) ."
2455,2456,772.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Characterization of the S. Typhimurium marT-fidL Operon An in silico analysis of sequences from S. Typhimurium SPI-3 suggested that the main factor responsible for the phenotypic changes could be marT , since its protein product exhibits similarity to the putative DNA binding domain of the CadC transcriptional activator of E. coli K-12 ."
2456,2457,1580.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2457,2458,1580.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2458,2459,1580.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2459,2460,1580.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2460,2461,1580.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2461,2462,1580.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2462,2463,1580.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2463,2464,1580.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2464,2465,1580.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2465,2466,1580.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2466,2467,1580.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent .
"
2467,2468,1580.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of umuD by all nine FQs is likely LexA dependent ."
2468,2469,2089.txt,1,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
2469,2470,2089.txt,2,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
2470,2471,2089.txt,3,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
2471,2472,2089.txt,4,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS ."
2472,2473,1594.txt,1,0,,,,FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in P-and L-ring assembly mutants by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .
2473,2474,766.txt,1,0,,,,"Five additional distinct SsrB-regulated genes outside SPI-2 were identified : srfI , srfD , srIG , srfL and srfM ."
2474,2475,996.txt,1,0,,,,"Interestingly , the genes encoding these proteins , STM4315 ( rtsA ) and STM4314 ( rtsB ) were among the most strongly Fis-activated genes detected in our microarray study ( supplementary data Tables S1 and S2 at http://mic ."
2475,2476,982.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , ansB is positively coregulated by Fnr ."
2476,2477,1351.txt,1,0,,,,"Evidence suggests that cysE may be activated by CysB .
"
2477,2478,1351.txt,2,0,,,,"This swarm-cell-specific induction of cysE is independent of CysB .
"
2478,2479,1351.txt,3,0,,,,"We reasoned that if cysE upregulation is driving induction of the CysB regulon by increasing NAS levels , adding NAS to swim cells should be able to induce the anti-biotic resistance phenotype in non-swarming cells ."
2479,2480,1437.txt,1,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2480,2481,1437.txt,2,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2481,2482,1437.txt,3,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2482,2483,1437.txt,4,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2483,2484,1437.txt,5,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2484,2485,1437.txt,6,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2485,2486,1437.txt,7,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2486,2487,1437.txt,8,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2487,2488,1437.txt,9,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2488,2489,1437.txt,10,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2489,2490,1437.txt,11,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2490,2491,1437.txt,12,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2491,2492,1437.txt,13,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2492,2493,1437.txt,14,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2493,2494,1437.txt,15,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2494,2495,1437.txt,16,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2495,2496,1437.txt,17,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2496,2497,1437.txt,18,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2497,2498,1437.txt,19,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2498,2499,1437.txt,20,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2499,2500,1437.txt,21,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2500,2501,1437.txt,22,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2501,2502,1437.txt,23,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External oleate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2502,2503,1437.txt,24,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External unsaturated LCFAs repress hilA transcription in a concentration-dependent manner .
"
2503,2504,1437.txt,25,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2504,2505,1437.txt,26,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2505,2506,1437.txt,27,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2506,2507,1437.txt,28,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2507,2508,1437.txt,29,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2508,2509,1437.txt,30,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2509,2510,1437.txt,31,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2510,2511,1437.txt,32,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2511,2512,1437.txt,33,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2512,2513,1437.txt,34,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2513,2514,1437.txt,35,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2514,2515,1437.txt,36,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2515,2516,1437.txt,37,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2516,2517,1437.txt,38,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2517,2518,1437.txt,39,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2518,2519,1437.txt,40,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH FadK HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2519,2520,1437.txt,41,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2520,2521,1437.txt,42,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2521,2522,1437.txt,43,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2522,2523,1437.txt,44,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC mM Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2523,2524,1437.txt,45,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2524,2525,1437.txt,46,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate mM Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2525,2526,1437.txt,47,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External palmitate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2526,2527,1437.txt,48,0,,,,"FadL Formate -LRB- + -RRB- Acetate LCFA Propionate RtsA HilD IM CoASH ATP FadD HilC AMP+PP i Oleate Myristate Palmitate Effectors InvF/SicA Butyrate FIG 2 External myristate LCFAs repress hilA transcription in a concentration-dependent manner .
"
2527,2528,1437.txt,49,0,,,,H-NS repression of hilA counteracts transcriptional activation by RtsA
2528,2529,1423.txt,1,0,,,,"This CsrA-mediated repression of hilD is caused by binding of CsrA to Dalgarno sequence of hilD mRNA .
"
2529,2530,1423.txt,2,0,,,,"This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine .
"
2530,2531,1423.txt,3,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2531,2532,1423.txt,4,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2532,2533,1423.txt,5,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2533,2534,1423.txt,6,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2534,2535,1423.txt,7,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2535,2536,1423.txt,8,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2536,2537,1423.txt,9,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2537,2538,1423.txt,10,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2538,2539,1423.txt,11,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2539,2540,1423.txt,12,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2540,2541,1423.txt,13,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2541,2542,1423.txt,14,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2542,2543,1423.txt,15,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2543,2544,1423.txt,16,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2544,2545,1423.txt,17,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
2545,2546,1423.txt,18,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD ."
2546,2547,49.txt,1,0,,,,"For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated ."
2547,2548,1345.txt,1,0,,,,an LysR-like transcriptional regulator represses flhDC transcription
2548,2549,809.txt,1,1,Salmonella,Salmonella,Salmonella,d in Salmonella it has been shown that transcription of the hns gene -- which influences expression of the Spi-1-encoded invasion genes through the regulator HilD -- is repressed by the iron homeostasis regulator F
2549,2550,61.txt,1,0,,,,"Interestingly , the same region upstream of the pagC translational start has been implicated in binding of the transcriptional regulatory protein SlyA ( J. Gunn and 700 : lacZ pagD : : .
"
2550,2551,61.txt,2,0,,,,"The pagC genes appear to be regulated by both SlyA , by a mechanism .
"
2551,2552,61.txt,3,1,Salmonella,Salmonella,Salmonella,"Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including pagC , in Salmonella .
"
2552,2553,61.txt,4,0,,,,"Although the previous result suggested that SlyA could bind to downstream of the transcription start of pagC , the ATTATT direct repeat we identified should represent namely , the SlyA box .
"
2553,2554,61.txt,5,0,,,,"Although the previous result suggested that SlyA could bind to downstream of the transcription start of pagC , the ATTATT direct repeat we identified should represent the SlyA recognition site .
"
2554,2555,61.txt,6,0,,,,"twice that _ controlled by up-1 in wild-type cells , indicating that SlyA also facilitates PhoP binding to the pagC promoter
"
2555,2556,61.txt,7,0,,,,"pagC genes are regulated by a similar mechanism , involving the coordinated actions of SlyA .
"
2556,2557,61.txt,8,0,,,,"Moreover , the pagC gene is positively regulated by SlyA .
"
2557,2558,61.txt,9,0,,,,"Within the virulence coincident genes , we determined that pagC is positively regulated by SlyA .
"
2558,2559,61.txt,10,0,,,,"Direct binding to promoter regions of virulence genes To determine whether SlyA regulates pagC genes in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in DslyA strains under conditions of oxidative-stress .
"
2559,2560,61.txt,11,0,,,,"Direct binding to promoter regions of virulence genes To determine whether SlyA regulates pagC genes in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT strains under conditions of oxidative-stress .
"
2560,2561,61.txt,12,0,,,,"Direct binding to promoter regions of metabolism genes To determine whether SlyA regulates pagC genes in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in DslyA strains under conditions of oxidative-stress .
"
2561,2562,61.txt,13,0,,,,"Direct binding to promoter regions of metabolism genes To determine whether SlyA regulates pagC genes in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT strains under conditions of oxidative-stress .
"
2562,2563,61.txt,14,0,,,,"SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of Fig. 4G , suggesting that SlyA directly regulates pagC expression .
"
2563,2564,61.txt,15,0,,,,"SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM , suggesting that SlyA directly regulates pagC expression .
"
2564,2565,61.txt,16,0,,,,Direct regulation of pagC genes by SlyA in response to ROS .
2565,2566,821.txt,1,0,,,,"To evaluate the role of the activators HilD and HilC in the regulation of rtsA transcription , the single-copy rtsA-lac transcriptional-fusion was tested in the hilD hilC background in the presence and absence of hha mutations ."
2566,2567,2102.txt,1,0,,,,"Thus , depending on the mechanisms of regulation of rpoS expression , Crl might be dispensable ."
2567,2568,2116.txt,1,0,,,,"Although RpoS is required for N starvation induction of stiC , separate additional signals appear to be involved in the response to individual starvation conditions .
"
2568,2569,2116.txt,2,0,,,,"Although RpoS is required for N starvation induction of stiC , separate additional signals appear to be involved in other conditions ."
2569,2570,75.txt,1,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;typhimu,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Conversely , two glyoxyate shunt genes under the positive control of CsrA in E. coli , aceA , were induced twofold in the S. typhimu-rium csrA mutant ."
2570,2571,1379.txt,1,0,,,,"Several studies have identi-fied the class 3 flagellar protein FliZ as an activator of hilA expression .
"
2571,2572,1379.txt,2,0,,,,"Moreover , studies have shown that FliZ , under the control of FlhDC , positively regulates hilA expression by controlling HilD post-translationally , through a mechanism independent of the Lon protease ."
2572,2573,835.txt,1,0,,,,"An example of an SprB-regulated gene , ( STM1841 ) , is shown in Fig ."
2573,2574,606.txt,1,0,,,,"However , the effect of oxygen seems to be indirect because the regulation by oxygen requires the PutA protein : putA mutants express the put operon at high constitutive levels regardless of the amount of oxygenation .
"
2574,2575,606.txt,2,0,,,,The phenotypes of putA mutants indicate that the PutA protein mediates the regulation of the put operon by proline .
2575,2576,1392.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , YncC acts in concert with S to activate transcription at the yciG promoter .
"
2576,2577,1392.txt,2,0,,,,"The position of the YncC binding site , centered at -- 101 with respect to the transcription start site of yciG , is 10 bp upstream of the most distant transcription activators at simple 70-dependent promoters ."
2577,2578,160.txt,1,0,,,,"For example , sopE seem to be regulated directly by InvF through modulation of invF expression .
"
2578,2579,160.txt,2,0,,,,Expression of sopE is controlled by the SPI-1-encoded proteins InvF and SicA .
2579,2580,174.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5-to 2-fold increase of hilA expression under in-vitro SPI-1-inducing conditions .
"
2580,2581,174.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5-to 2-fold increase of hilA expression under in-vitro high salt .
"
2581,2582,174.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5-to 2-fold increase of hilA expression under in-vitro low O2 ."
2582,2583,1386.txt,1,0,,,,"In the presence of leucine , binding of Lrp is reduced , resulting in reduced transcriptional activation of ilvIH expression .
"
2583,2584,1386.txt,2,0,,,,"It has been known that ilvIH promoter activity is under the positive control of Lrp .
"
2584,2585,1386.txt,3,2,Salmonella;unidentified plasmid;unidentified plasmid,Salmonella;plasmid;plasmid,Salmonella;unidentified plasmid,"Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) ."
2585,2586,612.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , nfsA .
"
2586,2587,612.txt,2,0,,,,"SoxS protein , activates sodA , nfsA ."
2587,2588,148.txt,1,0,,,,"Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon .
"
2588,2589,148.txt,2,0,,,,"RtsA can directly bind the hilA promoter .
"
2589,2590,148.txt,3,0,,,,"a model in which expression of hilA is controlled by the combined action of RtsA
"
2590,2591,148.txt,4,0,,,,"a model in which expression of hilA is controlled by the combined action of RtsA
"
2591,2592,148.txt,5,0,,,,"This is consistent with the feedforward loop model ; when neither RtsA are present , regulation of hilA is dampened , even though the primary signal is mediated through HilD .
"
2592,2593,148.txt,6,0,,,,"Studies have shown PheU that RtsA can each individually bind to the hilA promoter
"
2593,2594,148.txt,7,0,,,,"RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by the sic/sip operon -- in a fashion independent of HilA .
"
2594,2595,148.txt,8,0,,,,"RtsA , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through -- in a fashion independent of HilA .
"
2595,2596,148.txt,9,0,,,,"This work demonstrates the regulation of hilA by RtsA .
"
2596,2597,148.txt,10,0,,,,"In agreement with genetic data , we show that the purified RtsA protein , like HilD , binds to hilA promoters .
"
2597,2598,148.txt,11,0,,,,"In agreement with genetic data , we show that the purified RtsA protein , like HilC , binds to hilA promoters .
"
2598,2599,148.txt,12,0,,,,"Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; RtsA .
"
2599,2600,148.txt,13,0,,,,"Model 4 : Two feedforward loops with OR gate model of regulation of PhilA by heterodimers of HilC-HilD , HilC-RtsA and HilD-RtsA In this case functions s3 , s4 and s are m 5-1/4 : ð 1/2 HilD 1/2 HilC ÞH3 kH3 þ ð 1/2 HilD 1/2 HilC ÞH3 3 odified as follows : s 3 s 4 Model 2 : Two feedforward loops with OR gate logic for regulation of P by HilD , HilC and RtsA -LRB- monomer hilA activation -RRB- ðModel 4Þ s 5 In this case , the rate of change of HilA concentration is a additive function of the three input transactivators via the functions s3 , s4 and s5 corresponding to HilD , HilC and RtsA respectively and is represented as : d 1/2 HilA 1/4 1/2 þ 1/2 þ þ b3 b3 s3 s4 s5 s dt Model 3 : Two feedforward loops with OR gate model for regulation of PhilA by monomers of HilD , HilC and RtsA and addition of positive feedback on RtsA and HilC as well as cross activations of RtsA on HilC and vice versa where functions s7 and s9 represent the auto-activation of HilC and RtsA respectively and functions s8 and s10 represent the cross activation of HilC by RtsA and vice versa respectively .
"
2600,2601,148.txt,14,0,,,,"1/4 : ð 1/2 HilD 1/2 RtsA ÞH5 kH5 þ ð 1/2 HilD 1/2 RtsA ÞH5 2 : Two feedforward loops with OR gate for regulation of P by sA ( monomer hilA activ ðModel 4Þ s 5 This corresponds to activation via the heterodimeric complex of lD a with cooperativity H5 and threshold of activation K5 .
"
2601,2602,148.txt,15,0,,,,"1/4 : ð 1/2 HilD 1/2 RtsA ÞH5 kH5 þ ð 1/2 HilD 1/2 RtsA ÞH5 2 : Two feedforward loops with OR gate for regulation of P by sA ( monomer hilA activ ðModel 4Þ s 5 This corresponds to activation via the heterodimeric complex of lex with cooperativity H5 and threshold of activation K5 .
"
2602,2603,148.txt,16,0,,,,"1/4 : ð 1/2 HilD 1/2 RtsA ÞH5 kH5 þ ð 1/2 HilD 1/2 RtsA ÞH5 ÞH5 5 Mo for regulation of P by sA ( monomer hilA activ ðModel 4Þ s 5 This corresponds to activation via the heterodimeric complex of lD a with cooperativity H5 and threshold of activation K5 .
"
2603,2604,148.txt,17,0,,,,"1/4 : ð 1/2 HilD 1/2 RtsA ÞH5 kH5 þ ð 1/2 HilD 1/2 RtsA ÞH5 ÞH5 5 Mo for regulation of P by sA ( monomer hilA activ ðModel 4Þ s 5 This corresponds to activation via the heterodimeric complex of lex with cooperativity H5 and threshold of activation K5 .
"
2604,2605,148.txt,18,0,,,,"Earlier work on mathematical modeling of regulation of expression of hilA by RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .
"
2605,2606,148.txt,19,0,,,,"Differential expression of hilA , is influenced by RtsA
"
2606,2607,148.txt,20,0,,,,"LoiA activates expression of hilA gene through activating hilD As the expression of hilA is directly controlled by RtsA , we tested whether LoiA regulates HilA through any of these three regulators ."
2607,2608,1635.txt,1,0,,,,"Inactivation of ssrB in the ydgT background resulted in complete loss of virulence during systemic infection , consistent with the finding that deletion of ydgT does not override the requirement of SsrB for transcriptional activation of the SPI-2 pathogenicity island .
"
2608,2609,1635.txt,2,0,,,,"Taken together , these lines of evidence suggest that the Fur repressor could interfere with binding of the SsrB activator to the ssrB promoter , leading to repression of ssrB transcription ."
2609,2610,1153.txt,1,0,,,,"This pstS mutation only reduces hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilD .
"
2610,2611,1153.txt,2,0,,,,"This pstS mutation only reduces hilC expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilD ."
2611,2612,1147.txt,1,0,,,,TABLE 2 RT-qPCR analysis of KdgR-regulated genes Expression level kdgR mutant in FIG 5 Fitness of the mutants in kdgR-regulated genes in soft rots and intact tomatoes .
2612,2613,1621.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In addition , fimA expression from a fimA-lacZ reporter was increased in the absence of a functional FimW , in both a serovar Typhimurium background .
"
2613,2614,1621.txt,2,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In addition , fimA expression from a fimA-lacZ reporter was increased in the absence of a functional FimW , in both an E. coli Typhimurium background ."
2614,2615,1609.txt,1,0,,,,"The data show that all three genes , hilD , were repressed by H-NS and/or Hha ."
2615,2616,389.txt,1,0,,,,Fis repressed transcription of ndk .
2616,2617,362.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"ompR In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress _ mediating the reciprocal osmotic control of ompF
"
2617,2618,362.txt,2,0,,,,"Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompF is not clearly understood .
"
2618,2619,362.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Harlocker , Inouye , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2619,2620,362.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Harlocker , S.L. , Bergstrom , L. , , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2620,2621,362.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"ompR In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress _ mediating the reciprocal osmotic control of ompF
"
2621,2622,362.txt,6,0,,,,"Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompF is not clearly understood .
"
2622,2623,362.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"Harlocker , Inouye , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2623,2624,362.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,"Harlocker , S.L. , Bergstrom , L. , , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2624,2625,362.txt,9,1,Escherichia coli,Escherichia coli,Escherichia coli,"Harlocker , Inouye , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2625,2626,362.txt,10,1,Escherichia coli,Escherichia coli,Escherichia coli,"Harlocker , S.L. , Bergstrom , L. , , M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2626,2627,362.txt,11,1,Escherichia coli,Escherichia coli,Escherichia coli,"The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner .
"
2627,2628,362.txt,12,1,Escherichia coli,Escherichia coli,Escherichia coli,"The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner .
"
2628,2629,362.txt,13,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Expression of ompF genes in S. enterica serovar Typhi is under the control of OmpR .
"
2629,2630,362.txt,14,1,Escherichia coli,Escherichia coli,Escherichia coli,"Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2630,2631,362.txt,15,1,Escherichia coli,Escherichia coli,Escherichia coli,"Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli .
"
2631,2632,362.txt,16,1,Salmonella,Salmonella,Salmonella,"The two-component regulatory system OmpR = EnvZ regulates the porin genes ompF to osmolarity changes in Salmonella .
"
2632,2633,362.txt,17,0,,,,"Transcription regulation of ompF by OmpR .
"
2633,2634,362.txt,18,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"These results support the model where the LtrR protein directly induces ompR expression , upon which OmpR binds to the regulatory region of ompF to induce their synthesis in S. Typhi IMSS-1 .
"
2634,2635,362.txt,19,0,,,,"an OmpR-independent induction regulate ompF expression .
"
2635,2636,362.txt,20,0,,,,"Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .
"
2636,2637,362.txt,21,0,,,,Transcription regulation of ompF by OmpR .
2637,2638,1190.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , ansB is positively coregulated by cyclic-AMP-receptor-protein .
"
2638,2639,1190.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , ansB is positively coregulated by CRP ."
2639,2640,404.txt,1,0,,,,"PhoP also controls expression of Spi-2 by binding to the ssrB promoter the 5 ′ - UTR of the spiR transcript .
"
2640,2641,404.txt,2,1,Salmonella,Salmonella,Salmonella,"PhoP also controls expression of Salmonella pathogenicity island-2 by binding to the ssrB promoter the 5 ′ - UTR of the spiR transcript .
"
2641,2642,404.txt,3,0,,,,The response regulator PhoP controls Spi-2 by binding to the ssrB promoter the 5 ′ - UTR of the spiR transcript .
2642,2643,410.txt,1,0,,,,"STM1344 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .
"
2643,2644,410.txt,2,0,,,,"STM1344 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .
"
2644,2645,410.txt,3,0,,,,"Besides positive regulation of FlhDC , CsrA indirectly inhibits the expression of several GGDEF and/or EAL domain proteins STM1344 .
"
2645,2646,410.txt,4,0,,,,"Besides positive regulation of FlhDC , CsrA directly inhibits the expression of several GGDEF and/or EAL domain proteins STM1344 ."
2646,2647,1184.txt,1,0,,,,"The function of CsgD in rdar morphotype expression The csgD gene encodes for a transcriptional regulator of the LuxR superfamily .
"
2647,2648,1184.txt,2,0,,,,"In order to determine which CsgD-regulated factor , either curli fimbriae or cellulose , was responsible for restoring the biofilm phenotype in 3934 ∆ stm2689 [ pBR328 : : csgD ] , 3934 ∆ stm2689 strain was complemented with the adrA gene under the control of its own promoter , which exclusively activates cellulose A C Arabinose 0.1 % Glucose 0.1 % 3934 3934BADstm2689 B 3934BADstm2689 3934 3934 ara gluc ∆ stm2689 205 kD Fig. 3 .
"
2648,2649,1184.txt,3,0,,,,"To investigate on which level the regulation of CsgD expression occurs , the transcription of csgD was measured by real-time RT-PCR analysis .
"
2649,2650,1184.txt,4,0,,,,"Group III is represented by OmrA/B , which by binding directly to flhDC and csgD mRNA [ 62,75 ] , can down-regulate both motility and the expression of CsgD-controlled curli fibres and cellulose .
"
2650,2651,1184.txt,5,0,,,,"Alternatively , the leaf persistence competition defect of the STM4264 mutant may be unrelated to the regulation of CsgD since the csgD mutant had no defect in the phyllosphere .
"
2651,2652,1184.txt,6,0,,,,"The colony morphology of the csgD strain closely matched that of Fig. 6A that are regulated by CsgD .
"
2652,2653,1184.txt,7,0,,,,"The colony morphology of the csgD strain closely matched that of the WT strain that are regulated by CsgD .
"
2653,2654,1184.txt,8,0,,,,"To quantitate the degree of CsgD complementation in each strain , we measured the expression of csgD , coding for curli fimbria production , coding for a regulator of cellulose production , using promoter-lux operon fusion plasmids ."
2654,2655,376.txt,1,0,,,,CsgD controls the expression of bscA .
2655,2656,1812.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
2656,2657,438.txt,1,0,,,,"Transcription of the ibpB heat-shock gene is under control of s32-and s54-promoters .
"
2657,2658,438.txt,2,0,,,,Transcription of the ibpB heat-shock gene is under control of s32-and s54-promoters .
2658,2659,1806.txt,1,0,,,,"This pstS mutation only reduces hilD expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC .
"
2659,2660,1806.txt,2,0,,,,"This pstS mutation only reduces hilC expression to a small degree , so it seems unlikely that PhoB affects hilA by regulating the expression of hilC ."
2660,2661,1807.txt,1,0,,,,"Indeed , we showed that apo‐IscR , which prevails in an iscU mutant , down‐regulates the expression of the master regulator hilD and thereby of several downstream HilD‐regulated genes ."
2661,2662,1813.txt,1,0,,,,"In this study , we demonstrate that SsrB directly stimulates transcription of sifA by binding upstream of their respective promoters .
"
2662,2663,1813.txt,2,0,,,,"SsrB was able to activate transcription of sifA in 1.7-fold or absence -LRB- 3-fold -RRB- of CTD .
"
2663,2664,1813.txt,3,0,,,,SsrB was able to activate transcription of sifA in the C presence or absence -LRB- 3-fold -RRB- of CTD .
2664,2665,439.txt,1,0,,,,"The four PhoP-dependent genes were not strongly downregulated by the tdcA mutation in cultures , whereas the gene , showed significantly reduced expression in the tdcA mutant strains inside macrophages ."
2665,2666,1185.txt,1,0,,,,"Among the 38 genes , osmY were previously reported to be regulated by RpoS .
"
2666,2667,1185.txt,2,1,unidentified,unknown,unidentified,"The RpoS-regulated osmY gene encodes a periplasmic protein of unknown function that has been found to be induced by both osmotic and growth phase signals ( Yim and Villarejo , 1992 ) .
"
2667,2668,1185.txt,3,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , osmY are regulated by the alternative sigma factor RpoS ."
2668,2669,411.txt,1,0,,,,"In contrast , the presence of a hilD mutation completely blocked SirA induction of Fig. 5A .
"
2669,2670,411.txt,2,0,,,,"In contrast , the presence of a hilD mutation completely blocked SirA induction of rtsA .
"
2670,2671,411.txt,3,0,,,,"Thus SirA induction of csrBC prevents CsrA action , indirectly activating hilD expression post-transcriptionally .
"
2671,2672,411.txt,4,0,,,,"Thus SirA induction of csrBC prevents CsrA action , indirectly activating hilD expression post-transcriptionally .
"
2672,2673,411.txt,5,0,,,,"SirA , positively regulates hilD .
"
2673,2674,411.txt,6,0,,,,"SirA , independently of BarA , also activates hilD in response to the high acetate concentration ."
2674,2675,377.txt,1,0,,,,"Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon .
"
2675,2676,377.txt,2,0,,,,"RtsA have also been shown to regulate SPI-1 genes and flhDC , respectively ."
2676,2677,363.txt,1,0,,,,"Mutants defective at the gshA locus are unable to synthesize glutathione and display several phenotypes consistent with a defect in labile iron homeostasis and oxidative-stress , including increased expression of Furregulated genes , and decreased activity of Fe -- S cluster proteins ( Gralnick et al. , 2000 ; Thorgersen & Downs , 2008 ) ."
2677,2678,405.txt,1,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
2678,2679,405.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] ."
2679,2680,1191.txt,1,0,,,,this effect was reflected by induction of cspB and proteins ( CspA ) in response to preadaptation to cold-stress
2680,2681,388.txt,1,0,,,,"Since LeuO positively regulates the cas3-divergent cse1 gene , we evaluated the role of this LysR regulator in cas3 expression ."
2681,2682,1608.txt,1,0,,,,CpxR also can bind to the cpxR box located in the promoter region of target genes .
2682,2683,1146.txt,1,0,,,,"Teixido et al. showed evidence that transcription of narL , was regulated by the Fur protein regardless of oxygen conditions ."
2683,2684,1620.txt,1,0,,,,"Like STM1344 , STM1697 suppresses the transcription of class 3 flagella regulon genes by binding to FlhD .
"
2684,2685,1620.txt,2,0,,,,"Like STM1344 , STM1697 suppresses the transcription of class 2 flagella regulon genes by binding to FlhD .
"
2685,2686,1620.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella specific,Salmonella,"Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .
"
2686,2687,1620.txt,4,0,,,,"Both STM1344 and STM1697 suppress class 3 flagellum regulon genes by binding to FlhD
"
2687,2688,1620.txt,5,0,,,,"Both STM1344 and STM1697 suppress transcription of class 2 by binding to FlhD
"
2688,2689,1620.txt,6,0,,,,"complementation experiments demonstrated that STM1697 regulates virulence phenotypes through its interaction with FlhD .
"
2689,2690,1620.txt,7,0,,,,"complementation experiments demonstrated that STM1697 regulates flagellar formation through its interaction with FlhD .
"
2690,2691,1620.txt,8,0,,,,"Gene knockout demonstrated that STM1697 regulates virulence phenotypes through its interaction with FlhD .
"
2691,2692,1620.txt,9,0,,,,"Gene knockout demonstrated that STM1697 regulates flagellar formation through its interaction with FlhD .
"
2692,2693,1620.txt,10,0,,,,"A 2.0 Å resolution STM1697 -- FlhD structure reveals that STM1697 binds the same region of FlhD as STM134 .
"
2693,2694,1620.txt,11,0,,,,"experiments _ using SEC to determine if STM1697 can bind FlhD C to form STM16974FlhD4C2 complexes
"
2694,2695,1620.txt,12,0,,,,"experiments _ using SEC to determine if STM1697 can bind FlhD C to form STM1697 FlhD C 4 2 3 4 2
"
2695,2696,1620.txt,13,0,,,,"Therefore , we hypothesize that , when STM1697 binds to the FlhD subunits of steric exclusion prevents-70 RNA polymerase from binding to template DNA , thus blocking transcription .
"
2696,2697,1620.txt,14,0,,,,"Therefore , we hypothesize that , when STM1697 binds to the FlhD subunits of the FlhD4C2 complex prevents-70 RNA polymerase from binding to template DNA , thus blocking transcription .
"
2697,2698,1620.txt,15,0,,,,"The STM1697 mutants were unable to bind to FlhD in-vitro , as shown above .
"
2698,2699,1620.txt,16,0,,,,"STM1697 then binds to the peripheral FlhD of the FlhD4C2 complex .
"
2699,2700,1620.txt,17,0,,,,STM1697 then binds to the peripheral FlhD of the FlhD4C2 complex .
2700,2701,1634.txt,1,0,,,,"Conclusions : All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating global regulators .
"
2701,2702,1634.txt,2,0,,,,"Conclusions : All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network , integrating multiple environmental signals .
"
2702,2703,1634.txt,3,0,,,,"All these results together show that , at least under the tested conditions , RpoS is the central regulator in the hlyE regulatory network ."
2703,2704,1152.txt,1,1,Salmonella,Salmonella,Salmonella,"The genetic regulation of gogB in Salmonella is influenced by SsrB , under SPI-2-inducing conditions
"
2704,2705,1152.txt,2,1,Salmonella,Salmonella,Salmonella,"The genetic regulation of gogB in Salmonella is influenced by SsrB , under SPI-2-inducing conditions"
2705,2706,149.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
2706,2707,175.txt,1,0,,,,"we determined that SlyA positively regulates the fruK gene
"
2707,2708,175.txt,2,0,,,,"These results suggest that fruK is upregulated by SlyA .
"
2708,2709,175.txt,3,0,,,,"SlyA , thus , seems to upregulate fruK expression by directly binding to Fig. 4D .
"
2709,2710,175.txt,4,0,,,,"SlyA , thus , seems to upregulate fruK expression by directly binding to the promoter region ."
2710,2711,613.txt,1,0,,,,FliA-dependent activation of FlgM ensures an effectiv `` off 
2711,2712,1387.txt,1,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
2712,2713,1393.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .
"
2713,2714,1393.txt,2,1,Mus musculus,mouse,Mus musculus,"Activation of pmrC by PmrA suggests that the consequent pEtN modifications , are up-regulated during infection of the mouse
"
2714,2715,1393.txt,3,1,Mus musculus,mouse,Mus musculus,"Activation of pmrC by PmrA suggests that these loci , are up-regulated during infection of the mouse
"
2715,2716,1393.txt,4,1,Salmonella,Salmonella,Salmonella,"Although a non-cytotoxic form of polymyxin B -- termed polymyxin B nonapeptide ( Vaara and Vaara , 1983 ) -- could partially protect a Salmonella pmrA mutant from Fe ( III ) - mediated killing ( Chamnongpol et al. , 2002 ) inactivation of the PmrA-activated loci responsible for the lipid-A modification with 4-aminoarabinose ( i.e. pbgP ) or phosphoethanolamine ( i.e. pmrC ) did not render the organism susceptible to Fe ( III ) ( Lee et al. , 2004 ) .
"
2716,2717,1393.txt,5,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
2717,2718,1393.txt,6,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
2718,2719,1393.txt,7,0,,,,"Furthermore , a strain deleted for of all three pmrC , ugd and pmrG genes and harbouring the pmrA505 allele , which encodes a PmrA protein that promotes transcription of PmrA-activated genes even under noninducing conditions ( Kox et al. , 2000 ) , was as susceptible to Fe ( III ) as the DpmrAB mutant ( Table 1 ) .
"
2719,2720,1393.txt,8,1,Salmonella,Salmonella,Salmonella,"For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .
"
2720,2721,1393.txt,9,0,,,,S1 ) and that the ssrB promoter mutation had no effect on the expression of the PmrA-activated pmrC gene ( Fig. 5C ) .
2721,2722,607.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In the third multigene horizontal acquisition discovered ( Fig. 2 ) , an SsrB-regulated fusion ( srfH ) was found within a homologue of S. typhimurium type III secreted effectors sspH 1 ( P 10236 ) and sspH 2 ( P 10287 ) ."
2722,2723,161.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
2723,2724,2117.txt,1,0,,,,"Almiron et al. reported that expression of the dps gene is induced by the cessation of bacterial growth under S control of RpoS .
"
2724,2725,2117.txt,2,0,,,,"In addition , RpoS controls the expression of dps ."
2725,2726,834.txt,1,0,,,,"SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression and that of the spvABCD operon ( Chen et al. , 1995 ; Grob and Gui-ney , 1996 ; Grob et al. , 1997 ) ."
2726,2727,1378.txt,1,0,,,,"The two-component regulator PhoP/Q , represses hilA , whereas a member of the phosphorylated response regulator protein family , positively affects hilA .
"
2727,2728,1378.txt,2,0,,,,"The two-component regulator PhoP/Q , represses hilA , whereas SirA , positively affects hilA ."
2728,2729,74.txt,1,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , have been associated with tolC expression levels .
"
2729,2730,74.txt,2,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , MarA , have been associated with tolC expression levels .
"
2730,2731,74.txt,3,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , SoxS , have been associated with tolC expression levels .
"
2731,2732,74.txt,4,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , RamA , have been associated with tolC expression levels ."
2732,2733,820.txt,1,0,,,,Two StpA-repressed PhoP-dependent genes _ bound by ugtL
2733,2734,60.txt,1,0,,,,"IHF , also positively regulates hilA by displacing H-NS ."
2734,2735,2103.txt,1,0,,,,"IgaAmediated repression of the RcsB-YojN-RcsC system occurred at the post-translational level , as shown by chromosomal epitope tagging of the rcsC genes ."
2735,2736,1422.txt,1,0,,,,"Whereas this suggests that YfeR is a repressor of yfeH transcription , it is also apparent that factors other than YfeR modulate YfeH expression ."
2736,2737,808.txt,1,0,,,,"The chiP gene is under the transcriptional control of the NagC repressor As the next step in our comparative study , we examined the effects of nagC mutations on regulation of chiP ."
2737,2738,1344.txt,1,0,,,,"The class I flhDC operon is the master regulator , with FlhD ."
2738,2739,48.txt,1,0,,,,"Here in-vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals .
"
2739,2740,48.txt,2,0,,,,"Here in-vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation .
"
2740,2741,48.txt,3,0,,,,"Here in-vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP , providing a mechanism for the moderate upregulation of hlyE expression in response to oxygen .
"
2741,2742,48.txt,4,0,,,,"Thus , CRP enhances hlyE expression in response to FNR enhances hlyE expression in response to oxygen starvation .
"
2742,2743,48.txt,5,0,,,,"Thus , CRP enhances hlyE expression in response to glucose-starvation enhances hlyE expression in response to oxygen starvation .
"
2743,2744,48.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"Previous studies have shown that CRP contribute to hlyE expression when E. coli is grown on a solid medium .
"
2744,2745,48.txt,7,0,,,,"Thus , we concluded that CRP all contribute towards the regulation of hlyE expression .
"
2745,2746,48.txt,8,0,,,,"Footprinting studies have shown that CRP activate hlyE expression from the same site centered 61.5 bp upstream of the SlyA-associated transcription start site .
"
2746,2747,48.txt,9,0,,,,"CRP are known to activate hlyE expression
"
2747,2748,48.txt,10,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
2748,2749,48.txt,11,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
2749,2750,48.txt,12,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
2750,2751,48.txt,13,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
2751,2752,48.txt,14,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
2752,2753,48.txt,15,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
2753,2754,48.txt,16,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Escherichia coli;S. Typhi;Typhi,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"On the other hand , the transcriptional regulator Crp , previously described as an activator of hlyE transcription in Escherichia coli , is involved in transcriptional repression of hlyE in S. Typhi .
"
2754,2755,48.txt,17,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"The Crp regulator is involved in transcriptional repression of S. Typhi hlyE Crp is a transcriptional regulator previously reported to be an activator of hlyE transcription in E. coli .
"
2755,2756,48.txt,18,1,Escherichia coli,E. coli,Escherichia coli,CRP is a transcriptional regulator previously reported as an activator of the hlyE transcription in E. coli .
2756,2757,1350.txt,1,0,,,,"Upon completion of the basal body , the anti-sigma factor FlgM is secreted , allowing the alternative sigma factor FliA to initiate transcription of genes under control of fliC .
"
2757,2758,1350.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium;S. typhimurium;typhimurium;mice;S. typhimurium;typhimurium,Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium,"In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype ."
2758,2759,1436.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella-infected,Salmonella,srfH -- lacZ activity 20-fold _ mimicking the effect we observed with SsrB stimulation of srfH in Salmonella-infected macrophages
2759,2760,983.txt,1,0,,,,"fruBKA , under the control of FruR , was upregulated in the acrD mutant .
"
2760,2761,983.txt,2,0,,,,"The fructose operon , under the control of FruR , was upregulated in the acrD mutant ."
2761,2762,997.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
2762,2763,1595.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
2763,2764,1595.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
2764,2765,1595.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP ."
2765,2766,767.txt,1,0,,,,"When system is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein represses pmrD transcription .
"
2766,2767,767.txt,2,1,Salmonella,Salmonella,Salmonella,"When the Salmonella PmrA PmrB is activated independently of PmrD , such as by exposure to Fe3 , the PmrA protein represses pmrD transcription .
"
2767,2768,767.txt,3,2,Salmonella;Escherichia coli,Salmonella;E. coli,Escherichia coli;Salmonella,"We reasoned that if the PmrA-mediated repression of the Salmonella pmrD gene is designed to prevent the potentially detrimental production of PmrD protein , this negative feedback loop would be absent from E. coli because its PmrD protein is unable to activate the PmrA protein .
"
2768,2769,767.txt,4,1,Salmonella,Salmonella,Salmonella,"For example , the presence of a PmrA-binding site in the Salmonella pmrD promoter enables the PmrA protein to repress pmrD transcription
"
2769,2770,767.txt,5,0,,,,"The PhoP -- PmrA loop is closed by repression of pmrD expression by PmrA .
"
2770,2771,767.txt,6,0,,,,"The PhoP -- PmrD is closed by repression of pmrD expression by PmrA .
"
2771,2772,767.txt,7,0,,,,This loop can be deactivated by the transcriptional repression of pmrD by PmrA .
2772,2773,773.txt,1,0,,,,Another ` Fur-activated 
2773,2774,2088.txt,1,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,strain SL;SL1344;S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium,"MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of extracellular matrix formation in S. typhimurium .
"
2774,2775,2088.txt,2,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli,strain SL;SL1344;E. coli,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli;Sediminispirochaeta sinaica,"MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of extracellular matrix formation in E. coli .
"
2775,2776,2088.txt,3,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,strain SL;SL1344;S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium,"MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of aggregative morphology in S. typhimurium .
"
2776,2777,2088.txt,4,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli,strain SL;SL1344;E. coli,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli;Sediminispirochaeta sinaica,MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of aggregative morphology in E. coli .
2777,2778,1581.txt,1,0,,,,FlhD4C2 regulated STM3611
2778,2779,2063.txt,1,0,,,,"However , since operon is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between yghW .
"
2779,2780,2063.txt,2,0,,,,"However , since the hydrogenase 2 -LRB- hypO-hybABCDE -RRB- is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between yghW ."
2780,2781,798.txt,1,0,,,,"iroB genes are transcriptionally regulated by Fur
"
2781,2782,798.txt,2,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .
"
2782,2783,798.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"To verify if the S. Typhi siderophore salmochelin was regulated by Fur and/or by the sRNAs RfrA and RfrB , a transcriptional-fusion between the iroB promoter , the first gene of the iroBCDE operon , and the lacZ reporter gene was introduced to the different mutant strains .
"
2783,2784,798.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,S. Typhi;Typhi;plasmid,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"To verify if the S. Typhi siderophore salmochelin was regulated by Fur and/or by the sRNAs RfrA and RfrB , a transcriptional-fusion between the iroB promoter , the first gene of the iroBCDE operon , and the lacZ reporter gene was constructed in plasmid pRS415 .
"
2784,2785,798.txt,5,0,,,,that the transcription of iroB is regulated by Fur
2785,2786,940.txt,1,0,,,,SlyA is also involved in the regulation of sopD2
2786,2787,1218.txt,1,0,,,,"the molecular mechanism _ underlying the stationary-phase induction of yliH under LB with vigorous aeration , by analyzing its promoter activity in various mutant backgrounds,-lacking stationary-phase σ , RpoS , or stringent signal-molecules ppGpp , ∆ relA ∆
"
2787,2788,1218.txt,2,0,,,,"the molecular mechanism _ underlying the stationary-phase induction of yliH under the standard culture condition , by analyzing its promoter activity in various mutant backgrounds,-lacking stationary-phase σ , RpoS , or stringent signal-molecules ppGpp , ∆ relA ∆
"
2788,2789,1218.txt,3,0,,,,yliH expression was fur ther increased to 66.5-fold in RpoS-mutant background .
2789,2790,954.txt,1,0,,,,"Likewise , ugd transcription is co-ordinately induced with that of the cps genes by RcsB system , possibly because of its role in col-anic acid capsule synthesis .
"
2790,2791,954.txt,2,0,,,,The ugd gene are positively regulated under RcsB activating conditions .
2791,2792,2077.txt,1,0,,,,The CspE proteins increase stability of uspA mRNA facilitating steady-state expression .
2792,2793,1556.txt,1,0,,,,YdiV represses expression of yhjH .
2793,2794,1230.txt,1,0,,,,"Additionally , this strain harbored a HilD-regulated hilA "
2794,2795,1224.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the S. typhimurium hilA promoter .
"
2795,2796,1224.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the S. typhimurium hilA promoter .
"
2796,2797,1224.txt,3,0,,,,"First , an AraC/XylS family member , binds directly to several sites within de-represses hilA expression .
"
2797,2798,1224.txt,4,0,,,,"First , an AraC/XylS family member , binds directly to several sites within PhilA hilA expression .
"
2798,2799,1224.txt,5,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2799,2800,1224.txt,6,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2800,2801,1224.txt,7,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2801,2802,1224.txt,8,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2802,2803,1224.txt,9,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2803,2804,1224.txt,10,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2804,2805,1224.txt,11,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2805,2806,1224.txt,12,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SCHECHTER L.M. , LEE C.A. : AraC/XylS family members , directly bind the Salmonella typhimurium hilA promoter .
"
2806,2807,1224.txt,13,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2807,2808,1224.txt,14,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2808,2809,1224.txt,15,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2809,2810,1224.txt,16,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2810,2811,1224.txt,17,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2811,2812,1224.txt,18,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2812,2813,1224.txt,19,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2813,2814,1224.txt,20,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2814,2815,1224.txt,21,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Schechter LM , Lee CA : AraC/XylS family members , directly bind the Salmonella typhimurium hilA promoter .
"
2815,2816,1224.txt,22,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella Typhimurium hilA promoter .
"
2816,2817,1224.txt,23,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella Typhimurium hilA promoter .
"
2817,2818,1224.txt,24,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2818,2819,1224.txt,25,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2819,2820,1224.txt,26,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella Typhimurium hilA promoter .
"
2820,2821,1224.txt,27,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella Typhimurium hilA promoter .
"
2821,2822,1224.txt,28,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2822,2823,1224.txt,29,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2823,2824,1224.txt,30,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;typhi;typhi-murium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Schechter , L. M. , and C. A. Lee , 2001 AraC/XylS family members , HilD , directly bind the Salmonella typhi-murium hilA promoter .
"
2824,2825,1224.txt,31,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;typhi;typhi-murium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Schechter , L. M. , and C. A. Lee , 2001 AraC/XylS family members , HilC , directly bind the Salmonella typhi-murium hilA promoter .
"
2825,2826,1224.txt,32,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2826,2827,1224.txt,33,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2827,2828,1224.txt,34,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2828,2829,1224.txt,35,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter .
"
2829,2830,1224.txt,36,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella Typhimurium hilA promoter .
"
2830,2831,1224.txt,37,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella Typhimurium hilA promoter .
"
2831,2832,1224.txt,38,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;typhi;typhi-murium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhi-murium hilA promoter .
"
2832,2833,1224.txt,39,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;typhi;typhi-murium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhi-murium hilA promoter .
"
2833,2834,1224.txt,40,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Sal-monella;monella;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Sal-monella typhimurium hilA promoter .
"
2834,2835,1224.txt,41,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Sal-monella;monella;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Sal-monella typhimurium hilA promoter .
"
2835,2836,1224.txt,42,0,,,,"an AraC/XylS family member , binds directly to several sites within the hilA promoter .
"
2836,2837,1224.txt,43,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilD , directly bind the Salmonella typhimurium hilA promoter .
"
2837,2838,1224.txt,44,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"AraC/XylS family members , HilC , directly bind the Salmonella typhimurium hilA promoter ."
2838,2839,968.txt,1,0,,,,"Gel retardation assays indicated that Lrp binds a DNA region upstream of the traJ promoter .
"
2839,2840,968.txt,2,0,,,,"Because the 84 bp fragments both contain the region homologous to the Lrp binding site , these observations provided evidence that Lrp binds to the UAS of traJ .
"
2840,2841,968.txt,3,0,,,,"Because the 313 bp both contain the region homologous to the Lrp binding site , these observations provided evidence that Lrp binds to the UAS of traJ .
"
2841,2842,968.txt,4,0,,,,"Retardation of the DNA fragment under study is clearly observed , thereby confirming that Lrp binds the traJ UAS .
"
2842,2843,968.txt,5,0,,,,"We thus propose that binding of Lrp to the UAS upstream of traJ activates traJ transcription .
"
2843,2844,968.txt,6,0,,,,"We thus propose that binding of Lrp to the UAS upstream of traJ activates traJ transcription .
"
2844,2845,968.txt,7,1,unidentified plasmid,plasmid,unidentified plasmid,"In addition , Lrp controls the expression of the virulence plasmid traJ gene .
"
2845,2846,968.txt,8,2,Salmonella;unidentified plasmid;unidentified plasmid,Salmonella;plasmid;plasmid,Salmonella;unidentified plasmid,"Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) ."
2846,2847,1542.txt,1,0,,,,"The mgtC and pagC genes are both PhoP-activated genes required for intramacrophage growth [ 2,5 -- 7 ] .
"
2847,2848,1542.txt,2,1,Salmonella,Salmonella,Salmonella,"This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella 
"
2848,2849,1542.txt,3,0,,,,"This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to recruiting RNA polymerase .
"
2849,2850,1542.txt,4,0,,,,"This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to the mgtC promoter .
"
2850,2851,1542.txt,5,0,,,,"This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to the mgtC promoter .
"
2851,2852,1542.txt,6,1,Salmonella,Salmonella,Salmonella,"This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to recruiting RNA polymerase .
"
2852,2853,1542.txt,7,1,Salmonella,Salmonella,Salmonella,"This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .
"
2853,2854,1542.txt,8,1,Salmonella,Salmonella,Salmonella,"This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .
"
2854,2855,1542.txt,9,0,,,,"Although PhoP activates mgtC transcription initiation from a single promoter located in front of the mgtC gene , a computational approach found two other PhoP-binding sites .
"
2855,2856,1542.txt,10,0,,,,These effects are not specific to the phoP gene because they were also observed with the PhoP-activated mgtC gene ( Fig. 2B ) .
2856,2857,559.txt,1,0,,,,"the two-step regulon activates PmrD , which in turn activates the global regulator of efflux pumps , the MarA operon , eventually leads to the activation of acrB"
2857,2858,1973.txt,1,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"When induced at a similar level , SlyA tends to form more dimers in the wild-type strain than in a relA spoT mutant , suggesting that ppGpp probably induces a conformational change in SlyA structure that preferentially forms a dimer ."
2858,2859,1967.txt,1,0,,,,This demonstrates that FliZ is able to counter both YdiV-dependent and -- independent fliC repression at 5 hours .
2859,2860,565.txt,1,0,,,,"The authors further showed that , in addition to repression of the cadBA genes , OmpR was apparently also involved in activation of the atpB gene , encoding the α F0 subunit of the ATP synthase , thereby maintaining the cytoplasmic acidification in media at pH 5.6 ."
2860,2861,1797.txt,1,0,,,,"CsgD protein levels are downregulated in the STM1344 mutant .
"
2861,2862,1797.txt,2,0,,,,"Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .
"
2862,2863,1797.txt,3,0,,,,"Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .
"
2863,2864,1797.txt,4,0,,,,"Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .
"
2864,2865,1797.txt,5,0,,,,"Upon the deletion of STM1344 in STM1827 mutant backgrounds , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .
"
2865,2866,1797.txt,6,0,,,,"Upon the deletion of STM1344 in the STM4264 , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .
"
2866,2867,1797.txt,7,0,,,,"Upon the deletion of STM1344 in the STM4264 , the downregulation of CsgD expression to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .
"
2867,2868,1797.txt,8,0,,,,"Upon the deletion of STM1344 in the STM4264 , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in STM3611 mutant backgrounds , CsgD expression remained at the levels in the corresponding single mutants .
"
2868,2869,1797.txt,9,0,,,,"Upon the deletion of STM1344 in the STM4264 , the downregulation of rdar morphotype to the level in the UMR1 wild type was observed , while in the STM1703 , CsgD expression remained at the levels in the corresponding single mutants .
"
2869,2870,1797.txt,10,0,,,,"STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM3611 , required for the downregulation of CsgD expression .
"
2870,2871,1797.txt,11,0,,,,"STM1344 favors sessility by repressing the expression of the two phosphodiesterases , STM1703 , required for the downregulation of CsgD expression .
"
2871,2872,1797.txt,12,0,,,,"Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant ."
2872,2873,203.txt,1,0,,,,"Furthermore , this indicates that a relA-dependent source of ppGpp can compensate for any leucine-mediated inactivation of Lrp , either through elevated lrp expression or through other ppGpp-dependent mechanisms .
"
2873,2874,203.txt,2,0,,,,"In contrast , the presence of both lrp mutations in the donor strain restored the repression of pSLT transfer to a level similar to that of an Lrp-mutant .
"
2874,2875,203.txt,3,0,,,,"Lrp -- DNA interaction in this region was fully consistent with the observed repression of lrp transcription by this protein .
"
2875,2876,203.txt,4,0,,,,"that Lrp repressed the transcription of the lrp gene
"
2876,2877,203.txt,5,0,,,,"This pattern of protein -- DNA interaction is consistent with repression of the lrp promoter by Lrp promoter occlusion .
"
2877,2878,203.txt,6,0,,,,"lrp expression , is repressed , leading to low levels of Lrp
"
2878,2879,203.txt,7,0,,,,Lrp represses the expression of an lrp deletion mutant displays hypervirulence .
2879,2880,217.txt,1,0,,,,The finding that an S. Dublin phoQ mutant is negatively selected at all sites after oral dosing of calves is similarly consistent with the known role of PhoPQ in control of type III secretion .
2880,2881,1783.txt,1,0,,,,"STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC via FliA ."
2881,2882,571.txt,1,1,unidentified,not shown,unidentified,"However , phoP mutations did not affect induction of data not shown , indicating that it operates independently of the PhoPQ regulon .
"
2882,2883,571.txt,2,0,,,,"However , phoP mutations did not affect induction of the proposed pathway , indicating that it operates independently of the PhoPQ regulon .
"
2883,2884,571.txt,3,0,,,,"In the comparison of tolC strains in an Mg2-free buffer , the PhoPQ-activated modifica tions resulted in a more-than-fourfold increase in the barrier function against the penetration of a cationic dye , ethidium , in comparison with the phoP null mutant , in which the modification was absent ( Fig. 2 , left panel ) .
"
2884,2885,571.txt,4,0,,,,"the phagosome turns on various acid response genes provide protection against very low pH levels .31 The PhoPQ system is involved in controlling induction of the acid response genes and , not surprisingly , the phoP single mutant"
2885,2886,2261.txt,1,0,,,,"for cell , fliAZY expression was increased by inactivation of the ClpXP proteas
"
2886,2887,2261.txt,2,0,,,,"for cell , fliAZY expression was increased by inactivation of the ClpXP proteas"
2887,2888,1768.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2888,2889,1768.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2889,2890,1768.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2890,2891,1768.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2891,2892,1768.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2892,2893,1768.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2893,2894,1768.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2894,2895,1768.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2895,2896,1768.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2896,2897,1768.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2897,2898,1768.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent .
"
2898,2899,1768.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of sbmC by all nine FQs is likely LexA dependent ."
2899,2900,2275.txt,1,0,,,,FlhDC acts as a positive regulator for class flgM .
2900,2901,1032.txt,1,0,,,,"NsrR regulation of tehAB was not observed
"
2901,2902,1032.txt,2,0,,,,Previous studies indicated that NsrR binds to the promoter region of tehAB
2902,2903,1754.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , nfo .
"
2903,2904,1754.txt,2,0,,,,"SoxS protein , activates sodA , nfo ."
2904,2905,2249.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
2905,2906,2249.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
2906,2907,2249.txt,3,0,,,,"Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA ."
2907,2908,1740.txt,1,0,,,,"Next we focus our attention on the ArcA-activated proteins ( i.e. those proteins of lower levels in the arcA mutant , Fig. 1B ) ."
2908,2909,1998.txt,1,0,,,,"The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure ."
2909,2910,1026.txt,1,3,Salmonella;Salmonella enterica;Salmonella;unidentified,Salmonella;Salmonella enterica;enterica;unknown,Salmonella enterica;unidentified;Salmonella,"In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary-phase ( 4 ) ."
2910,2911,2271.txt,1,1,Vibrio vulnificus,Vibrio vulnificus,Vibrio vulnificus,"Lee , H.J. , Park , S.J. , Choi , S.H. , Lee , K.H. Vibrio vulnificus rpoS expression is repressed by direct binding of cAMP-CRP complex to its two promoter regions .
"
2911,2912,2271.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , CRP-cAMP represses rpoS transcription during logarithmic growth .
"
2912,2913,2271.txt,3,0,,,,"CRP participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .
"
2913,2914,2271.txt,4,1,Vibrio vulnificus,Vibrio vulnificus,Vibrio vulnificus,"Previously , it has been reported that rpoS expression is repressed by the cAMP-CRP complex in Vibrio vulnificus .
"
2914,2915,2271.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , CRP might repress hlyE expression by repressing rpoS in S. Typhi .
"
2915,2916,2271.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Altogether , these results suggest that CRP are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .
"
2916,2917,2271.txt,7,0,,,,"Figure 2 CRP participate in the repression of rpoS .
"
2917,2918,2271.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Here , we present genetic evidence indicating that CRP exerts down-regulation of hlyE by repressing rpoS in S. Typhi .
"
2918,2919,2271.txt,9,1,Vibrio vulnificus,Vibrio vulnificus,Vibrio vulnificus,"On the other hand , it has been reported that rpoS expression is repressed by direct binding of CRP-cAMP to its promoter region in Vibrio vulnificus ."
2919,2920,1778.txt,1,0,,,,"those _ observed in the hns single mutant upon induction of LeuO
"
2920,2921,1778.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Calva E LeuO positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Calva E Negative osmoregulation of gene independently of OmpR in an hns background .
"
2921,2922,1778.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Puente JL LeuO positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Puente JL Negative osmoregulation of gene independently of OmpR in an hns background ."
2922,2923,2265.txt,1,0,,,,"H-NS acts as a direct repressor of ftnA transcription , causing derepression of ftnA expression
"
2923,2924,2265.txt,2,0,,,,"H-NS acts as a direct repressor of ftnA transcription , thereby displacing H-NS
"
2924,2925,2265.txt,3,0,,,,"the his-tone-like nucleoid-associated protein acts as a direct repressor of ftnA transcription , thereby displacing H-NS"
2925,2926,1022.txt,1,0,,,,"PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .
"
2926,2927,1022.txt,2,0,,,,"Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) .
"
2927,2928,1022.txt,3,0,,,,"PmrA has been shown to bind ugd .
"
2928,2929,1022.txt,4,0,,,,"Results Mutation of the tolB locus promotes ugd transcription in a phoP-and pmrA-independent manner The ugd gene product participates in multiple cellular activities , suggesting that regulatory systems other than PhoP -- PmrA -- PmrB might also control ugd expression .
"
2929,2930,1022.txt,5,0,,,,"Collectively , these results strongly suggest that the pmrC , ugd and pmrG genes and the pbgPE operon are the only PmrA-regulated determinants required for Fe ( III ) resistance .
"
2930,2931,1022.txt,6,1,unidentified,not shown,unidentified,"The absence of transcriptional linkage between the RpoN and the PmrA regulons was corroborated because no significant differences were observed when the expression of PmrAcontrolled genes ( pmrI , pmrC , pmrF , and ugd ) was compared either in a RpoN or in a 1 DrpoN strain grown in LB ( exponential or stationary-phase ) or in a low-Mg N-21 minimal-medium , which are PhoP-and PmrA-inducing conditions ( Soncini & Groisman , 1996 ) ( Fig. 3a and data not shown ) .
"
2931,2932,1022.txt,7,0,,,,"( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain ."
2932,2933,1744.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Since the flhDC genes are regulated by the two-component system QseBC , a qseC mutant of S. Typhimurium was constructed to investigate the role of the QseC sensor kinase in norepinephrine-enhanced motility of S. Typhimurium .
"
2933,2934,1744.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Clarke , M.B. , and Sperandio , V. Transcriptional regulation of flhDC by QseBC in enterohaemorrhagic Escherichia coli .
"
2934,2935,1744.txt,3,0,,,,"10.1128 / JB.00635-00610 Clarke MB , Sperandio V Transcriptional regulation of flhDC by QseBC .
"
2935,2936,1744.txt,4,0,,,,"doi / JB.00635-00610 Clarke MB , Sperandio V Transcriptional regulation of flhDC by QseBC .
"
2936,2937,1744.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"Clarke M , Sperandio V. Transcriptional regulation of flhDC by QseBC in enterohaemorrhagic Escherichia coli .
"
2937,2938,1744.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"Transcriptional regulation of flhDC by QseBC ( FliA ) in enterohaemorrhagic Escherichia coli .
"
2938,2939,1744.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,Transcriptional regulation of flhDC by QseBC ( FliA ) in enterohaemorrhagic Escherichia coli .
2939,2940,2259.txt,1,0,,,,"A search for genetic factors unveiled LeuO as novel regulators of slrP .
"
2940,2941,2259.txt,2,0,,,,"We show that , under SPI1-inducing conditions , LeuO are indirect regulators of the slrP expression .
"
2941,2942,2259.txt,3,0,,,,Results support the model that LeuO regulate slrP in a manner dependent .
2942,2943,1988.txt,1,0,,,,"Thus , we investigated expression of the SsrB-activated ssaG gene , which is the first gene of a large operon ( from ssaG to ssaU ) and encodes a component of the Spi/Ssa T3SS ( 22 ) ."
2943,2944,1750.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for anaerobic induction of aniC in Salmonella typhimurium .
"
2944,2945,1750.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for acid-pH induction of aniC in Salmonella typhimurium ."
2945,2946,1036.txt,1,0,,,,"It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .
"
2946,2947,1036.txt,2,0,,,,It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .
2947,2948,549.txt,1,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified,strain SL;SL1344;not shown,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified;Sediminispirochaeta sinaica,"twenty six compounds were re-tested for inhibition of expression of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .
"
2948,2949,549.txt,2,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified,strain SL;SL1344;not shown,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified;Sediminispirochaeta sinaica,"twenty six compounds were re-tested for inhibition of growth of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .
"
2949,2950,549.txt,3,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified,strain SL;SL1344;not shown,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified;Sediminispirochaeta sinaica,"One hundred were re-tested for inhibition of expression of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .
"
2950,2951,549.txt,4,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified,strain SL;SL1344;not shown,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;unidentified;Sediminispirochaeta sinaica,One hundred were re-tested for inhibition of growth of the RpoS-dependent spvR gene in Samonella strain SL1344 ( data not shown ) .
2951,2952,1963.txt,1,0,,,,"It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .
"
2952,2953,1963.txt,2,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
2953,2954,1977.txt,1,0,,,,"Fig. 3 show that , in the presence of the -- AI-2 control reaction , low expression of the lsr -- lacZ-fusions occurs in the absence of luxS and , similar to what was shown in Fig. 2 , the fusions are induced to varying degrees Identification of LsrR : a protein responsible for mediating AI-2 regulation of transcription of the lsr operon The above results show that AI-2 induces the expression of the lsr operon ."
2954,2955,575.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , the global regulator ss .
"
2955,2956,575.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , phosphate regulation .
"
2956,2957,575.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , PhoB .
"
2957,2958,575.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , osmoregulation .
"
2958,2959,575.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , OmpR .
"
2959,2960,575.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , s32 of heat-shock response .
"
2960,2961,575.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses results from the activation of the s70-dependant uspA promoter of RpoS , RpoH ."
2961,2962,1787.txt,1,1,Escherichia coli,E. coli,Escherichia coli,LeuO is known to activate bglJ in E. coli while RcsB-BglJ heterodimers activate leuO transcription .
2962,2963,213.txt,1,1,Hypostomus robinii,tetA,Hypostomus robinii,"Influence of transcriptional activator RamA on expression of multidrug efflux pump Ac interdomain loop region of the tetA tetracycline resistance gene increase efflux of glycylcyclines .
"
2963,2964,213.txt,2,1,Hypostomus robinii,tetA,Hypostomus robinii,Influence of transcriptional activator RamA on expression of multidrug efflux pump Ac interdomain loop region of the tetA tetracycline resistance gene increase efflux of minocycline .
2964,2965,207.txt,1,0,,,,"In contrast , iron repression of the ssaG gene did not occur in Fig. 2C , suggesting that Fur represses SPI-2 expression in an iron-dependent fashion .
"
2965,2966,207.txt,2,0,,,,"In contrast , iron repression of the ssaG gene did not occur in the fur deletion mutant , suggesting that Fur represses SPI-2 expression in an iron-dependent fashion .
"
2966,2967,207.txt,3,0,,,,the same growth-condition was in contrast to the Fur repression of ssaG expression
2967,2968,1793.txt,1,0,,,,The flagellar master regulator FlhD4C2 is under autogenous control by FlhD4C2-dependent activation of the repressor rflM .
2968,2969,561.txt,1,0,,,,"for cell , fliAZY expression was increased by inactivation of the ClpXP proteas"
2969,2970,2073.txt,1,0,,,,"LeuO downregulates SPI-1 expression via hilD Because SPI-1 expression is responsive to multiple regulators , we devised a genetic screen to ascertain whether a single cell function might transmit LeuO-mediated regulation to SPI-1 ."
2970,2971,950.txt,1,0,,,,"This behavior reflects : first , that the PhoP-activated regulator RstA is necessary for transcription of feoB but not of mgtA in mildly acidic pH ( Choi , et al. , 2009 ) ."
2971,2972,788.txt,1,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while fruF likely are controlled by additional regulators .
"
2972,2973,788.txt,2,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while 2-keto-3-deoxyg-luconate kinase , araH , are controlled by additional regulators .
"
2973,2974,788.txt,3,0,,,,"Genes kduI -LRB- encoding 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase -RRB- appear to be most strongly controlled by KdgR , while kdgK , araH , are controlled by additional regulators ."
2974,2975,944.txt,1,0,,,,"RcsB-regulated genes can be divided into those that are RcsA dependent , such as the cps genes ( Gottesman et al. , 1985 ) ( Fig. 3 ) , and those that are RcsA independent , such as the ftsZ ( Carballes et al. , 1999 ; Costa and Anton , 2001 ) and osmC ( Davalos-Garcia et al. , 2001 ) genes ."
2975,2976,1208.txt,1,0,,,,IsrM can potentially negatively regulate SopA protein level at the translation level through its direct binding of the sopA mRNA and positively at the transcriptional level simultaneously through its down-regulation of the negative regulator HilE .
2976,2977,2067.txt,1,3,Iris germanica;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica;Iris germanica;unidentified,FLAG;14028s;flag;flag;unknown,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;unidentified;Iris germanica,"% surviva A B C 100 10 1 r r to to gtL c c u ve ve p e L tL + + + typ gt ug u-ild w pe P y o-t h ld p w i L e oP rA gtL h m u p p A r m p gt u yp-t ld w i A Mg2 + L L L H b-galactosidase activity YqjA-FLAG w ild-type 14028s p h o yqjA-flag P B yqjA w 10µM Mg2 + 2 + - flag ; phoP 10mM Mg ild-type 5 0 40 p Discussion The PhoP -- PhoQ regulatory system controls resistance to a variety of structurally different antimicrobial peptides ( Groisman et al. , 1992 ) , but the identity of the PhoP-regulated determinants mediating peptide resistance has remained largely unknown .
"
2977,2978,2067.txt,2,0,,,,"In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .
"
2978,2979,2067.txt,3,0,,,,"the yqjA gene we show is PhoP regulated for resistance to polymyxin B or defensin HNP-1
"
2979,2980,2067.txt,4,0,,,,"the yqjA gene we show is PhoP regulated for resistance to magainin 2 HNP-1
"
2980,2981,2067.txt,5,0,,,,"the yqjA gene we show is PhoP regulated for resistance to polymyxin B or defensin HNP-1
"
2981,2982,2067.txt,6,0,,,,"the yqjA gene we show is PhoP regulated for resistance to magainin 2 HNP-1
"
2982,2983,2067.txt,7,0,,,,"This raised the possibility that the yqjA and/or yqjB genes might be regulated by the PhoP protein .
"
2983,2984,2067.txt,8,0,,,,"two genes -- yqjA -- are both transcriptionally regulated by the PhoP
"
2984,2985,2067.txt,9,0,,,,Expression of the yqjA gene is controlled by the PhoP protein at the transcriptional level .
2985,2986,1546.txt,1,0,,,,"Third , the RstA-dependent activation of feoAB transcription increased Fe ( II ) uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells expressing the RstA protein ( Fig. 3 ) ."
2986,2987,1220.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Olsén , A. , Arnqvist , A. , Normar , S. The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .
"
2987,2988,1220.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Olsén , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , S. The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli .
"
2988,2989,1220.txt,3,0,,,,"The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .
"
2989,2990,1220.txt,4,0,,,,"Olsen , A. , Arnqvist , A. , Hammar , M. , Sukupolvi , S. , Normark , S. : The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .
"
2990,2991,1220.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"A. Olsen , A. Arnqvist , M. Hammar , S. Sukupolvi , S. Normark , The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli , Mol .
"
2991,2992,1220.txt,6,0,,,,The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA .
2992,2993,978.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA Our results suggested that HilD have independent effects on expression of sipC in S. typhimurium .
"
2993,2994,978.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA Our results suggested that HilD have independent effects on expression of sipA in S. typhimurium .
"
2994,2995,978.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA Our results suggested that HilD have independent effects on expression of invF in S. typhimurium .
"
2995,2996,978.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA Our results suggested that HilA have independent effects on expression of sipC in S. typhimurium .
"
2996,2997,978.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA Our results suggested that HilA have independent effects on expression of sipA in S. typhimurium .
"
2997,2998,978.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A subset of SPI1 genes is induced by HilD overexpression in the absence of hilA Our results suggested that HilA have independent effects on expression of invF in S. typhimurium .
"
2998,2999,978.txt,7,0,,,,"These data demonstrate that HilD can activate a subset of SPI1 genes in the absence of hilA .
"
2999,3000,978.txt,8,0,,,,"the key regulator hilA , we have focused on two activators of HilD .
"
3000,3001,978.txt,9,0,,,,"HilD can independently activate the hilA promoter .
"
3001,3002,978.txt,10,0,,,,"However , evidence from our laboratory indicates that HilD is a required activator of hilA expression necessary for recruitment of RNA polymerase at the hilA promoter .
"
3002,3003,978.txt,11,0,,,,"However , evidence from our laboratory indicates that HilD is a required activator of hilA expression necessary for contact of RNA polymerase at the hilA promoter .
"
3003,3004,978.txt,12,0,,,,"We wanted to determine if HilD could induce expression of hilA in the absence of the other regulators .
"
3004,3005,978.txt,13,0,,,,"The data in Fig. 2 demonstrate that HilD are able to induce expression of hilA in the absence of the other regulators .
"
3005,3006,978.txt,14,1,Terfezia pini,to 40,Terfezia pini,"Production of HilC induced expression of hilA ~ 120-fold , while HilD induced expression of hilA 30-to 40-fold , similar to previously reported values .
"
3006,3007,978.txt,15,0,,,,"We show that HilD can each independently activate expression of the hilA genes .
"
3007,3008,978.txt,16,0,,,,"However , HilD normally act in concert to activate hilA .
"
3008,3009,978.txt,17,0,,,,"However , our most striking results show that even though HilD appears to be the best hilA activator of the three in-vitro , when working alone it can not induce hilA enough to stimulate invasion .
"
3009,3010,978.txt,18,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella;enterica,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilD .
"
3010,3011,978.txt,19,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella;enterica,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilD .
"
3011,3012,978.txt,20,0,,,,"HilD can activate expression of hilA .
"
3012,3013,978.txt,21,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .
"
3013,3014,978.txt,22,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .
"
3014,3015,978.txt,23,0,,,,"Since HilD activates hilA transcription , it was surprising that reduced transcription of the central regulator HilA was not detected by microarray analysis .
"
3015,3016,978.txt,24,0,,,,"The mechanism by which HilD activate expression of hilA
"
3016,3017,978.txt,25,0,,,,"That means that at least hilA are induced by HilD .
"
3017,3018,978.txt,26,0,,,,"To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilD-lac chromosomal fusions .
"
3018,3019,978.txt,27,0,,,,"To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilC-lac .
"
3019,3020,978.txt,28,0,,,,"To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac .
"
3020,3021,978.txt,29,0,,,,"Under high-osmolarity conditions , HilD activate SPI1 genes indirectly through hilA .
"
3021,3022,978.txt,30,0,,,,"Under high-osmolarity conditions , HilD activate SPI1 genes directly through hilA .
"
3022,3023,978.txt,31,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .
"
3023,3024,978.txt,32,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilD .
"
3024,3025,978.txt,33,0,,,,"HilD are each capable of activating hilA transcription .
"
3025,3026,978.txt,34,0,,,,"HilD induces expression of the hilA gene by derepressing the silencing effect of Hha on the hilA promoter
"
3026,3027,978.txt,35,0,,,,"HilD induces expression of the hilA gene by derepressing the silencing effect of H-NS on the hilA promoter
"
3027,3028,978.txt,36,0,,,,"Earlier work on mathematical modeling of regulation of expression of hilA by HilD was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .
"
3028,3029,978.txt,37,0,,,,"Both HilC and HilD activate expression of SPI-1 genes by binding upstream of the master regulatory gene hilA to induce its expression .
"
3029,3030,978.txt,38,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; 2001 ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
3030,3031,978.txt,39,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lee ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
3031,3032,978.txt,40,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilD are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
3032,3033,978.txt,41,0,,,,"The AraC-like transcriptional regulator HilD , positively regulates the expression of the SPI-1 genes in a cascade fashion , mainly by directly inducing the expression of hilA .
"
3033,3034,978.txt,42,0,,,,"Several studies strongly support the idea that HilD induces the expression of hilA by counteracting the repression .
"
3034,3035,978.txt,43,0,,,,"hilA expression is induced by three transcriptional activators , HilD .
"
3035,3036,978.txt,44,0,,,,"Transcription of hilA is directly activated by HilD .
"
3036,3037,978.txt,45,0,,,,"HilD positively regulates hilA
"
3037,3038,978.txt,46,0,,,,"Previous studies indicate that HilD induces the expression of hilA by counteracting the repression hilA can be expressed independently of HilD .
"
3038,3039,978.txt,47,0,,,,"HilD is the key activator of hilA transcription
"
3039,3040,978.txt,48,0,,,,"HilD , activate directly the expression of hilA , independently of HilA .
"
3040,3041,978.txt,49,0,,,,"HilD , induces the expression of hilA .
"
3041,3042,978.txt,50,0,,,,"Altogether , these results suggest that HilD plays a pivotal role in activating hilA expression under the experimental conditions .
"
3042,3043,978.txt,51,0,,,,"It was found that LoiA positively regulates the expression of hilA -LRB- the master activator of SPI-1 -RRB- through direct activation of HilD under low O2 conditions , leading to the activation of SPI-1 genes for invasion .
"
3043,3044,978.txt,52,0,,,,"HilD in turn activates hilA expression
"
3044,3045,978.txt,53,1,unidentified,unknown,unidentified,"Briefly , ArcB responds to low oxygen conditions when bacteria undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA-P activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .
"
3045,3046,978.txt,54,1,unidentified,unknown,unidentified,"Briefly , ArcB responds to low oxygen conditions when bacteria undergoes autophosphorylation , following which the phosphate group is transferred to ArcA ; phosphorylated ArcA activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .
"
3046,3047,978.txt,55,1,unidentified,unknown,unidentified,"Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum ; phosphorylated ArcA-P activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .
"
3047,3048,978.txt,56,1,unidentified,unknown,unidentified,"Briefly , ArcB responds to low oxygen conditions when bacteria reach the distal ileum ; phosphorylated ArcA activates loiA gene expression indirectly through unknown regulator ; LoiA activates HilD directly through binding the hilD promoter ; HilD then activates hilA SPI-1 genes .
"
3048,3049,978.txt,57,0,,,,Transcription of the hilA gene is also stimulated by HilD .
3049,3050,1234.txt,1,0,,,,"HilA-activated expression also results in readthrough transcription of sicAsipBCDA from a promoter upstream of spaS ( Darwin and Miller , 1999b ) ."
3050,3051,1552.txt,1,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A role for FIS in the regulation of S. enterica topA expression has not been previously detected
"
3051,3052,1552.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"FIS does directly regulate the E. coli topA promoter
"
3052,3053,1552.txt,3,0,,,,"Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of topA might differ between the two species .
"
3053,3054,1552.txt,4,0,,,,"Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of topA might differ between the two species .
"
3054,3055,1552.txt,5,0,,,,"FIS control of topA gene expression .
"
3055,3056,1552.txt,6,0,,,,FIS control of topA expression .
3056,3057,993.txt,1,0,,,,"Moreover , studies have shown that FliZ , under the control of FlhDC , positively regulates hilA expression by controlling HilD post-translationally , through a mechanism independent of the Lon protease ."
3057,3058,987.txt,1,0,,,,"Repression by DeoR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .
"
3058,3059,987.txt,2,0,,,,Repression by DeoR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .
3059,3060,1585.txt,1,2,Cornu aspersum;Cantareus apertus,helix;helix,Cornu aspersum;Cantareus apertus,"The MarR-type regulator RovA , a dimeric winged-helix DNA-binding protein of the SlyA/Hor/Rap family activates invA transcription in response to temperature ."
3060,3061,777.txt,1,0,,,,Direct regulation of fruK genes by SlyA in response to ROS .
3061,3062,763.txt,1,0,,,,"The pattern of hilA-dependent regulation of prgH by BarA together with partially hilA-indepen-dent regulation of invF by BarA parallels the pattern recently reported for SirA .
"
3062,3063,763.txt,2,0,,,,the already depressed expression of invF in the sirA mutant further ( 36-and 8-fold respectively ) _ suggesting a SirA-independent means of control for these genes
3063,3064,2098.txt,1,0,,,,"Given that MarT is a member of the family of ToxR-like regulatory proteins , t3766 is a candidate target for regulation by the marT-fidL products ."
3064,3065,1591.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Hantke , K. Dual repression by Fe - Fur - MntR of the mntH gene , encoding an NRAMP-like Mn transporter in Escherichia coli .
"
3065,3066,1591.txt,2,0,,,,"The mntH transcription is also partially repressed by Fe2 via a global iron regulator , Fur .
"
3066,3067,1591.txt,3,0,,,,"Importantly , inactivation of Fur disrupts Fe2-dependent repression of mntH transcription .
"
3067,3068,1591.txt,4,0,,,,"Importantly , inactivation of Fur disrupts Fe2-dependent repression of mntH transcription ."
3068,3069,2107.txt,1,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;unidentified expression vector,S. Typhi;Typhi;S. Typhi;Typhi;GIFU10007;expression vector,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;unidentified expression vector;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR can Bind the Promoter Fragment of Putative Operon yehUTS in S. Typhi The gene ompR of S. Typhi GIFU10007 was successfully cloned into XhoI of the expression vector pET22b .
"
3069,3070,2107.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007,S. Typhi;Typhi;S. Typhi;Typhi;GIFU10007,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Salmonella enterica subsp. enterica serovar Typhimurium,OmpR can Bind the Promoter Fragment of Putative Operon yehUTS in S. Typhi The gene ompR of S. Typhi GIFU10007 was successfully cloned into the cloning sites NdeI .
3070,3071,1368.txt,1,3,unidentified plasmid;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;S. enterica;enterica;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Briefly , pNL3 is a pBR322-derived reporter plasmid in which the PhoP-activated phoN promoter region of S. enterica serovar Typhimurium is fused to the lacZ structural gene .
"
3071,3072,1368.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Chryseobacterium gallinarum,S. typhimurium;typhimurium;strain ( 100,Chryseobacterium gallinarum;Salmonella enterica subsp. enterica serovar Typhimurium,"The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB-medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg/mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) ."
3072,3073,64.txt,1,1,Salmonella,Salmonella,Salmonella,"A number of fusions to genes in known virulence regulons such as sodA ( manganese superoxide dismutase ) , pagJ ( a PhoPQ-activated gene ) and ssaE ( in Salmonella patho-genicity island 2 , SPI2 ) were identified ."
3073,3074,824.txt,1,0,,,,"They also con cents rm previous reports that the RcsA protein is not involved in stimulation of ftsZ expression by RcsB .
"
3074,3075,824.txt,2,0,,,,"Moreover , RcsB activates transcription of the cell division genes ftsZ and ftsA by acting speci cents cally on one of the ftsA1p governing expression of the ftsQAZ cluster .
"
3075,3076,824.txt,3,0,,,,"Moreover , RcsB activates transcription of the cell division genes ftsZ and ftsA by acting speci cents cally on one of the promoters governing expression of the ftsQAZ cluster ."
3076,3077,70.txt,1,0,,,,"the results of present study suggest that a structural homology exists between ToxR as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3077,3078,70.txt,2,0,,,,"the results of present study suggest that a structural homology exists between MarT as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3078,3079,70.txt,3,0,,,,"the results of present study suggest that a functional homology exists between ToxR as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3079,3080,70.txt,4,0,,,,"the results of present study suggest that a functional homology exists between MarT as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3080,3081,70.txt,5,0,,,,"Some previous reports suggest that a structural homology exists between ToxR as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3081,3082,70.txt,6,0,,,,"Some previous reports suggest that a structural homology exists between MarT as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3082,3083,70.txt,7,0,,,,"Some previous reports suggest that a functional homology exists between ToxR as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
"
3083,3084,70.txt,8,0,,,,Some previous reports suggest that a functional homology exists between MarT as i -RRB- MarT can bind to the misL promoter region ; ii -RRB- ToxR is a transcriptional regulator .
3084,3085,830.txt,1,0,,,,"On the other hand , LeuO has only been found for ompS2 , although there is the distinct possibility that there is such a regulator for ompS1 .
"
3085,3086,830.txt,2,1,Salmonella,Salmonella,Salmonella,"We report here that LeuO are the main negative regulators of ompS1 expression in Salmonella .
"
3086,3087,830.txt,3,1,Salmonella,Salmonella,Salmonella,"We report here that LeuO are the main positive regulators of ompS1 expression in Salmonella .
"
3087,3088,830.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,S. Typhi;Typhi;plasmid,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"To test whether LeuO regulated the ompS1 gene , LeuO was expressed in S. Typhi wild type from plasmid pFMTrcleuO-50
"
3088,3089,830.txt,5,0,,,,"Interestingly , the pRO310 ompS1 was also positively regulated by LeuO .
"
3089,3090,830.txt,6,0,,,,"Hence , LeuO regulated positively the ompS1 gene .
"
3090,3091,830.txt,7,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3091,3092,830.txt,8,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3092,3093,830.txt,9,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3093,3094,830.txt,10,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3094,3095,830.txt,11,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3095,3096,830.txt,12,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3096,3097,830.txt,13,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3097,3098,830.txt,14,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how LeuO regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
3098,3099,830.txt,15,0,,,,"that LeuO bound upstream from the ompS1 regulatory region , overlapping with one binding site of StpA , but not interacting with the promoter region and promoting a change in the local DNA architecture
"
3099,3100,830.txt,16,0,,,,"that LeuO bound upstream from the ompS1 regulatory region , overlapping with one binding site of H-NS , but not interacting with the promoter region and promoting a change in the local DNA architecture
"
3100,3101,830.txt,17,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"The observation that both ompS1 were regulated by LeuO at different levels of induction opens the possibility that there is a regulon in S. enterica .
"
3101,3102,830.txt,18,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,Salmonella;Typhi;plasmid;Salmonella;Typhi;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .
"
3102,3103,830.txt,19,0,,,,"LeuO regulates the ompS1 , ompS2 , dsrA , and rovA genes .
"
3103,3104,830.txt,20,0,,,,"LeuO are involved in regulation of ompS1 .
"
3104,3105,830.txt,21,1,Salmonella,Salmonella,Salmonella,"Moreover it has been reported that LeuO are the main negative regulators of ompS1 expression in Salmonella .
"
3105,3106,830.txt,22,1,Salmonella,Salmonella,Salmonella,Moreover it has been reported that LeuO are the main positive regulators of ompS1 expression in Salmonella .
3106,3107,2113.txt,1,0,,,,"IgaA controls the RcsC-YojN-RcsB system at a post-translational level To decipher the mechanism by which IgaA exerts negative control of the RcsC-YojN-RcsB system , isogenic strains , yojN genes were constructed ."
3107,3108,1432.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
3108,3109,1354.txt,1,0,,,,HilD binds directly to the regulatory regions of the coding regions of ssrB .
3109,3110,58.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"With regard to transcriptional regulation of thefru operon , the results summarized here and previously , as well as unpublished results -LRB- Cao and Saier -RRB- suggest that the fru regulon in S. typhimurium is complex ; that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru -LRB- Cao and Saier , unpublished results -RRB- ; that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; that it may be regulated at the transcriptional level by two or more distinct mechanisms -LRB- possibly involving two distinct inducers , fructose-i-phos-phate and fructose -RRB- which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation .
"
3110,3111,58.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"With regard to transcriptional regulation of thefru operon , the results summarized here and previously , as well as unpublished results -LRB- Cao and Saier -RRB- suggest that the fru regulon in S. typhimurium is complex ; that it may consist of at least three or four operons , one encoding the IIIFm-FPr protein , fructose-i-phosphate kinase , and IIFru , a second encoding a fructose-inducible enzyme I-like protein , a third encoding the fructose repressor , FruR , and possibly a fourth encoding a cryptic 11Fru -LRB- Cao and Saier , unpublished results -RRB- ; that it is unique in its response to the loss of the cyclic AMP-CRP complex as a result of mutations in the cya , crp , or pts gene ; that it may be regulated at the transcriptional level by two or more distinct mechanisms -LRB- possibly involving two distinct inducers , fructose-i-phos-phate and fructose -RRB- which together account for induction by fructose , or that low-level expression of cryptic fru genes accounts for the anomalous fru operon induction behavior ; and that the proteins of the fructose-specific PTS may play a direct or indirect role in transcriptional regulation ."
3111,3112,818.txt,1,0,,,,"a 1.1 1.1 a membran , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant"
3112,3113,1340.txt,1,0,,,,"It is surprising that either glycerol can serve as effectors of PocR for induction of the cob operons , yet only propanediol is able to induce pocR transcription .
"
3113,3114,1340.txt,2,0,,,,"It is surprising that either glycerol can serve as effectors of PocR for induction of the pdu operons , yet only propanediol is able to induce pocR transcription .
"
3114,3115,1340.txt,3,0,,,,"It is surprising that either propanediol can serve as effectors of PocR for induction of the cob operons , yet only propanediol is able to induce pocR transcription .
"
3115,3116,1340.txt,4,0,,,,"It is surprising that either propanediol can serve as effectors of PocR for induction of the pdu operons , yet only propanediol is able to induce pocR transcription .
"
3116,3117,1340.txt,5,1,unidentified plasmid,plasmid,unidentified plasmid,"In this manner , we were able to isolate clones of pocR in which expression of pocR was not increased by transcription from Plac on the plasmid , since high-level expression of pocR by Plac led to constitutive -LRB- 1,2-PDL-indepen-dent -RRB- PocR activity in-vivo ."
3117,3118,1426.txt,1,0,,,,"Mutation of the cognate response regulator gene rcsB restored full virulence to the rcsC constitutive mutant , indicating that virulence attenuation results from aberrant expression of RcsB-regulated genes.The virulence attenuation phenotype was partially dependent on the regulatory gene rcsA , which is necessary for transcription of certain RcsB-regulated genes , and on the RcsB-and RcsA-dependent colanic acid capsule synthesis cps operon ."
3118,3119,159.txt,1,0,,,,FliA-dependent activation of FlgM ensures an effectiv `` off 
3119,3120,165.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Furthermore , addition of NO to E. coli cultures leads to upregulation of norV via transcriptional activation by the regulator NorR .
"
3120,3121,165.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"The NorR protein of Escherichia coli activates expression of the Flavorubredoxin gene norV in response to reactive-nitrogen-species .
"
3121,3122,165.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,The NorR protein of Escherichia coli activates expression of the flavorubredoxin gene norV in response to reactive-nitrogen-species .
3122,3123,603.txt,1,1,unidentified,unidentified,unidentified,"Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) ."
3123,3124,1397.txt,1,0,,,,"Taken together , these results show that CpxR represses the autoregulation of sseB located in SPI-2 ."
3124,3125,1383.txt,1,0,,,,"that acnA expression was regulated by SoxR , oxidative-stress"
3125,3126,617.txt,1,0,,,,The mgtB promoter is regulated by the PhoP/PhoQ system .
3126,3127,171.txt,1,4,Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Felis catus;Clostridium aminobutyricum,Typhimurium;E. coli;cat;Clostridium aminobutyricum,Felis catus;Clostridium aminobutyricum;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Apart from the PhoP/PhoQ-regulated ugd ( pagA ) gene , which in serovar Typhimurium has been demonstrated to be transcriptionally active inside macrophages and to be necessary for growth in a low-magnesium environment ( 1 , 19 , 20 ) , two genes were identified with homology to the E. coli tdh gene and the cat2 gene in Clostridium aminobutyricum ."
3127,3128,398.txt,1,0,,,,"7 min 25 min hilD AraC-family SPI1 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of ( groEL , groES , grpE , SEN1800 and ht encoding heat-shock proteins .
"
3128,3129,398.txt,2,0,,,,"7 min 25 min hilD AraC-family transcriptional regulator 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of ( groEL , groES , grpE , SEN1800 and ht encoding heat-shock proteins ."
3129,3130,1618.txt,1,0,,,,"Thus , the LeuO regulators positively regulate ompS2 .
"
3130,3131,1618.txt,2,0,,,,"The experiments described above indicated that both the LeuO were involved in the positive regulation of ompS2 expression .
"
3131,3132,1618.txt,3,0,,,,"LeuO participates in the regulation of ompS2 .
"
3132,3133,1618.txt,4,0,,,,"LeuO bound to the 5 upstream regulatory region of ompS2 in two .
"
3133,3134,1618.txt,5,0,,,,"IMSSTN103 where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2
"
3134,3135,1618.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"the original S. Typhi Tn-10 insertion mutant where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2
"
3135,3136,1618.txt,7,0,,,,"IMSSTN103 where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2
"
3136,3137,1618.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"the original S. Typhi Tn-10 insertion mutant where the transposon insertion allowed us to identify LeuO as a positive regulator of ompS2
"
3137,3138,1618.txt,9,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"The observation that both ompS2 were regulated by LeuO at different levels of induction opens the possibility that there is a regulon in S. enterica .
"
3138,3139,1618.txt,10,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,Salmonella;Typhi;plasmid;Salmonella;Typhi;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .
"
3139,3140,1618.txt,11,0,,,,"A previous report showed that LeuO bound to the promoter region of ompS2 at 93 to 109 to the transcription start site .
"
3140,3141,1618.txt,12,0,,,,"ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action
"
3141,3142,1618.txt,13,0,,,,ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action
3142,3143,1156.txt,1,0,,,,"For genes , we found two genes , ydhJ are negatively regulated by SlyA ."
3143,3144,1630.txt,1,0,,,,"However , the sirA knock-out does not lead to a complete loss in HilD levels since HilD is regulated by other factors ."
3144,3145,1624.txt,1,0,,,,"The two-component regulatory OmpR/EnvZ function through HilD , thus inducing hilC ."
3145,3146,1142.txt,1,0,,,,"This anti-correlation in the levels of RpoS proteins recalled an earlier observation that Fis is a repressor of rpoS gene transcription , at least in exponential-phase cultures .
"
3146,3147,1142.txt,2,0,,,,"This anti-correlation in the levels of the Fis recalled an earlier observation that Fis is a repressor of rpoS gene transcription , at least in exponential-phase cultures .
"
3147,3148,1142.txt,3,0,,,,"Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .
"
3148,3149,1142.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Altogether , these results suggest that Fis are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .
"
3149,3150,1142.txt,5,0,,,,"Fis participate in the repression of rpoS .
"
3150,3151,1142.txt,6,0,,,,"On the other hand , Fis precludes the RpoS accumulation by repressing the rpoS transcription ."
3151,3152,1817.txt,1,0,,,,"The expression of rob is negatively regulated by SoxS in response to sodium salicylate and paraquat , respectively .
"
3152,3153,1817.txt,2,0,,,,"rob is negatively regulated by SoxS The transcript levels of rob in the DsoxS strains were repressed after treatment with NaOCl as in the wild type .
"
3153,3154,1817.txt,3,0,,,,"rob is negatively regulated by SoxS The transcript levels of rob in the DmarA strains were repressed after treatment with NaOCl as in the wild type .
"
3154,3155,1817.txt,4,0,,,,"SoxS bind the promoter region of rob To determine whether the repression was due to a direct interaction between SoxS with the promoter of rob , we performed a bioinformatic analysis .
"
3155,3156,1817.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"other studies _ performed in E. coli where rob was shown to be negatively regulated by both SoxS by a direct interaction with its promoter region
"
3156,3157,1817.txt,6,0,,,,"EMSAs _ demonstrating that SoxS bind to the promoter region of rob , indicating that the repression exerted by SoxS is due to a direct interaction with the DNA"
3157,3158,1803.txt,1,0,,,,"IgaA controls the RcsC-YojN-RcsB system at a post-translational level To decipher the mechanism by which IgaA exerts negative control of the RcsC-YojN-RcsB system , isogenic strains , rcsB genes were constructed ."
3158,3159,429.txt,1,0,,,,"A novel NsrR-regulated gene designated STM1808 has been identified , along with hmp , hcp-hcr , yeaR-yoaG , ygbA and ytfE .
"
3159,3160,429.txt,2,1,Salmonella,Salmonella,Salmonella,"Moreover , the operons of yeaR-yoaG , previously shown to be regulated by NsrR in Salmonella , were found to be induced 678.1 - , 314.5 - , 130.2 - , 123.7-and 15.9-fold , respectively , by the absence of NsrR .
"
3160,3161,429.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Moreover , the operons of yeaR-yoaG , previously shown to be regulated by NsrR in Escherichia coli - , 123.7-and 15.9-fold , respectively , by the absence of NsrR .
"
3161,3162,429.txt,4,0,,,,"These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) ."
3162,3163,1195.txt,1,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : slyA .
"
3163,3164,1195.txt,2,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : slyA .
"
3164,3165,1195.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"The PhoP Protein Binds to the Promoter of the slyA Gene -- Investigation of PhoP-controlled slyA transcription has been carried out using plasmid-borne constructs harboring the slyA promoter region ( 20 ) .
"
3165,3166,1195.txt,4,1,unidentified plasmid,plasmid,unidentified plasmid,"The PhoP Protein Binds to the Promoter of the slyA Gene -- Investigation of PhoP-controlled slyA transcription has been carried out using plasmid-borne constructs harboring the slyA promoter region ( 20 ) .
"
3166,3167,1195.txt,5,0,,,,"The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .
"
3167,3168,1195.txt,6,1,unidentified,unknown,unidentified,"Although the mechanism remains unknown , it has been suggested that the PhoP protein regulates slyA expression indirectly because a PhoP box could not be identified in the slyA promoter region .
"
3168,3169,1195.txt,7,0,,,,"that the PhoP protein binds to the slyA promoter
"
3169,3170,1195.txt,8,0,,,,"It has been suggested that the PhoP protein regulates the slyA gene indirectly because a PhoP box could not be identified in the slyA promoter .
"
3170,3171,1195.txt,9,0,,,,"The PhoP protein binds to the slyA promoter .
"
3171,3172,1195.txt,10,0,,,,"These results indicate that the PhoP protein controls slyA transcription directly .
"
3172,3173,1195.txt,11,0,,,,"Although others have proposed that the PhoP protein regulates slyA transcription indirectly -LRB- i.e. by modulating the expression of another regulatory protein -RRB- , our results argue that PhoP controls slyA transcription directly -LRB- i.e. by binding to the slyA promoter .
"
3173,3174,1195.txt,12,0,,,,"Although others have proposed that the PhoP protein regulates slyA transcription indirectly -LRB- i.e. by modulating the expression of another regulatory protein -RRB- , our results argue that PhoP controls slyA transcription directly -LRB- i.e. by binding to the slyA promoter .
"
3174,3175,1195.txt,13,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
3175,3176,401.txt,1,0,,,,"FlhDC acts as a positive regulator for class fliA .
"
3176,3177,401.txt,2,0,,,,"To investigate whether z66 is regulated by FlhDC like other biphasic S. fliA mutants were affected by the osmotic environment , an ompR mutant was also prepared ."
3177,3178,367.txt,1,0,,,,"Previously , we dem-onstrated that HilD directly induces the expression of the ssrAB operon .
"
3178,3179,367.txt,2,0,,,,"This suggests that HilD induces the expression of ssrAB also by counteracting H-NS-me-diated repression of its promoter .
"
3179,3180,367.txt,3,0,,,,"All together , these results indicate that HilD induces the expression of ssrAB by displacing the H-NS nucleoprotein complex from the promoter of this operon .
"
3180,3181,367.txt,4,0,,,,"Furthermore , our results indicate that HilD induces the expression of ssrAB by binding to one located on .
"
3181,3182,367.txt,5,0,,,,"Furthermore , our results indicate that HilD induces the expression of ssrAB by binding to at least two different AT-rich regions .
"
3182,3183,367.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Interestingly , when S. Typhimurium is grown to late stationary-phase in LB-medium , HilD directly induces the expression of the ssrAB operon .
"
3183,3184,367.txt,7,0,,,,"HilD can activate the ssrAB operon by specifically interacting with its regulatory region to upregulate SPI-2 .
"
3184,3185,367.txt,8,0,,,,HilD can also induce expression of SPI-2 by direct binding to the promoter of ssrAB .
3185,3186,373.txt,1,0,,,,"To study the DNA-binding properties of CsgD we used DNase I footprint analysis to show that unphosphorylated CsgD-His6 binds specifically to the csgBA .
"
3186,3187,373.txt,2,0,,,,"To study the DNA-binding properties of CsgD we used electrophoretic-mobility-shift assays to show that unphosphorylated CsgD-His6 binds specifically to the csgBA .
"
3187,3188,373.txt,3,0,,,,a negative control furthermore demonstrated the specificity of the binding of CsgD-His6 to the csgBA
3188,3189,415.txt,1,0,,,,"Under conditions of low-osmolarity , the transcription of sipB is negatively controlled by the RcsB regulator , acting in concert with the TviA protein ."
3189,3190,1181.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"As the RstA binding site is identical apart from a single nucleotide , the RstA ortholog STM1475 might directly control csgD transcription in S. Typhimurium ."
3190,3191,372.txt,1,0,,,,"CsrA regulates translation of cstA , by blocking ribosome access to the cstA transcript ."
3191,3192,1180.txt,1,0,,,,"These results are consistent with the role of FimW as a negative regulator of fimbrial expression , acting either directly on the fimA promoter to indirectly through the activity of other regulatory molecules .
"
3192,3193,1180.txt,2,0,,,,"These results are consistent with the role of FimW as a negative regulator of fimbrial expression , acting either directly on the fimA promoter to repress transcription .
"
3193,3194,1180.txt,3,0,,,,"that the regulatory effect of FimW is not due to the binding of FimW alone at the fimA promoter
"
3194,3195,1180.txt,4,0,,,,"These results demonstrate that the fimZ gene encodes a positive regulator for fimA , while FimW is a repressor for fimA ."
3195,3196,414.txt,1,1,Escherichia coli,E. coli,Escherichia coli,locus STM2628 whose hypothetical product shows similarity to the DicA repressor of the E. coli K-12 cryptic Qin prophage
3196,3197,400.txt,1,0,,,,"These results indicated that the transcription of tviB was under negative control of OmpR , respectively .
"
3197,3198,400.txt,2,0,,,,"These results indicated that the transcription of tviB was under positive control of OmpR , respectively ."
3198,3199,1194.txt,1,0,,,,"The last two ORFs of srgB , encode a transcriptional regulator of the AraC family respectively ."
3199,3200,366.txt,1,0,,,,"Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels which are simply accomplished by iron .
"
3200,3201,366.txt,2,1,Salmonella,Salmonella,Salmonella,"We propose that the RstA-induced feoB expression allows Salmonella cells to take up more Fe ( II ) , thereby promoting Fur activity [ as evidenced by Fur-Fe ( II ) levels ] based on the following .
"
3201,3202,366.txt,3,0,,,,"Activation of feoB transcription by the RstA protein is necessary for repression of iron-responsive genes .
"
3202,3203,366.txt,4,0,,,,"Together with the finding that induction of the feoB gene was necessary for repression of the iron response by the RstA protein ( Fig. 3B ) , our results suggest that iron signaling via the RstA-induced FeoB promotes Fur activity beyond the levels .
"
3203,3204,366.txt,5,0,,,,"This emphasizes that , in the presence of iron , the feoB gene should be induced by the RstA protein to repress iron-responsive genes ."
3204,3205,1802.txt,1,0,,,,This tolerance appeared to be reflected in the upregulation of rpoE of the RpoS regulon .
3205,3206,428.txt,1,0,,,,These experiments indicate that the putative yojN rcsB operon requires the OmpR response regulator for expression .
3206,3207,1816.txt,1,0,,,,"In the presence of Mn , MntR represses the expression of mntH , through direct binding of specific sites within the promoter regions of these genes .
"
3207,3208,1816.txt,2,1,Bacillus subtilis,Bacillus subtilis,Bacillus subtilis,"MntR , plays a major role in regulating mntH expression in Bacillus subtilis .
"
3208,3209,1816.txt,3,1,Salmonella,Salmonella,Salmonella,"Expression of Salmonella mntH gene is regulated by both MntR-dependent and-independent mechanisms .
"
3209,3210,1816.txt,4,0,,,,"The Fur-and MntR-controlled mntH gene , also involved in Mn2 + and Fe2 + uptake ( with a preference for Mn2 + ) , was also induced but in lesser extent ( up to 2.1-fold at 45 min ) ."
3210,3211,1625.txt,1,0,,,,"The ssaH promoter was previously shown to be regulated by EnvZ through SsrB -- both protein pairs being two-component regulators -- and not by PhoQ .
"
3211,3212,1625.txt,2,0,,,,"The ssaH promoter was previously shown to be regulated by EnvZ through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .
"
3212,3213,1625.txt,3,0,,,,"The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoQ .
"
3213,3214,1625.txt,4,0,,,,"The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .
"
3214,3215,1625.txt,5,0,,,,There was no evidence of SsrB binding at ssaH .
3215,3216,1143.txt,1,0,,,,"These results show that HilD positively controls the expression of the gtgE genes , independently of InvF .
"
3216,3217,1143.txt,2,0,,,,"These results show that HilD positively controls the expression of the gtgE genes , independently of HilA .
"
3217,3218,1143.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"HilD induces the expression of gtgE , in the absence of other Salmonella-specific regulators .
"
3218,3219,1143.txt,4,0,,,,"Thus , HilD positively regulates the expression of the gtgE genes , and positively .
"
3219,3220,1143.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD positively regulates gtgE in S. Typhimurium .
"
3220,3221,1143.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"HilD induces the expression of gtgE , in E. coli MC4100 ."
3221,3222,1157.txt,1,0,,,,ssaJ are regulated by HilC
3222,3223,1631.txt,1,2,unidentified plasmid;Prairie vole hantavirus,plasmid;pVV,Prairie vole hantavirus;unidentified plasmid,"We used a low copy plasmid , pVV448 , in which the HilA-activated invF promoter region ( -319 bp to +128 bp , relative to the HilA-activated +1 ) is cloned upstream of lacZ .
"
3223,3224,1631.txt,2,1,Prairie vole hantavirus,pVV,Prairie vole hantavirus,"As expected , HilA activates lacZ expression from pVV448 up to 50-fold ."
3224,3225,1619.txt,1,0,,,,PmrAB activation results in upregulation of cld .
3225,3226,399.txt,1,0,,,,"Expression of STY3070 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx in an hns background , suggesting that this global regulatory protein has a positive effect .
"
3226,3227,399.txt,2,0,,,,"Expression of assT was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx in an hns background , suggesting that this global regulatory protein has a positive effect .
"
3227,3228,399.txt,3,0,,,,"Expression of ompS1 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for tpx in an hns background , suggesting that this global regulatory protein has a positive effect .
"
3228,3229,399.txt,4,0,,,,"Interestingly , the results indicate that H-NS is a positive regulator of tpx ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .
"
3229,3230,399.txt,5,0,,,,global microarray analysis indicated that H-NS represses tpx expression .
3230,3231,616.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Nou , X. , Braaten , B. , Kaltenbach , L. , regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for anaerobic induction of aniC in Salmonella typhimurium .
"
3231,3232,616.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Nou , X. , Braaten , B. , Kaltenbach , L. , regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for acid-pH induction of aniC in Salmonella typhimurium .
"
3232,3233,616.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for anaerobic induction of aniC in Salmonella typhimurium .
"
3233,3234,616.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for acid-pH induction of aniC in Salmonella typhimurium ."
3234,3235,1382.txt,1,0,,,,"In addition , HilC directly activate sipC in non-HilA dependent manner ."
3235,3236,170.txt,1,0,,,,"Among these , we identified the GolS-target operators from the golTS operon and the golB gene ( Checa et al. , 2007 ) , as well as the CueR-controlled operators from cueO and copA genes ( Kim et al. , 2002 ; Espariz et al. , 2007 ) .
"
3236,3237,170.txt,2,0,,,,CueR regulates cueO .
3237,3238,164.txt,1,0,,,,"This work demonstrates the regulation of hilC by RtsA .
"
3238,3239,164.txt,2,0,,,,"In agreement with genetic data , we show that the purified RtsA protein , like HilD , binds to the hilC , hilD , rtsA .
"
3239,3240,164.txt,3,0,,,,"In agreement with genetic data , we show that the purified RtsA protein , like HilC , binds to the hilC , hilD , rtsA ."
3240,3241,1396.txt,1,0,,,,"STM3388 additively influence the CsgD expression level , while AdrA primarily activates cellulose biosynthesis through the creation of different c-di-GMP pools ."
3241,3242,602.txt,1,0,,,,"FimZ is known to negatively regulate flhD expression .
"
3242,3243,602.txt,2,0,,,,It is possible that the increase in FimZ in the ΔinvS background strain led to the decrease of flhD expression .
3243,3244,158.txt,1,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , wraB are regulated by the alternative sigma factor RpoS ."
3244,3245,1341.txt,1,0,,,,"Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .
"
3245,3246,1341.txt,2,0,,,,"In addition , the lack of consensus PmrA-binding sites in the promoters of STM3968 suggested that these genes may be indirectly activated by PmrA ."
3246,3247,1427.txt,1,0,,,,"The SoxRS-and MarRAB-regulated genes that contribute t broad antibiotic resistance include the acrAB operon encoding a multidrug efflux pump ( 22 , 25 , 30 ) and the micF gene encoding an antisense RNA that inhibits synthesis of the OmpF outer membrane porin ( 6 , 7 , 32 ) ."
3247,3248,1433.txt,1,1,Salmonella,Salmonella,Salmonella,"of the RcsC/YojN/RcsB regulatory system due to the rcsC11 allele in the sensor RcsC renders Salmonella that inactivation of the response regulator gene rcsB restores full virulence to the rcsC11 mutant , indicative that its attenuated phenotype results from aberrant expression of RcsB-regulated genes .
"
3248,3249,1433.txt,2,1,unidentified plasmid,plasmid,unidentified plasmid,"rcsB overexpression represses PrcsDB activity RESULTS RcsB overproduction represses rcsD transcription We have previously demonstrated that rcsB overexpression from plasmid prcsB results in strong repression of rcsD gene expression , while its own expression is not affected ."
3249,3250,819.txt,1,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella,Salmonella;Typhi;Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression Matías and Juan A Fuentes1 ,3 * Abstract Background : SPI-18 is a pathogenicity island found in some Salmonella enterica serovars , including S. T .
"
3250,3251,819.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression Matías 1 , Alejandro A Hida .
"
3251,3252,819.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression Matías , Nicolás A Villa .
"
3252,3253,819.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression Matías , Leonardo M Rodrígu .
"
3253,3254,819.txt,5,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"R E S E A R C H A R T I C L E Open Access RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression Matías R Jofr .
"
3254,3255,819.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates global regulators , to control S. Typhi hlyE expression .
"
3255,3256,819.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates multiple environmental signals , to control S. Typhi hlyE expression .
"
3256,3257,819.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates PhoP signaling pathways , to control S. Typhi hlyE expression .
"
3257,3258,819.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates Fis , to control S. Typhi hlyE expression .
"
3258,3259,819.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates CRP , to control S. Typhi hlyE expression .
"
3259,3260,819.txt,11,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression .
"
3260,3261,819.txt,12,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,RpoS integrates PhoP signaling pathways to control Salmonella Typhi hlyE expression .
3261,3262,59.txt,1,0,,,,"genetic analyses indicate that this process is regulated by Fnr controlling the expression of lpxO .
"
3262,3263,59.txt,2,0,,,,"Biochemical analyses indicate that this process is regulated by Fnr controlling the expression of lpxO .
"
3263,3264,59.txt,3,0,,,,"Thus , the oxygen-dependent regulation of lpxO expression is lost when fnr is deleted , indicating that Fnr is a negative regulator of lpxO expression under anaerobic conditions .
"
3264,3265,59.txt,4,0,,,,"Thus , the oxygen-dependent regulation of lpxO expression is lost when fnr is deleted , indicating that Fnr is a negative regulator of lpxO expression under anaerobic conditions .
"
3265,3266,59.txt,5,0,,,,"These results indicate that Fnr regulate lpxO expression through direct binding to its promoter region .
"
3266,3267,59.txt,6,0,,,,"In addition , we also demonstrate that global regulators Fnr control the oxygen-dependent lipid-A hydroxylation by directly regulating the expression of lpxO .
"
3267,3268,59.txt,7,0,,,,"Our results also showed that both Fnr are able to bind in-vitro to the promoter regions of lpxO , strongly suggesting a direct role for these regulators in the control of lpxO transcription .
"
3268,3269,59.txt,8,0,,,,"Our results also showed that both Fnr are able to bind in-vitro to the promoter regions of lpxO , strongly suggesting a direct role for these regulators in the control of lpxO transcription .
"
3269,3270,59.txt,9,1,Salmonella,Enteritidis,Salmonella,a model in which Fnr control the expression of lpxO in S. Enteritidis to achieve a fine-tuning of lipid-A hydroxylation levels
3270,3271,1355.txt,1,0,,,,The LysR-type regulator LeuO has been shown to activate hilE transcription to repress HilD activity .
3271,3272,831.txt,1,0,,,,"To the functional category related to the `` cell envelope 
"
3272,3273,831.txt,2,0,,,,"PhoPQ-regulated genes include lpxO , whose product results in the addition of 2-hydroxymyristate to the 3 = position of lipid-A ( A ) ; pagL , whose product results in deacylation at the 3 = position of lipid-A ( B ) ; and pagP , whose product results in the addition of a palmitate chain to the 2 = position of lipid-A ( C ) ."
3273,3274,71.txt,1,0,,,,"that OmpR binds directly to ssrB regulatory regions to affect their expression
"
3274,3275,71.txt,2,0,,,,"Previous results from gene fusions suggest that regulation of ssrB by OmpR is distinct .
"
3275,3276,71.txt,3,0,,,,"Previous results from gene fusions suggest that regulation of ssrB by OmpR is uncoupled .
"
3276,3277,71.txt,4,1,synthetic construct,primer,synthetic construct,"Previous results from primer-extension analysis suggest that regulation of ssrB by OmpR is distinct .
"
3277,3278,71.txt,5,1,synthetic construct,primer,synthetic construct,"Previous results from primer-extension analysis suggest that regulation of ssrB by OmpR is uncoupled .
"
3278,3279,71.txt,6,0,,,,"Other examples of genes include ssrB known regulators of SPI-2 previously reported to be influenced by OmpR Figure 7 .
"
3279,3280,71.txt,7,0,,,,"Other examples of genes include ssrB known regulators of SPI-2 previously reported to be influenced by OmpR Figure 7 .
"
3280,3281,71.txt,8,1,Salmonella,Salmonella,Salmonella,"previous work in Salmonella has shown that phosphorylated OmpR can bind to either ssrB within SPI-2
"
3281,3282,71.txt,9,0,,,,"In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrB genes .
"
3282,3283,71.txt,10,0,,,,"Under low osmolality , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .
"
3283,3284,71.txt,11,0,,,,"Under acidic pH , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .
"
3284,3285,71.txt,12,0,,,,"The OmpR protein regulates the transcription of the ssrB genes , partly by acting there as a conventional TF .
"
3285,3286,71.txt,13,0,,,,"The OmpR protein regulates the transcription of the ssrB genes , partly by acting there by acting as an anti-repressor .
"
3286,3287,71.txt,14,0,,,,"For example , OmpR promotes SPI-2 expression by directly binding to both ssrB promoters ."
3287,3288,2112.txt,1,0,,,,The pagP genes are regulated by PhoP-PhoQ
3288,3289,2106.txt,1,0,,,,"Here , we show that the chiP gene , like the chbBCARFG operon , is also downregulated at the transcriptional level by the NagC repressor .
"
3289,3290,2106.txt,2,0,,,,"Inactivation of the NagC repressor causes chiP expression to increase no more than twofold to threefold in ΔchiX background .
"
3290,3291,2106.txt,3,0,,,,"The NagC repressor inhibits chiP transcription under uninduced conditions through binding to the chiP promoter .
"
3291,3292,2106.txt,4,0,,,,"The NagC repressor inhibits chiP transcription under uninduced conditions through binding to the chiP promoter .
"
3292,3293,2106.txt,5,0,,,,"However , in both organisms repression of chiP by NagC is inefficient resulting in a relatively high basal level of chiP transcription in the absence of chitobi-ose .
"
3293,3294,2106.txt,6,0,,,,"Second , as the flux of chitobiose through the ChbBCA ChbFG enzymes relieves repression by NagC of both chiP operons .
"
3294,3295,2106.txt,7,0,,,,"Second , as the flux of chitobiose through the ChbBCA transporter enzymes relieves repression by NagC of both chiP operons .
"
3295,3296,2106.txt,8,0,,,,"In uninduced the chb , chiP operons are repressed by NagC .
"
3296,3297,2106.txt,9,0,,,,"In the absence-of-chitosugars the chb , chiP operons are repressed by NagC ."
3297,3298,825.txt,1,0,,,,"the former _ being regulated by a promoter located upstream of the pstS gene regulated by CRP
"
3298,3299,825.txt,2,0,,,,the former _ being regulated by a promoter located upstream of the pstS gene regulated by CRP
3299,3300,65.txt,1,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels were approximately fourfold higher in wild-type S. Typh-imurium than in a fur mutant in Fe-rich-medium .
"
3300,3301,65.txt,2,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( d .
"
3301,3302,65.txt,3,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( ( Fig. .
"
3302,3303,65.txt,4,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( d .
"
3303,3304,65.txt,5,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( ( Fig. .
"
3304,3305,65.txt,6,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( d .
"
3305,3306,65.txt,7,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( ( Fig. .
"
3306,3307,65.txt,8,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( d .
"
3307,3308,65.txt,9,0,,,,"Consistent with positive regulation by Fur , ftnA mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( ( Fig. .
"
3308,3309,65.txt,10,0,,,,"Thus , ftnA genes are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .
"
3309,3310,65.txt,11,0,,,,"In the absence of Fe and/or Fur , repression of ryhB is relieved , leading to negative regulation of ftnA .
"
3310,3311,65.txt,12,0,,,,Both bfr and ftnA are under positive regulation by Fur
3311,3312,1369.txt,1,0,,,,"Instead , FimW may function by influencing the ability of FimZ to activate transcription from this promoter , either by inhibiting the binding of FimZ to the fimA promoter or by inhibiting activation by FimZ once this protein has bound .
"
3312,3313,1369.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Also , since FimZ regulates S. typhimurium fimA expression , we constructed a fimZ-lacZ fusion to investigate the expression of this important regulator of the fimbrial system .
"
3313,3314,1369.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Also , since FimZ regulates S. typhimurium fimA expression , we constructed a fimZ-lacZ fusion to investigate the expression of this important regulator of the fimbrial system .
"
3314,3315,1369.txt,4,0,,,,"this , along with our previous reports of FimZ , indicates that FimZ can bind to the fimA promoter region
"
3315,3316,1369.txt,5,0,,,,"However , our in-vitro results indicate that FimZ alone will bind to the fimA promoter .
"
3316,3317,1369.txt,6,0,,,,"However , when FimZ binds in-vitro to the fimA promoter , many molecules of FimZ are associated with the DNA fragments , creating a large DNA-pro-tein complex .
"
3317,3318,1369.txt,7,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"FimZ binds the Salmonella typhimurium fimA promoter .
"
3318,3319,1369.txt,8,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;typhimu,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"FimZ binds the Salmonella typhimu-rium fimA promoter .
"
3319,3320,1369.txt,9,0,,,,"FimZ was shown to bind the fimA promoter to activate fimbrial expression .
"
3320,3321,1369.txt,10,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhimu,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,FimZ binds the Salmonella Typhimu-rium fimA promoter .
3321,3322,762.txt,1,3,Salmonella;Salmonella;Escherichia coli;Erwinia amylovora;Salmonella,S. enterica;enterica;E. coli;Erwinia amylovora;Salmonella,Escherichia coli;Salmonella;Erwinia amylovora,"Microarray analyses of rcsB-and/or rcsB rcsA-dependent changes in genes expression in S. enterica , E. coli and Erwinia amylovora identified dozens of genes that are directly or indirectly controlled by these regulators ( Wang et al. , 2007 ; 2012 ) To determine which members of the Rcs regulon contribute to persistence within tomatoes , we chose a two-pronged approach : we first defined a set of likely direct RcsAB targets , and then que-ried results of a recently completed high-throughput screen of transposon-tagged Salmonella mutants ( de Moraes et al. , submitted ) to determine which of the RcsAB-regulated genes contribute to the reduced fitness of the mutants ."
3322,3323,1590.txt,1,0,,,,"The substitutions assT 688/assT 80 LBS-B 80 LBS-C , decreased LeuO-mediated assT activation by 35 % , respectively , whereas no changes in transcriptional activity were detected from assT 688/assT 80 LBS-D , containing a 3-bp substitution in LBS I .
"
3323,3324,1590.txt,2,0,,,,"The substitutions assT 688/assT 80 LBS-B 80 LBS-C , decreased LeuO-mediated assT activation by 53 , respectively , whereas no changes in transcriptional activity were detected from assT 688/assT 80 LBS-D , containing a 3-bp substitution in LBS I ."
3324,3325,2099.txt,1,0,,,,this effect was reflected by induction of cspB and proteins ( CspC ) in response to preadaptation to cold-stress
3325,3326,1584.txt,1,4,Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli;Felis catus;Clostridium aminobutyricum,Typhimurium;E. coli;cat;Clostridium aminobutyricum,Felis catus;Clostridium aminobutyricum;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Apart from the PhoP/PhoQ-regulated ugd ( pagA ) gene , which in serovar Typhimurium has been demonstrated to be transcriptionally active inside macrophages and to be necessary for growth in a low-magnesium environment ( 1 , 19 , 20 ) , two genes were identified with homology to the E. coli tdh gene and the cat2 gene in Clostridium aminobutyricum ."
3326,3327,776.txt,1,1,Salmonella,Salmonella,Salmonella,ZupT determines changes in intracellular zinc concentration of Lack Previous studies have shown that zinT are coregulated by Zur and that ZinT accumulation is strongly induced by EDTA and repressed by zinc .23 The addition of 0.5 μM ZnSO4 to the culture medium causes the complete abrogation of ZinT accumulation in a wild type Salmonella strai
3327,3328,986.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"Among kanamycin-resistant tranductants , the presence of the lexA ( Ind ) mutation was confirmed through β-galactosidase assay after introduction of the pGE108 plasmid ( Table 2 ) which contains a LexA-regulated cea ∷ lacZ fusion ( Salles et al. , 1987 ) .
"
3328,3329,986.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"The LexA-based genetic system detects in-vivo protein dimerization in E. coli SU101 , in which the reporter fusion sulA : : lacZ is controlled by the LexA dimer -LRB- dimerization is essential for operator recognition -RRB- ."
3329,3330,992.txt,1,0,,,,"Thus , we investigated expression of the SsrB-activated ssaG gene , which is the first gene of a large operon ( from ssaG to ssaU ) and encodes a component of the Spi/Ssa T3SS ( 22 ) ."
3330,3331,1235.txt,1,0,,,,"slyA _ controlled by the PmrA/PmrB , to promote intracellular bacterial survival in the phagosome"
3331,3332,979.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , BasR binds directly to the csgD promoter to activate transcription ."
3332,3333,1553.txt,1,3,unidentified plasmid;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;S. enterica;enterica;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Briefly , pNL3 is a pBR322-derived reporter plasmid in which the PhoP-activated phoN promoter region of S. enterica serovar Typhimurium is fused to the lacZ structural gene .
"
3333,3334,1553.txt,2,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
3334,3335,1553.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .
"
3335,3336,1553.txt,4,0,,,,"RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .
"
3336,3337,1553.txt,5,0,,,,"Two additional PhoP-activated genes , slyB and phoN , were used as positive and negative controls , respectively , since previous experiments have shown direct interaction of PhoP with the promoter of slyB but not with the promoter of phoN ( 50 ) ."
3337,3338,1547.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Even though Rho has been proposed to play an indirect role in gene control by riboswitches [ i.e. , by prematurely terminating transcription of those mRNAs , our results demonstrate that the E. coli ribB riboswitch operates in a distinct manner ."
3338,3339,1221.txt,1,1,Escherichia coli,E. coli,Escherichia coli,It was later demonstrated that E. coli SdiA activates ftsQ in response to AHL .
3339,3340,1209.txt,1,0,,,,"Although the O1-site downstream of the transcriptional start site appears to be the most important for csgD expression , binding of Cra to operators O3 located upstream commonly appears to be important for maximal transcription .
"
3340,3341,1209.txt,2,0,,,,"Although the O1-site downstream of the transcriptional start site appears to be the most important for csgD expression , binding of Cra to operators O2 upstream commonly appears to be important for maximal transcription ."
3341,3342,945.txt,1,0,,,,Transcription of the sic/sip operon is activated directly by the SPI-1 encoded transcription factor InvF could therefore be mediated through direct regulation of invF .
3342,3343,2066.txt,1,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3343,3344,2066.txt,2,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3344,3345,2066.txt,3,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3345,3346,2066.txt,4,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3346,3347,2066.txt,5,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3347,3348,2066.txt,6,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3348,3349,2066.txt,7,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3349,3350,2066.txt,8,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3350,3351,2066.txt,9,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3351,3352,2066.txt,10,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3352,3353,2066.txt,11,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3353,3354,2066.txt,12,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3354,3355,2066.txt,13,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3355,3356,2066.txt,14,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3356,3357,2066.txt,15,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3357,3358,2066.txt,16,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 2809 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3358,3359,2066.txt,17,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3359,3360,2066.txt,18,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3360,3361,2066.txt,19,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3361,3362,2066.txt,20,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3362,3363,2066.txt,21,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3363,3364,2066.txt,22,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3364,3365,2066.txt,23,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3365,3366,2066.txt,24,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu Haruo Watanabe1 1Department of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3366,3367,2066.txt,25,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3367,3368,2066.txt,26,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3368,3369,2066.txt,27,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3369,3370,2066.txt,28,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Sexually Transmitted Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3370,3371,2066.txt,29,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3371,3372,2066.txt,30,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxA , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3372,3373,2066.txt,31,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for invasion genes , in Shigella sonnei .
"
3373,3374,2066.txt,32,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Shigella sonnei,Salmonella;Salmonella enterica;enterica;Typhimurium;Shigella sonnei,Salmonella enterica;Shigella sonnei;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 149 -- 2817 Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium Shu-ichi Nakayama ,1 Akira Kushiro ,2 Takashi Asahara ,2 Ryu-ichiro Tanaka ,2 Lan Hu ,3 Dennis J. Kopecko3 of Bacteriology , National Institute of Infectious Diseases , Toyama , 1-23-1 , Shinjuku-Ku , Tokyo 162-8640 , Japan Correspondence Haruo Watanabe 2Yakult Central Institute for Microbiological Research , Yaho 1796 , Kunitachi-Shi , Tokyo 186-8650 , Japan haruwata@nih.go.jp 3Laboratory of Enteric Diseases , Center for Biologics Evaluation and Research , FDA , Bldg 29 , 8800 Rockville Pike , Bethesda , MD 20892 , USA A two-component regulatory system , cpxR , plays an important role in the pH-dependent regulation of virF , a global activator for virulence determinants , in Shigella sonnei .
"
3374,3375,2066.txt,33,2,Salmonella;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Sal-monella;monella;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .
"
3375,3376,2066.txt,34,2,Salmonella;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Sal-monella;monella;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Sal-monella enterica serovar Typhimurium .
"
3376,3377,2066.txt,35,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium .
"
3377,3378,2066.txt,36,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Activation of hilA expression at low pH requires the cognate response regulator CpxR , in Salmonella enterica serovar Typhimurium ."
3378,3379,2072.txt,1,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , RpoS , DnaJ , DnaK , GrpE .
"
3379,3380,2072.txt,2,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , RpoS , heat-shock .
"
3380,3381,2072.txt,3,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , stationary-phase , DnaJ , DnaK , GrpE .
"
3381,3382,2072.txt,4,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , H-NS , stationary-phase , heat-shock .
"
3382,3383,2072.txt,5,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , RpoS , DnaJ , DnaK , GrpE .
"
3383,3384,2072.txt,6,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , RpoS , heat-shock .
"
3384,3385,2072.txt,7,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , stationary-phase , DnaJ , DnaK , GrpE .
"
3385,3386,2072.txt,8,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , OmpR , DNA structure , stationary-phase , heat-shock .
"
3386,3387,2072.txt,9,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , RpoS , DnaJ , DnaK , GrpE .
"
3387,3388,2072.txt,10,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , RpoS , heat-shock .
"
3388,3389,2072.txt,11,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , stationary-phase , DnaJ , DnaK , GrpE .
"
3389,3390,2072.txt,12,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , H-NS , stationary-phase , heat-shock .
"
3390,3391,2072.txt,13,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , RpoS , DnaJ , DnaK , GrpE .
"
3391,3392,2072.txt,14,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , RpoS , heat-shock .
"
3392,3393,2072.txt,15,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , stationary-phase , DnaJ , DnaK , GrpE .
"
3393,3394,2072.txt,16,0,,,,"The flhDC master operon is influenced by catabolite-repression , OmpR , DNA structure , stationary-phase , heat-shock .
"
3394,3395,2072.txt,17,0,,,,"Transcription of the flhDC operon is known to be regulated by signals from a network of OmpR .
"
3395,3396,2072.txt,18,0,,,,"Emerging evidence indicates that OmpR regulates regulation of the flagellar operon flhDC .
"
3396,3397,2072.txt,19,0,,,,"Emerging evidence indicates that OmpR regulates regulation of the flagellar operon flhDC .
"
3397,3398,2072.txt,20,0,,,,"fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC by OmpR .
"
3398,3399,2072.txt,21,0,,,,"Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of flagellation by activation of the flagellar operon flhDC .
"
3399,3400,2072.txt,22,0,,,,"Recently , it was also demonstrated that OmpR of Yersinia is involved in the control of motility by activation of the flagellar operon flhDC .
"
3400,3401,2072.txt,23,1,Yersinia pseudotuberculosis,Yersinia pseudotuberculosis,Yersinia pseudotuberculosis,"Positive regulation of flhDC expression by OmpR in Yersinia pseudotuberculosis .
"
3401,3402,2072.txt,24,1,Yersinia enterocolitica,Yersinia enterocolitica,Yersinia enterocolitica,OmpR controls Yersinia enterocolitica motility by positive regulation of flhDC expression .
3402,3403,789.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , CsrA is known to control the expression of STM3611 ."
3403,3404,951.txt,1,0,,,,"The regulation of OmpR on hfq may be in a indirect manner .
"
3404,3405,951.txt,2,0,,,,The regulation of OmpR on hfq may be in a direct manner .
3405,3406,1792.txt,1,0,,,,"When growth took place in LB-rich-medium , a significant 6.6-fold increase of expression of pdxK was observed in the DptsJ strain with respect to Fig. 1B , con-firming the repressor role of PtsJ .
"
3406,3407,1792.txt,2,0,,,,"When growth took place in LB-rich-medium , a significant 6.6-fold increase of expression of pdxK was observed in the DptsJ strain with respect to wild-type , con-firming the repressor role of PtsJ ."
3407,3408,206.txt,1,0,,,,"In addition , Lrp represses expression of the spvABCD operon ."
3408,3409,560.txt,1,0,,,,"Lack of AraC suppressed hilA repression by 0.2 % L-arabinose .
"
3409,3410,560.txt,2,0,,,,"hilA expression was increasingly repressed in an AraCˉ background as the L-arabinose concentration increase
"
3410,3411,560.txt,3,0,,,,"When araE was expressed constitutively , lack of AraC no longer suppressed hilA repression by L-arabinose ."
3411,3412,574.txt,1,0,,,,"Later , LeuO was determined to reduce rpoS translation ( which encodes S sigma factor ) by repression of the small regulatory DsrA-RNA ."
3412,3413,212.txt,1,0,,,,"Likewise , lacZ in the phoP mutant indicated that PhoP is involved in the regulation of tlpA .
"
3413,3414,212.txt,2,0,,,,"Likewise , the higher expression of tlpA : indicated that PhoP is involved in the regulation of tlpA .
"
3414,3415,212.txt,3,0,,,,"To further investigate the possibility that PhoP regulates tlpA , we constructed OG2008 .
"
3415,3416,212.txt,4,0,,,,"To further investigate the possibility that PhoP regulates tlpA , we constructed a double mutant strain .
"
3416,3417,212.txt,5,0,,,,"These results indicate that PhoP plays a pivotal role as a repressor in the regulation of tlpA .
"
3417,3418,212.txt,6,0,,,,"Therefore , the regulation of tlpA by PhoP may provide a molecular mechanism to the suppressed expression of tlpA under MgM medium , containing low Mg 2þ concentration .
"
3418,3419,212.txt,7,0,,,,"Therefore , the regulation of tlpA by PhoP may explain a molecular mechanism to the suppressed expression of tlpA under MgM medium , containing low Mg 2þ concentration ."
3419,3420,1786.txt,1,0,,,,Fis somewhat increased the expression of cspH upon nutritional up-shift .
3420,3421,1976.txt,1,0,,,,"a 1.1 1.1 a a rbsA 1.1 ABC superfamily -LRB- -RRB- , -- D-ribose high-affinity transport protein ABC superfamily -LRB- -RRB- , D-ribose transport protein ABC superfamil , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant"
3421,3422,548.txt,1,0,,,,"RcsB-regulated genes can be divided into those that are RcsA dependent , such as the cps genes ( Gottesman et al. , 1985 ) ( Fig. 3 ) , and those that are RcsA independent , such as the ftsZ ( Carballes et al. , 1999 ; Costa and Anton , 2001 ) and osmC ( Davalos-Garcia et al. , 2001 ) genes ."
3422,3423,1962.txt,1,0,,,,"Although HilD regulate two promoters upstream of hilC , they activate one and repress the other , such that overall HilD appear to have no effect on hilC expression .
"
3423,3424,1962.txt,2,0,,,,"These results indicate that Lon is involved in the autoregulation of hilC transcription by modulating amounts of HilD .
"
3424,3425,1962.txt,3,0,,,,"This work demonstrates the regulation of hilC by HilD .
"
3425,3426,1962.txt,4,0,,,,"The HilD proteins bind to the common DNA sites at hilC promoters .
"
3426,3427,1962.txt,5,0,,,,"To check if both regulators are important , the regulation of hilC gene expression by HilD is considered to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .
"
3427,3428,1962.txt,6,0,,,,"To check if both regulators are important , the regulation of hilC gene expression by HilD is considered to function as gate , this dependency is taken as an OR gate .
"
3428,3429,1962.txt,7,0,,,,"To check if both regulators are important , the regulation of hilC gene expression by HilD is considered to function as an , this dependency is taken as an OR gate .
"
3429,3430,1962.txt,8,0,,,,"HilD also directly controls the expression of hilC .
"
3430,3431,1962.txt,9,0,,,,HilD-or HilC-Sumo proteins bind to a 210-bp fragment of the hilC promoter .
3431,3432,1751.txt,1,0,,,,"In order to further elucidate the contribution of single RamA to the ciprofloxacin resistance of SI3 , RamA was overexpressed in SI2R ( SI2ramA : : aph ) ."
3432,3433,1989.txt,1,0,,,,"gyrB promoter DNA was incubated with increasing concentrations of Fis protein prior to digestion with DNase I .
"
3433,3434,1989.txt,2,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS 
"
3434,3435,1989.txt,3,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS "
3435,3436,2258.txt,1,0,,,,"Partial induction of the lpxO gene by growth on low Mg2 and the role of the PhoP/PhoQ system in the transcription of lpxO .
"
3436,3437,2258.txt,2,0,,,,Partial induction of A reporter construct ( Fig. 5A ) and the role of the PhoP/PhoQ system in the transcription of lpxO .
3437,3438,1037.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Of 93 CsrA-induced genes identified in-vitro , we found that 88 % were downregulated during infection of J774A .1 macrophages by S. typhimurium ; consistent with this , csrA was also downregulated threefold ( Figure 1 ) [ 19,30 ] ."
3438,3439,1023.txt,1,0,,,,"PhoPQ , seem to convert pH decreases into the regulation of different virulence-factors while the primary role of fur appears to be protection against acid stress itself ."
3439,3440,1745.txt,1,0,,,,"SsrB also appears to activate ssrA , although the mechanism of regulation remains to be determined
"
3440,3441,1745.txt,2,0,,,,"L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .
"
3441,3442,1745.txt,3,0,,,,"R. Oropeza suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .
"
3442,3443,1745.txt,4,0,,,,"1134 X. Feng suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .
"
3443,3444,1745.txt,5,0,,,,"SsrB , in turn , activates ssrA .
"
3444,3445,1745.txt,6,0,,,,"SsrB , in turn , activates ssrA .
"
3445,3446,1745.txt,7,0,,,,"SsrB activates transcription in the absence of ssrA Previous work from our laboratory demonstrated that transcription of ssrB genes occurs from separate promoters .
"
3446,3447,1745.txt,8,0,,,,SsrB activates transcription in the absence of ssrA Previous work from our laboratory demonstrated that transcription of the adjacent ssrA occurs from separate promoters .
3447,3448,2264.txt,1,0,,,,"sseB were used as controls for PhoP-and SsrB-dependent expression , respectively ."
3448,3449,1779.txt,1,0,,,,"This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS-and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) .
"
3449,3450,1779.txt,2,0,,,,"This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS-and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) ."
3450,3451,2270.txt,1,0,,,,a Rho-dependent terminator inhibits transcription elongation into the ribB coding region in the presence of FMN
3451,3452,1009.txt,1,0,,,,"Schematic diagram _ illustrating the interplay between STM1344 in the regulation of FlhD4C2 functionality
"
3452,3453,1009.txt,2,0,,,,"STM1344 suppress the functionality of the master regulator of the flagella regulatory cascade , FlhD4C2 ."
3453,3454,2266.txt,1,0,,,,"However , entC mRNA levels in the fur deletion strain were constitutively higher than those , indicating that Fur functions to repress entC expression inside macrophages .
"
3454,3455,2266.txt,2,1,Salmonella,Salmonella,Salmonella,"Expression of these genes is downregulated in Salmonella , as evidenced by the finding that Fur represses expression of the entC gene inside Fig. 1C .
"
3455,3456,2266.txt,3,1,Salmonella,Salmonella,Salmonella,"Expression of these genes is downregulated in Salmonella , as evidenced by the finding that Fur represses expression of the entC gene inside macrophages ."
3456,3457,2272.txt,1,0,,,,"The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiA , has been characterized .
"
3457,3458,2272.txt,2,0,,,,"Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during P starvation .
"
3458,3459,2272.txt,3,0,,,,"Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during N .
"
3459,3460,2272.txt,4,0,,,,"Nonetheless , it is clear from these results that RpoS is involved in the positive regulation of both stiA and stiC during C .
"
3460,3461,2272.txt,5,0,,,,"Since the stiA are regulated by RpoS , we wanted to examine the combined effects of sti mutations on starvation survival .
"
3461,3462,2272.txt,6,0,,,,"Since the stiA are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .
"
3462,3463,2272.txt,7,0,,,,"On the basis of the fact that stiA are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .
"
3463,3464,2272.txt,8,0,,,,"On the basis of the fact that stiA are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA are not induced and/or because stiB is overexpressed in an rpoS mutant ."
3464,3465,589.txt,1,0,,,,"A model for SPI1 regulation Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : RtsA .
"
3465,3466,589.txt,2,0,,,,"A model for SPI1 regulation Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilD .
"
3466,3467,589.txt,3,0,,,,"A model for SPI1 regulation Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC .
"
3467,3468,589.txt,4,0,,,,"Expression of hilA is directly controlled by three AraC-like activators : RtsA .
"
3468,3469,589.txt,5,0,,,,"Expression of hilA is directly controlled by three AraC-like activators : HilD .
"
3469,3470,589.txt,6,0,,,,"Expression of hilA is directly controlled by three AraC-like activators : HilC .
"
3470,3471,589.txt,7,2,Cornu aspersum;Cantareus apertus;Cornu aspersum;Cantareus apertus,helix;helix;helix;helix,Cornu aspersum;Cantareus apertus,"In addition to the BarA/SirA system , the AraC-like regulator RitA directly controls the hilA expression , while a helix-turn-helix DNA binding protein , negatively regulates the expression of the flhDC .
"
3471,3472,589.txt,8,0,,,,"In addition to the BarA/SirA system , the AraC-like regulator RitA directly controls the hilA expression , while RitB , negatively regulates the expression of the flhDC .
"
3472,3473,589.txt,9,0,,,,"Three AraC-like transcriptional activators have been reported to bind to the hilA promoter : RtsA .
"
3473,3474,589.txt,10,0,,,,"Three AraC-like transcriptional activators have been reported to bind to the hilA promoter : HilD .
"
3474,3475,589.txt,11,0,,,,"Three AraC-like transcriptional activators have been reported to bind to the hilA promoter : HilC .
"
3475,3476,589.txt,12,0,,,,"Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : RtsA .
"
3476,3477,589.txt,13,0,,,,"Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilD .
"
3477,3478,589.txt,14,0,,,,"Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC .
"
3478,3479,589.txt,15,0,,,,"Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : RtsA .
"
3479,3480,589.txt,16,0,,,,"Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilD .
"
3480,3481,589.txt,17,0,,,,"Expression of hilA is controlled by the combined action of three AraC-like transcriptional activators : HilC .
"
3481,3482,589.txt,18,0,,,,"The expression of hilA , is directly controlled by three AraC-like regulators , RtsA , .
"
3482,3483,589.txt,19,0,,,,"The expression of hilA , is directly controlled by three AraC-like regulators , HilC , .
"
3483,3484,589.txt,20,0,,,,"The expression of hilA , is directly controlled by three AraC-like regulators , HilD , .
"
3484,3485,589.txt,21,0,,,,"Expression of hilA is directly controlled by three AraC-like regulators , RtsA , .
"
3485,3486,589.txt,22,0,,,,"Expression of hilA is directly controlled by three AraC-like regulators , HilC , .
"
3486,3487,589.txt,23,0,,,,"Expression of hilA is directly controlled by three AraC-like regulators , HilD , .
"
3487,3488,589.txt,24,0,,,,"Differential expression of hilA , is influenced by three AraC-like regulators
"
3488,3489,589.txt,25,0,,,,Expression of hilA is directly controlled by three AraC-like transcriptional regulators
3489,3490,1035.txt,1,0,,,,"However , unlike spf -- CRP complex , cyaR is activated by CRP .
"
3490,3491,1035.txt,2,0,,,,"However , unlike spf -- CRP complex , cyaR is activated by CRP ."
3491,3492,1753.txt,1,0,,,,FliA-dependent activation of FlgM ensures an effectiv `` off 
3492,3493,1747.txt,1,0,,,,"PhoR/PhoB can increase the expression of the hilE invasion repressor gene
"
3493,3494,1747.txt,2,0,,,,"PhoR/PhoB can increase the expression of the hilE invasion repressor gene
"
3494,3495,1747.txt,3,0,,,,"PhoR/PhoB can increase the expression of the hilE invasion repressor gene
"
3495,3496,1747.txt,4,0,,,,"PhoR/PhoB can increase the expression of the hilE invasion repressor gene
"
3496,3497,1747.txt,5,0,,,,"PhoR/PhoB can increase the expression of the hilE invasion repressor gene
"
3497,3498,1747.txt,6,0,,,,PhoR/PhoB can increase the expression of the hilE invasion repressor gene
3498,3499,1021.txt,1,0,,,,"These results suggest that the induction of sifB expression by acidic pH inside the vacuole is mediated by both B and OmpR -- EnvZ .
"
3499,3500,1021.txt,2,0,,,,These results suggest that the induction of sifB expression by acidic pH inside the vacuole is mediated by both SsrA and OmpR -- EnvZ .
3500,3501,238.txt,1,2,Salmonella;Salmonella;Escherichia coli,S. enterica;enterica;E. coli,Escherichia coli;Salmonella,"In electro-phoretic mobility-shift assays , Fis was found to bind to both the gyrA of S. enterica , despite the strong divergence from the E. coli sequence on the part of the former .
"
3501,3502,238.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"The retention of Fis-mediated repression of gyrA in S. enterica despite the radically different nucleotide sequence found immediately upstream of the Pribnow box is indicative of the physiological importance for the cell of regulation of gyrase expression by Fis .
"
3502,3503,238.txt,3,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Fis also binds to and represses the promoters of the gyrA genes in both E. coli and S. Typhimurium , resulting in reduced levels of DNA supercoiling .
"
3503,3504,238.txt,4,2,Escherichia coli;Salmonella;Salmonella,E. coli;S. enterica;enterica,Escherichia coli;Salmonella,"In E. coli , FIS binds the gyrA promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrA .
"
3504,3505,238.txt,5,0,,,,"Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrA might differ between the two species .
"
3505,3506,238.txt,6,0,,,,"Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrA might differ between the two species .
"
3506,3507,238.txt,7,0,,,,FIS control of gyrA .
3507,3508,1974.txt,1,0,,,,"The ssaH promoter was previously shown to be regulated by EnvZ through SsrA -- both protein pairs being two-component regulators -- and not by PhoP .
"
3508,3509,1974.txt,2,0,,,,The ssaH promoter was previously shown to be regulated by EnvZ through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .
3509,3510,1960.txt,1,0,,,,"In addition , HilC directly activate sipA in non-HilA dependent manner ."
3510,3511,562.txt,1,0,,,,"Likewise , ugd transcription is co-ordinately induced with that of the cps genes by the RcsA protein , possibly because of its role in col-anic acid capsule synthesis ."
3511,3512,204.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources .
"
3512,3513,204.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ."
3513,3514,1790.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Considering the overexpression of qseB in the absence of qseC , the repression of invF transcription in DqseC provides further evidence that QseB can attenuate the invasion of epithelial cells by S. Typhi ."
3514,3515,1948.txt,1,0,,,,"Detection of Mutations in the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , RamR exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers .
"
3515,3516,1948.txt,2,0,,,,"Detection of Mutations in the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , MarA exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers .
"
3516,3517,1948.txt,3,0,,,,"Detection of Mutations in the soxRS , marRAB , acrR and ramR regulatory loci ( as it is already known , the transcriptional regulators SoxS exert a positive effect on AcrAB/TolC expression , whereas AcrR is the local repressor ) was performed using the corresponding primers ."
3517,3518,1784.txt,1,0,,,,"ACYC184-HA-CadC , was expressed under the control of the cadC promoter in the cadC strain ."
3518,3519,210.txt,1,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in hcp , ygbA , ytfE , STM1808 and yeaR ( Experimental Procedures ) ."
3519,3520,576.txt,1,0,,,,"that HilD are each capable of independently inducing expression of the hilC genes
"
3520,3521,576.txt,2,0,,,,"We demonstrate that HilD are each capable of inducing expression of hilC .
"
3521,3522,576.txt,3,0,,,,"We wanted to determine if HilD could induce expression of hilC in the absence of the other regulators .
"
3522,3523,576.txt,4,0,,,,"HilD also induced expression of hilC .
"
3523,3524,576.txt,5,0,,,,"HilD induced expression of hilC approximately threeto fourfold .
"
3524,3525,576.txt,6,0,,,,"These data show that HilD are each capable of independently inducing expression of hilC , consistent with our model that HilD constitute a feed forward regulatory loop .
"
3525,3526,576.txt,7,0,,,,"We show that HilD can each independently activate expression of the hilC genes .
"
3526,3527,576.txt,8,0,,,,"HilD are all also capable of activating expression of hilC independent of each other and comprise a complex feed forward regulatory loop .
"
3527,3528,576.txt,9,0,,,,"For this purpose , we analyzed the effect of L-arabinose on the expression of three HilD-activated genes ( hilC , rtsA , and invH ) .
"
3528,3529,576.txt,10,0,,,,"Furthermore , HilD activates transcription of hilC and of hilD itself by direct binding to both promoters ."
3529,3530,2064.txt,1,0,,,,"HilD , regulates the expression of lpxR .
"
3530,3531,2064.txt,2,0,,,,"that HilD directly controls the expression of the lpxR genes
"
3531,3532,2064.txt,3,0,,,,"HilD binds to the regulatory regions of lpxR .
"
3532,3533,2064.txt,4,0,,,,"To further define whether the HilD-mediated regulation of lpxR is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .
"
3533,3534,2064.txt,5,0,,,,"To further define whether the HilD-mediated regulation of lpxR is direct , we analyzed the interaction of HilD with the regulatory region of these genes .
"
3534,3535,2064.txt,6,0,,,,"Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the lpxR genes .
"
3535,3536,2064.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,S. Typhimurium;S. Typhimurium SL1344;Typhimurium;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium,"In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : lpxR .
"
3536,3537,2064.txt,8,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of lpxR .
"
3537,3538,2064.txt,9,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of lpxR .
"
3538,3539,2064.txt,10,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of lpxR .
"
3539,3540,2064.txt,11,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of lpxR .
"
3540,3541,2064.txt,12,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of lpxR .
"
3541,3542,2064.txt,13,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of lpxR .
"
3542,3543,2064.txt,14,2,Felis catus;Escherichia coli,cat;E. coli,Felis catus;Escherichia coli,"Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of lpxR .
"
3543,3544,2064.txt,15,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of lpxR .
"
3544,3545,2064.txt,16,2,Felis catus;Salmonella;Salmonella,cat;Salmonella;Salmonella-specific,Felis catus;Salmonella,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of lpxR .
"
3545,3546,2064.txt,17,0,,,,"Thus , HilD directly regulates the expression of the lpxR genes , and positively .
"
3546,3547,2064.txt,18,0,,,,"Whether the regulation by HilD implies that the lpxR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .
"
3547,3548,2064.txt,19,0,,,,"Whether the regulation by HilD implies that the lpxR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .
"
3548,3549,2064.txt,20,1,Salmonella,Salmonella,Salmonella,"Whether the regulation by HilD implies that the lpxR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .
"
3549,3550,2064.txt,21,1,Salmonella,Salmonella,Salmonella,"Whether the regulation by HilD implies that the lpxR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .
"
3550,3551,2064.txt,22,0,,,,HilD binds to the regulatory region of lpxR .
3551,3552,947.txt,1,0,,,,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of glpT , in H7 .
"
3552,3553,947.txt,2,0,,,,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of glpT , in O157 .
"
3553,3554,947.txt,3,0,,,,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of glpT , in the enterohemorrhagic EHEC strain .
"
3554,3555,947.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of glpT , in the enterohemorrhagic E. coli strain ."
3555,3556,953.txt,1,0,,,,"As well as being regulated by RpoE , degP , is also CpxR ."
3556,3557,1579.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Just one work reported that a S. Typhimurium 1phoP mutant presents wild-type levels of lpxO expression , indicating that this gene is not regulated by PhoP/PhoQ ."
3557,3558,2070.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In vitro binding of FruR , to icd operons of Salmonella typhimurium .
"
3558,3559,2070.txt,2,0,,,,"In vitro binding of FruR , to icd operons of Esche-richia coli ."
3559,3560,1551.txt,1,0,,,,HilD binds directly to the regulatory regions of the coding regions of ssrA .
3560,3561,2058.txt,1,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"YncC also Binds to the E. coli K-12 yciGFE Promoter Region -- The ortholog of yncC in E. coli K-12 -LRB- named mcbR -RRB- , regulates colanic acid production by repressing expression of the ybiM gene ."
3561,3562,1237.txt,1,0,,,,"Moreover , while we did not detect a HilC-regulated transfrag for DapZ using Rockhopper , we did detect strong binding of HilC upstream of dapZ ( see Fig .
"
3562,3563,1237.txt,2,0,,,,"Moreover , while we did not detect a HilC-regulated transfrag for DapZ , we did detect strong binding of HilC upstream of dapZ ( see Fig ."
3563,3564,1223.txt,1,0,,,,"Au activates the expression of cpxP , the archetypical CpxR/CpxA-regulated gene To test if in the presence of Au , other members of the Cpx regulon are induced , we measured the expression of cpxP , coding for a key component of the CpxR/CpxA signal transduction pathway known to acts as a CpxA modulator ( Hunke et al. , 2012 ; Raivio , 2014 ; Grabowicz and Silhavy , 2016 ) .
"
3564,3565,1223.txt,2,0,,,,"Au activates the expression of cpxP , the archetypical CpxR/CpxA-regulated gene To test if in the presence of Au , other members of the Cpx regulon are induced , we measured the expression of cpxP , coding for a key component of the CpxR/CpxA signal transduction pathway known to acts as a CpxA modulator ( Hunke et al. , 2012 ; Raivio , 2014 ; Grabowicz and Silhavy , 2016 ) ."
3565,3566,1545.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene Marcos Fernández - d Edmundo Calva * Departamento de Microbiolog Molecular , Instituto de Biotecnología , Universidad Nacional Autónoma de México , Cuernavaca , Morelos 62210 , México The Salmonella enterica serovar Typhi ompS2 gene codes for es for a 362-amino-acid outer membrane .
"
3566,3567,1545.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene Marcos Fernández - José Luis Puen Molecular , Instituto de Biotecnología , Universidad Nacional Autónoma de México , Cuernavaca , Morelos 62210 , México The Salmonella enterica serovar Typhi ompS2 gene codes for es for a 362-amino-acid outer membrane .
"
3567,3568,1545.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene Marcos Fernández - Mor Molecular , Instituto de Biotecnología , Universidad Nacional Autónoma de México , Cuernavaca , Morelos 62210 , México The Salmonella enterica serovar Typhi ompS2 gene codes for es for a 362-amino-acid outer membrane ."
3568,3569,984.txt,1,0,,,,"However , since operon is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO .
"
3569,3570,984.txt,2,0,,,,"However , since the hydrogenase 2 -LRB- hypO-hybABCDE -RRB- is differentially expressed under conditions , we hypothesized that FhlA , stimulates transcription from the 54-dependent promoter in the intergenic region between hypO ."
3570,3571,748.txt,1,1,Salmonella,Salmonella,Salmonella,"Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates other genes of srgB ."
3571,3572,990.txt,1,0,,,,"In addition to HilD , the expression of lpxR in SPI-1-inducing conditions is positively regulated by SlyA ."
3572,3573,1592.txt,1,0,,,,"Together , these data suggest that although there is some regulation of hilE transcription and translation , this regulation is not dramatic under normal conditions and/or the identified regulators have effects on the system of HilE ."
3573,3574,760.txt,1,0,,,,"To study the DNA-binding properties of CsgD we used DNase I footprint analysis to show that unphosphorylated CsgD-His6 binds specifically to adrA promoter regions .
"
3574,3575,760.txt,2,0,,,,"To study the DNA-binding properties of CsgD we used electrophoretic-mobility-shift assays to show that unphosphorylated CsgD-His6 binds specifically to adrA promoter regions .
"
3575,3576,760.txt,3,0,,,,a negative control furthermore demonstrated the specificity of the binding of CsgD-His6 to adrA promoter regions
3576,3577,774.txt,1,0,,,,"In addition , katE is not resistant to Crl activation per se because it responded to Crl activation when S levels were decreased by the rpoSLT2 mutation ."
3577,3578,1586.txt,1,0,,,,"fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of fliA by OmpR .
"
3578,3579,1586.txt,2,0,,,,fljB : z66 at low-osmolarity is associated with the inhibition of To clarify whether the expression of fljB is regulated by OmpR the expression of flhDC by OmpR .
3579,3580,2110.txt,1,0,,,,"HilC do not seem to regulate expression of hilD .
"
3580,3581,2110.txt,2,0,,,,"These results indicate that Lon is involved in the autoregulation of hilD transcription by modulating amounts of HilC .
"
3581,3582,2110.txt,3,0,,,,"Thus , HilC are also apparently indirectly regulating hilD , contributing to the feedforward loop .
"
3582,3583,2110.txt,4,0,,,,"This work demonstrates the regulation of hilD by HilC .
"
3583,3584,2110.txt,5,0,,,,"When the hilD translational fusion was placed under control of the lacUV5 promoter , overproduction of HilC had no effect .
"
3584,3585,2110.txt,6,0,,,,"Thus , although HilD is capable of auto-regulation , the results could not be due to the loss of this regulatory protein controlling its own expres ¬ Pat post-transcriptionally regulates HilD The regulation of hilD is complex ; hilD is also regulated by the transcriptional regulators HilC and RtsA , which constitute a feed-forward circuit to control the downstream SPI1 regulator Hil ."
3585,3586,1419.txt,1,0,,,,"The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS .
"
3586,3587,1419.txt,2,0,,,,The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS .
3587,3588,73.txt,1,0,,,,that either SdiA regulates luxS
3588,3589,833.txt,1,0,,,,"Besides the mgtA gene , only 2 of slyB were directly regulated by the PhoPQ two-component system organisms .
"
3589,3590,833.txt,2,0,,,,"Besides the mgtA gene , only 2 of slyB were directly regulated by the PhoPQ two-component system in ."
3590,3591,67.txt,1,0,,,,"However , DNA sequence analysis suggest that the regulation of sirA by CRP is probably indirect .
"
3591,3592,67.txt,2,0,,,,"However , gel mobility-shift experiments suggest that the regulation of sirA by CRP is probably indirect .
"
3592,3593,67.txt,3,0,,,,"To test the hypothesis that the CRP binds directly to the sirA promoter , we used in-vitro gel mobility-shift assays .
"
3593,3594,67.txt,4,0,,,,"that the regulation of sirA by CRP is indirect
"
3594,3595,67.txt,5,0,,,,"Based on these observations , it seems unlikely that CRP directly controls sirA expression .
"
3595,3596,67.txt,6,0,,,,"CRP functions as crp is necessary for SPI-1 genes expression by binding to its regulator sirA .
"
3596,3597,67.txt,7,0,,,,CRP functions as a transcriptional activator is necessary for SPI-1 genes expression by binding to its regulator sirA .
3597,3598,827.txt,1,0,,,,"Since the PhoBR signal regulates hilA via hilE , it was logical to examine whether the regulatory signal was transmitted through fimZ similar to that ."
3598,3599,199.txt,1,0,,,,"Direct binding to promoter regions of virulence genes To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in DslyA strains under conditions of oxidative-stress .
"
3599,3600,199.txt,2,0,,,,"Direct binding to promoter regions of virulence genes To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT strains under conditions of oxidative-stress .
"
3600,3601,199.txt,3,0,,,,"Direct binding to promoter regions of metabolism genes To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in DslyA strains under conditions of oxidative-stress .
"
3601,3602,199.txt,4,0,,,,"Direct binding to promoter regions of metabolism genes To determine whether SlyA regulates sopD , sopE2 , hilA fruk , glpA , kgtP in-vivo , the promoter activity of each gene was evaluated using the vector pGLO in WT strains under conditions of oxidative-stress .
"
3602,3603,199.txt,5,0,,,,"Direct regulation of sopD genes by SlyA in response to ROS .
"
3603,3604,199.txt,6,0,,,,"Our results showed that at 3 h post-infection only , sopD were negatively regulated by SlyA , with DslyA expression increased two-and five-times , respectively ."
3604,3605,2104.txt,1,0,,,,"The ORF of malS is regulated by MalT , the activator of the maltose system in E. col ."
3605,3606,1425.txt,1,0,,,,"HilA , is believed to directly activate expression from the prgH promoters in SPI1 .
"
3606,3607,1425.txt,2,0,,,,"These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .
"
3607,3608,1425.txt,3,0,,,,"HilA directly activates the prgH promoter .
"
3608,3609,1425.txt,4,0,,,,"By binding upstream of prgH , HilA directly activates expression of the prgH operons that encode the components of the TTS apparatus ."
3609,3610,1343.txt,1,0,,,,"SpvR regulates the spvABCD operon
"
3610,3611,1343.txt,2,0,,,,"the spvABCD genes _ regulated by the SpvR protein
"
3611,3612,1343.txt,3,0,,,,"SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , that of the spvABCD operon ."
3612,3613,1357.txt,1,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
3613,3614,2138.txt,1,0,,,,"For example , sopE seem to be regulated directly indirectly by HilA through modulation of invF expression ."
3614,3615,9.txt,1,0,,,,"Plumbridge , the NagC repressor acts as an activator for the transcription of the glmUS operon ."
3615,3616,1431.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
3616,3617,1431.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
3617,3618,628.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Expression of ptsG is regulated by ArcA in Escherichia coli .
3618,3619,172.txt,1,0,,,,"that acnA expression was regulated by CRP , glucose-starvation"
3619,3620,1380.txt,1,0,,,,"These data suggest that CRP activates ompF expression in exponential-growth .
"
3620,3621,1380.txt,2,0,,,,These data suggest that CRP activates ompF expression during stationary-phase .
3621,3622,614.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
3622,3623,614.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
3623,3624,600.txt,1,0,,,,the already depressed expression of sipC in the sirA mutant further ( 36-and 8-fold respectively ) _ suggesting a SirA-independent means of control for these genes
3624,3625,1394.txt,1,0,,,,dps transcription is regulated in a sigma S-and IHF-dependent manner
3625,3626,98.txt,1,0,,,,"In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .
"
3626,3627,98.txt,2,0,,,,"In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .
"
3627,3628,98.txt,3,0,,,,"In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .
"
3628,3629,98.txt,4,0,,,,"In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .
"
3629,3630,98.txt,5,0,,,,"PhoP binds to the upstream region of the macA gene , resulting in regulation of macAB .
"
3630,3631,98.txt,6,0,,,,"PhoP binds to the upstream region of the macA gene , resulting in regulation of macAB ."
3631,3632,166.txt,1,0,,,,"OmpR-P also binds to the ssrB region
"
3632,3633,166.txt,2,0,,,,"The effect of OmpR appears to be direct , based on our observation that OmpR-P binds to the intergenic region between ssrB .
"
3633,3634,166.txt,3,0,,,,"Altogether , our data indicate that OmpR-P binds around the intergenic region between ssrB .
"
3634,3635,166.txt,4,0,,,,"In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrB genes ."
3635,3636,1169.txt,1,0,,,,The Mlc global regulator has been shown to downregulate an hilE promoter .
3636,3637,1141.txt,1,0,,,,Most of these genes were induced at a higher level in the RpoS-mutant background with sseB .
3637,3638,1627.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
3638,3639,1633.txt,1,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
3639,3640,1633.txt,2,0,,,,"Despite synthesizing the PhoP protein constitutively , there was no occupancy of PhoP-activated promoters ( Fig. 3C ) or transcription of PhoP-activated genes ( Fig. 3D ) in the strain with the -- 35 sequence in the phoPQ promoter growing under repressing conditions .
"
3640,3641,1633.txt,3,0,,,,"a regulated promoter is activated by the PhoP protein transcription in one with the wild-type phoPQ promoter -LSB- is , harboring the PhoP box is responsible for transcriptional autoregulation
"
3641,3642,1633.txt,4,0,,,,"a regulated promoter is activated by the PhoP protein transcription in one with the wild-type phoPQ promoter -LSB- is , harboring the PhoP box is responsible for transcriptional autoregulation"
3642,3643,1155.txt,1,0,,,,"BaeR-P binds to the mdtA promoter region Electrophoretic mobility-shift assays were performed with phosphorylated BaeR-6 a 600 bp DNA fragment of the upstream region of mdtA as described in methods .
"
3643,3644,1155.txt,2,0,,,,BaeR-P binds to the mdtA promoter region Electrophoretic mobility-shift assays were performed with phosphorylated BaeR-6 # His as described in methods .
3644,3645,1800.txt,1,0,,,,"32 6 Although the divergently transcribed cas3 genes share a 5 cents intergenic region , we found that LeuO only control cse1 expression .
"
3645,3646,1800.txt,2,0,,,,"32 6 Although the divergently transcribed cse1 genes share a 5 cents intergenic region , we found that LeuO only control cse1 expression ."
3646,3647,1814.txt,1,0,,,,"Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we postulate that the RstA/RstB systems might coregulate iraP to control RpoS ."
3647,3648,358.txt,1,0,,,,"Our results indicate that only the PmrA regulator binds to the wzz promoter , inducing fepE gene expression ."
3648,3649,416.txt,1,0,,,,"As previously shown , Crl production was increased by the rpoS mutation by a mechanism ."
3649,3650,1182.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"SirA-dependent regulation of serovar Typhimurium sopB .
"
3650,3651,1182.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"SirA-dependent regulation of serovar Typhimurium sopB .
"
3651,3652,1182.txt,3,0,,,,"SirA-dependent regulation of sopB chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar .
"
3652,3653,1182.txt,4,0,,,,A screen revealed that SirA regulates not only expression of SPI1-encoded genes but also the transcription of SPI5-encoded sopB .
3653,3654,370.txt,1,0,,,,"our previous study in which SlyA enhanced PhoP binding to the promoter of phoP , lacZ expression
"
3654,3655,370.txt,2,1,synthetic construct,primer,synthetic construct,"Our results from primer-extension demonstrate that transcriptions of the identified loci are activated by SlyA because the mRNA level of transcripts is reduced significantly in the phoP mutants grown in low-Mg2 conditions -LRB- Fig .
"
3655,3656,370.txt,3,0,,,,SlyA can also activate phoP genes
3656,3657,1828.txt,1,0,,,,"The PhoP/PhoQ regulatory system has been shown to regulate the expression of a variety including pagC .
"
3657,3658,1828.txt,2,0,,,,"The PhoP/PhoQ regulatory system has been shown to regulate the expression of pagC .
"
3658,3659,1828.txt,3,0,,,,"Because PhoP/PhoQ regulates more than 40 genes , additional PhoP/PhoQ-activated genes , including pmrD and pagD , were examined to determine if bile specifically regulated pagC , or if it has a general effect on PhoP/PhoQ-regulated genes .
"
3659,3660,1828.txt,4,0,,,,"The results establish that other PhoP/PhoQ-regulated genes were unaffected by the presence of bile ( as exemplified by pagD and pmrD , Fig. 2 ) , suggesting that pagC is specifically affected by bile .
"
3660,3661,1828.txt,5,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus musculus,S. Typhimurium;Typhimurium;mouse,Mus musculus;Salmonella enterica subsp. enterica serovar Typhimurium,"pagC was originally identified as a PhoP/PhoQ-regulated gene required for S. Typhimurium virulence in a mouse model and for its survival within macrophages ( Miller et al. , 1989 ) .
"
3661,3662,1828.txt,6,0,,,,"pagC is a macrophage-inducible promoter is controlled by the PhoP/PhoQ two-component regulatory system .
"
3662,3663,1828.txt,7,0,,,,"recombinants express these genes under the control of the macrophage-inducible pagC promoter , controlled by the PhoP/PhoQ two-component regulatory system has been found to be an effective in-vivo-inducible promoter when compared to others
"
3663,3664,1828.txt,8,0,,,,"recombinants express these genes under the control of the macrophage-inducible pagC promoter , controlled by the PhoP/PhoQ two-component regulatory system has been found to be an effective in-vivo-inducible promoter when compared to others
"
3664,3665,1828.txt,9,0,,,,The PhoP-activated gene pagC _ regulated by the PhoP/PhoQ system
3665,3666,364.txt,1,0,,,,"The genes slrP and dsbA are also induced by HilC independently of InvF .
"
3666,3667,364.txt,2,0,,,,The genes slrP and dsbA are also induced by HilC independently of both HilA .
3667,3668,1196.txt,1,0,,,,"mutually repressing repressors wherein FliZ repression of ydiV is predicted to increase flagellar class II gene expression because YdiV inhibits binding of the FlhD4C2 complex to DNA
"
3668,3669,1196.txt,2,0,,,,mutually repressing repressors wherein FliZ repression of ydiV is predicted to increase flagellar class II gene expression because YdiV inhibits binding of the FlhD4C2 complex to DNA
3669,3670,402.txt,1,0,,,,"We show that HilC can directly bind invF .
"
3670,3671,402.txt,2,0,,,,"Overproduction of HilC activate the expression of a chromosomal invF-lacZ fusion in the absence of hilA In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilA , respectively , under the control of the arabinose-inducible PBAD promoter .
"
3671,3672,402.txt,3,0,,,,"Overproduction of HilC activate the expression of a chromosomal invF-lacZ fusion in the absence of hilA In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilC , respectively , under the control of the arabinose-inducible PBAD promoter .
"
3672,3673,402.txt,4,0,,,,"Overproduction of HilC activate the expression of a chromosomal invF-lacZ fusion in the absence of hilA In order to study the activation of invF by HilC , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilD , respectively , under the control of the arabinose-inducible PBAD promoter .
"
3673,3674,402.txt,5,0,,,,"These results suggest that HilC might directly activate invF expression by binding to sequences upstream of invF .
"
3674,3675,402.txt,6,0,,,,"HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
3675,3676,402.txt,7,0,,,,"HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
3676,3677,402.txt,8,0,,,,"In addition to binding upstream of invF , HilC also bind to sites upstream of hilC .
"
3677,3678,402.txt,9,0,,,,"In addition to binding upstream of invF , HilC also bind within S. Akbar , unpublished results .
"
3678,3679,402.txt,10,0,,,,"In addition to binding upstream of invF , HilC also bind within the prgH-hilD intergenic region .
"
3679,3680,402.txt,11,0,,,,"These gel shift assays indicate that HilC each bind sequences downstream of the HilD-and HilC-dependent invF promoter .
"
3680,3681,402.txt,12,0,,,,"These gel shift assays indicate that HilC each bind sequences upstream of the HilD-and HilC-dependent invF promoter .
"
3681,3682,402.txt,13,0,,,,Dam-dependent regulation of invF was still observed in HilC
3682,3683,365.txt,1,1,unidentified,unknown,unidentified,"In the presence of an unknown environmental condition , HilC may activate invF expression .
"
3683,3684,365.txt,2,0,,,,"If a condition exists in which hilA is repressed while invF expression is induced through HilC , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?
"
3684,3685,365.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3685,3686,365.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3686,3687,365.txt,5,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3687,3688,365.txt,6,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3688,3689,365.txt,7,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3689,3690,365.txt,8,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3690,3691,365.txt,9,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3691,3692,365.txt,10,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3692,3693,365.txt,11,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.A.Lee Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3693,3694,365.txt,12,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3694,3695,365.txt,13,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3695,3696,365.txt,14,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3696,3697,365.txt,15,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3697,3698,365.txt,16,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3698,3699,365.txt,17,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3699,3700,365.txt,18,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3700,3701,365.txt,19,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3701,3702,365.txt,20,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , C.P.Lostroh Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3702,3703,365.txt,21,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3703,3704,365.txt,22,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3704,3705,365.txt,23,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- HilC , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3705,3706,365.txt,24,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3706,3707,365.txt,25,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3707,3708,365.txt,26,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- HilD , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3708,3709,365.txt,27,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , and Catherine A. Lee * Department of Microbiology and Molecular Genetics , Harvard Medical School , 200 Longwood Avenue , Boston , MA 02115 .
"
3709,3710,365.txt,28,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , , ‡ C. Phoebe Lostr .
"
3710,3711,365.txt,29,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC directly activate invF expressionS.Akbar , L.M.Schechter Molecular Microbiology 47 , 715 -- 728 AraC/XylS family members , directly activate virulence gene expression independently of HilA in Salmonella typhimurium Samina Akbar , † Lisa M. Schecht .
"
3711,3712,365.txt,30,0,,,,"Our studies show that HilC activate transcription of invF from a promoter .
"
3712,3713,365.txt,31,0,,,,"We show that HilC can directly activate invF .
"
3713,3714,365.txt,32,0,,,,"We propose that HilC can independently activate invF expression .
"
3714,3715,365.txt,33,0,,,,"HilC do not activate invF expression from the HilA-dependent invF promoter Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .
"
3715,3716,365.txt,34,2,unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus,plasmid;pVV;pVV,Prairie vole hantavirus;unidentified plasmid,"These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilC to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD-and HilC-dependent +1 of invF .
"
3716,3717,365.txt,35,0,,,,"It is possible that HilC , activates invF expression from a second promoter .
"
3717,3718,365.txt,36,1,Escherichia coli,E. coli,Escherichia coli,"In order to address whether additional S. typhimuriumspecific genes are required for HilC to activate invF , we examined both pSA7 reporters in E. coli TOP-10 cells .
"
3718,3719,365.txt,37,2,Prairie vole hantavirus;Escherichia coli,pVV;E. coli,Escherichia coli;Prairie vole hantavirus,"In order to address whether additional S. typhimuriumspecific genes are required for HilC to activate invF , we examined both pVV448 reporters in E. coli TOP-10 cells .
"
3719,3720,365.txt,38,1,Escherichia coli,E. coli,Escherichia coli,"We found that HilC induce invF expression from pSA7 in E. coli , comparable to that .
"
3720,3721,365.txt,39,1,Prairie vole hantavirus,pVV,Prairie vole hantavirus,"We also found that HilC , activates invF expression from pVV448 , also comparable to that .
"
3721,3722,365.txt,40,0,,,,"These results suggest that HilC might directly activate invF expression by binding to sequences upstream of invF .
"
3722,3723,365.txt,41,0,,,,"These results suggest that HilC might directly activate invF expression by binding to sequences upstream of invF .
"
3723,3724,365.txt,42,0,,,,"HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
3724,3725,365.txt,43,0,,,,"HilC bind to the invF promoter fragment in-vitro To examine whether HilC might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
3725,3726,365.txt,44,0,,,,"HilC directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
3726,3727,365.txt,45,0,,,,"HilC directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
3727,3728,365.txt,46,0,,,,"HilC directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
3728,3729,365.txt,47,0,,,,"HilC directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
3729,3730,365.txt,48,0,,,,"HilC directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
3730,3731,365.txt,49,0,,,,"HilC directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
3731,3732,365.txt,50,0,,,,"Discussion HilD directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
3732,3733,365.txt,51,0,,,,"Discussion HilD directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
3733,3734,365.txt,52,0,,,,"HilC appear to activate transcription of invF from a HilD/C-dependent start site .
"
3734,3735,365.txt,53,0,,,,"Our studies also suggest that the downstream binding site is required for HilC to activate invF .
"
3735,3736,365.txt,54,0,,,,"In fact , there is evidence that HilC directly activate invF expression 723 can be secreted independently of SPI1 .
"
3736,3737,365.txt,55,0,,,,"HilC are each capable of partially activating invF
"
3737,3738,365.txt,56,0,,,,"HilC activate transcription from the p promoters in an apparently redundant invF sicA manner .
"
3738,3739,365.txt,57,0,,,,"HilC activate transcription from the p promoters in an apparently redundant invF sicA manner .
"
3739,3740,365.txt,58,0,,,,"In addition , HilC directly activate invF in non-HilA dependent manner .
"
3740,3741,365.txt,59,0,,,,"HilC can activate expression of the invF and sicA/sip transcriptional units independently of HilA .
"
3741,3742,365.txt,60,0,,,,"HilC , activate directly the expression of the invF operon , independently of HilA .
"
3742,3743,365.txt,61,0,,,,HilC all positively regulate invF .
3743,3744,1829.txt,1,0,,,,"Consequently , we conclude that besides upregulation of RpoS , other Hfq-dependent factor are required to restore rdar morphotype expression in the hfq mutant of UMR1 ."
3744,3745,403.txt,1,0,,,,"Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB-medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) ."
3745,3746,1197.txt,1,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,Salmonella;Typhi;plasmid;Salmonella;Typhi;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene ."
3746,3747,1183.txt,1,0,,,,"Interestingly , the results indicate that H-NS is a positive regulator of tpx ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS ."
3747,3748,417.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"mcpC , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI4-encoded genes , and repressed by SsrB .
"
3748,3749,417.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"mcpC , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-associated genes , and repressed by SsrB .
"
3749,3750,417.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"mcpC , are predicted to encode Salmo-nella-specific methyl-accepting chemotaxis proteins and display similar expression patterns to the SPI1-encoded genes , and repressed by SsrB ."
3750,3751,371.txt,1,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3751,3752,371.txt,2,0,,,,"Miller , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3752,3753,371.txt,3,0,,,,"J.S. , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3753,3754,371.txt,4,0,,,,"Gunn , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3754,3755,371.txt,5,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3755,3756,371.txt,6,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3756,3757,371.txt,7,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3757,3758,371.txt,8,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3758,3759,371.txt,9,0,,,,"PhoP-PhoQ activates transcription o pmrAB .
"
3759,3760,371.txt,10,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3760,3761,371.txt,11,0,,,,"Miller , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3761,3762,371.txt,12,0,,,,"J.S. , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3762,3763,371.txt,13,0,,,,"Gunn , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3763,3764,371.txt,14,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3764,3765,371.txt,15,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3765,3766,371.txt,16,0,,,,"Gunn JS , Miller SI : PhoP-PhoQ activates transcription of pmrAB .
"
3766,3767,371.txt,17,0,,,,"Miller , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3767,3768,371.txt,18,0,,,,"J.S. , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3768,3769,371.txt,19,0,,,,"Gunn , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3769,3770,371.txt,20,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3770,3771,371.txt,21,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3771,3772,371.txt,22,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3772,3773,371.txt,23,0,,,,"Miller , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3773,3774,371.txt,24,0,,,,"J.S. , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3774,3775,371.txt,25,0,,,,"Gunn , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3775,3776,371.txt,26,0,,,,"Miller , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3776,3777,371.txt,27,0,,,,"J.S. , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3777,3778,371.txt,28,0,,,,"Gunn , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3778,3779,371.txt,29,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3779,3780,371.txt,30,0,,,,"Gunn , J. , Miller , S. PhoP-PhoQ activates transcription of pmrAB .
"
3780,3781,371.txt,31,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3781,3782,371.txt,32,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3782,3783,371.txt,33,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3783,3784,371.txt,34,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3784,3785,371.txt,35,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3785,3786,371.txt,36,0,,,,"Gunn JS , Miller SI PhoP-PhoQ activates transcription of pmrAB .
"
3786,3787,371.txt,37,0,,,,"Miller , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3787,3788,371.txt,38,0,,,,"J.S. , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3788,3789,371.txt,39,0,,,,"Gunn , S.I. PhoP-PhoQ activates transcription of pmrAB .
"
3789,3790,371.txt,40,0,,,,"PhoP-PhoQ activates transcription of pmrAB .
"
3790,3791,371.txt,41,0,,,,PhoP-PhoQ activates transcription of pmrAB .
3791,3792,359.txt,1,0,,,,"However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with Fig. 3D .
"
3792,3793,359.txt,2,0,,,,"However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / also with the double substitution pKK8/ompR -134 -1 / E .
"
3793,3794,359.txt,3,0,,,,"However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / Fig. 3D -134 -1 / E .
"
3794,3795,359.txt,4,0,,,,"However , the AAA nucleotides , located at 116 to 114 bp upstream of the translational start-site of the OmpR regulatory protein , have a fundamental role in ompR activation , since a clear decrease of transcriptional expression was observed with substitution pKK8/ompR -134 -1 / D -134 -1 / E .
"
3795,3796,359.txt,5,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A
"
3796,3797,359.txt,6,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at this locus
"
3797,3798,359.txt,7,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A
"
3798,3799,359.txt,8,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at this locus
"
3799,3800,359.txt,9,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A
"
3800,3801,359.txt,10,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at this locus
"
3801,3802,359.txt,11,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A
"
3802,3803,359.txt,12,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at this locus
"
3803,3804,359.txt,13,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A
"
3804,3805,359.txt,14,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at this locus
"
3805,3806,359.txt,15,0,,,,"the ompR mutant _ suggesting that OmpR functions as a repressor at Fig 5A
"
3806,3807,359.txt,16,0,,,,the ompR mutant _ suggesting that OmpR functions as a repressor at this locus
3807,3808,1815.txt,1,0,,,,"Additionally , since it has been suggested that insertions in pduF may exert polarity onto the downstream pocR gene , pduF mutants may also have decreased amounts of PocR protein ."
3808,3809,1801.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Fis also stimulates transcription of E. coli topA , when the bacteria experience oxidative-stress , something , although the severity of the oxidative-stress is unclear from an examination of the responses of classic oxidative-stress response genes .
"
3809,3810,1801.txt,2,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"Transcription of E. coli topA is driven by the interplay of at least four transcription start sites , allowing FIS to be both an activator of E. coli topA expression .
"
3810,3811,1801.txt,3,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS 
"
3811,3812,1801.txt,4,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS 
"
3812,3813,1801.txt,5,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS 
"
3813,3814,1801.txt,6,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS 
"
3814,3815,1801.txt,7,2,Escherichia coli;Salmonella;Salmonella,E. coli;S. enterica;enterica,Escherichia coli;Salmonella,"E. coli topA was upregulated in the absence of FIS in both exponential-growth and stationary-phase , whereas S. enterica topA expression was elevated in stationary-phase relative to wild-type cells .
"
3815,3816,1801.txt,8,2,Escherichia coli;Salmonella;Salmonella,E. coli;S. enterica;enterica,Escherichia coli;Salmonella,"E. coli topA was upregulated in the absence of FIS in both exponential-growth and stationary-phase , whereas S. enterica topA expression was unaffected in Dfis cells during exponential-growth .
"
3816,3817,1801.txt,9,2,unidentified plasmid;Escherichia coli;unidentified plasmid,plasmid;E. coli;plasmid,Escherichia coli;unidentified plasmid,"Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare 4A -RRB- .
"
3817,3818,1801.txt,10,2,unidentified plasmid;Escherichia coli;unidentified plasmid,plasmid;E. coli;plasmid,Escherichia coli;unidentified plasmid,"Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare Figs 3A -RRB- ."
3818,3819,1632.txt,1,0,,,,"Pon , C.L. Antagonistic H-NS proteins in the transcriptional control of hns expression .
"
3819,3820,1632.txt,2,0,,,,"C.O. H-NS proteins in the transcriptional control of hns expression .
"
3820,3821,1632.txt,3,0,,,,"Gualerzi H-NS proteins in the transcriptional control of hns expression .
"
3821,3822,1632.txt,4,0,,,,"A. H-NS proteins in the transcriptional control of hns expression .
"
3822,3823,1632.txt,5,0,,,,"La Teana H-NS proteins in the transcriptional control of hns expression .
"
3823,3824,1632.txt,6,0,,,,"A. H-NS proteins in the transcriptional control of hns expression .
"
3824,3825,1632.txt,7,0,,,,"Brandi H-NS proteins in the transcriptional control of hns expression .
"
3825,3826,1632.txt,8,0,,,,"M. H-NS proteins in the transcriptional control of hns expression .
"
3826,3827,1632.txt,9,0,,,,"Falconi H-NS proteins in the transcriptional control of hns expression .
"
3827,3828,1632.txt,10,0,,,,"Antagonistic involvement of H-NS proteins in the transcriptional control of hns expression .
"
3828,3829,1632.txt,11,0,,,,"Interestingly , the results indicate that H-NS is a positive regulator of STY1978 ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS .
"
3829,3830,1632.txt,12,0,,,,"As suggested by our previous study , establishing the Mg2-responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level remains high in high-Mg2 conditions in the hns mutant .
"
3830,3831,1632.txt,13,0,,,,"As suggested by our previous study , establishing the Mg2-responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level remains high in PhoP-repressing conditions in the hns mutant .
"
3831,3832,1632.txt,14,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Consistent with the pleiotropic effects of hns mutations were regulated by H-NS in S. Typhimurium .
"
3832,3833,1632.txt,15,0,,,,"SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sseJ loci .
"
3833,3834,1632.txt,16,0,,,,"SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including sifB .
"
3834,3835,1632.txt,17,0,,,,"SPI-2 Effector Genes Are Repressed by hns -- Previous array studies revealed preferential binding of H-NS to horizontally acquired AT-rich DNA , including the sifA .
"
3835,3836,1632.txt,18,0,,,,"Nevertheless , when F7 was divided into F9 , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3836,3837,1632.txt,19,0,,,,"Nevertheless , when F7 was divided into F9 , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3837,3838,1632.txt,20,0,,,,"Nevertheless , when F7 was divided into F8 , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3838,3839,1632.txt,21,0,,,,"Nevertheless , when F7 was divided into F8 , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3839,3840,1632.txt,22,0,,,,"Nevertheless , when F7 was divided into two smaller fragments , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3840,3841,1632.txt,23,0,,,,"Nevertheless , when F7 was divided into two smaller fragments , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F9 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3841,3842,1632.txt,24,0,,,,"Nevertheless , when F7 was divided into two smaller fragments , containing the 5 3 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3842,3843,1632.txt,25,0,,,,"Nevertheless , when F7 was divided into two smaller fragments , containing the 5 = regions of F7 , respectively , no H-NS affinity for both F8 was detected , suggesting nonspecific binding of H-NS to F7 in accordance with the null effect of the hns mutation on dsbL expression .
"
3843,3844,1632.txt,26,1,unidentified plasmid,plasmid,unidentified plasmid,Effect of low-temperature on the regulation of the plasmid-encoded hns gene R27 encode a protein related to the global modulator H-NS .
3844,3845,1154.txt,1,0,,,,"These results demonstrate that the fimZ gene encodes a positive regulator for fimA , while FimW is a repressor for fimA ."
3845,3846,1140.txt,1,0,,,,"Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of motility , at least during acid adaptation .
"
3846,3847,1140.txt,2,0,,,,"Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of fla-gellation , at least during acid adaptation ."
3847,3848,1626.txt,1,0,,,,"SoxS _ regulated , including soxS itself"
3848,3849,1168.txt,1,0,,,,"it has been suggested that ytfE becomes activated by NarL upon exposure to nitrite
"
3849,3850,1168.txt,2,0,,,,it has been suggested that ytfE becomes activated by NarL upon exposure to nitrate
3850,3851,99.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .
"
3851,3852,99.txt,2,0,,,,"NsrR regulates expression of not only hmp .
"
3852,3853,99.txt,3,0,,,,"A novel NsrR-regulated gene designated STM1808 has been identified , along with hmp , hcp-hcr , yeaR-yoaG , ygbA and ytfE .
"
3853,3854,99.txt,4,1,Salmonella,Salmonella,Salmonella,"Collectively , these findings demonstrate that NsrR-regulated genes in addition to hmp are important for NO · detoxification , nitrosative-stress resistance and Salmonella virulence .
"
3854,3855,99.txt,5,0,,,,"In addition , double mutant strains lacking both hmp and other NsrR-regulated genes were constructed to determine the contribution to nitrosative-stress resistance in the absence of NO · detoxification by Hmp .
"
3855,3856,99.txt,6,1,Salmonella,Salmonella,Salmonella,"These data confirm previous findings with regard to hmp , and additionally demonstrate that the NsrR-regulated ytfE and STM1808 genes contribute to Salmonella virulence .
"
3856,3857,99.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The NsrR-regulated hmp gene encodes a flavohemoglobin that is capable of detoxifying NO · under both aerobic and anaerobic conditions and is required for S. Typhimurium virulence ( Bang et al. , 2006 ; Crawford and Goldberg , 1998 ; Stevanin et al. , 2002 ) .
"
3857,3858,99.txt,8,1,Mus sp.,mice,Mus sp.,"We have identified a novel NsrR-regulated gene designated STM1808 , and demonstrated a role for specific NsrR-regulated genes in promoting growth during nitrosative-stress in-vitro ( hmp , STM1808 , ygbA and hcp ) and during systemic infection of mice in-vivo ( hmp , STM1808 , ytfE ) .
"
3858,3859,99.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium the principal regulator of hmp expression during nitrosative-stress is the transcriptional repressor NsrR .
"
3859,3860,99.txt,10,0,,,,"NsrR-dependent expression of hmp was significantly greater at DEA/NO concentrations as low as 1 μM in comparison to genes regulated by Sox .
"
3860,3861,99.txt,11,0,,,,"NsrR-dependent expression of hmp was significantly greater at DEA/NO concentrations as low as 1 μM in comparison to genes regulated by Fu .
"
3861,3862,99.txt,12,0,,,,"NsrR-dependent expression of hmp was significantly greater at DEA/NO concentrations as low as 1 μM in comparison to genes regulated by Nor .
"
3862,3863,99.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Microarray analysis of the S. Typhimurium NsrR regulon In previous studies , NsrR was identified as the major regulator of hmp transcription in S. Typhimurium ."
3863,3864,1395.txt,1,0,,,,"( B ) Alignment of the promoter region of slrP and six PhoP-activated genes with a similar architecture .
"
3864,3865,1395.txt,2,0,,,,"To study if PhoP was a direct activator of slrP transcription , first we analyzed the promoter region of this gene ."
3865,3866,601.txt,1,1,Escherichia coli,E. coli,Escherichia coli,A very recent report has shown that DsbA acts as a periplasmic oxidant and that deletion of dsbA leads to increased transcription of PhoP-regulated genes in E. coli .
3866,3867,167.txt,1,0,,,,"On the other hand , the FlhD2C2 activator complex at the top of the flagellar regulon hierarchy downregulates STM1344 expression ."
3867,3868,173.txt,1,0,,,,"The regulator of aromatic amino-acid metabolism , TyrR , controls the tyrosine requirement for hyaB expression ."
3868,3869,615.txt,1,0,,,,"In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .
"
3869,3870,615.txt,2,0,,,,"In environments , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .
"
3870,3871,615.txt,3,0,,,,"In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of expression of somA .
"
3871,3872,615.txt,4,0,,,,"In low Mg2 , PhoP binds to the intergenic region between the macA , resulting in downregulation of macAB of somA .
"
3872,3873,615.txt,5,0,,,,"macA transcript levels are elevated in 12 h postinfection , consistent with potential rapid inactivation of PhoP .
"
3873,3874,615.txt,6,0,,,,"macA transcript levels are elevated in 8 h postinfection , consistent with potential rapid inactivation of PhoP .
"
3874,3875,615.txt,7,0,,,,"macA transcript levels are elevated in 4 h postinfection , consistent with potential rapid inactivation of PhoP ."
3875,3876,1381.txt,1,0,,,,"B A ∆ DnaK ∆ ∆ ClpP 400 400 300 300 200 200 100 100 ore , the marked decrease of transcription from the A an pro might be due to excessive degradation of the FlhD2C2 complex by the ClpXP protease if this accumulates in the ∆ dnaK cells .
"
3876,3877,1381.txt,2,0,,,,"B A ∆ DnaK ∆ ∆ ClpP 400 400 300 300 200 200 100 100 ore , the marked decrease of transcription from the m th pro might be due to excessive degradation of the FlhD2C2 complex by the ClpXP protease if this accumulates in the ∆ dnaK cells .
"
3877,3878,1381.txt,3,0,,,,"B A DnaK ∆ ClpP 400 400 300 300 200 200 100 100 ore , the marked decrease of transcription from the A an pro might be due to excessive degradation of the FlhD2C2 complex by the ClpXP protease if this accumulates in the ∆ dnaK cells .
"
3878,3879,1381.txt,4,0,,,,"B A DnaK ∆ ClpP 400 400 300 300 200 200 100 100 ore , the marked decrease of transcription from the m th pro might be due to excessive degradation of the FlhD2C2 complex by the ClpXP protease if this accumulates in the ∆ dnaK cells .
"
3879,3880,1381.txt,5,0,,,,"B A 500 500 DnaK ∆ ClpP 400 400 300 300 200 200 100 100 ore , the marked decrease of transcription from the A an pro might be due to excessive degradation of the FlhD2C2 complex by the ClpXP protease if this accumulates in the ∆ dnaK cells .
"
3880,3881,1381.txt,6,0,,,,"B A 500 500 DnaK ∆ ClpP 400 400 300 300 200 200 100 100 ore , the marked decrease of transcription from the m th pro might be due to excessive degradation of the FlhD2C2 complex by the ClpXP protease if this accumulates in the ∆ dnaK cells ."
3881,3882,629.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .
"
3882,3883,629.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .
"
3883,3884,629.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression .
"
3884,3885,629.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating soxS expression ."
3885,3886,1356.txt,1,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimu,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , STM4118 may be a PmrA-activated gene responsible for modification of LPS core with pEtN in S. enterica serovar Typhimu-rium .
"
3886,3887,1356.txt,2,0,,,,"Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .
"
3887,3888,1356.txt,3,0,,,,"Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays ."
3888,3889,1430.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Rentschler AE , Lovrich SD , Fitton R , Enos-Berlage J , Schwan WR OmpR regulation of the uropathogenic Escherichia coli fimB gene in an acidic/high osmolality environment ."
3889,3890,8.txt,1,0,,,,"HilA , regulates the expression of sinR ."
3890,3891,2139.txt,1,0,,,,"Upon phosphoryl transfer , the response regulator UhpA -LRB- presumably phosphorylated on the conserved Asp-54 -RRB- shows enhanced affinity for the uhpT promoter , initiates uhpT transcription ."
3891,3892,1424.txt,1,0,,,,CsgDD59N-His6 bound with affinities comparable to wildtype CsgD to both the csgBA .
3892,3893,1342.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
3893,3894,826.txt,1,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones are , therefore , introduced in this list with its function if known .
"
3894,3895,826.txt,2,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones are , therefore , introduced in this list with their corresponding gene if known .
"
3895,3896,826.txt,3,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones show no expression in spleen , therefore , introduced in this list with its function if known .
"
3896,3897,826.txt,4,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones show no expression in spleen , therefore , introduced in this list with their corresponding gene if known .
"
3897,3898,826.txt,5,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones show medium expression levels in tumor , therefore , introduced in this list with its function if known .
"
3898,3899,826.txt,6,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones show medium expression levels in tumor , therefore , introduced in this list with their corresponding gene if known .
"
3899,3900,826.txt,7,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones show high expression levels in tumor , therefore , introduced in this list with its function if known .
"
3900,3901,826.txt,8,1,Escherichia coli,E.coli,Escherichia coli,"Gene Function Fold induction by hypoxia 59.7 27.4 Putative cytoplasmic protein sn-glycerol-3-phosphate transporter ydiH glpT bcsG mltD mdh mtfA frdA pfkA pflE nirB glpA ybaL 4 48 0.3 1.1 1.9 15.4 1368.1 14.6 150.1 65.3 886.6 0.4 Membrane protein ; endoglucanase Membrane-bound lytic murein transglycosylase D Malate dehydrogenase Mlc titration factor-A Fumarate reductase flavoprotein subunit Similar to E.coli 6-phosphofructokinase I Putative pyruvate formate lyase : : proton antiport protein 92-134-154-156 172-185-212-271 301 310 Clones show high expression levels in tumor , therefore , introduced in this list with their corresponding gene if known ."
3901,3902,66.txt,1,1,unidentified,not shown,unidentified,"To determine whether LeuO is the casA activator in N-minimal-medium , the pKK-375 fusion was introduced into the IMSS-1 leuO strain : we found that LeuO does not induce casA expression in N-minimal-medium , since the activity values in the leuO-deficient strain were the same as those in the wild-type strain -LRB- data not shown -RRB- ."
3902,3903,2105.txt,1,0,,,,phoN are known to be regulated by SlyA
3903,3904,198.txt,1,0,,,,"While initially defined as an activator of the catalase gene katE , RpoS seems to participate in the ATRs"
3904,3905,1418.txt,1,0,,,,"It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .
"
3905,3906,1418.txt,2,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment .
"
3906,3907,1418.txt,3,1,unidentified,unidentified,unidentified,"Moreover as rck is also regulated by an unidentified SdiA-independent system at 42 , it is conceivable that Rck invasion mechanism is not restricted to the gastrointestinal tract .
"
3907,3908,1418.txt,4,1,unidentified,unidentified,unidentified,"Moreover as rck is also regulated by an unidentified SdiA-independent system at 37 ° , it is conceivable that Rck invasion mechanism is not restricted to the gastrointestinal tract .
"
3908,3909,1418.txt,5,1,Salmonella,Salmonella,Salmonella,"rck operons are controlled by the Salmonella N-Acyl homoserine lactone receptor SdiA
"
3909,3910,1418.txt,6,1,Salmonella,Salmonella,Salmonella,"rck operons are controlled by the Salmonella N-Acyl homoserine lactone receptor SdiA
"
3910,3911,1418.txt,7,0,,,,"To decipher the regulation of rck by SdiA , we first confirmed the operon organization of the pefI-srgC locus .
"
3911,3912,1418.txt,8,0,,,,"These results demonstrate that the transcriptional regulation of rck by SdiA previously observed also modulates Rck protein expression .
"
3912,3913,1418.txt,9,0,,,,"We thus decided to further characterize the mechanism of transcriptional regulation of rck by SdiA .
"
3913,3914,1418.txt,10,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella,S. Typhimurium;Typhimurium;plasmid;Enteritidis,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Different rck regulation by SdiA between S. Typhimurium is due to differences in the promoter region of the pefI-srgC operon As mentioned in the Introduction part , the pefI-srgC operon is present in its complete form only on the virulence plasmid of Enteritidis .
"
3914,3915,1418.txt,11,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;plasmid;Typhimu,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"Different rck regulation by SdiA between S. Typhimurium is due to differences in the promoter region of the pefI-srgC operon As mentioned in the Introduction part , the pefI-srgC operon is present in its complete form only on the virulence plasmid of the two broad-host-range serotypes Typhimu-rium .
"
3915,3916,1418.txt,12,2,Salmonella;unidentified plasmid;Salmonella,Enteritidis;plasmid;Enteritidis,Salmonella;unidentified plasmid,"Different rck regulation by SdiA between S. Enteritidis is due to differences in the promoter region of the pefI-srgC operon As mentioned in the Introduction part , the pefI-srgC operon is present in its complete form only on the virulence plasmid of Enteritidis .
"
3916,3917,1418.txt,13,3,Salmonella;unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,Enteritidis;plasmid;Typhimu,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;unidentified plasmid,"Different rck regulation by SdiA between S. Enteritidis is due to differences in the promoter region of the pefI-srgC operon As mentioned in the Introduction part , the pefI-srgC operon is present in its complete form only on the virulence plasmid of the two broad-host-range serotypes Typhimu-rium .
"
3917,3918,1418.txt,14,1,Salmonella,Enteritidis,Salmonella,"The PefIP2 promoters are absent in S. Enteritidis , suggesting a mechanism of regulation of rck expression by SdiA different between these two sero-types .
"
3918,3919,1418.txt,15,1,Salmonella,Enteritidis,Salmonella,"The PefIP1 promoters are absent in S. Enteritidis , suggesting a mechanism of regulation of rck expression by SdiA different between these two sero-types .
"
3919,3920,1418.txt,16,0,,,,"This result demonstrates that the regulation of rck expression by SdiA is different between these two serotypes .
"
3920,3921,1418.txt,17,0,,,,"H-NS negatively regulates Rck expression at 37 °C As our results were not supporting an involvement of SdiA in the transcriptional regulation of rck at low-temperature , we searched for another regulatory mechani .
"
3921,3922,1418.txt,18,0,,,,"In this study , we first confirmed that the transcriptional regulation of rck by SdiA resulted in an increase of Rck protein expression .
"
3922,3923,1418.txt,19,1,Salmonella,Salmonella,Salmonella,"Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 1 , 61 ) .
"
3923,3924,1418.txt,20,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"AI-1 Signaling in Salmonella Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 19 , 35 ) .
"
3924,3925,1418.txt,21,4,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Gardnerella vaginalis;unidentified plasmid,S. enterica;enterica;Typhimurium;ATCC 14018;plasmid,unidentified plasmid;Gardnerella vaginalis;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Abed et al. also showed that the promoter region of the rck operon , located on the S. enterica serovar Typhimurium ATCC 14018 plasmid , is regulated by the SdiA protein in the presence of AHL ."
3925,3926,2111.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
3926,3927,832.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
3927,3928,832.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
3928,3929,72.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In this study , we generated two S. Typhimurium aroA strains , genetically modified to express Stx2 AB , as orally delivered vectors for the control of HUS .
"
3929,3930,72.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In this study , we generated two S. Typhimurium aroA strains , genetically modified to express a nontoxic Stx2 derivative , as orally delivered vectors for the control of HUS ."
3930,3931,775.txt,1,0,,,,CsrA in turn affects an inhibition of the AvrA protein production of chromo-somal-encoded avrA
3931,3932,1587.txt,1,0,,,,"However , Lee et al. [ 21 ] demonstrated that the loss of pmrC and the pmrHFIJKLM operon ( also called the pbg operon ) resulted in PM resistance equal to that of a pmrA mutant strain , suggesting a limited role for PmrAB-regulated core modification in PM resistance ."
3932,3933,1593.txt,1,0,,,,"We did not expect regulation of bcsA by RpoS , as Zogaj et al. found in an RpoS-independent manner .
"
3933,3934,1593.txt,2,0,,,,"We did not expect regulation of bcsA by RpoS , as Zogaj et al. found that a bcsA-lacZ gene fusion was indeed partially induced in the stationary-phase ."
3934,3935,761.txt,1,0,,,,"Furthermore , STM2585 are regulated by SlyA ."
3935,3936,991.txt,1,0,,,,"In vitro characterization of transcriptional-fusions to virulence genes As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) ."
3936,3937,749.txt,1,0,,,,"The expression of rob is negatively regulated by MarA in response to sodium salicylate and paraquat , respectively .
"
3937,3938,749.txt,2,0,,,,"rob is negatively regulated by MarA The transcript levels of rob in the DsoxS strains were repressed after treatment with NaOCl as in the wild type .
"
3938,3939,749.txt,3,0,,,,"rob is negatively regulated by MarA The transcript levels of rob in the DmarA strains were repressed after treatment with NaOCl as in the wild type .
"
3939,3940,749.txt,4,0,,,,"MarA bind the promoter region of rob To determine whether the repression was due to a direct interaction between MarA with the promoter of rob , we performed a bioinformatic analysis .
"
3940,3941,749.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"other studies _ performed in E. coli where rob was shown to be negatively regulated by both MarA by a direct interaction with its promoter region
"
3941,3942,749.txt,6,0,,,,"EMSAs _ demonstrating that MarA bind to the promoter region of rob , indicating that the repression exerted by MarA is due to a direct interaction with the DNA"
3942,3943,985.txt,1,0,,,,"Similarly , CRP controls OmpD expression , however , different from S , CRP activates ompD transcription ."
3943,3944,1222.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Paratyphi,S. Typhimurium;Typhimurium;Paratyphi,Salmonella enterica subsp. enterica serovar Paratyphi;Salmonella enterica subsp. enterica serovar Typhimurium,"In contrast to S. Typhimurium and S. Paratyphi B dT , no pagK ( encoding a PhoPQ-activated protein ) was detected , but stkC was present ."
3944,3945,1544.txt,1,1,Salmonella,Salmonella,Salmonella,"A number of fusions to genes in known virulence regulons such as sodA ( manganese superoxide dismutase ) , pagJ ( a PhoPQ-activated gene ) and ssaE ( in Salmonella patho-genicity island 2 , SPI2 ) were identified ."
3945,3946,2059.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"It has been reported that StpA can negatively regulate expression of a reporter gene under the control of the hns promoter in E. coli ; although this could only be observed in the absence of hns , this raised the possibility that StpA-dependent gene expression could simply reflect changes in the level of H-NS ."
3946,3947,1550.txt,1,0,,,,"In the presence of Mn , MntR represses the expression of sitABCD , through direct binding of specific sites within the promoter regions of these genes ."
3947,3948,1236.txt,1,0,,,,"the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes include dinP
"
3948,3949,1236.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3949,3950,1236.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3950,3951,1236.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3951,3952,1236.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinP are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3952,3953,1236.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3953,3954,1236.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3954,3955,1236.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3955,3956,1236.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"dinB are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3956,3957,1236.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3957,3958,1236.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses much like umuDC , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3958,3959,1236.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is LexA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent .
"
3959,3960,1236.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"coli are two names for one gene , there is no dinB in S. typhimurium .8 ) The sbmC gene was originally identified by its ability to confer resistance to MccB17 at high copy number .9 MccB17 is a peptide antibiotic , possesses a quasicanonical LexA box , the expression of sbmC is RecA dependent .9 Thus , upregulation of dinP by all nine FQs is likely LexA dependent ."
3960,3961,952.txt,1,0,,,,"Five of the HilD/HilC/RtsA-bound regions associated with direct transcription activation of protein-coding genes outside SPI-1 overlap regions that are likely bound by H-NS ( HilD/HilC/RtsA binding sites associated with regulation of lpxR , , siiA , mcpC , and ssaG ) .
"
3961,3962,952.txt,2,0,,,,"HilD/HilC/RtsA binding sites _ associated with regulation of lpxR ,"
3962,3963,2071.txt,1,1,Salmonella,Salmonella,Salmonella,"Given the inhibitory effects of the DksA-dependent regulation of the transcription of amino-acid synthesis and transport , we tested whether the addition of amino-acids had any effect on the marked susceptibility of dksA mutant Salmonella strains to chemically generated NO .
"
3963,3964,2071.txt,2,0,,,,These results indicated that DksA is a positive regulator of genes suggested that invasion phenotypes of the dksA mutant were at least in part due to the lower expression of these genes in the absence of DksA .
3964,3965,1578.txt,1,0,,,,"Thus , it is possible that HilC can regulate the expression of ssrAB ."
3965,3966,2065.txt,1,0,,,,"Also , in Gram-positive bacteria , inactivation of rpoN or the s54-controlled PTS permeases has been reported to increase resistance to membrane-permeabilizing peptides of the subclass IIa bacteriocins ."
3966,3967,946.txt,1,0,,,,"Thus , SsrB regulates transcription of sifB by both relief of H-NS repression .
"
3967,3968,946.txt,2,0,,,,"Thus , SsrB regulates transcription of sifB by both direct activation of H-NS repression ."
3968,3969,211.txt,1,0,,,,"In 2 þ addition , the mgtCB operon is also regulated at the transcriptional level by a PhoPQ-independent mechanis .
"
3969,3970,211.txt,2,0,,,,"In 2 þ addition , the mgtCB operon is also regulated at the transcriptional level by a PhoPQ-independent mechanis .
"
3970,3971,211.txt,3,0,,,,Discussion Multiple regulatory pathways control the MgtC protein The mgtCB operon is known to be regulated at the transcriptional level by the PhoPQ two-component system in response to external Mg concentration .
3971,3972,1785.txt,1,0,,,,"AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA ."
3972,3973,577.txt,1,0,,,,H-NS/Hha negatively regulate the hilA genes under low-osmolarity conditions .
3973,3974,563.txt,1,0,,,,"Transcription of the hilA , invF is repressed by Lrp ."
3974,3975,2298.txt,1,0,,,,"Additive effect of STM1344 on virulence As STM1344 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
3975,3976,2298.txt,2,0,,,,"Additive effect of STM1344 on virulence As STM1697 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
3976,3977,2298.txt,3,0,,,,"Additive effect of STM1344 on rdar biofilm formation As STM1344 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
3977,3978,2298.txt,4,0,,,,"Additive effect of STM1344 on rdar biofilm formation As STM1697 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
3978,3979,2298.txt,5,0,,,,"Additive effect of STM1344 on motility As STM1344 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
3979,3980,2298.txt,6,0,,,,"Additive effect of STM1344 on motility As STM1697 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
3980,3981,2298.txt,7,0,,,,"As FlhD4C2 is a highly conserved protein , we hypothesize that even STM1344 homologues as a common phenotype affect motility through inhibition of FlhD4C2 functionality also in other bacteria ."
3981,3982,1949.txt,1,0,,,,"These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cAMP and cAMP-receptor-protein -LRB- CRP -RRB- .
"
3982,3983,1949.txt,2,0,,,,These genes are contained in divergently transcribed operons whose 70-dependent promoters are activated by MalT ; transcription of malT is positively regulated by cyclic AMP and cAMP-receptor-protein -LRB- CRP -RRB- .
3983,3984,1791.txt,1,0,,,,"Using site directed mutagenesis , Marchal et al. demonstrated that the fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 promoters .
"
3984,3985,1791.txt,2,0,,,,"Using site directed mutagenesis , Marchal et al. demonstrated that the third positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1269 promoters ."
3985,3986,205.txt,1,0,,,,"In vitro studies provide insights into how PrpR may activate prpBCDE expression .
"
3986,3987,205.txt,2,0,,,,The 2-MC-activated PrpR nd activates transcription of prpBCDE from Pp .
3987,3988,1961.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor 02/11/12 http://dx.doi.org/10.4161/rna.19682 Results Hf affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3988,3989,1961.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor 02/11/12 http://dx.doi.org/10.4161/rna.19682 Results Hf affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3989,3990,1961.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor 02/11/12 http://dx.doi.org/10.4161/rna.19682 Results Hf affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3990,3991,1961.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3991,3992,1961.txt,5,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3992,3993,1961.txt,6,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3993,3994,1961.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3994,3995,1961.txt,8,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3995,3996,1961.txt,9,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3996,3997,1961.txt,10,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3997,3998,1961.txt,11,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3998,3999,1961.txt,12,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
3999,4000,1961.txt,13,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4000,4001,1961.txt,14,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4001,4002,1961.txt,15,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why S. Typhimurium varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4002,4003,1961.txt,16,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4003,4004,1961.txt,17,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4004,4005,1961.txt,18,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4005,4006,1961.txt,19,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 ArcZ UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4006,4007,1961.txt,20,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4007,4008,1961.txt,21,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4008,4009,1961.txt,22,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4009,4010,1961.txt,23,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 RprA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4010,4011,1961.txt,24,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4011,4012,1961.txt,25,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for c-di-GMP signaling has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4012,4013,1961.txt,26,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Ute.Romling@ki.se Submitted : 08/19/1 ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 .
"
4013,4014,1961.txt,27,3,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;Salmonella;Salmonella typhimurium;typhimurium,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"However , whereas OxyS negatively influences RpoS abundance ,15 DsrA UTR , a process is reflected in the strong decrease of cellular RpoS levels in hfq mutant strains , while rpoS mRNA levels display only a minor reduction .22,23 Currently it is unclear why E. coli varies among both species .24 Whereas the relevance of RpoS for rdar morphotype development has been studied in great detail ,6,25 * Correspondence to : Ute Römling ; Emai ; Revised : 02/08/12 ; Accepte affects rdar morphotype expression in Salmonella typhimurium UMR1 ."
4014,4015,1975.txt,1,0,,,,"The pattern of hilA-dependent regulation of prgH by BarA together with partially hilA-indepen-dent regulation of invF by BarA parallels the pattern recently reported for SirA .
"
4015,4016,1975.txt,2,0,,,,It is known that prgH is under the regulation of SirA .
4016,4017,239.txt,1,0,,,,"Previous work has shown that the global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site .
"
4017,4018,239.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"Previous studies have shown that FNR contribute to hlyE expression when E. coli is grown on a solid medium .
"
4018,4019,239.txt,3,0,,,,"Thus , we concluded that FNR all contribute towards the regulation of hlyE expression .
"
4019,4020,239.txt,4,0,,,,"Footprinting studies have shown that FNR activate hlyE expression from the same site centered 61.5 bp upstream of the SlyA-associated transcription start site .
"
4020,4021,239.txt,5,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
4021,4022,239.txt,6,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
4022,4023,239.txt,7,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
4023,4024,239.txt,8,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
4024,4025,239.txt,9,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
4025,4026,239.txt,10,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when FNR act synergistically by binding at different sites within the ansB promoter .
"
4026,4027,239.txt,11,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site at the promoter region in response to oxygen depletion and glucose-starvation , respectively ."
4027,4028,1746.txt,1,0,,,,"b-Galactosidase activity -LRB- Miller units SlyA also regulates ssrA From the results , it seemed probable that additional regulators of ssrA/ssrB existed .
"
4028,4029,1746.txt,2,0,,,,"b-Galactosidase activity -LRB- Miller units SlyA also regulates ssrA From the results , it seemed probable that additional regulators of ssrA/ssrB existed .
"
4029,4030,1746.txt,3,0,,,,Our recent observations indicate that SlyA exerts a direct effect by binding at ssrA .
4030,4031,1020.txt,1,0,,,,that hcp transcription is activated by S-nitrosylation of OxyR during anaerobic nitrate respiration
4031,4032,1034.txt,1,0,,,,"We reason that metE is not a true target of AI-2 regulation but , instead , metE transcription is induced in the wild-type luxS strain relative to the luxS null strain because homocysteine is produced during the generation of AI-2 in the LuxS strain ."
4032,4033,1752.txt,1,0,,,,"Transcription of the flhDC operon is known to be regulated by signals from a network of CRP .
"
4033,4034,1752.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"The cAMP-CRP complex also regulates the transcription of the flhDC operon in S. enterica , although YdiV apparently masks the effect , at least under the conditions ."
4034,4035,2273.txt,1,0,,,,"It is interesting to note that several regulators of InvF , were found in significantly lower levels in the dam mutant ."
4035,4036,588.txt,1,1,Escherichia coli;Escherichia coli,Escherichia coli;Escherichia coli,Escherichia coli,"The cellular concentration of the rs subunit of RNA polymerase in Escherichia coli is controlled at Hu , R. Regulation in the rpoS regulon of Escherichia coli .
"
4036,4037,588.txt,2,1,Escherichia coli;Escherichia coli,Escherichia coli;Escherichia coli,Escherichia coli,"The cellular concentration of the rs subunit of RNA polymerase in Escherichia coli is controlled at Hu , R. Regulation in the rpoS regulon of Escherichia coli ."
4037,4038,1008.txt,1,1,Salmonella,Salmonella,Salmonella,The pagD and pagC genes are PhoP-activated genes ( 9 ) located next to each other in the Salmonella chromosome but transcribed in opposite directions from a shared intergenic region .
4038,4039,2267.txt,1,0,,,,"Alternatively , CsgD could stimulate bapA transcription indirectly via the activation of an intermediate regulatory gene ."
4039,4040,1777.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene Marcos Fernández - d Edmundo Calva * Departamento de Microbiolog Molecular , Instituto de Biotecnología , Universidad Nacional Autónoma de México , Cuernavaca , Morelos 62210 , México The Salmonella enterica serovar Typhi ompS2 gene codes for es for a 362-amino-acid outer membrane .
"
4040,4041,1777.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene Marcos Fernández - José Luis Puen Molecular , Instituto de Biotecnología , Universidad Nacional Autónoma de México , Cuernavaca , Morelos 62210 , México The Salmonella enterica serovar Typhi ompS2 gene codes for es for a 362-amino-acid outer membrane .
"
4041,4042,1777.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR Positively Regulate the Salmonella enterica Serovar Typhi ompS2 Porin Gene Marcos Fernández - Mor Molecular , Instituto de Biotecnología , Universidad Nacional Autónoma de México , Cuernavaca , Morelos 62210 , México The Salmonella enterica serovar Typhi ompS2 gene codes for es for a 362-amino-acid outer membrane ."
4042,4043,1011.txt,1,1,Salmonella,Salmonella,Salmonella,"Transcription of katN is RpoS and growth phase dependent Salmonella strains carrying the Tn5B21 inserts G57 and I28 were initially selected because they contain RpoSregulated lacZ gene fusions ( Ibanez-Ruiz et al. , 2000 ) .
"
4043,4044,1011.txt,2,0,,,,"Thirty-eight unique mutants _ carrying transcriptional lacZ gene fusions positively regulated by RpoS
"
4044,4045,1011.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Vijayakumar , S.R. , Kirchhof , M.G. , Patten , C.L. , and Schellhorn , H.E. ( 2004 ) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .
"
4045,4046,1011.txt,4,0,,,,"To further examine the SraL regulation by RpoS , we analyzed sraL promoter response in a transcriptional-fusion to lacZ reporter gene in both rpoS mutant genetic backgrounds .
"
4046,4047,1011.txt,5,0,,,,"To further examine the SraL regulation by RpoS , we analyzed sraL promoter response in a transcriptional-fusion to lacZ reporter gene in both wild-type .
"
4047,4048,1011.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"Vijayakumar SRV , Kirchhof MG , Patten CL & Schellhorn HE ( 2004 ) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .
"
4048,4049,1011.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis .
4049,4050,585.txt,1,0,,,,Lrp binds to sequences upstream of the spvABCD operon
4050,4051,591.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"LrhA is a positive regulator of flhDC in E. coli .
"
4051,4052,591.txt,2,0,,,,LrhA is also a known regulator of flhDC .
4052,4053,1005.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"However , translational regulator for flhD expression in E. coli in z66 revealed that OmpR did condition .
"
4053,4054,1005.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"However , translational regulator for flhD expression in E. coli in the high-osmolarity expression investigation of fljB revealed that OmpR did condition ."
4054,4055,1763.txt,1,0,,,,"pmrD expression post-translationally activates the PmrAB TCS
"
4055,4056,1763.txt,2,0,,,,pmrD expression post-translationally activates the PmrAB TCS
4056,4057,2242.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,three genetically separated operator elements are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor
4057,4058,1993.txt,1,0,,,,We also observed negative regulation of flgM by RtsB .
4058,4059,1039.txt,1,0,,,,"In turn , fliA is positively controlled by the gene products FlhD .
"
4059,4060,1039.txt,2,0,,,,The FlhD proteins act together in an FlhD2C2 hetero-tetramer to activate the σ70 promoter of fliA gene .
4060,4061,1987.txt,1,0,,,,"Indeed , deletion of yhjH in the arcZ mutant lead to 3-fold upregulation of CsgD levels ( Fig. 6D ; Fig ."
4061,4062,2256.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
4062,4063,2256.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
4063,4064,2256.txt,3,0,,,,"Interestingly , a novel virulence factor gtgE , a synonym of STM1055 , was recently shown to be activated by SlyA ."
4064,4065,220.txt,1,0,,,,"Arnqvist , Normark , S s-dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in-vivo by s in the absence of 70 the nucleoid-associated protein H-NS .
"
4065,4066,220.txt,2,0,,,,"Arnqvist , A s-dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in-vivo by s in the absence of 70 the nucleoid-associated protein H-NS .
"
4066,4067,220.txt,3,0,,,,"Arnqvist , Olsé s-dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in-vivo by s in the absence of 70 the nucleoid-associated protein H-NS .
"
4067,4068,220.txt,4,0,,,,"Arnqvist , A. s-dependent s growth-phase induction of the csgBA promoter in Escher-ichia coli can be achieved in-vivo by s in the absence of 70 the nucleoid-associated protein H-NS ."
4068,4069,546.txt,1,0,,,,"InvF , regulates the expression of phoH ."
4069,4070,552.txt,1,0,,,,"The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of r70 , while the class-3 promoter in operon flgKL is regulated by FliA .
"
4070,4071,552.txt,2,0,,,,"The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of r70 , while the class-3 promoter in operon flgKL is regulated by FliA .
"
4071,4072,552.txt,3,0,,,,"The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC , while the class-3 promoter in operon flgKL is regulated by FliA .
"
4072,4073,552.txt,4,0,,,,"The class-2 promoter of the operon flgBCDEFGHIJKL is regulated by a complex of FlhDC , while the class-3 promoter in operon flgKL is regulated by FliA ."
4073,4074,234.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , fpr .
"
4074,4075,234.txt,2,0,,,,"SoxS protein , activates sodA , fpr ."
4075,4076,1978.txt,1,0,,,,The FlhD levels were determined by immunoblotting analysis at various times after flhC transcription was induced by 50 µM IPTG .
4076,4077,1788.txt,1,0,,,,"cobA-lacZ transcription was used as negative control of a gene whose transcription is not controlled by the PocR/1 ,2-PDL system ; under both conditions , cobA transcription remained unaffected .
"
4077,4078,1788.txt,2,0,,,,"cobA-lacZ transcription was used as negative control of a gene whose transcription is not controlled by the PocR/1 ,2-PDL system ; under both conditions , cobA transcription remained unaffected ."
4078,4079,1950.txt,1,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA -- hmp intergenic region .
"
4079,4080,1950.txt,2,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA -- hmp intergenic region .
"
4080,4081,1950.txt,3,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser 
"
4081,4082,1950.txt,4,0,,,,A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser 
4082,4083,2281.txt,1,1,Hypostomus robinii,tetA,Hypostomus robinii,Strains contained HilD/HilC-repressible lac fusion under the control of a tetA promoter .
4083,4084,2295.txt,1,0,,,,"Thus , the LeuO regulators positively regulate ompS2 .
"
4084,4085,2295.txt,2,0,,,,"LeuO positively regulates ompS2 .
"
4085,4086,2295.txt,3,0,,,,"Moreover , the LeuO activator of the LysR family was identified as a regulator for ompS2 .
"
4086,4087,2295.txt,4,0,,,,"Interestingly , we had shown previously that LeuO positively regulates ompS2 .
"
4087,4088,2295.txt,5,0,,,,"Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter , the induction of ompS1 can occur independent of OmpR .
"
4088,4089,2295.txt,6,1,unidentified plasmid,plasmid,unidentified plasmid,"For ompS2 , we found that in the absence of IPTG considerable transcriptional activity was detected only at 12 h , showing that , as observed for STY3070 , the basal expression from the recombinant LeuO plasmid was enough for induction of the putative operon .
"
4089,4090,2295.txt,7,1,unidentified plasmid,plasmid,unidentified plasmid,"For ompS2 , we found that in the absence of IPTG considerable transcriptional activity was detected only at 12 h , showing that , as observed for STY3070 , the basal expression from the recombinant LeuO plasmid was enough for induction of the quiescent porin .
"
4090,4091,2295.txt,8,0,,,,"if the amount of LeuO increased , ompS2 expression diminished , supporting the observation that an ompS2 gene fusion is expressed at higher levels at an OD of 0.6 upon induction of LeuO with 20 M IPTG from pFMTrcleuO-50
"
4091,4092,2295.txt,9,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4092,4093,2295.txt,10,0,,,,"ompS2 is positively regulated by the LeuO regulator by derepressing the HN-S action
"
4093,4094,2295.txt,11,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4094,4095,2295.txt,12,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4095,4096,2295.txt,13,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4096,4097,2295.txt,14,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4097,4098,2295.txt,15,0,,,,"LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 , consistent with LeuO .
"
4098,4099,2295.txt,16,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva , E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4099,4100,2295.txt,17,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva , E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4100,4101,2295.txt,18,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In Salmonella enterica serovar Typhi , LeuO activates the expression of ompS2 .
"
4101,4102,2295.txt,19,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
4102,4103,2295.txt,20,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
4103,4104,208.txt,1,0,,,,"The sitABCD operon is induced under iron-deficient conditions in the testinal tant is gesting is repressed by Fur .
"
4104,4105,208.txt,2,0,,,,"The sitABCD operon is induced under iron-deficient conditions in-vitro is gesting is repressed by Fur .
"
4105,4106,208.txt,3,0,,,,"The sit locus was constitutively expressed in the fur background , indicating that Fur acts as a repressor of sitABCD .
"
4106,4107,208.txt,4,0,,,,"Fur is reported to repress the host-inducible , virulence-associated sitABCD iron acquisition genes .
"
4107,4108,208.txt,5,1,Salmonella,Salmonella,Salmonella,"For example , Fur has previously been shown to repress sitABCD , in Salmonella .
"
4108,4109,208.txt,6,0,,,,that Fur represses the sitABCD operon in the lumen
4109,4110,1944.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"This result demonstrates that in E. coli RamA can mediate an MDR phenotype independently of a functionally intact marA , likely by direct activation of MarA-controlled genes .
"
4110,4111,1944.txt,2,0,,,,"The expression of MarA is further activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes involved in adaptation to stress conditions , such as oxidative-stress , heavy metals or antimicrobials .10 A well-known example of an adaptive phenotype controlled by MarA is increased tolerance to antibiotics such as tetracycline , chloramphenicol and fluoroquinolones ,11,12 and to other anti-microbial compounds such as triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16 which encodes an antisense RNA involved in the regulation of outer membrane protein F ( OmpF ) , through which hydrophilic substances enter the cell ."
4111,4112,787.txt,1,0,,,,"As ppGpp regulation may require DksA , we also tested whether inactivation of dksA would result in a decreased resistance towards streptomycin ."
4112,4113,1213.txt,1,0,,,,"These data indicate that in STM4264 mutants , CsgD expression is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4113,4114,1213.txt,2,0,,,,"These data indicate that in STM4264 mutants , the rdar morphotype is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4114,4115,1213.txt,3,0,,,,"These data indicate that in STM1703 , STM1827 , STM3611 , CsgD expression is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4115,4116,1213.txt,4,0,,,,"These data indicate that in STM1703 , STM1827 , STM3611 , the rdar morphotype is upregulated , whereby STM4264 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4116,4117,1213.txt,5,0,,,,"In order to demonstrate that upregulation of the rdar morphotype in the STM4264 mutants is mediated by CsgD , csgD was knocked out in the STM4264 mutants ."
4117,4118,1575.txt,1,0,,,,"Five of the HilD/HilC/RtsA-bound regions associated with direct transcription activation of protein-coding genes outside SPI-1 overlap regions that are likely bound by H-NS ( HilD/HilC/RtsA binding sites associated with regulation of lpxR , , siiA , mcpC , and ssaG ) ."
4118,4119,1561.txt,1,0,,,,"Fur repressed ssrB expression both under acidic conditions , which we ascribe to the direct binding of Fur to the ssrB promoter .
"
4119,4120,1561.txt,2,0,,,,"Fur repressed ssrB expression both inside macrophages , which we ascribe to the direct binding of Fur to the ssrB promoter .
"
4120,4121,1561.txt,3,0,,,,"We reveal that Fur provide evidence that Fur represses SsrB production by binding to the ssrB promoter .
"
4121,4122,1561.txt,4,0,,,,"Fur represses expression of the ssrB gene .
"
4122,4123,1561.txt,5,0,,,,"Fur negatively controls SPI-2 expression via repression of ssrB transcription .
"
4123,4124,1561.txt,6,0,,,,"Fur negatively controls SPI-2 expression via repression of ssrB transcription .
"
4124,4125,1561.txt,7,0,,,,"Given that that Fur represses ssrB expression , it is possible that the Fur regulator controls SPI-2 genes in a fashion dependent on the SsrB regulator .
"
4125,4126,1561.txt,8,0,,,,"We further reasoned that if Fur controls SPI-2 genes via the repression of ssrB transcription , Fur repression of SPI-2 expression would be impaired when the ssrB gene is ectopically expressed from a heterologous promoter .
"
4126,4127,1561.txt,9,0,,,,"We further reasoned that if Fur controls SPI-2 genes via the repression of ssrB transcription , Fur repression of SPI-2 expression would be impaired when the ssrB gene is ectopically expressed from a heterologous promoter .
"
4127,4128,1561.txt,10,0,,,,"We further reasoned that if Fur controls SPI-2 genes via the repression of ssrB transcription , Fur repression of SPI-2 expression would be impaired when the ssrB gene is ectopically expressed from a heterologous promoter .
"
4128,4129,1561.txt,11,0,,,,"Taken together , these results illustrate that Fur repression of ssrB transcription leads to repression of SPI-2 genes under acidic conditions .
"
4129,4130,1561.txt,12,0,,,,"Taken together , these results illustrate that Fur repression of ssrB transcription leads to repression of SPI-2 genes under acidic conditions .
"
4130,4131,1561.txt,13,0,,,,"FIG 3 The Fur regulator represses expression of the ssrB gene under acidic conditions .
"
4131,4132,1561.txt,14,0,,,,"FIG 3 The Fur regulator represses expression of the ssrB gene inside macro-phages .
"
4132,4133,1561.txt,15,0,,,,"We determined that Fur represses ssrB transcription by directly binding to Fig. 4B .
"
4133,4134,1561.txt,16,0,,,,"We determined that Fur represses ssrB transcription by directly binding to the ssrB promoter .
"
4134,4135,1561.txt,17,0,,,,"We determined that Fur represses ssrB transcription by directly binding to the ssrB promoter .
"
4135,4136,1561.txt,18,0,,,,"FIG 5 Fur repression of ssrB expression leads to repression of SPI-2 expression .
"
4136,4137,1561.txt,19,0,,,,FIG 5 Fur repression of ssrB expression leads to repression of SPI-2 expression .
4137,4138,2068.txt,1,0,,,,"T. Wada , Y. Tanabe , K. Kutsukake , FliZ acts as a repressor of he ydiV gene .
"
4138,4139,2068.txt,2,0,,,,"FliZ directly represses ydiV transcription
"
4139,4140,2068.txt,3,0,,,,"FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .
"
4140,4141,2068.txt,4,0,,,,"YdiV are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .
"
4141,4142,2068.txt,5,0,,,,"FliZ acts as a repressor of the ydiV gene .
"
4142,4143,2068.txt,6,0,,,,"FliZ acts as a repressor of the ydiV gene .
"
4143,4144,2068.txt,7,0,,,,"FliZ represses ydiV transcriptionally .
"
4144,4145,2068.txt,8,0,,,,"mutually repressing repressors wherein FliZ repression of ydiV is predicted to increase flagellar class II gene expression because YdiV targets the complex for ClpXP-mediated proteolysis
"
4145,4146,2068.txt,9,0,,,,"mutually repressing repressors wherein FliZ repression of ydiV is predicted to increase flagellar class II gene expression because YdiV inhibits binding of the FlhD4C2 complex to DNA
"
4146,4147,2068.txt,10,0,,,,"mutually repressing repressors wherein FliZ repression of ydiV is predicted to increase flagellar class II gene expression because YdiV targets the complex for ClpXP-mediated proteolysis
"
4147,4148,2068.txt,11,0,,,,"mutually repressing repressors wherein FliZ repression of ydiV is predicted to increase flagellar class II gene expression because YdiV inhibits binding of the FlhD4C2 complex to DNA
"
4148,4149,2068.txt,12,0,,,,"These data demonstrate that FliZ represses ydiV to a greater extent as cells approach stationary-phase .
"
4149,4150,2068.txt,13,0,,,,"both the kinetic pattern of ydiV repression by FliZ support our fliC transcription timecourse .
"
4150,4151,2068.txt,14,0,,,,"FliZ represses ydiV transcription .
"
4151,4152,2068.txt,15,0,,,,"The positive feedback loops _ formed when FliZ decreases ydiV transcription
"
4152,4153,2068.txt,16,0,,,,"neither coordinated downregulation of ydiV by FliZ as flagellar gene expression increases
"
4153,4154,2068.txt,17,0,,,,"FliZ represses ydiV .
"
4154,4155,2068.txt,18,0,,,,"Wada T , Tanabe Y , Kutsukake K. FliZ acts as a repressor of he ydiV gene .
"
4155,4156,2068.txt,19,0,,,,"FliZ represses the class II repressor ydiV ; thus ydiV are mutually repressing repressors with opposing effects upon class II transcription .
"
4156,4157,2068.txt,20,0,,,,"FliZ represses the class II repressor ydiV ; thus fliZ are mutually repressing repressors with opposing effects upon class II transcription .
"
4157,4158,2068.txt,21,0,,,,"Kutsukake , K. FliZ acts as a repressor of the ydiV gene .
"
4158,4159,2068.txt,22,0,,,,"Y. , K. FliZ acts as a repressor of the ydiV gene .
"
4159,4160,2068.txt,23,0,,,,"Tanabe , K. FliZ acts as a repressor of the ydiV gene .
"
4160,4161,2068.txt,24,0,,,,"T. , K. FliZ acts as a repressor of the ydiV gene .
"
4161,4162,2068.txt,25,0,,,,"Wada , K. FliZ acts as a repressor of the ydiV gene .
"
4162,4163,2068.txt,26,0,,,,"J Bacteriol 184:645 -- 653 Wada T , Tanabe Y , Kutsukake K FliZ acts as a repressor of the ydiV gene .
"
4163,4164,2068.txt,27,0,,,,"FliZ acts as a repressor of the ydiV gene .
"
4164,4165,2068.txt,28,0,,,,"Wada T , Tanabe Y , Kutsukake K FliZ acts as a repressor of the ydiV gene .
"
4165,4166,2068.txt,29,0,,,,FliZ represses ydiV transcription .
4166,4167,1207.txt,1,0,,,,"Like marRAB , acrAB are positively regulated by Rob .
"
4167,4168,1207.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"While Rosenberg et al. presented evidence that mar is not necessary for bile-salt-mediated activation of acrAB in E. coli , they observed that induction of acrAB by bile-salts is dependent upon Rob .
"
4168,4169,1207.txt,3,1,Salmonella,Salmonella,Salmonella,"Other regulators of Rob did not contrib-ute to acrAB induction by indole in Salmonella .
"
4169,4170,1207.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"Also , acrAB is reportedly induced by bile in a Robdependent manner in E. coli .
"
4170,4171,1207.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcriptional factor Rob plays a major role in inducing acrAB expression in response to bile .
"
4171,4172,1207.txt,6,0,,,,"8 -- 13 _ shown that Rob , play a role in antimicrobial resistance by activating acrAB
"
4172,4173,1207.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcriptional factor Rob plays a major role in inducing acrAB expression in response to bile ."
4173,4174,793.txt,1,0,,,,"2.3 IscR binds on the promoter of hilD Because the ISC machinery was found to play a role in the regulation of Spi1 TTSS gene expression , we aimed at identifying a protein involved in the control of the Spi1 TTSS apparatus .
"
4174,4175,793.txt,2,0,,,,"2.3 IscR binds on the promoter of hilD Because the ISC machinery was found to play a role in the regulation of Spi1 TTSS gene expression , we aimed at identifying a protein involved in the control of the Spi1 TTSS apparatus .
"
4175,4176,793.txt,3,0,,,,"2.3 IscR binds on the promoter of hilD Because the ISC machinery was found to play a role in the regulation of Spi1 TTSS gene expression , we aimed at identifying a protein involved in the control of the Spi1 TTSS apparatus .
"
4176,4177,793.txt,4,0,,,,"2.3 IscR binds on the promoter of hilD Because the ISC machinery was found to play a role in the regulation of Spi1 TTSS gene expression , we aimed at identifying a protein matured by ISC .
"
4177,4178,793.txt,5,0,,,,"2.3 IscR binds on the promoter of hilD Because the ISC machinery was found to play a role in the regulation of Spi1 TTSS gene expression , we aimed at identifying a protein matured by ISC .
"
4178,4179,793.txt,6,0,,,,"FIGURE 3 IscR binds to the hilD promoter in-vitro .
"
4179,4180,793.txt,7,0,,,,"Because the extent of the regulatory effect was only 1.5 fold , we tested whether the IscR‐mediated regulation of hilD had any effect on the expression of downstream HilD‐regulated genes ."
4180,4181,963.txt,1,0,,,,"The heat-shock protein DnaK has been shown to inhibit RpoS proteolysis , with a significant decrease in RpoS stability in dnaK mutants ."
4181,4182,1549.txt,1,0,,,,Significant transcriptional repression of zraP is observed during overexpression of BaeR .
4182,4183,2040.txt,1,0,,,,"hilC whose product is an AraC/XylS-type transcription activator for hilA
"
4183,4184,2040.txt,2,0,,,,"hilD whose products are both AraC/XylS-type transcription activators for hilA
"
4184,4185,2040.txt,3,0,,,,"hilC whose products are both AraC/XylS-type transcription activators for hilA
"
4185,4186,2040.txt,4,0,,,,"Transcription of hilA is directly activated by members of the AraC/XylS family of transcriptional regulators .
"
4186,4187,2040.txt,5,0,,,,"This effect was specific for HilD since the other AraC/XylS type activators of hilA , was sufficient to activate SPI-1 expression at Fig. 6 .
"
4187,4188,2040.txt,6,0,,,,"This effect was specific for HilD since the other AraC/XylS type activators of hilA , was sufficient to activate SPI-1 expression at 42 ° .
"
4188,4189,2040.txt,7,0,,,,Transcription of the hilA gene is also stimulated by the SPI1-encoded AraC/XylS-like regulatory proteins HilC .
4189,4190,2054.txt,1,0,,,,"The genes slrP and dsbA are also induced by HilC independently of InvF .
"
4190,4191,2054.txt,2,0,,,,"The genes slrP and dsbA are also induced by HilC independently of both HilA .
"
4191,4192,2054.txt,3,0,,,,"In this context , slrP is induced by overexpression of HilC independently of the central SPI1 regulator HilA , with RtsA ."
4192,4193,977.txt,1,0,,,,"To better characterize the contribution of RcsB to persistence within tomatoes , rcsB genes were deleted"
4193,4194,744.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
4194,4195,750.txt,1,0,,,,A similar arrangement of binding sites has been observed in the regulation of pstS by PhoP in B. subtilis .
4195,4196,988.txt,1,0,,,,"Transcription of selected PhoPQ-regulated genes , hmpA and rpoD was determined by standard PCR using the synthesized cDNAs and the primers listed in table S4 ."
4196,4197,778.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4197,4198,2083.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Although fimY gene of Salmonella typhimurium is involved in regulating the amino-acid sequence of FimY shares very little homology with other known prokaryotic proteins in the GenBank database .
4198,4199,2097.txt,1,1,Leiostomus xanthurus;Leiostomus xanthurus;Leiostomus xanthurus;Leiostomus xanthurus,spoT;spoT;spoT;spoT,Leiostomus xanthurus,"The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both relA spoT strain , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of RtsA/B on the expression in the relA spoT strain was not due to repression by these of a hilA-lacZ fusion in relA spoT strains .
"
4199,4200,2097.txt,2,1,Leiostomus xanthurus;Leiostomus xanthurus,spoT;spoT,Leiostomus xanthurus,"The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both the wild type , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of RtsA/B on the expression in the relA spoT strain was not due to repression by these of a hilA-lacZ fusion in the wild types ."
4200,4201,1367.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhi;typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Emerging evidence indicates that OmpR regulates ompS2 in S. typhi .
"
4201,4202,1367.txt,2,0,,,,"Thus , the OmpR regulators positively regulate ompS2 .
"
4202,4203,1367.txt,3,0,,,,The experiments described above indicated that both the OmpR regulators were involved in the positive regulation of ompS2 expression .
4203,4204,2108.txt,1,0,,,,"the anti-HPV16 VLP IgG titers _ induced by a PhoPc asd strain ,"
4204,4205,195.txt,1,0,,,,"Lastly , yiaJ is a repressor of transcription in the IclR family ."
4205,4206,1401.txt,1,0,,,,"These results show that HilD positively controls the expression of the lpxR genes , independently of InvF .
"
4206,4207,1401.txt,2,0,,,,"These results show that HilD positively controls the expression of the lpxR genes , independently of HilA .
"
4207,4208,1401.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"HilD induces the expression of lpxR , in the absence of other Salmonella-specific regulators .
"
4208,4209,1401.txt,4,0,,,,"Thus , HilD positively regulates the expression of the lpxR genes , and positively .
"
4209,4210,1401.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD positively regulates lpxR in S. Typhimurium .
"
4210,4211,1401.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"HilD induces the expression of lpxR , in E. coli MC4100 ."
4211,4212,1415.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
4212,4213,1415.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4213,4214,181.txt,1,0,,,,"qor is known to be upregulated by RpoS-inducing conditions , including growth at 23 ° .
"
4214,4215,181.txt,2,0,,,,"qor is known to be upregulated by RpoS-inducing conditions , including starvation at 23 ° ."
4215,4216,1373.txt,1,0,,,,"In addition , CsrA stimulates expression of STM3611 tenfold ."
4216,4217,57.txt,1,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in ygbA ."
4217,4218,817.txt,1,0,,,,"One possible explanation of this finding is that the pstS mutation increases protein levels of FimZ , potentially activating transcription of its own gene , consistent with previous work by Yeh et al. ( 43 ) ."
4218,4219,2134.txt,1,0,,,,Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .
4219,4220,5.txt,1,0,,,,"While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .
"
4220,4221,5.txt,2,0,,,,"As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in mlrA mutant .
"
4221,4222,5.txt,3,0,,,,"As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in the wild type .
"
4222,4223,5.txt,4,0,,,,"As MlrA has been described to activate transcription of csgD , we also examined the levels of bapA mRNA in csgD mutant .
"
4223,4224,5.txt,5,1,unidentified,unknown,unidentified,"Under the influence of unknown environmental signals , MlrA induces the csgD expression .
"
4224,4225,5.txt,6,0,,,,"Moreover , transcriptional expression of csgD , is activated by the regulator MlrA .
"
4225,4226,5.txt,7,0,,,,It has been described that csgD expression is stimulated by MlrA .
4226,4227,2120.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"Research A Proteomic Analysis Reveals Differential S - Regulation of katN Locus by H-NS in Salmonella r , and Françoise Norel § Norel § ¶ ‡ The stationary-phase s controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Esch .
"
4227,4228,2120.txt,2,0,,,,"The results reveal differential regulation of katN locus by H-NS in these two closely related bacteria .
"
4228,4229,2120.txt,3,1,Salmonella,Salmonella,Salmonella,"However , the sequence , the length , , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by H-NS .
"
4229,4230,2120.txt,4,1,Salmonella,Salmonella,Salmonella,"However , the position of H-NS binding regions , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by H-NS .
"
4230,4231,2120.txt,5,1,Salmonella,Salmonella,Salmonella,"However , the position of the McbR/YncC , relative to katN promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by H-NS .
"
4231,4232,2120.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"A proteomic analysis reveals differential regulation of katN locus by H-NS in Escherichia coli K-12 .
"
4232,4233,2120.txt,7,1,Salmonella,Salmonella,Salmonella,A proteomic analysis reveals differential regulation of katN locus by H-NS in Salmonella .
4233,4234,1429.txt,1,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) ."
4234,4235,43.txt,1,0,,,,"Results Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by ¯ iA * mutan .
"
4235,4236,43.txt,2,0,,,,"Results Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by Flg ."
4236,4237,803.txt,1,0,,,,YdcR activates the expression of srfN at the transcriptional level .
4237,4238,630.txt,1,0,,,,"The PmrA-P protein controls its own levels by positively regulating transcription of the pmrCAB operon , by repressing expression of the pmrD gene .
"
4238,4239,630.txt,2,0,,,,"The PmrA-P protein controls its own levels by positively regulating transcription of the pmrCAB operon , by an intrinsic feedback mechanism ."
4239,4240,156.txt,1,0,,,,"We did not observe a decrease in Δ in a wza yjb rcsB mutant beyond what is observed in the rcsB mutant , suggesting that no additional RcsB-regulated factors are required for PMF maintenance ( see Fig ."
4240,4241,142.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,The opposite regulation of pagM by the Salmo-nella PhoP/PhoQ system is reminiscent of the control .
4241,4242,624.txt,1,0,,,,Most of these genes were induced at a higher level in the RpoS-mutant background with sptP .
4242,4243,94.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"For example , in E. coli , IHF has been shown to regulate transcription of the ompR ."
4243,4244,1398.txt,1,0,,,,"These observations suggest that the sE-dependent increase in fdhD expression is not specific to Crp4-induced damage but rather signifies a generalized stress response to cytoplasmic membrane damage .
"
4244,4245,1398.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of rpoE Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between fdhD .
"
4245,4246,1398.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of rpoE Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between sE .
"
4246,4247,1398.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of fdhD Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between fdhD .
"
4247,4248,1398.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of fdhD Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between fdhD .
"
4248,4249,1398.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of fdhD Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between sE .
"
4249,4250,1398.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp4 induce expression of fdhD Complementation of P2 susceptibility of rpoE mutant S. Typhimurium by fdhD overexpression suggested a possible regulatory link between sE .
"
4250,4251,1398.txt,8,1,Salmonella,Salmonella,Salmonella,"While it is clear that Crp4 kill Salmonella by distinct actions , the targeting of the cytoplasmic membrane in both cases may be responsible for the common ability of these peptides to activate the E s-dependent induction of fdhD expression ."
4251,4252,80.txt,1,0,,,,"Like marRAB , acrAB are positively regulated by SoxS .
"
4252,4253,80.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"In S. enterica the global regu-2 SoxS regulate the acrAB operon by binding to mar/sox boxes .
"
4253,4254,80.txt,3,1,Salmonella,Salmonella,Salmonella,"Other regulators of SoxS did not contrib-ute to acrAB induction by indole in Salmonella .
"
4254,4255,80.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcription of acrAB is controlled by SoxS .
"
4255,4256,80.txt,5,0,,,,"In particular , the expression of acrAB is regulated by SoxS .
"
4256,4257,80.txt,6,1,Salmonella,Salmonella,Salmonella,"For example , acrAB transcription in Salmonella is controlled by SoxS .
"
4257,4258,80.txt,7,0,,,,"At a global level , acrAB expression is regulated by SoxS ."
4258,4259,618.txt,1,0,,,,"FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
"
4259,4260,618.txt,2,0,,,,"FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
"
4260,4261,618.txt,3,0,,,,"FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
"
4261,4262,618.txt,4,0,,,,"Pruss , B.M. , Liu , X. , Hendrickson , W. , and Matsumura , P. ( 2001 ) FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
"
4262,4263,618.txt,5,0,,,,"FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
"
4263,4264,618.txt,6,0,,,,"FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
"
4264,4265,618.txt,7,0,,,,FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions .
4265,4266,1603.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcription of micF is controlled by the homologous proteins MarA .
"
4266,4267,1603.txt,2,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4267,4268,1603.txt,3,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4268,4269,1603.txt,4,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4269,4270,1603.txt,5,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4270,4271,1603.txt,6,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4271,4272,1603.txt,7,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4272,4273,1603.txt,8,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4273,4274,1603.txt,9,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4274,4275,1603.txt,10,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4275,4276,1603.txt,11,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4276,4277,1603.txt,12,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4277,4278,1603.txt,13,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4278,4279,1603.txt,14,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4279,4280,1603.txt,15,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4280,4281,1603.txt,16,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4281,4282,1603.txt,17,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4282,4283,1603.txt,18,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4283,4284,1603.txt,19,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4284,4285,1603.txt,20,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4285,4286,1603.txt,21,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4286,4287,1603.txt,22,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4287,4288,1603.txt,23,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4288,4289,1603.txt,24,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4289,4290,1603.txt,25,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4290,4291,1603.txt,26,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4291,4292,1603.txt,27,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4292,4293,1603.txt,28,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4293,4294,1603.txt,29,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4294,4295,1603.txt,30,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4295,4296,1603.txt,31,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4296,4297,1603.txt,32,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4297,4298,1603.txt,33,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4298,4299,1603.txt,34,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4299,4300,1603.txt,35,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4300,4301,1603.txt,36,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4301,4302,1603.txt,37,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4302,4303,1603.txt,38,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4303,4304,1603.txt,39,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4304,4305,1603.txt,40,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4305,4306,1603.txt,41,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4306,4307,1603.txt,42,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4307,4308,1603.txt,43,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4308,4309,1603.txt,44,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4309,4310,1603.txt,45,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4310,4311,1603.txt,46,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4311,4312,1603.txt,47,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4312,4313,1603.txt,48,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4313,4314,1603.txt,49,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4314,4315,1603.txt,50,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4315,4316,1603.txt,51,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4316,4317,1603.txt,52,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4317,4318,1603.txt,53,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4318,4319,1603.txt,54,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4319,4320,1603.txt,55,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4320,4321,1603.txt,56,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4321,4322,1603.txt,57,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4322,4323,1603.txt,58,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4323,4324,1603.txt,59,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4324,4325,1603.txt,60,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4325,4326,1603.txt,61,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4326,4327,1603.txt,62,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4327,4328,1603.txt,63,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4328,4329,1603.txt,64,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4329,4330,1603.txt,65,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4330,4331,1603.txt,66,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4331,4332,1603.txt,67,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4332,4333,1603.txt,68,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4333,4334,1603.txt,69,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4334,4335,1603.txt,70,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4335,4336,1603.txt,71,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4336,4337,1603.txt,72,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4337,4338,1603.txt,73,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16"
4338,4339,397.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
4339,4340,397.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
4340,4341,397.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
4341,4342,397.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
4342,4343,397.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed treR genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
4343,4344,397.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP ."
4344,4345,1165.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Cooperative interaction between Fnr in the regulation of the cydAB operon of Escherichia coli .
"
4345,4346,1165.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in activation .
"
4346,4347,1165.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in repression .
"
4347,4348,1165.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in activation .
"
4348,4349,1165.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in repression .
"
4349,4350,1165.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in activation .
"
4350,4351,1165.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of Fnr in repression .
"
4351,4352,1165.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,Cooperative interaction between Fnr in the regulation of the cydAB operon of Escherichia coli .
4352,4353,1171.txt,1,0,,,,"RtsA/B was capable of increasing the expression of hilA , hilC , hilD ,"
4353,4354,383.txt,1,0,,,,The FlhC levels were determined by immunoblotting analysis at various times after flhD transcription was induced by 50 µM IPTG .
4354,4355,1617.txt,1,0,,,,"This might explain the inhibition of cspH expression by gyrase inhibitor , i.e. a reduction of Fis levels and a decrease in the superhelical density of the cspH promoter ."
4355,4356,1159.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , five transcription factors have been implicated : hmp transcription is repressed by Fur .
"
4356,4357,1159.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , five transcription factors have been implicated : hmp transcription is repressed by Fur ."
4357,4358,1818.txt,1,1,Salmonella,Salmonella,Salmonella,"Transcription of katN is RpoS and growth phase dependent Salmonella strains carrying the Tn5B21 inserts G57 and I28 were initially selected because they contain RpoSregulated lacZ gene fusions ( Ibanez-Ruiz et al. , 2000 ) .
"
4358,4359,1818.txt,2,1,Salmonella,Salmonella,Salmonella,"Consistent with a role for RpoS in the regulation of katN was not produced in the Salmonella rpoS Fig. 2A .
"
4359,4360,1818.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,Salmonella;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella,Consistent with a role for RpoS in the regulation of katN was not produced in the Salmonella rpoS mutant SL1344K .
4360,4361,354.txt,1,1,synthetic construct,primer,synthetic construct,"Among the SPI-5 genes , primer-extension analysis revealed that pipC were induced at entry into the stationary-phase under standard growt conditions independently of RpoS ."
4361,4362,432.txt,1,0,,,,"Emerging evidence indicates that OmpR regulates cryptic porins ompS1 .
"
4362,4363,432.txt,2,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4363,4364,432.txt,3,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4364,4365,432.txt,4,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4365,4366,432.txt,5,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in IMSS-1 , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4366,4367,432.txt,6,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4367,4368,432.txt,7,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in IMSS-41 , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4368,4369,432.txt,8,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in STYhns99 and in the hns ompR double mutant -LRB- STY9941 -RRB- .
"
4369,4370,432.txt,9,0,,,,"LeuO derepressed both ompS1 promoters To elucidate how OmpR regulate ompS1 expression , the effect of LeuO was evaluated in the wild type , in the ompR mutant , in the hns mutant and in the hns ompR double mutant -LRB- STY9941 -RRB- ."
4370,4371,426.txt,1,0,,,,"However while SirA inhibits CsrA activity via the activation of csrB , SirA does not regulate the transcription of csrA .
"
4371,4372,426.txt,2,0,,,,"No further increase in PefA expression was apparent in TS133 , thus the lack of inactivation of the SirA-regulated genes csrB and csrC produced similar effects on PefA expression .
"
4372,4373,426.txt,3,0,,,,"No further increase in PefA expression was apparent in a sirA csrB csrC DfimAICDHF mutant , thus the lack of inactivation of the SirA-regulated genes csrB and csrC produced similar effects on PefA expression ."
4373,4374,340.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
4374,4375,1824.txt,1,0,,,,"The expression of ssrAB is , in turn , regulated by the OmpR-EnvZ two-component system ."
4375,4376,368.txt,1,0,,,,expression of activity of FlhD proteins in initiating the transcription of fliA-fused lacZ gene after induction of IPTG-controlled flhDC genes in cells depleted either of DnaK or of both DnaK and ClpP .
4376,4377,1830.txt,1,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgH remains unaffected .
"
4377,4378,1830.txt,2,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgH remains unaffected .
"
4378,4379,1830.txt,3,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgH remains unaffected ."
4379,4380,1831.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,the expression of the SPI-1 genes when S. Typhimurium is grown in the presence of cpxR _ indicating that the absence of CpxA leads to the repression of the SPI-1 genes through CpxR
4380,4381,369.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
4381,4382,1825.txt,1,0,,,,"Among the 38 genes , otsBA were previously reported to be regulated by RpoS ."
4382,4383,427.txt,1,0,,,,"IHF , have been suggested to repress SPI-2 gene expression indirectly , since no binding of these proteins to ssrA and/or ssrB promoters has been demonstrated ."
4383,4384,341.txt,1,0,,,,"We have previously shown that pnp have opposing effects on biofilm formation at decreased growth temperatures with NlpI , respectively , suppressing biofilm formation .
"
4384,4385,341.txt,2,0,,,,"We have previously shown that pnp have opposing effects on biofilm formation at decreased growth temperatures with NlpI , respectively , enhancing biofilm formation ."
4385,4386,355.txt,1,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
4386,4387,355.txt,2,0,,,,"Together with a bioinformatic analysis of other Enterobacteriaceae species , these data identify a conserved AraC regulon that includes 7 previously described AraC-regulated genes ( araB , araA , araD , araE , araF , araG , and araH ) as well as three novel targets identified in this work ( ytfQ , araT , and araU ) ."
4387,4388,1819.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"As mentioned in the Introduction , the expression of ilvIH in E. coli K-12 is activated by Lrp .
"
4388,4389,1819.txt,2,0,,,,"Lrp activates ilvIH expression .
"
4389,4390,1819.txt,3,0,,,,"Lrp , activates transcription of ilvIH ."
4390,4391,433.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Moreover , these results also demonstrate that the S. typhimurium Fur positively regulates the expression of the flhD master operon .
"
4391,4392,433.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Moreover , the S. typhimurium flhD master operon , is positively regulated by Fur through an iron-independent mechanism ."
4392,4393,1158.txt,1,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
4393,4394,1158.txt,2,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Lee , H. , Hsu , F.F. , Turk , J. , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanola-mine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4394,4395,1158.txt,3,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"[ 21 ] Lee , H. , Hsu , F.F. , Turk , J. and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4395,4396,1158.txt,4,0,,,,"pmrC , a PmrA-regulated gene necessary for the addition of pEtN to lipid-A , did not affect core pEtN addition .
"
4396,4397,1158.txt,5,0,,,,"Recently , the PmrA-regulated pmrC gene product was shown to mediate the addition of pEtN to the 1-position of lipid-A and affect resistance to PM ( 22 ) .
"
4397,4398,1158.txt,6,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid a and poly-myxin resistance in Salmonella enterica .
"
4398,4399,1158.txt,7,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Lee , H. , Hsu , F.F. , Turk , J. , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanola-mine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4399,4400,1158.txt,8,0,,,,"Collectively , these results strongly suggest that the pmrC , ugd and pmrG genes and the pbgPE operon are the only PmrA-regulated determinants required for Fe ( III ) resistance .
"
4400,4401,1158.txt,9,0,,,,"pmrC mediates the PmrA-PmrB-regulated attachment of phosphoethanolamine to lipid-A ( 27 ) .
"
4401,4402,1158.txt,10,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .
"
4402,4403,1158.txt,11,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"68 , 6139 -- 6146 58 Lee , H. et al. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4403,4404,1158.txt,12,0,,,,"PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid-A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase .
"
4404,4405,1158.txt,13,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Lee H , Hsu FF , Turk J & Groisman EA ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4405,4406,1158.txt,14,1,unidentified,not shown,unidentified,"The absence of transcriptional linkage between the RpoN and the PmrA regulons was corroborated because no significant differences were observed when the expression of PmrAcontrolled genes ( pmrI , pmrC , pmrF , and ugd ) was compared either in a RpoN or in a 1 DrpoN strain grown in LB ( exponential or stationary-phase ) or in a low-Mg N-21 minimal-medium , which are PhoP-and PmrA-inducing conditions ( Soncini & Groisman , 1996 ) ( Fig. 3a and data not shown ) .
"
4406,4407,1158.txt,15,0,,,,"( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain .
"
4407,4408,1158.txt,16,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .
"
4408,4409,1158.txt,17,0,,,,"After being phosphorylated by PmrB , PmrA can effectively bind to the transcriptional sites of pmrC .
"
4409,4410,1158.txt,18,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4410,4411,1158.txt,19,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and poly-myxin resistance in Salmonella enterica .
"
4411,4412,1158.txt,20,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica .
"
4412,4413,1158.txt,21,0,,,,"Importantly , the enrichment in ssrB promoter DNA was comparable to that of other known PmrA-regulated genes , including pmrC ( Fig. 4C ) .
"
4413,4414,1158.txt,22,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Lee , H. , Hsu , F.F. , Turk , J , and Groisman , E.A. ( 2004 ) The PmrA-regulated pmrC gene mediates phosphoethanol-amine modification of lipid a and polymyxin resistance in Salmonella enterica .
"
4414,4415,1158.txt,23,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"[ 75 ] H. Lee , F.F. Hsu , J. Turk , E.A. Groisman , The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid-A and polymyxin resistance in Salmonella enterica , J. Bacteriol ."
4415,4416,1170.txt,1,1,Escherichia coli,E : coli,Escherichia coli,InvF are sufficient to activate transcription of sigD ± lacZYA in E : coli CC118lpir .
4416,4417,1616.txt,1,0,,,,"As rpoS is upregulated in these mutants , activities of ArcA under microaerobiosis in the wild-type cells lead to the downregulation of rpoS .
"
4417,4418,1616.txt,2,0,,,,the response regulator ArcA directly inhibits rpoS transcription
4418,4419,382.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
4419,4420,382.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4420,4421,396.txt,1,0,,,,IHF activates the transcription of ilvBN .
4421,4422,1602.txt,1,0,,,,"As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .
"
4422,4423,1602.txt,2,0,,,,"As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation .
"
4423,4424,1602.txt,3,0,,,,"According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .
"
4424,4425,1602.txt,4,0,,,,"Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling .
"
4425,4426,1602.txt,5,0,,,,"The response regulator PhoP represses hilA , whereas transcription of pag is activated .
"
4426,4427,1602.txt,6,0,,,,"The response regulator PhoP represses hilA , whereas transcription of PhoP-activated genes is activated ."
4427,4428,1164.txt,1,0,,,,"As both ArcA and Fnr contribute to regulation of respiration , the same explanation may be relevant for the GNS phenotype of the fnr mutants .
"
4428,4429,1164.txt,2,0,,,,"Our results also provide evidence that nipAB expression is regulated by Fnr , as induction is completely abolished in an fnr mutant background ."
4429,4430,619.txt,1,0,,,,We next compared the mRNA levels of fhuF between the wild-type and feoA promoter mutant strains grown in LB me-dium and found that the lack of RstA-activated feoAB transcription abrogates repression of the Fur target gene even in the strain expressing the RstA protein ( Fig. 3B ) .
4430,4431,81.txt,1,0,,,,"The suppressive effects of spermine NONOate on PhoP-dependent gene transcription appear to be directly related to the production of RNS because the polyamine base spermine did not suppress the acid-induced expression of the PhoP-activated loci lpxO , pqaA , and pcgE ( fig. 6B -- D ) .
"
4431,4432,81.txt,2,0,,,,"The acid-inducible expression of the PhoP-activated loci lpxO , pqaA and pcgE were monitored in the presence or absence of 250 mM spermine , 250 mM spermine NONOate or 500 mM NaNO2 ( B -- D ) ."
4432,4433,1399.txt,1,0,,,,"Thus , we investigated the role of the PhoP-activated pagP and pgtE genes , because they had been implicated in resistance to the alpha-helical peptide C18G ( Guo et al. , 1998 ; Guina et al. , 2000 ) .
"
4433,4434,1399.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] .
"
4434,4435,1399.txt,3,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .
"
4435,4436,1399.txt,4,0,,,,These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- pgtE .
4436,4437,95.txt,1,0,,,,"SsrBC Stimulates Transcription of sseJ in Vitro in the Absence of Additional Factors -- To determine whether SsrB could directly activate transcription , we used purified SsrBC in an in-vitro-transcription assay ."
4437,4438,143.txt,1,0,,,,"In line with this hypothesis , in a cpxR mutant csgA transcription was only slightly enhanced , indicating that under those environmental conditions repression by CpxR plays a minor role ."
4438,4439,625.txt,1,1,Salmonella,Salmonella,Salmonella,the PhoP-PhoQ _ activated Salmonella genes pagK and pagJ
4439,4440,631.txt,1,0,,,,"the RstA protein bound to the feoA promoter
"
4440,4441,631.txt,2,1,unidentified,unknown,unidentified,"When activated under iron-replete conditions by unknown signal , the RstA protein binds to the feoA promoter to activate transcription of the feoAB operon ."
4441,4442,157.txt,1,0,,,,"OmpR binds to its own promoter Although the evidence suggests that OmpR can regulate its own expression , OmpR autoregulation could be indirect , with OmpR controlling the expression of a second gene , the product of which directly controls the ompR promoter .
"
4442,4443,157.txt,2,0,,,,"The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .
"
4443,4444,157.txt,3,0,,,,"Consequently , DNA mobility-shift assays were performed to determine whether OmpR actually binds to the ompR promoter region .
"
4444,4445,157.txt,4,0,,,,"The results clearly demonstrate that phosphorylated OmpR protein binds to the ompR promoter region with a greater affinity than that of unphosphorylated OmpR .
"
4445,4446,157.txt,5,0,,,,"OmpR footprint In vitro DNA footprinting experiments were then conducted to determine which of the three potential OmpR binding sites in the ompR promoter are actually bound by OmpR .
"
4446,4447,157.txt,6,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4447,4448,157.txt,7,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4448,4449,157.txt,8,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4449,4450,157.txt,9,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4450,4451,157.txt,10,0,,,,"OmpR binds to its own promoter Although the evidence suggests that OmpR can regulate its own expression , OmpR autoregulation could be indirect , with OmpR controlling the expression of a second gene , the product of which directly controls the ompR promoter .
"
4451,4452,157.txt,11,0,,,,"The results presented here reveal that H-NS represses ompR , and that OmpR protein directly autoregulates its own expression in response to acid shock by overcoming H-NS repression .
"
4452,4453,157.txt,12,0,,,,"Consequently , DNA mobility-shift assays were performed to determine whether OmpR actually binds to the ompR promoter region .
"
4453,4454,157.txt,13,0,,,,"The results clearly demonstrate that phosphorylated OmpR protein binds to the ompR promoter region with a greater affinity than that of unphosphorylated OmpR .
"
4454,4455,157.txt,14,0,,,,"OmpR footprint In vitro DNA footprinting experiments were then conducted to determine which of the three potential OmpR binding sites in the ompR promoter are actually bound by OmpR .
"
4455,4456,157.txt,15,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4456,4457,157.txt,16,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4457,4458,157.txt,17,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4458,4459,157.txt,18,0,,,,"the ompR promoter region serve as internal controls for spurious binding of OmpR
"
4459,4460,157.txt,19,0,,,,"Lee et al. established that loss of virulence in ompR mutants could be partly attributed to the loss of the transcriptional regulator of the SsrA-SsrB system-the OmpR protein .
"
4460,4461,157.txt,20,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .
"
4461,4462,157.txt,21,0,,,,"Since previous studies have demonstrated that OmpR is a regulator of Agf expression , we decided to determine whether the TnphoA insertion in 2 final candidate mutants is in the ompR gene .
"
4462,4463,157.txt,22,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"ompR are required for resistance to the bile salt sodium deoxycholate in S. Typhi We have shown that LtrR has a role in the synthesis of the major outer membrane proteins OmpF and OmpC through its direct regulation of OmpR .
"
4463,4464,157.txt,23,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"The ompR mutant was also complemented with the ompR coding region from Escheri-chia coli under the control of pQE60ompR ; this construct was used since it is identical to the S. Typhi OmpR protein .
"
4464,4465,157.txt,24,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"The ompR mutant was also complemented with the ompR coding region from Escheri-chia coli under the control of an IPTG-inducible promoter ; this construct was used since it is identical to the S. Typhi OmpR protein .
"
4465,4466,157.txt,25,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"CadC interacts directly with OmpR Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to RNA polymerase .
"
4466,4467,157.txt,26,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"CadC interacts directly with OmpR Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter .
"
4467,4468,157.txt,27,0,,,,"Thus , OmpR only directly regulates two , i.e. , ompR , of the four genes ."
4468,4469,1428.txt,1,0,,,,"Because PhoP/PhoQ regulates more than 40 genes , additional PhoP/PhoQ-activated genes , including pmrD and pagD , were examined to determine if bile specifically regulated pagC , or if it has a general effect on PhoP/PhoQ-regulated genes ."
4469,4470,2121.txt,1,0,,,,"Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of and its homolog FlrC in the upstream regions and ORFs of rcsB , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .
"
4470,4471,2121.txt,2,0,,,,"Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA in the upstream regions and ORFs of rcsB , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .
"
4471,4472,2121.txt,3,0,,,,"In the present study , rcsB were also predicted to have binding sites of YfhA within their ORFs .
"
4472,4473,2121.txt,4,0,,,,"Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA mediated regulation of rcsB ."
4473,4474,802.txt,1,1,Salmonella,Salmonellae,Salmonella,"sseC , were induced much more than two-fold in the RpoS-mutant than in the wild type Salmonellae ."
4474,4475,42.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,Putative regulation by the global regulators RcsB was evaluated by generating three isogenic S. Typhi deletion mutants of fur .
4475,4476,816.txt,1,0,,,,"Furthermore , STM2585 are regulated by PhoP ."
4476,4477,56.txt,1,0,,,,"Like marRAB , tolC are positively regulated by MarA ."
4477,4478,4.txt,1,0,,,,"These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , .
"
4478,4479,4.txt,2,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4479,4480,4.txt,3,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4480,4481,4.txt,4,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4481,4482,4.txt,5,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4482,4483,4.txt,6,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4483,4484,4.txt,7,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4484,4485,4.txt,8,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4485,4486,4.txt,9,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4486,4487,4.txt,10,0,,,,"increased repression of hilA _ encoding the SPI-1 transcriptional activator HilA
"
4487,4488,4.txt,11,0,,,,"Differential expression of the hilA gene The HilA protein decreases in expression of the hilA gene typically decrease on invasion .
"
4488,4489,4.txt,12,0,,,,Differential expression of the hilA gene The HilA protein decreases in expression of the hilA gene typically have a corresponding increase .
4489,4490,2135.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Autoregulator of the Escherichia coli crp gene : CRP is a transcriptional repressor for its own gene .
"
4490,4491,2135.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,Autoregulation of the Escherichia coli crp gene : CRP is a transcriptional repressor for its own gene .
4491,4492,180.txt,1,1,Salmonella,Salmonella,Salmonella,PmrA Reduces Salmonella Virulence by Repressing ssrB Transcription .
4492,4493,1414.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
4493,4494,1372.txt,1,0,,,,"Under low osmolality , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
4494,4495,1372.txt,2,0,,,,"Under acidic pH , the ssrA genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
4495,4496,1372.txt,3,0,,,,"Since PhoP regulates expression of ssrA , it also regulates expression of genes in the SsrB regulon ."
4496,4497,1366.txt,1,0,,,,"also suppressed the negative effect of the AT4 region , the 72 bp gene silencer region located between the leuO gene , by delimiting the transcriptional repression by H-NS through the binding of LeuO to the promoter region
"
4497,4498,1366.txt,2,0,,,,H-NS are involved in regulation of leuO .
4498,4499,1400.txt,1,0,,,,"With the exception of cysK and sbp , mutants in all other CysB-regulated genes showed little or no activity on swim plates .
"
4499,4500,1400.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium,typhimu,Salmonella enterica subsp. enterica serovar Typhimurium,"Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9-minimal-medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative-stress ."
4500,4501,194.txt,1,0,,,,this effect was reflected by induction of cspD and proteins ( CspA ) in response to preadaptation to cold-stress
4501,4502,2109.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In vitro binding of FruR , to the fru , pps , ace , pts of Salmonella typhimurium .
"
4502,4503,2109.txt,2,0,,,,"In vitro binding of FruR , to the fru , pps , ace , pts of Esche-richia coli ."
4503,4504,2096.txt,1,1,synthetic construct,Primer,synthetic construct,"Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM ."
4504,4505,779.txt,1,0,,,,"PmrAB-regulated genes include pmrHFIJKL , whose product results in the addition of aminoarabinose to the 1 and 4 = phosphates of lipid-A ( D ) ; pmrC , whose product results in the addition of phosphoethanolamine to the 1 and 4 = phosphates of lipid-A ( E ) ; cptA , whose product results in the addition of phosphoethanolamine to the LPS core ( F ) ; pmrG , whose product results in the addition of phosphate to heptose present in the LPS core ( G ) ; and cld , whose product results in an O-antigen chain length determinant ( H ) ."
4505,4506,2082.txt,1,0,,,,"HilD , regulates the expression of sinR .
"
4506,4507,2082.txt,2,0,,,,"that HilD directly controls the expression of the sinR genes
"
4507,4508,2082.txt,3,0,,,,"HilD binds to the regulatory regions of sinR .
"
4508,4509,2082.txt,4,0,,,,"To further define whether the HilD-mediated regulation of sinR is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .
"
4509,4510,2082.txt,5,0,,,,"To further define whether the HilD-mediated regulation of sinR is direct , we analyzed the interaction of HilD with the regulatory region of these genes .
"
4510,4511,2082.txt,6,0,,,,"Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the sinR genes .
"
4511,4512,2082.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,S. Typhimurium;S. Typhimurium SL1344;Typhimurium;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium,"In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : sinR .
"
4512,4513,2082.txt,8,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of sinR .
"
4513,4514,2082.txt,9,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of sinR .
"
4514,4515,2082.txt,10,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of sinR .
"
4515,4516,2082.txt,11,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of sinR .
"
4516,4517,2082.txt,12,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of sinR .
"
4517,4518,2082.txt,13,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of sinR .
"
4518,4519,2082.txt,14,2,Felis catus;Escherichia coli,cat;E. coli,Felis catus;Escherichia coli,"Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of sinR .
"
4519,4520,2082.txt,15,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of sinR .
"
4520,4521,2082.txt,16,2,Felis catus;Salmonella;Salmonella,cat;Salmonella;Salmonella-specific,Felis catus;Salmonella,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of sinR .
"
4521,4522,2082.txt,17,0,,,,"Thus , HilD directly regulates the expression of the sinR genes , and positively .
"
4522,4523,2082.txt,18,0,,,,"Whether the regulation by HilD implies that the sinR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .
"
4523,4524,2082.txt,19,0,,,,"Whether the regulation by HilD implies that the sinR genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .
"
4524,4525,2082.txt,20,1,Salmonella,Salmonella,Salmonella,"Whether the regulation by HilD implies that the sinR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .
"
4525,4526,2082.txt,21,1,Salmonella,Salmonella,Salmonella,"Whether the regulation by HilD implies that the sinR genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .
"
4526,4527,2082.txt,22,0,,,,HilD binds to the regulatory region of sinR .
4527,4528,989.txt,1,0,,,,"Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is LexA .
"
4528,4529,989.txt,2,0,,,,"Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS .
"
4529,4530,989.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"The Escherichia coli SOS gene sbmC is regulated by H-NS during stationary growth phase .
"
4530,4531,989.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,The Escherichia coli SOS gene sbmC is regulated by H-NS during the SOS-induction .
4531,4532,751.txt,1,1,Salmonella virus P22,P22,Salmonella virus P22,"One such isolate was re-constructed by P22 HT transduction to confirm that the Tn10dCm insertion suppressed hilC : : lac downregulation by LeuO .
"
4532,4533,751.txt,2,1,Salmonella virus P22,P22,Salmonella virus P22,"One such isolate was purified by P22 HT transduction to confirm that the Tn10dCm insertion suppressed hilC : : lac downregulation by LeuO .
"
4533,4534,751.txt,3,0,,,,"Use of a HilE − null mutant constructed ad ( strain SV55 provided independent evidence that lack of HilE suppressed hilC : : lac downregulation by LeuO .
"
4534,4535,751.txt,4,0,,,,Use of a HilE − null mutant constructed ad d h provided independent evidence that lack of HilE suppressed hilC : : lac downregulation by LeuO .
4535,4536,745.txt,1,0,,,,"pagJ are known to be regulated by PhoP ,56"
4536,4537,2055.txt,1,0,,,,"The araBAD promoter is induced in the presence of arabinose by the positive regulator AraC .
"
4537,4538,2055.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"E. coli AraC activates transcription of the araBAD , araFGH , araE in the presence of its inducer , L-arabinose ."
4538,4539,976.txt,1,0,,,,"Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .
"
4539,4540,976.txt,2,0,,,,"Induction of the feoB gene is necessary for downregulation of the Fur-repressed genes upon RstA activation .
"
4540,4541,976.txt,3,0,,,,"the RstA-dependent activation of feoAB transcription increased Fe uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells .
"
4541,4542,976.txt,4,0,,,,"Third increased Fe uptake , whereas mutation of the RstA-binding sequences on the feoA promoter or deletion of the feoB gene abolished repression of Fur-regulated genes in cells ."
4542,4543,962.txt,1,2,unidentified plasmid;Escherichia coli,plasmid;E. coli,Escherichia coli;unidentified plasmid,"RESULTS AND DISCUSSIONS Screen for Fur-regulated Promoters and Sequence Analyses of DNA Regions Identified by FURTA Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .
"
4543,4544,962.txt,2,2,unidentified plasmid;Escherichia coli,plasmid;E. coli,Escherichia coli;unidentified plasmid,"RESULTS AND DISCUSSIONS Screen for Fur-regulated Promoters and Sequence Analyses of DNA Regions Identified by FURTA Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .
"
4544,4545,962.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi;plasmid;S. Typhimurium;Typhimurium,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"To determine whether Fur regulation of tcf was specific to S. Typhi , lacZ reporter plasmid was transformed into S. Typhimurium .
"
4545,4546,962.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,S. Typhi;Typhi;plasmid,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"To determine whether Fur regulation of tcf was specific to S. Typhi , lacZ reporter plasmid was transformed into their isogenic fur mutants .
"
4546,4547,962.txt,5,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Escherichia coli,S. Typhi;Typhi;plasmid;E. coli,unidentified plasmid;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"To determine whether Fur regulation of tcf was specific to S. Typhi , lacZ reporter plasmid was transformed into E. coli K-12 ."
4547,4548,2041.txt,1,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,Salmonella;Typhi;plasmid;Salmonella;Typhi;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene .
"
4548,4549,2041.txt,2,0,,,,"The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code during biofilm formation .
"
4549,4550,2041.txt,3,0,,,,"The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code in the exponential-growth-phase .
"
4550,4551,2041.txt,4,0,,,,The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme .
4551,4552,1548.txt,1,0,,,,"H-NS binds to structural gene in a temperature-dependent manner To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 37 ◦ .
"
4552,4553,1548.txt,2,0,,,,"H-NS binds to structural gene in a temperature-dependent manner To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 25 .
"
4553,4554,1548.txt,3,0,,,,"H-NS binds to the hilC promoter in a temperature-dependent manner To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 37 ◦ .
"
4554,4555,1548.txt,4,0,,,,"H-NS binds to the hilC promoter in a temperature-dependent manner To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 37 ◦ .
"
4555,4556,1548.txt,5,0,,,,"H-NS binds to the hilC promoter in a temperature-dependent manner To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 25 .
"
4556,4557,1548.txt,6,0,,,,"H-NS binds to the hilC promoter in a temperature-dependent manner To demonstrate the direct involvement of H-NS in the thermo-regulation of hilC , we studied the binding of H-NS by competitive gel-retardation assays at 25 .
"
4557,4558,1548.txt,7,0,,,,Another interesting observation from these experiments is that H-NS binds to the hilC structural gene in addition to the promoter .
4558,4559,2069.txt,1,0,,,,"With the exception of cysK and sbp , mutants in all other CysB-regulated genes showed little or no activity on swim plates .
"
4559,4560,2069.txt,2,0,,,,"Stoichiometry of binding of CysB to cysK .
"
4560,4561,2069.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"In this regard , it has been reported that expression of cysK in E. coli is under the control of CysB .
"
4561,4562,2069.txt,4,0,,,,Stoichiometry of binding of CysB to cysK .
4562,4563,1560.txt,1,0,,,,"It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .
"
4563,4564,1560.txt,2,0,,,,It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .
4564,4565,792.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Fis represses transcription of the gyrA genes in E. coli .
"
4565,4566,792.txt,2,2,Salmonella;Salmonella;Escherichia coli;Salmonella;Salmonella,S.enterica;enterica;E. coli;S. enterica;enterica,Escherichia coli;Salmonella,") Discussion The finding that the sequences of S.enterica gyrA genes diverge significantly upstream of the -- 10 box of the promoter raised the possibility that the well-characterized Fis-mediated repression of gyrA transcription seen in E. coli might not be reproduced in S. enterica .
"
4566,4567,792.txt,3,2,Escherichia coli;Escherichia coli;Salmonella;Salmonella,E. coli;E. coli;S. enterica;enterica,Escherichia coli;Salmonella,") Discussion The finding that the sequences of the E. coli gyrA genes diverge significantly upstream of the -- 10 box of the promoter raised the possibility that the well-characterized Fis-mediated repression of gyrA transcription seen in E. coli might not be reproduced in S. enterica .
"
4567,4568,792.txt,4,2,Salmonella;Salmonella;Escherichia coli,S. enterica;enterica;E. coli,Escherichia coli;Salmonella,"Thus , Fis has the potential to act as a repressor at the S. enterica gyrA promoter by interfering with RNA polymerase binding , as it does in E. coli .
"
4568,4569,792.txt,5,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"The retention of Fis-mediated repression of gyrA in S. enterica despite the radically different nucleotide sequence found immediately upstream of the Pribnow box is indicative of the physiological importance for the cell of regulation of gyrase expression by Fis .
"
4569,4570,792.txt,6,0,,,,"the Fis protein is a repressor of gyrA transcription
"
4570,4571,792.txt,7,2,Escherichia coli;Salmonella;Salmonella,E. coli;S. enterica;enterica,Escherichia coli;Salmonella,"In E. coli , FIS binds the gyrA promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrA ."
4571,4572,1206.txt,1,0,,,,"Inactivation of LsrR by the presence of phosphorylated AI-2 allows SPI-1 and fliC , fliD gene transcription ."
4572,4573,1212.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The yncE gene is induced under iron restriction through the action of the global iron regulator Fur in E. coli ; however , the iron restriction did not affect the transcription of the yncD gene .
"
4573,4574,1212.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"The yncE gene is induced under iron restriction through the action of the global iron regulator Fur in E. coli ; however , the regulator did not affect the transcription of the yncD gene ."
4574,4575,786.txt,1,0,,,,"This means that a strong induction of and a sequential induction of acrAB is expected only when MarR is inactivated as , indeed , occurs with SAL .
"
4575,4576,786.txt,2,0,,,,"This means that a strong induction of and a sequential induction of acrAB is expected only when MarR is inactivated as , indeed , occurs with SAL ."
4576,4577,1574.txt,1,1,unidentified plasmid;unidentified plasmid,plasmid;plasmid,unidentified plasmid,"Effect of lrp mutations on conjugal plasmid transfer Together , the results suggest that Lrp might act as an activator of conjugal plasmid transfer .
"
4577,4578,1574.txt,2,1,unidentified plasmid;unidentified plasmid,plasmid;plasmid,unidentified plasmid,"This magnification of the difference in the absence of fertility inhibition further supports the model that Lrp acts as an activator of pSLT plasmid transfer : a FinO-plasmid is no longer derepressed when an lrp mutation reduces traJ transcription .
"
4578,4579,1574.txt,3,0,,,,"When leucine was added to the MOPS culture , the level of lrp-gfp expression increased by between 1.5-and 2-fold , provided the Lrp protein was present ; leucine did not have this effect in the lrp knockout mutant ."
4579,4580,1945.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Clarke M , Sperandio V. Transcriptional regulation of flhDC by sigma-28 in enterohaemorrhagic Escherichia coli .
"
4580,4581,1945.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,Transcriptional regulation of flhDC by sigma-28 ( FliA ) in enterohaemorrhagic Escherichia coli .
4581,4582,209.txt,1,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .
"
4582,4583,209.txt,2,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE ."
4583,4584,2294.txt,1,0,,,,"Mutations in the promoter region of ramA appear to play a role in the up-regulation of RamA
"
4584,4585,2294.txt,2,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in and INRA , UMR 6175 Plateforme d
"
4585,4586,2294.txt,3,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in and INRA , UMR 6175 Plateforme d
"
4586,4587,2294.txt,4,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in , UPR4301 , Orléans , Fra et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4587,4588,2294.txt,5,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in , UPR4301 , Orléans , Fra et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4588,4589,2294.txt,6,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in ; Centre de Biophysique Moléculaire C et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4589,4590,2294.txt,7,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in ; Centre de Biophysique Moléculaire C et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4590,4591,2294.txt,8,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in UR1282 Infectiologie Animale et Santé Publique , Nouzilly , Franc et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4591,4592,2294.txt,9,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in UR1282 Infectiologie Animale et Santé Publique , Nouzilly , Franc et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4592,4593,2294.txt,10,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in a Franck Coste , b Sylvie Canepa , c Marie-Christine Maurel , c Etienne Giraud , a Françoise Culard , b Bertrand Castaing , b Alain Roussel , b * and Axel Cloeckaerta INR et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4593,4594,2294.txt,11,0,,,,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in a Franck Coste , b Sylvie Canepa , c Marie-Christine Maurel , c Etienne Giraud , a Françoise Culard , b Bertrand Castaing , b Alain Roussel , b * and Axel Cloeckaerta INR et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4594,4595,2294.txt,12,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in Salmonella enterica Serovar Typhimurium Sylvie Baucheron et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4595,4596,2294.txt,13,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Binding of the RamR Repressor to Mutated Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in Salmonella enterica Serovar Typhimurium Sylvie Baucheron et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4596,4597,2294.txt,14,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in and INRA , UMR 6175 Plateforme d
"
4597,4598,2294.txt,15,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in and INRA , UMR 6175 Plateforme d
"
4598,4599,2294.txt,16,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in , UPR4301 , Orléans , Fra et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4599,4600,2294.txt,17,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in , UPR4301 , Orléans , Fra et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4600,4601,2294.txt,18,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in ; Centre de Biophysique Moléculaire C et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4601,4602,2294.txt,19,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in ; Centre de Biophysique Moléculaire C et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4602,4603,2294.txt,20,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in UR1282 Infectiologie Animale et Santé Publique , Nouzilly , Franc et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4603,4604,2294.txt,21,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in UR1282 Infectiologie Animale et Santé Publique , Nouzilly , Franc et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4604,4605,2294.txt,22,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in a Franck Coste , b Sylvie Canepa , c Marie-Christine Maurel , c Etienne Giraud , a Françoise Culard , b Bertrand Castaing , b Alain Roussel , b * and Axel Cloeckaerta INR et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4605,4606,2294.txt,23,0,,,,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in a Franck Coste , b Sylvie Canepa , c Marie-Christine Maurel , c Etienne Giraud , a Françoise Culard , b Bertrand Castaing , b Alain Roussel , b * and Axel Cloeckaerta INR et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4606,4607,2294.txt,24,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in Salmonella enterica Serovar Typhimurium Sylvie Baucheron et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in nce by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4607,4608,2294.txt,25,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Binding of the RamR Repressor to Wild-Type Promoters of the ramA Gene Involved in Efflux-Mediated Multidrug Resistance in Salmonella enterica Serovar Typhimurium Sylvie Baucheron et moléculaires , Nouzilly , Francec The transcriptional activator RamA is involved in ed in multidrug resi by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenic Enterobacteriaceae .
"
4608,4609,2294.txt,26,0,,,,"that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in other Enterobacter-iaceae .11 -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
4609,4610,2294.txt,27,1,Salmonella,Salmonella,Salmonella,"that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
4610,4611,2294.txt,28,0,,,,"that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in other Enterobacter-iaceae .11 -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
4611,4612,2294.txt,29,1,Salmonella,Salmonella,Salmonella,"that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
4612,4613,2294.txt,30,0,,,,"that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in other Enterobacter-iaceae .11 -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
4613,4614,2294.txt,31,1,Salmonella,Salmonella,Salmonella,"that the transcriptional activator RamA , plays the dominant role in the regulation of AcrAB -- TolC in Salmonella -- 17 To date have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
4614,4615,2294.txt,32,0,,,,"This derepression presumably results , as previously observed with other known ramA inducers , in increased levels of the RamA protein .27,28 Using in-vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .
"
4615,4616,2294.txt,33,0,,,,"This derepression presumably results , as previously observed with chlorpromazine , in increased levels of the RamA protein .27,28 Using in-vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region .
"
4616,4617,2294.txt,34,0,,,,"This derepression presumably results , as previously observed with indole , in increased levels of the RamA protein .27,28 Using in-vitro acellular experiments , we showed that bile achieves this effect by inhibiting the binding of the RamR repressor to the ramA promoter region ."
4617,4618,2280.txt,1,0,,,,"Interestingly , lacZ fusion was also positively regulated by LeuO ."
4618,4619,1951.txt,1,0,,,,Experiments with purified CsgD are needed to determine whether CsgD can activate transcription by E S and/or E 70 at the csgB promoters .
4619,4620,1789.txt,1,1,Escherichia coli,E. coli,Escherichia coli,S2 based on the report that E. coli KdgR contributes to the regulation of eda .
4620,4621,553.txt,1,0,,,,The involvement of Fis in negative regulation of ndk was of interest .
4621,4622,1979.txt,1,0,,,,"While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .
"
4622,4623,1979.txt,2,0,,,,"In addition , the possibility that ArcZ is required for RpoS-regulated expression of csgD irrespectively of RpoS levels can not be excluded .
"
4623,4624,1979.txt,3,0,,,,"In addition , the RpoS-dependent sRNA SdsR controls csgD expression most likely via a transcriptional regulator .
"
4624,4625,1979.txt,4,0,,,,RpoS can bind to the csgD promoter .
4625,4626,235.txt,1,0,,,,"To confirm that CpxR regulates hilA through not directly , we analyzed the effect of CpxR on the expression of hilA in the presence or not of HilD .
"
4626,4627,235.txt,2,0,,,,"To confirm that CpxR regulates hilA through HilD , we analyzed the effect of CpxR on the expression of hilA in the presence or not of HilD .
"
4627,4628,235.txt,3,0,,,,"mutant _ indicating that CpxR regulates hilA through not directly
"
4628,4629,235.txt,4,0,,,,"mutant _ indicating that CpxR regulates hilA through HilD
"
4629,4630,235.txt,5,0,,,,"mutant _ indicating that CpxR regulates hilA through not directly
"
4630,4631,235.txt,6,0,,,,mutant _ indicating that CpxR regulates hilA through HilD
4631,4632,221.txt,1,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
4632,4633,221.txt,2,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .
"
4633,4634,221.txt,3,1,Salmonella,Salmonella,Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
4634,4635,221.txt,4,1,Salmonella,Salmonella,Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd in-vitro , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .
"
4635,4636,221.txt,5,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
4636,4637,221.txt,6,2,Salmonella;Escherichia coli,Salmonella;Escherichia coli,Escherichia coli;Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes Escherichia coli is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- .
"
4637,4638,221.txt,7,1,Salmonella,Salmonella,Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- E.A.G. , unpublished results -RRB- .
"
4638,4639,221.txt,8,1,Salmonella,Salmonella,Salmonella,"Despite the lack of conservation in this atypically located regulatory site , we demonstrated that the PhoP protein binds to the Salmonella ugd promoter in-vivo , inactivation of the PhoP box in the ugd promoter abolishes PhoP-dependent ugd transcription is unable to promote ugd transcription under the PhoP-dependent conditions -LRB- C. Mouslim , unpublished results -RRB- ."
4639,4640,547.txt,1,0,,,,Dam-dependent regulation of invF was still observed in RtsA backgrounds
4640,4641,1038.txt,1,0,,,,"RcsA-RcsB-regulated genes are primarily involved in exopolysaccharide ( EPS ) production and include the 19-gene colanic acid capsular operon and the yjbEFGH operon , which encodes the biosynthesis of a distinct EPS ( 18 , 19 ) ."
4641,4642,2257.txt,1,0,,,,"These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) ."
4642,4643,1986.txt,1,1,unidentified plasmid;unidentified plasmid,plasmid;plasmid,unidentified plasmid,We next examined transcription of the two Fur-repressed genes in the strain that carried deletions of the rstA and fur genes and harbored either the RstA expression plasmid or the plasmid vector ; analysis determined that the mRNA levels of fhuA and fhuF were similar to those in the fur deletion strain regardless of RstA expression ( Fig. 1B ) .
4643,4644,1992.txt,1,0,,,,"csrB binds CsrA , thereby reducing the level of free CsrA protein .
"
4644,4645,1992.txt,2,0,,,,"csrB binds CsrA , titrating it .
"
4645,4646,1992.txt,3,0,,,,"CsrA also activates transcription of csrB , possibly through indirect regulation of a transcription factor ."
4646,4647,2243.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4647,4648,1004.txt,1,1,Escherichia coli,E. coli,Escherichia coli,LeuO has also been shown to repress the acid stress regulator cadC in E. coli
4648,4649,590.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Fis represses transcription of the gyrB genes in E. coli .
"
4649,4650,590.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"Given the strong sequence similarity between the S. enterica gyrB gene , we anticipated that its promoter would show evidence of repression by Fis to a similar degree to approximately 1.5-fold .
"
4650,4651,590.txt,3,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"Given the strong sequence similarity between the S. enterica gyrB gene , we anticipated that its promoter would show evidence of repression by Fis to a similar degree to that .
"
4651,4652,590.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , Fis-mediated repression of the gyrB promoter acts not through blocking of RNA polymerase binding but through interference with the formation of an open transcription complex by the bound polymerase .
"
4652,4653,590.txt,5,0,,,,"the Fis protein is a repressor of gyrB transcription
"
4653,4654,590.txt,6,2,Escherichia coli;Salmonella;Salmonella,E. coli;S. enterica;enterica,Escherichia coli;Salmonella,"In E. coli , FIS binds the gyrB promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrB ."
4654,4655,1762.txt,1,0,,,,"PmrA has been shown to bind the promoters of other PmrA-regulated loci , including pmrCAB , pmrHFIJKLM , and pmrE ( ugd ) ( 1 , 56 ) .
"
4655,4656,1762.txt,2,0,,,,"PmrA has been shown to bind pmrCAB .
"
4656,4657,1762.txt,3,0,,,,"In addition , PmrA can autoregulate the pmrCAB operon to increase expression of th regulatory system in response to induction signals ."
4657,4658,1776.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"This lowering of acnA transcription was not observed when b-galactosidase activity from PacnA-lacZ was measured in anaerobic cultures of the S. Typhimurium fnr mutant , suggesting that FNR represses acnA expression ."
4658,4659,584.txt,1,0,,,,"We establish that this surface migration is dependent on the PhoP-activated MgtA-dependent pagM gene .
"
4659,4660,584.txt,2,1,Salmonella,Salmonella,Salmonella,"This motility requires the PhoP-activated mgtA , mgtC , and pagM genes , which specify a Mg2 + transporter , an inhibitor of Salmonella "
4660,4661,1010.txt,1,2,Cornu aspersum;Cantareus apertus,helix;helix,Cornu aspersum;Cantareus apertus,"We evaluated the utilities of these vectors by fusing the-helix domains of PspA and pneumococcal surface protein C ( PspC ) , to bla SS under the control of the Ptrc promoter .
"
4661,4662,1010.txt,2,2,Cornu aspersum;Cantareus apertus,helix;helix,Cornu aspersum;Cantareus apertus,"We evaluated the utilities of these vectors by fusing the-helix domains of pneumococcal surface protein A and pneumococcal surface protein C ( PspC ) , to bla SS under the control of the Ptrc promoter ."
4662,4663,2269.txt,1,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4663,4664,2269.txt,2,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4664,4665,2269.txt,3,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4665,4666,2269.txt,4,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4666,4667,2269.txt,5,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4667,4668,2269.txt,6,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4668,4669,2269.txt,7,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4669,4670,2269.txt,8,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4670,4671,2269.txt,9,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4671,4672,2269.txt,10,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4672,4673,2269.txt,11,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4673,4674,2269.txt,12,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4674,4675,2269.txt,13,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4675,4676,2269.txt,14,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4676,4677,2269.txt,15,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4677,4678,2269.txt,16,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4678,4679,2269.txt,17,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4679,4680,2269.txt,18,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4680,4681,2269.txt,19,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4681,4682,2269.txt,20,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4682,4683,2269.txt,21,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4683,4684,2269.txt,22,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4684,4685,2269.txt,23,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4685,4686,2269.txt,24,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
4686,4687,2269.txt,25,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"However , micF are also induced by stress signals in additional ways , it was suggested that S. enterica to salicylate activates MarA through binding to its repressor , MarR .
"
4687,4688,2269.txt,26,1,Escherichia coli,E. coli,Escherichia coli,"However , micF are also induced by stress signals in additional ways , it was suggested that exposure of E. coli activates MarA through binding to its repressor , MarR .
"
4688,4689,2269.txt,27,0,,,,"These results , together with the results of the induction of micF by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
4689,4690,2269.txt,28,0,,,,"These results , together with the results of the induction of micF by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
4690,4691,2269.txt,29,0,,,,"These results , together with the results of the induction of micF by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate ."
4691,4692,1760.txt,1,0,,,,"IscR was also demonstrated to repress hilD and subsequently Spi1 gene expression , consistent with the observation that an IscR mutant is hyper invasive in epithelial cells .
"
4692,4693,1760.txt,2,0,,,,"2.4 IscR represses the expression of hilD gene Next , to investigate the regulatory role of IscR on hilD , the expression of the hilD fusion was found to be about 1.5 fold up‐reg-ulated in an iscR muta .
"
4693,4694,1760.txt,3,0,,,,"2.4 IscR represses the expression of hilD gene Next , to investigate the regulatory role of IscR on hilD , the expression of the hilD fusion was measured to be about 1.5 fold up‐reg-ulated in an iscR muta .
"
4694,4695,1760.txt,4,0,,,,"The iscR mutation led to a 5.5 fold increase in hilD mRNA level compared to the wild‐type strain , confirming that IscR acts as a repressor of hilD ."
4695,4696,592.txt,1,1,Salmonella,Salmonella,Salmonella,Transcription of the Salmonella pcgL gene is regulated by the PhoP-PhoQ two-component system .
4696,4697,1006.txt,1,0,,,,"List of genes Description List of genes Description DNA-binding transcriptional dual regulator , global regulator of anaerobic-growth spaM Needle complex assembly protein fnr Type III secretion apparatus protein Needle complex export protein hilA fliA Invasion protein transcriptional activator RNA polymerase , sigma-28 factor invG invA Putative regulatory protein for type III secretion apparatus Type III secretion low calcium response chaperone LcrH/SycD ATP-dependent Clp protease proteolytic subunit invF clpP Needle complex pathogenicity 1 island effector Description for the genes in Figure 11b .
"
4697,4698,1006.txt,2,0,,,,"List of genes Description List of genes Description DNA-binding transcriptional dual regulator , global regulator of anaerobic-growth spaM Needle complex assembly protein fnr Type III secretion apparatus protein Needle complex export protein hilA fliA Invasion protein transcriptional activator RNA polymerase , sigma-28 factor invG invA Putative regulatory protein for type III secretion apparatus Type III secretion low calcium response chaperone LcrH/SycD ATP-dependent Clp protease proteolytic subunit invF clpP Needle complex inner membrane protein Description for the genes in Figure 11b .
"
4698,4699,1006.txt,3,0,,,,"List of genes Description List of genes Description DNA-binding transcriptional dual regulator , global regulator of anaerobic-growth spaM Needle complex assembly protein fnr Type III secretion apparatus protein Needle complex export protein hilA fliA Invasion protein transcriptional activator RNA polymerase , sigma-28 factor invG invA Putative regulatory protein for type III secretion apparatus Type III secretion low calcium response chaperone LcrH/SycD ATP-dependent Clp protease proteolytic subunit invF clpP Needle complex pathogenicity 1 island effector protein sicA/spaT prgH Surface presentation of antigens protein SpaS Invasion-associated .
"
4699,4700,1006.txt,4,0,,,,"List of genes Description List of genes Description DNA-binding transcriptional dual regulator , global regulator of anaerobic-growth spaM Needle complex assembly protein fnr Type III secretion apparatus protein Needle complex export protein hilA fliA Invasion protein transcriptional activator RNA polymerase , sigma-28 factor invG invA Putative regulatory protein for type III secretion apparatus Type III secretion low calcium response chaperone LcrH/SycD ATP-dependent Clp protease proteolytic subunit invF clpP Needle complex inner membrane protein protein sicA/spaT prgH Surface presentation of antigens protein SpaS Invasion-associated ."
4700,4701,1012.txt,1,0,,,,"The expression of ilvIH gene products is inhibited by leucine , apparently due to a requirement for Lrp for activation of ilvIH transcription .
"
4701,4702,1012.txt,2,0,,,,"The expression of AHAS III is inhibited by leucine , apparently due to a requirement for Lrp for activation of ilvIH transcription ."
4702,4703,586.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"More recently , it was shown that leuO expression in E. coli can be activated by the BglJ regulators .
"
4703,4704,586.txt,2,0,,,,"Also , LeuO expression was detected in a phosphate-restricted media ; and recently it was shown that the expression of the leuO gene can be activated by BglJ regulators LeuO HAS SEVERAL FUNCTIONS IN VIVO Even though LeuO is expressed at very low level in standard laboratory conditions , it seems that in-vivo it has a role in bacterial survival ."
4704,4705,1774.txt,1,0,,,,"Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- S -RSB- cluster is reversibly inactivated by NO .
"
4705,4706,1774.txt,2,0,,,,"Expression of hmpA is under the control of the redox active repressor NsrR , whose -LSB- Fe is reversibly inactivated by NO ."
4706,4707,1984.txt,1,0,,,,"These results indicate that the autoregulation of tufB gene expression is independent from transcriptional initiation of its regulation by Fis .
"
4707,4708,1984.txt,2,0,,,,"These results indicate that the autoregulation of tufB gene expression is independent from transcriptional initiation of its regulation by Fis .
"
4708,4709,1984.txt,3,0,,,,"These results indicate that the autoregulation of tufB gene expression is independent from transcriptional initiation of the operon by Fis .
"
4709,4710,1984.txt,4,1,Salmonella,Salmonella,Salmonella,"The gene Fis-binding sites upstream of the promoter ( Van Delft independent regulation of the tufB gene in Salmonella , Fig. 9 ."
4710,4711,2255.txt,1,0,,,,"Furthermore , PAT DE4 was positive for the outer membrane receptor gene instead of but no signal was obtained for the islet genes htrE ( probable porin/fimbrial assembly protein ) , sopD2 ( secreted effector protein ) , srfJ ( putative virulence factor , activated by transcription factor SsrB ) and sseK2 ( translocated effector protein SSEK2 by type III secretion system ) while pagK ( PhoPQ-activated protein ) was present only in this array type ."
4711,4712,2241.txt,1,0,,,,phoN is transcriptionally activated by PhoP-PhoQ
4712,4713,1990.txt,1,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Pectinatus brassicae;Thermococcus aggregans,S. Typhi;Typhi;strain Ty;strain Ty,Thermococcus aggregans;Pectinatus brassicae;Salmonella enterica subsp. enterica serovar Typhimurium,"The influence of SlyASTy on the expression of clyASTy could not be directly studied in S. Typhi , because a non-virulent aroA mutant of strain Ty2 , was hence rather unsuitable as host strain
"
4713,4714,1990.txt,2,3,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Pectinatus brassicae;Thermococcus aggregans,S. Typhi;Typhi;strain Ty;strain Ty,Thermococcus aggregans;Pectinatus brassicae;Salmonella enterica subsp. enterica serovar Typhimurium,"The influence of SlyASTy on the expression of clyASTy could not be directly studied in S. Typhi , because a non-virulent aroA mutant of strain Ty2 , grew poorly on standard agar plates"
4714,4715,1748.txt,1,0,,,,"As previously reported , yggX mutant strains have increased expression of the SoxR reporter fpr ."
4715,4716,237.txt,1,0,,,,"Since the PhoP/PhoQ system represses hilA expression , it can be speculated that either both hilA are regulated by PhoP/PhoQ in an opposite way or VirK negatively influences hilA expression ."
4716,4717,551.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In fact , inactivation of stpA only has phenotypic effects in the absence of hns , indicating that the deletion of stpA is fully compensated by H-NS in E. coli .
"
4717,4718,551.txt,2,0,,,,One mechanism is mediated by the negative cross-regulation that both proteins exert on each other ; H-NS represses stpA transcription more strongly than StpA controls hns .
4718,4719,545.txt,1,1,Escherichia coli,E. coli,Escherichia coli,the V. cholerae CytR protein is able to repress transcription of the udp gene of E. coli in-vivo
4719,4720,223.txt,1,0,,,,"There is a much closer correspondence between the effects of IHF among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either IHF , as are the genes .
"
4720,4721,223.txt,2,0,,,,"There is a much closer correspondence between the effects of HU among the genes of the SPI2 pathogenicity island : the ssrA ssrB regulatory genes are downregulated in the absence of either IHF , as are the genes ."
4721,4722,2296.txt,1,1,Vibrio vulnificus,Vibrio vulnificus,Vibrio vulnificus,"Lee , H.J. , Park , S.J. , Choi , S.H. , Lee , K.H. Vibrio vulnificus rpoS expression is repressed by direct binding of cAMP-CRP complex to its two promoter regions .
"
4722,4723,2296.txt,2,0,,,,"The binding of cAMP-CRP complex to rpoS promoter were proved through exogenous cAMP addition , respectively .
"
4723,4724,2296.txt,3,0,,,,"The binding of cAMP-CRP complex to rpoS promoter were proved through lacZ fusion , respectively .
"
4724,4725,2296.txt,4,0,,,,"The binding of cAMP-CRP complex to rpoS promoter were proved through electrophoretic-mobility-shift assay , respectively .
"
4725,4726,2296.txt,5,1,unidentified,not shown,unidentified,"The whole rpoS promoter bound to CRP in data not shown .
"
4726,4727,2296.txt,6,0,,,,"The whole rpoS promoter bound to CRP in EMSA .
"
4727,4728,2296.txt,7,0,,,,"The cAMP-CRP complex is thought to be involved in the control of rpoS transcription
"
4728,4729,2296.txt,8,0,,,,"cAMP-CRP specifically bound to two sites of the rpoS promoter in-vitro .
"
4729,4730,2296.txt,9,0,,,,"It suggests that , except for cAMP-CRP , additional factors may also be involved in the regulation of rpoS transcription .
"
4730,4731,2296.txt,10,1,Vibrio vulnificus,Vibrio vulnificus,Vibrio vulnificus,"On the other hand , it has been reported that rpoS expression is repressed by direct binding of CRP-cAMP to its promoter region in Vibrio vulnificus .
"
4731,4732,2296.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Sun demonstrated direct binding of CRP to the rpoS promoter region in S. Typhimurium , where it is able to bind to two sites in this sequence .
"
4732,4733,2296.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Cheng demonstrated direct binding of CRP to the rpoS promoter region in S. Typhimurium , where it is able to bind to two sites in this sequence .
"
4733,4734,2296.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Both sites are conserved in S. Typhi rpoS promoter , suggesting a dir-ect binding by CRP .
"
4734,4735,2296.txt,14,0,,,,"This versatility can be explained , at least in part , by the fact that CRP is regulating rpoS ."
4735,4736,1947.txt,1,0,,,,"The otsBA operon is transcribed by the RpoSRNA polymerase holoenzyme ; therefore , the observation that the induction of the otsB gene occurs after the induction of rpoS is consistent with this transcriptional activation cascade .
"
4736,4737,1947.txt,2,0,,,,"The otsBA operon is transcribed by the RpoSRNA polymerase holoenzyme ; therefore , the observation that the induction of the otsB gene occurs after the induction of rpoS is consistent with this transcriptional activation cascade ."
4737,4738,579.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,Putative regulation by Fur was evaluated by generating three isogenic S. Typhi deletion mutants of argR .
4738,4739,1953.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4739,4740,2282.txt,1,0,,,,The CspC proteins increase stability of uspA mRNA facilitating steady-state expression .
4740,4741,948.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"PhoP-suppressed genes include prgH and fliC [ 55 -- 57 ] , PhoP-activated genes include pmrAB , another two-component signal transduction system involved primarily in the protection of Salmo-nella to cationic antimicrobial peptides ( CAMP , see below ) [ 58 ] , mgtA and mgtCB encoding Mg transport 2 + systems , phoN , a periplasmic non-specific acid phospha-tase , pcgL encoding a periplasmic D-Ala -- D-Ala dipeptidase , or pagL , pagP and pgtE which contribute to increased resistance to CAMPs [ 59 -- 62 ] ."
4741,4742,1204.txt,1,0,,,,"Moreover , s-54 N is involved in the growth-dependent regulation of rfaH ."
4742,4743,790.txt,1,0,,,,"slyA is positively regulated by HilD
"
4743,4744,790.txt,2,0,,,,slyA is positively regulated by HilD
4744,4745,1562.txt,1,0,,,,"One possible explanation of this finding is that the pstS mutation increases protein levels of FimZ , potentially activating transcription of its own gene , consistent with previous work by Yeh et al. ."
4745,4746,1576.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
4746,4747,1576.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4747,4748,784.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"The Escherichia coli SOS gene sbmC is regulated by RpoS during stationary growth phase .
"
4748,4749,784.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,The Escherichia coli SOS gene sbmC is regulated by RpoS during the SOS-induction .
4749,4750,1210.txt,1,0,,,,"plasmids _ expressing HhaD48N under control of the native hha promoter
"
4750,4751,1210.txt,2,0,,,,"plasmids _ expressing HhaD48N under control of the native hha promoter
"
4751,4752,1210.txt,3,0,,,,plasmids _ expressing HhaD48N under control of the native hha promoter
4752,4753,974.txt,1,0,,,,"To investigate whether z66 is regulated by FlhDC like other biphasic S. flhDC mutants were affected by the osmotic environment , an ompR mutant was also prepared ."
4753,4754,1238.txt,1,0,,,,"These data indicate that in STM4264 mutants , CsgD expression is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4754,4755,1238.txt,2,0,,,,"These data indicate that in STM4264 mutants , the rdar morphotype is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4755,4756,1238.txt,3,0,,,,"These data indicate that in STM1703 , STM1827 , STM3611 , CsgD expression is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4756,4757,1238.txt,4,0,,,,"These data indicate that in STM1703 , STM1827 , STM3611 , the rdar morphotype is upregulated , whereby STM1703 mutants showed the most pronounced upregulation of the rdar morphotype and expression of its master regulator CsgD .
"
4757,4758,1238.txt,5,0,,,,"In order to demonstrate that upregulation of the rdar morphotype in the STM1703 mutants is mediated by CsgD , csgD was knocked out in the STM1703 mutants ."
4758,4759,2057.txt,1,0,,,,"Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does upregulate hilE in an FimZ-dependent manner .
"
4759,4760,2057.txt,2,0,,,,"Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does not affect fimZ expression ."
4760,4761,2043.txt,1,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity ; Fis has also been shown to bind to the ssrA promoter .
"
4761,4762,2043.txt,2,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to have a positive influence on ssrA promoter activity ; Fis has also been shown to bind to the ssrA promoter .
"
4762,4763,2043.txt,3,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in bacteria ; Fis has also been shown to bind to the ssrA promoter .
"
4763,4764,2043.txt,4,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in bacteria ; Fis has also been shown to bind to the ssrA promoter .
"
4764,4765,2043.txt,5,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in LB medium ; Fis has also been shown to bind to the ssrA promoter .
"
4765,4766,2043.txt,6,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in Bertani medium ; Fis has also been shown to bind to the ssrA promoter .
"
4766,4767,2043.txt,7,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in LB medium ; Fis has also been shown to bind to the ssrA promoter .
"
4767,4768,2043.txt,8,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in Bertani medium ; Fis has also been shown to bind to the ssrA promoter .
"
4768,4769,2043.txt,9,0,,,,"Fis levels influence the ssrA promoter The Fis protein has been shown previously to influence the homeostatic control of DNA supercoiling in Escheri-chia coli .
"
4769,4770,2043.txt,10,0,,,,A role for Fis in the positive regulation of SPI-2 genes is also supported by a dem-onstration -- DNA complexes at the promoter regions of the ssrA .
4770,4771,960.txt,1,0,,,,"In addition to being a positive regulator of FlhD4C2 activity , FliZ posttranslationally activates the regulatory protein HilD , which , in turn , positively regulates the expression of hilA ."
4771,4772,753.txt,1,0,,,,"Rather , the FliA loop contributes to bistability by ensuring that expression of FliZ is strongly enhanced by FlhD4C2 due to fliZ ."
4772,4773,747.txt,1,0,,,,"Expression of genes under the control of MalT was , however , significantly reduced in the csrA mutant , approximately threeto 10-fold below the levels of the wild type ."
4773,4774,2094.txt,1,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin CAP , CRP family STM3466 crp 10.1371 / journal.ppat .1000306 .
"
4774,4775,2094.txt,2,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin CAP , CRP family STM3466 crp doi .
"
4775,4776,2094.txt,3,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin CAP , cyclic-AMP-receptor-protein STM3466 crp 10.1371 / journal.ppat .1000306 .
"
4776,4777,2094.txt,4,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin CAP , cyclic-AMP-receptor-protein STM3466 crp doi .
"
4777,4778,2094.txt,5,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin catabolite activator protein , CRP family STM3466 crp 10.1371 / journal.ppat .1000306 .
"
4778,4779,2094.txt,6,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin catabolite activator protein , CRP family STM3466 crp doi .
"
4779,4780,2094.txt,7,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin catabolite activator protein , cyclic-AMP-receptor-protein STM3466 crp 10.1371 / journal.ppat .1000306 .
"
4780,4781,2094.txt,8,0,,,,"g001 STM1444 slyA transcriptional regulator for hemolysin catabolite activator protein , cyclic-AMP-receptor-protein STM3466 crp doi ."
4781,4782,2080.txt,1,0,,,,the PhoP/Q _ regulated locus pagO
4782,4783,1589.txt,1,0,,,,"SsrB , in turn , activates ssaB .
"
4783,4784,1589.txt,2,0,,,,"SsrB , in turn , activates ssaB ."
4784,4785,1370.txt,1,0,,,,"7 min 25 min hilD AraC-family SPI1 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of f gen encoding heat-shock proteins .
"
4785,4786,1370.txt,2,0,,,,7 min 25 min hilD AraC-family transcriptional regulator 0.36 0.20 0.16 invA 0.34 0.25 0.17 EscV/YscV/HrcV family type III secretion system export apparatus protein Induction of Genes caused up regulation of f gen encoding heat-shock proteins .
4786,4787,1416.txt,1,0,,,,"While the results suggest that PgtABC , are most likely involved in the regulation of expression of the pgtP gene , alternatively , it is possible , although highly unlikely , that these polypeptides might be involved in posttranslational modulation of the PgtP activity
"
4787,4788,1416.txt,2,0,,,,These results indicate that PgtABC are involved in the regulation of expression of pgtP gene .
4788,4789,182.txt,1,0,,,,"The following studies show that PhoBR regulate hilE expression via the fimZ gene .
"
4789,4790,182.txt,2,0,,,,"Since the PhoBR signal regulates hilA via hilE , it was logical to examine whether the regulatory signal was transmitted through fimZ similar to that ."
4790,4791,196.txt,1,1,Escherichia coli,E. coli,Escherichia coli,LeuO has also been shown to repress the small RNA dsrA in E. coli
4791,4792,1402.txt,1,0,,,,"These data suggest that dps are negatively regulated by Fur in Fe-rich-medium .
"
4792,4793,1402.txt,2,0,,,,"hence are expressed under iron-replete conditions consistent with iron storage/detoxification roles , while dps are negatively regulated by Fur"
4793,4794,68.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
4794,4795,68.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
4795,4796,1364.txt,1,0,,,,"In agreement with the inability of the rcsA mutation to restore invasion to the rcsC11 mutant , the inhibition of transcription of the invG gene was RcsA Fig. 3D .
"
4796,4797,1364.txt,2,0,,,,"In agreement with the inability of the rcsA mutation to restore invasion to the rcsC11 mutant , the inhibition of transcription of the invG gene was RcsA independent ."
4797,4798,828.txt,1,0,,,,"It is interesting to note that several regulators of HilD , were found in significantly lower levels in the dam mutant ."
4798,4799,40.txt,1,0,,,,"Fis binds to a 280-bp spvR gene fragment .
"
4799,4800,40.txt,2,0,,,,"A DNA sequence from the promoter of the spvR gene , known not to be Fis-regulated ( our unpublished data ; see also supplementary data Tables S1 and S2 at http://mic.sgmjournals.org ) , was used as a negative control ."
4800,4801,800.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"-LRB- A to D -RRB- The expression of the master regulator of rdar morphotype expression , CsgD , in the STM1344 mutant was downregulated in comparison to that in wild-type S. Typhimurium UMR1 .
"
4801,4802,800.txt,2,0,,,,"STM1344 positively affects the expression of the major regulator of CsgD , through the downregulation of the expression of the phosphodiesterases STM1703 and STM3611 .
"
4802,4803,800.txt,3,0,,,,"Römlin , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .
"
4803,4804,800.txt,4,0,,,,"Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .
"
4804,4805,800.txt,5,0,,,,"Römlin , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .
"
4805,4806,800.txt,6,0,,,,"Simm , R. , Remminghorst , U. , Ahmad , I. , Zakikhany , K. , , U. A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility .
"
4806,4807,800.txt,7,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility in Salmonella enterica serovar Typhimurium .
4807,4808,2123.txt,1,0,,,,"DISCUSSION Because our previous operon fusion study indicated that the fliA mutations have no significant effect on the expression level of the class 2 operons , the FliA-FlgM regulatory system has been believed to be specific for the transcriptional control of class 3 ."
4808,4809,2137.txt,1,0,,,,"In the case of SPI-3 , MarTSTm regulates the transcription of misL ."
4809,4810,6.txt,1,0,,,,"Taken together , these results show that CpxR represses the autoregulation of ssrB located in SPI-2 ."
4810,4811,54.txt,1,0,,,,All of the genes belong to the phoPQ regulon although the ugd genes are regulated by PhoPQ indirectly through the PmrAB signal transduction system .
4811,4812,1358.txt,1,0,,,,"the mechanism _ resulting in regulation of csgD expression by MltC
"
4812,4813,1358.txt,2,0,,,,"Therefore , the MltE MltC-dependent regulation of csgD expression occurs regulating biofilm formation , suggesting the existence of a novel signaling pathway .
"
4813,4814,1358.txt,3,0,,,,"Therefore , the MltE MltC-dependent regulation of csgD expression occurs independently of major signaling pathways sensing turnover , suggesting the existence of a novel signaling pathway .
"
4814,4815,1358.txt,4,0,,,,"Therefore , the MltE MltC-dependent regulation of csgD expression occurs independently of major signaling pathways sensing cell wall disturbance , suggesting the existence of a novel signaling pathway ."
4815,4816,814.txt,1,0,,,,"potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD promoters .
"
4816,4817,814.txt,2,0,,,,"In vitro transcription assays with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the csgD promoters .
"
4817,4818,814.txt,3,1,Salmonella,Salmonella,Salmonella,"In vitro transcription experiments with purified Crl protein of Salmonella showed that Crl stimulates S-dependent transcription at the csgD promoters .
"
4818,4819,814.txt,4,0,,,,"Crl protein activates in-vitro-transcription by E S from the csgD promoters .
"
4819,4820,814.txt,5,0,,,,"Together , these results showed that Crl enhanced both the rate of formation of open complexes by E S from the csgD promoters .
"
4820,4821,814.txt,6,0,,,,"Together , these results showed that Crl enhanced both the quantity of open complexes by E S from the csgD promoters .
"
4821,4822,814.txt,7,0,,,,"In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the csgD genes ; these genes are involved in the biosynthesis of cellulose .
"
4822,4823,814.txt,8,0,,,,In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the csgD genes ; these genes are involved in the biosynthesis of curli .
4823,4824,627.txt,1,0,,,,kan parent strain _ indicating that HilD can overcome the decreased expression of invF
4824,4825,141.txt,1,0,,,,"A role for Fis in the positive regulation of SPI-2 genes is also supported by a dem-onstration -- DNA complexes at the promoter regions of the ssaG genes .
"
4825,4826,141.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Ryu , S. Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .
"
4826,4827,141.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Ryu , S. Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .
"
4827,4828,141.txt,4,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .
"
4828,4829,141.txt,5,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .
"
4829,4830,141.txt,6,0,,,,"Fis binds directly to the promoter regions of ssaG
"
4830,4831,141.txt,7,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Fis is required for proper regulation of ssaG expression in Salmonella enterica serovar Typhimurium .
4831,4832,155.txt,1,1,synthetic construct;synthetic construct,Synthetic;Synthetic,synthetic construct,"Synthetic minimal-medium with limiting ( PCN-P media ) was used for the analyses of promoters under control of the SsrB regulatory system in-vitro as described .33 Synthetic medium was supplemented with 1 mM adenine for growth of the auxotrophic purD strain .
"
4832,4833,155.txt,2,1,synthetic construct;synthetic construct,Synthetic;Synthetic,synthetic construct,"Synthetic minimal-medium with PCN media amounts of phosphate was used for the analyses of promoters under control of the SsrB regulatory system in-vitro as described .33 Synthetic medium was supplemented with 1 mM adenine for growth of the auxotrophic purD strain .
"
4833,4834,155.txt,3,1,synthetic construct;synthetic construct,Synthetic;Synthetic,synthetic construct,Synthetic minimal-medium with non-limiting amounts of phosphate was used for the analyses of promoters under control of the SsrB regulatory system in-vitro as described .33 Synthetic medium was supplemented with 1 mM adenine for growth of the auxotrophic purD strain .
4834,4835,633.txt,1,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"A mutation in the S. enterica serovar Typhimurium phoQ gene which results in a threonine residue at codon 48 being replaced with an isoleucine results in overexpression of several PhoP-activated genes ( 8 , 19 , 20 , 24 ) .
"
4835,4836,633.txt,2,0,,,,"PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl .
"
4836,4837,633.txt,3,0,,,,"a phoQ mutation results in increased expression of PhoP-activated genes
"
4837,4838,633.txt,4,1,Salmonella,Salmonella,Salmonella,"Transcriptional regulation of Salmonella virulence -- a phoQ periplasmic domain mutation results in increased net phosphotransfer to PhoP .
"
4838,4839,633.txt,5,4,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Mus sp.,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;mice,Salmonella enterica;Mus sp.;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Inactivation of the phoP or levels of the PhoP-activated genes increased , phoQ genes renders Salmonella enterica serovar reached a peak that was lower than that obtained Typhimurium five orders of magnitude less when Salmonella was induced at 50 mM Mg2 + virulent for mice and unable to proliferate within ( except for the mgtA gene , which reached the phagocytic cells ( 4-6 ) .
"
4839,4840,633.txt,6,0,,,,"RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) .
"
4840,4841,633.txt,7,0,,,,"If MgtA exerts its regulatory function by removing Mg2 + away from PhoQ , deletion of the mgtA gene should not affect expression of PhoP-activated genes in a strain lacking the phoQ gene .
"
4841,4842,633.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhimurium strains with mutations in phoQ that have variable expression of PhoP-activated genes ( pag ) were constructed to study GPL regulation .
"
4842,4843,633.txt,9,1,Salmonella;Salmonella;Salmonella;Salmonella;Salmonella;Salmonella,S. enterica;enterica;S. enterica;enterica;S. enterica;enterica,Salmonella,"A S. enterica strain expressing PhoQ ( N67D , E112D ) from its normal chromosomal location induced the PhoP-activated phoP gene like the isogenic strain with the wild-type S. enterica phoQ gene ( Fig. 3A ) ; this result argues that these periplasmic residues are not essential for the response to acidic pH. The PhoQ proteins from both S. enterica and S. bongori harbor a histidine residue at position 157 ."
4843,4844,83.txt,1,0,,,,"These data suggest that FadR act independently to control hilA expression .
"
4844,4845,83.txt,2,0,,,,FadR apparently functions independently to control hilA transcription .
4845,4846,169.txt,1,0,,,,NagC is the repressor of the divergent nagE -- nagBACD operon .
4846,4847,97.txt,1,0,,,,"Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of and its homolog FlrC in the upstream regions and ORFs of sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .
"
4847,4848,97.txt,2,0,,,,"Probable role of YfhA in osmoregulation of T6SS The presence of several binding sites of YfhA in the upstream regions and ORFs of sciS , coupled to the fact that YfhA is also a non-cognate response regulator of EnvZ , strongly indicates the involvement of YfhA in osmoregulation of T6SS .
"
4848,4849,97.txt,3,0,,,,"In the present study , sciS were also predicted to have binding sites of YfhA within their ORFs .
"
4849,4850,97.txt,4,0,,,,"Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA mediated regulation of sciS ."
4850,4851,380.txt,1,0,,,,These results imply that Lrp-mediated regulation of the hilA affects expression of the SPI-1 effectors .
4851,4852,1614.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"that McbR are both able to induce expression of the yciGFE locus in E. coli K-12
"
4852,4853,1614.txt,2,1,Salmonella,Salmonella,Salmonella,that McbR are both able to induce expression of the yciGFE locus in Salmonella
4853,4854,1172.txt,1,0,,,,"5 100 2 prpR JE4766 JE4593 PrpR -LRB- WT -RRB- PrpR -LRB- DA domain -RRB- c 940 ± 45 62 prpR234 prpR235 prpR236 JE6634 JE6635 180 ± 26 260 ± 26 19 28 12 17 F129L E50K prpR237 prpR238 JE6636 JE6637 190 ± 4 980 ± 15 20 13 65 D37N A162T 104 S33R F49L prpR239 prpR240 JE6638 JE6639 580 ± 22 415 ± 21 62 44 38 28 E172G F49S prpR241 prpR242 JE6672 JE6673 65 ± 4 170 ± 9 7 4 18 11 S33N E142K prpR243 prpR244 JE6674 JE6675 500 ± 4 530 ± 77 53 56 33 35 R24S prpR245 prpR246 JE6865 JE6762 490 ± 10 85 ± 12 52 9 32 6 Y180H L47P S21P prpR247 prpR248 JE6763 JE6764 360 ± 22 90 ± 5 38 24 9 6 R24H G104E prpR249 prpR250 JE6765 JE6766 350 ± 47 70 ± 14 37 23 7 5 K81H F178C prpR251 prpR252 JE6767 JE6768 350 ± 12 570 ± 13 37 23 61 36 38 23 340 ± 34 JE6769 D31G prpR253 PrpR is different from other well-studied members of this family of activators , such as XylR and DmpR , in which the region linking the sensing and catalytic domains contains a coiled-coil structure that is important for controlling binding of the effector molecule and activation of the protein ."
4854,4855,1166.txt,1,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) ."
4855,4856,1600.txt,1,0,,,,"Activation of the acrAB operon is achieved through the direct binding of a positive regulator of the AraC/XylS family , to the operator regions of these genes .
"
4856,4857,1600.txt,2,0,,,,"Activation of the acrAB operon is achieved through the direct binding of a positive regulator of the AraC/XylS family , to the operator regions of these genes .
"
4857,4858,1600.txt,3,1,Salmonella,Salmonella,Salmonella,"For example , acrAB transcription in Salmonella is controlled by the AraC/XylS-like regulators RamA ."
4858,4859,394.txt,1,0,,,,"Furthermore , PmrA activates the expression of several pags , including pmrCAB itself , under low cation conditions in a PhoP-dependent manner ; however , PmrA can also induce these genes under acid conditions in the absence of PhoPQ regardless of cation concentrations ."
4859,4860,1628.txt,1,1,unidentified,unknown,unidentified,"A previous study concluded that FadD positively regulates hilA expression in the absence of external LCFAs by an unknown FadR-independent mechanism .
"
4860,4861,1628.txt,2,0,,,,"The authors suggested that fatty acid and/or their derivatives , activated by FadD , may act as intracellular signals to regulate hilA expression , it has also been demonstrated that LCUFAs , present in the bacterial growth medium , exert a repressive action on the PhoP/PhoQ system activity .
"
4861,4862,1628.txt,3,0,,,,"The authors suggested that fatty acid and/or their derivatives , activated by FadD , may act as intracellular signals to regulate hilA expression , it has also been demonstrated that long chain unsaturated free fatty-acids , present in the bacterial growth medium , exert a repressive action on the PhoP/PhoQ system activity ."
4862,4863,343.txt,1,0,,,,"Furthermore , CreB is also known to positively regulate pta ."
4863,4864,425.txt,1,0,,,,"These data confirmed that RcsB positively controls dps expression , mainly playing the role of an inductor during the exponential phase .
"
4864,4865,425.txt,2,0,,,,"These results indicated that the most important contribution of RcsB in dps induction is produced when the PrcsDB promoter is activated during the exponential phase .
"
4865,4866,425.txt,3,0,,,,"In this sense , our micro-array results showed that RcsB induces transcription of dps in an RcsA-independent pathway , because gene expression was not affected in the rcsC11 rcsA mutant relative to those levels .
"
4866,4867,425.txt,4,0,,,,RcsB activates transcription of genes responsible for the dps gene .
4867,4868,431.txt,1,0,,,,"In addition , the lack of consensus PmrA-binding sites in the promoters of STM1257 suggested that these genes may be indirectly activated by PmrA ."
4868,4869,357.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
4869,4870,1833.txt,1,0,,,,"InvF positively regulates effector proteins within sipB and located outside -LRB- sopE -RRB- with the help of chaperone SicA .
"
4870,4871,1833.txt,2,0,,,,"InvF positively regulates effector proteins within sipB and located outside -LRB- sopD -RRB- with the help of chaperone SicA .
"
4871,4872,1833.txt,3,0,,,,"InvF positively regulates effector proteins within sipB and located outside -LRB- sopB -RRB- with the help of chaperone SicA .
"
4872,4873,1833.txt,4,0,,,,InvF induces the expression of sipB -LSB- 14e16 -RSB- .
4873,4874,419.txt,1,0,,,,"The sroC expression was quantified by qRT-PCR , revealing an induction of ∼ 6 times in WT cells at t late-log pha , indicating a positive effect of RpoS on SroC expression ."
4874,4875,1199.txt,1,0,,,,It has been demonstrated that CreB can control the expression of talA .
4875,4876,1827.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
4876,4877,1198.txt,1,2,Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;Salmonella;Salmonella-specific;plasmid,Salmonella;unidentified plasmid,"Evaluation of the specificity o Salmonella P using various intestinal bacterial species * f CR primers virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .
"
4877,4878,1198.txt,2,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) ."
4878,4879,1826.txt,1,0,,,,Inactivation of sirA lowered the levels of two known inhibitors of CsrA activity .
4879,4880,1832.txt,1,0,,,,"the concentration of ssDNA returns to normal levels , cleavage of LexA is terminated -LRB- the lexA gene is itself regulated by LexA -RRB-
"
4880,4881,1832.txt,2,0,,,,"the concentration of ssDNA returns to normal levels , cleavage of LexA is terminated -LRB- the lexA gene is itself regulated by LexA -RRB-
"
4881,4882,1832.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"Among kanamycin-resistant tranductants , the presence of the lexA ( Ind ) mutation was confirmed through β-galactosidase assay after introduction of the pGE108 plasmid ( Table 2 ) which contains a LexA-regulated cea ∷ lacZ fusion ( Salles et al. , 1987 ) .
"
4882,4883,1832.txt,4,0,,,,"However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .
"
4883,4884,1832.txt,5,0,,,,"The increase in mutation rates in the lexA ( def ) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho .
"
4884,4885,1832.txt,6,0,,,,"To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .
"
4885,4886,1832.txt,7,0,,,,"This increase in DNA breaks in the lexA ( def ) strain is mediated by two endonucleases , UvrC and Cho , and the LexAcontrolled UvrB protein ( Koskiniemi and Andersson 2009 ) ."
4886,4887,418.txt,1,0,,,,"The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .
"
4887,4888,418.txt,2,0,,,,"Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .
"
4888,4889,418.txt,3,0,,,,"Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes ."
4889,4890,430.txt,1,0,,,,"Transcrip-2 + tion of PmrA-activated genes is induced in low Mg in a process that requires the PhoP and PhoQ proteins , the PhoP-activated pmrD gene as well as the PmrA and PmrB proteins ( Kox et al. , 2000 ) .
"
4890,4891,430.txt,2,2,Escherichia coli;Salmonella;Escherichia coli;Salmonella,E. coli;Salmonella;E. coli;Salmonella,Escherichia coli;Salmonella,"The highly divergent PmrD protein is responsible for this phenotype as replacement of the E. coli pmrD gene by its Salmonella counterpart resulted in an E. coli strain that transcribed PmrA-activated genes and displayed poly-myxin B resistance under the same conditions as Salmonella .
"
4891,4892,430.txt,3,2,Escherichia coli;Salmonella;Escherichia coli,E. coli;Salmonella;E. coli,Escherichia coli;Salmonella,"This behavior is due to the highly divergent PmrD protein ( Figs. 6 and 7 ) , because replacement of the E. coli pmrD gene by the Salmonella pmrD gene endowed E. coli with the ability to transcribe the PmrA-activated pbgP gene and to exhibit resistance to polymyxin B in response to the low Mg2 signal ( Fig. 3 ) ."
4892,4893,356.txt,1,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , Nore , F. 1997 Relationships between H-NS , sigma S , growt phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4893,4894,356.txt,2,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , Nore , F. 1997 Relationships between H-NS , sigma S , Spv phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4894,4895,356.txt,3,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , L , F. 1997 Relationships between H-NS , sigma S , growt phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4895,4896,356.txt,4,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , L , F. 1997 Relationships between H-NS , sigma S , Spv phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4896,4897,356.txt,5,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , Kowart , F. 1997 Relationships between H-NS , sigma S , growt phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4897,4898,356.txt,6,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , Kowart , F. 1997 Relationships between H-NS , sigma S , Spv phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4898,4899,356.txt,7,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , F , F. 1997 Relationships between H-NS , sigma S , growt phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4899,4900,356.txt,8,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schae ¡ er , F , F. 1997 Relationships between H-NS , sigma S , Spv phase in the control of spvR , the regulatory gene of the Salmonella dublin virulence plasmid .
"
4900,4901,356.txt,9,0,,,,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4901,4902,356.txt,10,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4902,4903,356.txt,11,0,,,,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4903,4904,356.txt,12,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4904,4905,356.txt,13,0,,,,"Norel , F. Relationships between H-NS S phase in the control of spvR , the regulatory gene of operon .
"
4905,4906,356.txt,14,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Norel , F. Relationships between H-NS S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4906,4907,356.txt,15,0,,,,"Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4907,4908,356.txt,16,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4908,4909,356.txt,17,0,,,,"Relationships between H-NS phase in the control of spvR , the regulatory gene of operon .
"
4909,4910,356.txt,18,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4910,4911,356.txt,19,0,,,,"Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , rowth phase in the control of spvR , the regulatory gene of peron .
"
4911,4912,356.txt,20,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , rowth phase in the control of spvR , the regulatory gene of he Salmonella plasmid virulence .
"
4912,4913,356.txt,21,0,,,,"Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , pvR phase in the control of spvR , the regulatory gene of peron .
"
4913,4914,356.txt,22,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule V , Schaeffer F , Kowarz L , Norel F. Relationships between H-NS , sigma S , pvR phase in the control of spvR , the regulatory gene of he Salmonella plasmid virulence .
"
4914,4915,356.txt,23,0,,,,"Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4915,4916,356.txt,24,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4916,4917,356.txt,25,0,,,,"Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4917,4918,356.txt,26,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4918,4919,356.txt,27,0,,,,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4919,4920,356.txt,28,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
4920,4921,356.txt,29,0,,,,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of operon .
"
4921,4922,356.txt,30,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , growth phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence ."
4922,4923,342.txt,1,0,,,,"RtsA can directly induce the hilA expression independent of HilD .
"
4923,4924,342.txt,2,0,,,,"RtsA can directly induce the hilA expression independent of HilC .
"
4924,4925,342.txt,3,0,,,,"In the present study , the expression from lac fusion was retained after disruption in Fig. 2A in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
4925,4926,342.txt,4,0,,,,"In the present study , the expression from the hilA was retained after disruption in Fig. 2A in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
4926,4927,342.txt,5,0,,,,"RtsA increases invasion gene expression by increasing transcription of hilA .
"
4927,4928,342.txt,6,0,,,,"These data suggest that RtsA may activate hilA expression in response to a set of signals .
"
4928,4929,342.txt,7,0,,,,"Like HilD , RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression .
"
4929,4930,342.txt,8,0,,,,"Like HilC , RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression .
"
4930,4931,342.txt,9,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , RtsA can independently induce expression of rtsA We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .
"
4931,4932,342.txt,10,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , RtsA can independently induce expression of rtsA We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .
"
4932,4933,342.txt,11,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , RtsA can independently induce expression of hilD We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .
"
4933,4934,342.txt,12,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , RtsA can independently induce expression of hilD We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .
"
4934,4935,342.txt,13,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , RtsA can independently induce expression of hilC We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .
"
4935,4936,342.txt,14,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , RtsA can independently induce expression of hilC We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .
"
4936,4937,342.txt,15,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , HilD can independently induce expression of rtsA We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .
"
4937,4938,342.txt,16,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , HilD can independently induce expression of rtsA We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .
"
4938,4939,342.txt,17,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , HilD can independently induce expression of hilD We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .
"
4939,4940,342.txt,18,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , HilD can independently induce expression of hilD We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .
"
4940,4941,342.txt,19,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , HilD can independently induce expression of hilC We have shown that RtsA , like HilD , induces expression of hilA by binding to the HilA promoter region .
"
4941,4942,342.txt,20,0,,,,"Thus these regulators form a self-reinforcing feed forward regulatory loop and increased expression or activity of one regulator leads to an increase in expression of the other regulators Results HilC , HilD can independently induce expression of hilC We have shown that RtsA , like HilC , induces expression of hilA by binding to the HilA promoter region .
"
4942,4943,342.txt,21,0,,,,"We wanted to determine if RtsA could induce expression of hilA in the absence of the other regulators .
"
4943,4944,342.txt,22,0,,,,"The data in Fig. 2 demonstrate that RtsA are able to induce expression of hilA in the absence of the other regulators .
"
4944,4945,342.txt,23,1,Terfezia pini,to 40,Terfezia pini,"Production of HilC induced expression of hilA ~ 120-fold , while RtsA induced expression of hilA 30-to 40-fold , similar to previously reported values .
"
4945,4946,342.txt,24,0,,,,"We show that RtsA can each independently activate expression of the hilA genes .
"
4946,4947,342.txt,25,0,,,,"However , RtsA normally act in concert to activate hilA .
"
4947,4948,342.txt,26,0,,,,"RtsA can activate expression of hilA .
"
4948,4949,342.txt,27,0,,,,"The mechanism by which RtsA activate expression of hilA
"
4949,4950,342.txt,28,0,,,,"That means that at least hilA are induced by RtsA proteins .
"
4950,4951,342.txt,29,0,,,,"Under high-osmolarity conditions , RtsA activate SPI1 genes indirectly through hilA .
"
4951,4952,342.txt,30,0,,,,"Under high-osmolarity conditions , RtsA activate SPI1 genes directly through hilA .
"
4952,4953,342.txt,31,0,,,,"RtsA are each capable of activating hilA transcription .
"
4953,4954,342.txt,32,0,,,,"Earlier work on mathematical modeling of regulation of expression of hilA by RtsA was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .
"
4954,4955,342.txt,33,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; 2001 ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
4955,4956,342.txt,34,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lee ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
4956,4957,342.txt,35,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RtsA are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
4957,4958,342.txt,36,0,,,,"hilA expression is induced by three transcriptional activators , RtsA .
"
4958,4959,342.txt,37,0,,,,"Inducible expression RtsA protein was sufficient to activate hilA following growth at 42 °C .
"
4959,4960,342.txt,38,0,,,,Transcription of the hilA gene is also stimulated by RtsA .
4960,4961,424.txt,1,0,,,,"yciF was initially identified by a screen for RpoSregulated genes and a putative RpoS-dependent promoter has been located upstream of yciG [ 39 ] .
"
4961,4962,424.txt,2,0,,,,"Because yciF was identified in a screen for RpoSregulated genes , we examined transcription of yciG : : luc with and without RpoS to determine if activation of yciGFE-katN by bile was dependent upon RpoS .
"
4962,4963,424.txt,3,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , yciF are regulated by the alternative sigma factor RpoS ."
4963,4964,1629.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Previously , a Salmonella enterica sero-var Typhimurium phoP locus mutant ( pho24 ) was isolated that constitutively expressed PhoP-activated genes ( pag ) and repressed PhoP-repressed genes ( prg ) ( 21 , 24 ) .
"
4964,4965,1629.txt,2,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .
"
4965,4966,1629.txt,3,0,,,,"Moreover , the macB genes were expressed to higher levels in a phoP mutant than in Fig. 4A , suggesting that these genes are repressed by PhoP as low Mg2 .
"
4966,4967,1629.txt,4,0,,,,"Moreover , the macB genes were expressed to higher levels in a phoP mutant than in the wild-type strain , suggesting that these genes are repressed by PhoP as low Mg2 .
"
4967,4968,1629.txt,5,0,,,,"Moreover , the macA genes were expressed to higher levels in a phoP mutant than in Fig. 4A , suggesting that these genes are repressed by PhoP as low Mg2 .
"
4968,4969,1629.txt,6,0,,,,"Moreover , the macA genes were expressed to higher levels in a phoP mutant than in the wild-type strain , suggesting that these genes are repressed by PhoP as low Mg2 .
"
4969,4970,1629.txt,7,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Inactivation of the phoP or levels of the PhoP-activated genes increased , phoQ genes renders Salmonella enterica serovar reached a peak .
"
4970,4971,1629.txt,8,0,,,,The expression profile of phoP is rather consistent with the proposed role of PhoP as a repressor of SPI-1 genes since phoP was expressed when the SPI-1 regulators have become to decline .
4971,4972,1167.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium;S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"While it may be tempting to speculate that repression of cadA transcription by Fis may represent a step in the expression of virulence in S. typhimurium , it is not known if lysine decarboxylase activity plays any role in S. typhimurium virulence ."
4972,4973,395.txt,1,0,,,,"RpoS is also required for the expression of MlrA and , at the same time activates the repressor cpxR ."
4973,4974,1601.txt,1,0,,,,"Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadC .
"
4974,4975,1601.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in SCV of macrophages .
"
4975,4976,1601.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both the cadC in the Salmonellacontaining vacuole of macrophages .
"
4976,4977,1601.txt,4,0,,,,"Activated OmpR then represses the cadC/BA operon by directly binding to both the cadC , leading to cytoplasmic acidification ."
4977,4978,1615.txt,1,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Escherichia coli;S. Typhi;Typhi,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"On the other hand , the transcriptional regulator Crp , previously described as an activator of hlyE transcription in Escherichia coli , is involved in transcriptional repression of hlyE in S. Typhi .
"
4978,4979,1615.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"The Crp regulator is involved in transcriptional repression of S. Typhi hlyE Crp is a transcriptional regulator previously reported to be an activator of hlyE transcription in E. coli .
"
4979,4980,1615.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"increased b-galactosidase activity in comparison with the parental strain _ suggesting that Crp is involved in downregulation of hlyE transcription in S. Typhi
"
4980,4981,1615.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"All these results together suggest that Crp is involved in downregulation of hlyE in S. Typhi .
"
4981,4982,1615.txt,5,0,,,,"Moreover , the addition of glucose to the growth medium results in decreasing the hlyE mRNA , suggesting that there is another factor related to catabolite-repression , different from Crp , involved in downregulation of hlyE Fig. 2 .
"
4982,4983,1615.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"In addition , we found that Crp is involved in downregulation of hlyE in S. Typhi .
"
4983,4984,1615.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Crp is involved in transcriptional repression of S. Typhi hlyE .
"
4984,4985,1615.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi;S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Nevertheless , addition of glucose to the growth medium results in a decrease of hlyE mRNA in S. Typhi Δcrp mutant , suggesting that there is another factor related to catabolite-repression , different from CRP , involved in down-regulation of hlyE in S. Typhi .
"
4985,4986,1615.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Nevertheless , genetic experiments showed that CRP participates in the negative regulation of hlyE in S. Typhi since crp deletion led to increased β-galactosidase activit .
"
4986,4987,1615.txt,10,0,,,,"Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .
"
4987,4988,1615.txt,11,0,,,,"CRP participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .
"
4988,4989,1615.txt,12,0,,,,"CRP participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay .
"
4989,4990,1615.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , CRP might repress hlyE expression by repressing rpoS in S. Typhi ."
4990,4991,381.txt,1,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , RpoS , DnaJ , DnaK , GrpE .
"
4991,4992,381.txt,2,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , RpoS , heat-shock .
"
4992,4993,381.txt,3,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , stationary-phase , DnaJ , DnaK , GrpE .
"
4993,4994,381.txt,4,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , osmolarity , H-NS , stationary-phase , heat-shock .
"
4994,4995,381.txt,5,0,,,,"The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , RpoS , DnaJ , DnaK , GrpE .
"
4995,4996,381.txt,6,0,,,,"The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , RpoS , heat-shock .
"
4996,4997,381.txt,7,0,,,,"The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , stationary-phase , DnaJ , DnaK , GrpE .
"
4997,4998,381.txt,8,0,,,,"The flhDC master operon is influenced by catabolite-repression , osmolarity , H-NS , stationary-phase , heat-shock .
"
4998,4999,381.txt,9,0,,,,"Transcription of the flhDC operon is known to be regulated by signals from a network of H-NS .
"
4999,5000,381.txt,10,0,,,,H-NS also regulate cell motility by interacting with the flhDC promoter .
5000,5001,1173.txt,1,0,,,,"FimZ is an activator of type was shown to represses flhDC .
"
5001,5002,1173.txt,2,0,,,,FimZ is an activator of type 1 fimbriae flhDC .
5002,5003,168.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .
"
5003,5004,168.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Levy demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .
"
5004,5005,168.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inhibited , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression .
"
5005,5006,168.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Ruiz demonstrated that when the AcrAB-TolC pump in Escherichia coli is inactivated , cellular metabolites accumulate , inactivating AcrR and/or upregulating marA expression ."
5006,5007,96.txt,1,0,,,,"Since a Tn5 insertion in this region disrupts the negative regulation by FIS we currently do not know if the transposon insertion decreases normal expression of hupB .
"
5007,5008,96.txt,2,0,,,,Since a Tn5 insertion in this region disrupts the negative regulation by FIS we currently do not know if the transposon insertion increases normal expression of hupB .
5008,5009,82.txt,1,0,,,,"Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of any other position along the whole operon .
"
5009,5010,82.txt,2,0,,,,"Although the regulation of the pefI-srgC operon is SdiA-dependent , no SdiA-box was found upstream of pefI along the whole operon .
"
5010,5011,82.txt,3,0,,,,"Second , we described the mechanism of regulation by SdiA on the promoter region located upstream of pefI .
"
5011,5012,82.txt,4,0,,,,a relatively high affinity _ demonstrating a direct regulation of the pefI-srgC operon by SdiA
5012,5013,154.txt,1,0,,,,"CsrA binds the 50-UTR of the fimAICDHF transcript To further investigate the mechanism , we determined whether CsrA can bind to the 50-UTR of the fimAICDHF transcript by an EMSA .
"
5013,5014,154.txt,2,0,,,,"CsrA binds the 50-UTR of the fimAICDHF transcript To further investigate the mechanism , we determined whether CsrA can bind to the 50-UTR of the fimAICDHF transcript by an EMSA .
"
5014,5015,154.txt,3,0,,,,"These results suggested that CsrA specifically binds the 50-UTR of the fimAICDHF transcript .
"
5015,5016,154.txt,4,0,,,,"These data suggested that CsrA bound specifically to GGA binding sites in the 50-UTR of the fimAICDHF transcript .
"
5016,5017,154.txt,5,0,,,,"Our finding that CsrA binds the 50-UTR of the fimAICDHF transcript raised the possibility that the fimAICDHF genes antagonized the regulatory effects of CsrA by a similar mechanism .
"
5017,5018,154.txt,6,0,,,,"Similarly , binding of CsrA to the 50-UTR of the fimAICDHF transcript had little effect on expression of FimA .
"
5018,5019,154.txt,7,0,,,,"little effect on expression of FimA _ suggesting that the main function 0 for the binding of CsrA to the 5-UTR of the fimAICDHF transcript was not to regulate expression of the
"
5019,5020,154.txt,8,0,,,,"Instead , our data raised the intriguing possibility that binding of the fimAICDHF mRNA to CsrA functioned mainly in regulating CsrA activity .
"
5020,5021,154.txt,9,0,,,,"In contrast , CsrA binding of mRNAs will be affected to a lesser extent by fluctuations in fimAICDHF-transcript levels .
"
5021,5022,154.txt,10,0,,,,"Thus , differences in the affi-nities of different mRNA targets for CsrA are predicted to determine the magnitude by which expression of each target is regulated by the 50-UTR of the fimAICDHF transcript ."
5022,5023,632.txt,1,0,,,,"Therefore , the slower increasing of FlhD proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of s ClpAP , HslVU and L .
"
5023,5024,632.txt,2,0,,,,"Therefore , the slower increasing of FlhD proteins in the ∆ dnaK cells could be due to the degradation of both monomers by the increased level of f protea ."
5024,5025,626.txt,1,0,,,,"There was a reprodu-cible decrease of approximately 200 Miller units in the rpoS null strain background suggesting either a small or indirect RpoS-mediated e ¡ ec
"
5025,5026,626.txt,2,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + spoT : : Apr-carry-ing strains DA2260 , respectively .
"
5026,5027,626.txt,3,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + spoT : : Apr-carry-ing strains DA2246 , respectively .
"
5027,5028,626.txt,4,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + spoT : : Apr-carry-ing strains DA2247 , respectively .
"
5028,5029,626.txt,5,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + relA : : Apr-carry-ing strains DA2260 , respectively .
"
5029,5030,626.txt,6,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + relA : : Apr-carry-ing strains DA2246 , respectively .
"
5030,5031,626.txt,7,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : : Apr into the crp + relA : : Apr-carry-ing strains DA2247 , respectively .
"
5031,5032,626.txt,8,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2173 strain : : Apr-carry-ing strains DA2260 , respectively .
"
5032,5033,626.txt,9,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2173 strain : : Apr-carry-ing strains DA2246 , respectively .
"
5033,5034,626.txt,10,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2173 strain : : Apr-carry-ing strains DA2247 , respectively .
"
5034,5035,626.txt,11,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2238 : : Apr-carry-ing strains DA2260 , respectively .
"
5035,5036,626.txt,12,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2238 : : Apr-carry-ing strains DA2246 , respectively .
"
5036,5037,626.txt,13,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2238 : : Apr-carry-ing strains DA2247 , respectively .
"
5037,5038,626.txt,14,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : its crp-803 : : Apr-carry-ing strains DA2260 , respectively .
"
5038,5039,626.txt,15,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : its crp-803 : : Apr-carry-ing strains DA2246 , respectively .
"
5039,5040,626.txt,16,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : its crp-803 : : Apr-carry-ing strains DA2247 , respectively .
"
5040,5041,626.txt,17,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2210 derivatives to obtain rpoS : : Apr-carry-ing strains DA2260 , respectively .
"
5041,5042,626.txt,18,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2210 derivatives to obtain rpoS : : Apr-carry-ing strains DA2246 , respectively .
"
5042,5043,626.txt,19,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : DA2210 derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , respectively .
"
5043,5044,626.txt,20,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : ppGpp0 derivatives to obtain rpoS : : Apr-carry-ing strains DA2260 , respectively .
"
5044,5045,626.txt,21,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : ppGpp0 derivatives to obtain rpoS : : Apr-carry-ing strains DA2246 , respectively .
"
5045,5046,626.txt,22,0,,,,"To that purpose , RpoS was inactivated by introducing mutation rpoS : ppGpp0 derivatives to obtain rpoS : : Apr-carry-ing strains DA2247 , respectively .
"
5046,5047,626.txt,23,0,,,,rpoS translation may inhibit flhDC transcription through an RpoS-mediated mechanism
5047,5048,140.txt,1,0,,,,"SoxS _ regulated , including fpr"
5048,5049,7.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
5049,5050,2136.txt,1,0,,,,The ArcAB system can also act as a positive regulator by the induction of cydAB
5050,5051,815.txt,1,0,,,,"-RRB- , narG -LRB- are positively regulated by SlyA"
5051,5052,1359.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"crl transcription in E. coli W3110 is repressed by Crl -LRB- by more than 10-fold -RRB- .
"
5052,5053,1359.txt,2,0,,,,These results suggested that crl transcription is not repressed by Crl in ATCC 14028 .
5053,5054,55.txt,1,0,,,,"HilD binds directly to the regulatory regions of the ssrAB operon .
"
5054,5055,55.txt,2,0,,,,"HilD binds to the regulatory region of ssrAB , promoting OmpR binding .
"
5055,5056,55.txt,3,0,,,,"HilD binds to the regulatory region of ssrAB , thereby counteracting H-NS mediated repression .
"
5056,5057,55.txt,4,0,,,,"Furthermore , electrophoretic-mobility-shift assays showed that both HilD bind to the ssrAB region containing the repressing sequences .
"
5057,5058,55.txt,5,0,,,,"the mechanism by which HilD regulate the expression of ssrAB for the first time that HilD is able to displace H-NS from one of its target genes
"
5058,5059,55.txt,6,0,,,,"RESULTS cis elements required for the regulation of ssrAB by HilD .
"
5059,5060,55.txt,7,0,,,,"all the cis elements _ required for the HilD-mediated regulation of ssrAB
"
5060,5061,55.txt,8,0,,,,"the 302/478 region _ required for the regulation of ssrAB by HilD
"
5061,5062,55.txt,9,0,,,,"negative regulatory sequences are required to maintain the HilD-mediated regulation of ssrAB
"
5062,5063,55.txt,10,0,,,,"the cis elements _ required for the HilD-mediated regulation of ssrAB
"
5063,5064,55.txt,11,1,Felis catus,cat,Felis catus,"The expression analysis of ssrAB-cat 10 fusions in the hilD mutant revealed that consecutive deletions of the 240 / FIG 3 Analysis of the cis-acting sequences required for the HilD-mediated regulation of ssrAB .
"
5064,5065,55.txt,12,1,Felis catus,cat,Felis catus,"The expression analysis of ssrAB-cat 69 revealed that consecutive deletions of the 240 / FIG 3 Analysis of the cis-acting sequences required for the HilD-mediated regulation of ssrAB .
"
5065,5066,55.txt,13,1,Felis catus,cat,Felis catus,"The expression analysis of ssrAB-cat 119 revealed that consecutive deletions of the 240 / FIG 3 Analysis of the cis-acting sequences required for the HilD-mediated regulation of ssrAB .
"
5066,5067,55.txt,14,1,Felis catus,cat,Felis catus,"The expression analysis of ssrAB-cat 240 revealed that consecutive deletions of the 240 / FIG 3 Analysis of the cis-acting sequences required for the HilD-mediated regulation of ssrAB .
"
5067,5068,55.txt,15,1,Felis catus,cat,Felis catus,"The expression analysis of the ssrAB-cat 336 revealed that consecutive deletions of the 240 / FIG 3 Analysis of the cis-acting sequences required for the HilD-mediated regulation of ssrAB .
"
5068,5069,55.txt,16,0,,,,"Our data from the expression analysis showed that HilD regulate the expression of ssrAB mainly by acting on the 119/336 regions , respectively .
"
5069,5070,55.txt,17,0,,,,"Our data from the expression analysis showed that HilD regulate the expression of ssrAB mainly by acting on the 55/240 regions , respectively .
"
5070,5071,55.txt,18,0,,,,"To further dissect ated regulation of ssrAB , we analyzed the interaction of HilD to different segments of the 302/478 region by EMSAs .
"
5071,5072,55.txt,19,0,,,,"To further dissect ated regulation of ssrAB , we analyzed the interaction of HilD to different segments of the 302/478 region by electro-phoretic mobility-shift assays .
"
5072,5073,55.txt,20,0,,,,"FIG 5 HilD bind to the same regions of ssrAB .
"
5073,5074,55.txt,21,0,,,,"DISCUSSION In this study , we elucidated the mechanism by which HilD regulate the expression of ssrAB .
"
5074,5075,55.txt,22,0,,,,"the cis elements _ required for positive HilD-mediated regulation of ssrAB
"
5075,5076,55.txt,23,0,,,,"HilD binds to close to most of the sites of ssrAB .
"
5076,5077,55.txt,24,0,,,,"The regions _ required for the regulation of ssrAB by HilD
"
5077,5078,55.txt,25,0,,,,"To determine how HilD to regulate the expression of ssrAB in response to different growth-conditions is a matter of future studies .
"
5078,5079,55.txt,26,0,,,,"To determine how HilD to regulate the expression of ssrAB in response to different growth-conditions is a matter of our current .
"
5079,5080,55.txt,27,0,,,,"HilD cooperate to directly control the expression of ssrAB in our unpublished results .
"
5080,5081,55.txt,28,0,,,,"HilD cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions .
"
5081,5082,55.txt,29,0,,,,"reciprocally , SPI-1-encoded HilD upregulates SPI-2 gene expression by directly binding the ssrAB operon"
5082,5083,801.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .
"
5083,5084,801.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .
"
5084,5085,801.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .
"
5085,5086,801.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Norel , F. Growth SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes .
"
5086,5087,801.txt,5,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Coynault , C. , Robbe-Saule , V. , Popoff , M.Y. , SpvR regulation of transcription of Salmonella typhimurium spvABC virulence genes ."
5087,5088,41.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"Both hypotheses need to be tested , but we already know that expression of sdiA from a plasmid increases the expression of SdiA-regulated genes in the absence of signal ( 1 , 22 ) .
"
5088,5089,41.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Given that the Salmo-nella promoters are confirmed to respond to chromosomal sdiA and AHL , whereas the ftsQP2 promoter is not , we suspect that the binding of SdiA to the ftsQP2 promoter may not be physiologically relevant .
"
5089,5090,41.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Bos taurus,S. Typhimurium;Typhimurium;cow,Bos taurus;Salmonella enterica subsp. enterica serovar Typhimurium,"Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in cow models of infection .
"
5090,5091,41.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Gallus gallus,S. Typhimurium;Typhimurium;chicken,Gallus gallus;Salmonella enterica subsp. enterica serovar Typhimurium,"Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in chicken .
"
5091,5092,41.txt,5,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus musculus,S. Typhimurium;Typhimurium;mouse,Mus musculus;Salmonella enterica subsp. enterica serovar Typhimurium,"Despite the regulation of putative virulence genes by SdiA , we have previously reported that an sdiA mutant of S. Typhimurium is not attenuated in mouse .
"
5092,5093,41.txt,6,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"Despite the regulation of putative virulence genes by SdiA , a sdiA mutant of S. enterica sv .
"
5093,5094,41.txt,7,0,,,,"Therefore , binding of plant compounds to SdiA can not explain the lack of sdiA expression in planta .
"
5094,5095,41.txt,8,0,,,,"It seems that SdiA needs the binding of AHLs for proper protein folding before interacting with DNA although some studies suggested that the overexpression of sdiA could be sufficient to activate it -LRB- without AHLs -RRB- .
"
5095,5096,41.txt,9,1,Mus sp.;Mus sp.,mice;mice,Mus sp.,"In mice , infection with a sdiA mutant resulted in increased bacterial loads in the livers of infected mice indicating that SdiA may be a negative regulator of virulence .
"
5096,5097,41.txt,10,1,Mus sp.;Mus sp.,mice;mice,Mus sp.,"In mice , infection with a sdiA mutant resulted in increased fecal shedding in the livers of infected mice indicating that SdiA may be a negative regulator of virulence .
"
5097,5098,41.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To test this hypothesis , we determined that S. typhimurium encodes SdiA regulated by sdiA ."
5098,5099,2122.txt,1,0,,,,"Rho-dependent transcriptional termination regulates tufB expression To further investigate the regulation of the tufB gene we decided to focus on two transcriptionally fused tufB-yfp alleles : a wild-type allele and a tufB G-29A allele .
"
5099,5100,2122.txt,2,0,,,,"Rho-dependent transcriptional termination regulates tufB expression To further investigate the regulation of the tufB gene we decided to focus on two transcriptionally fused tufB-yfp alleles : a wild-type allele and a tufB G-29A allele .
"
5100,5101,2122.txt,3,0,,,,"Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .
"
5101,5102,2122.txt,4,0,,,,"Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .
"
5102,5103,2122.txt,5,0,,,,"Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .
"
5103,5104,2122.txt,6,0,,,,"Using this experimental system we tested two hypotheses : that regulation of EF-TuB levels is influenced by RNase Emediated tufB mRNA degradation ; that the regulation of EF-TuB levels is influenced by Rho-dependent transcription termination .
"
5104,5105,2122.txt,7,0,,,,"The relative expression in the G-29A mutant was significantly reduced in the presence of the rho-111 allele indicating that Rho activity is involved in regulating the amount of tufB transcript -LRB- Supporting Information Table S4 -RRB- .
"
5105,5106,2122.txt,8,0,,,,"that Rho-dependent transcriptional termination is involved in the regulation of tufB gene expression
"
5106,5107,2122.txt,9,1,Salmonella,Salmonella,Salmonella,that the independent regulation of the tufB gene in Salmonella involves Rho-dependent transcription termination
5107,5108,1403.txt,1,0,,,,"Hence , it is likely that there exists a similar mechanism of phosphorylated YfhA-P mediated regulation of sciS ."
5108,5109,197.txt,1,0,,,,"Thus , the attenuated phenotype of aflgM mutant may be a consequence of overexpression of a FliA-regulated gene whose expression is normally modulated in a flgM 
"
5109,5110,197.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium;S. typhimurium;typhimurium;mice;S. typhimurium;typhimurium,Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium,"In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype .
"
5110,5111,197.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium;S. typhimurium;typhimurium;mice;S. typhimurium;typhimurium,Mus sp.;Salmonella enterica subsp. enterica serovar Typhimurium,"In this investigation , we observed that ( i ) the in-vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable , as were the amounts of flagellin produced by the strains ; ( ii ) the 50 % lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice ; and ( iii ) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype ."
5111,5112,829.txt,1,5,Salmonella;Salmonella enterica;Salmonella;Escherichia coli;Cornu aspersum;Cantareus apertus,Salmonella;Salmonella enterica;enterica;Escherichia coli;helix;helix,Cantareus apertus;Salmonella;Salmonella enterica;Cornu aspersum;Escherichia coli,"Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Ribosome Function in Salmonella enterica Biochemistry , Brown University , 60 Olive Street , Providence , Rhode Island 029122 The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine ( ) modifications at positions 1911 , 1915 , and 1917 in helix 69 of 23S rRNA .
"
5112,5113,829.txt,2,5,Salmonella;Salmonella enterica;Salmonella;Escherichia coli;Cornu aspersum;Cantareus apertus,Salmonella;Salmonella enterica;enterica;Escherichia coli;helix;helix,Cantareus apertus;Salmonella;Salmonella enterica;Cornu aspersum;Escherichia coli,"Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Growth Function in Salmonella enterica Biochemistry , Brown University , 60 Olive Street , Providence , Rhode Island 029122 The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine ( ) modifications at positions 1911 , 1915 , and 1917 in helix 69 of 23S rRNA ."
5113,5114,1365.txt,1,0,,,,"Fusion junction sequence determination Creating an inducible ssrB allele The fusion junctions of 10 SsrB-regulated fusions unlinked to SPI-2 were determined .
"
5114,5115,1365.txt,2,0,,,,"The next column demonstrates the specificity of the regulation to the intracellular environment by comparing the expression ratio of the three most highly SsrB-regulated fusions in a wild-type versus ssrB : : cm background in DMEM .
"
5115,5116,1365.txt,3,0,,,,"Results from DNase-I-protection assays provide direct evidence that SsrB binds at ssrB , although the binding sites lie within the .
"
5116,5117,1365.txt,4,0,,,,"Expression of an episomal copy of ssrB resulted in expression of SPI-2 genes in each mutant background , suggesting that SsrB is epistatic to other regulators for SPI-2 transcription .
"
5117,5118,1365.txt,5,0,,,,"Thus , one explanation for the transcription we observe following overexpression of ssrB may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins .
"
5118,5119,1365.txt,6,0,,,,"In addition , the SsrB regulator also directly binds and autoregulates the ssrB promoters to activate their expression .
"
5119,5120,1365.txt,7,0,,,,"Taken together , these lines of evidence suggest that the Fur repressor could interfere with binding of the SsrB activator to the ssrB promoter , leading to repression of ssrB transcription .
"
5120,5121,1365.txt,8,0,,,,"Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation .
"
5121,5122,1365.txt,9,0,,,,"To confirm that SsrA-dependent phosphorylation was not required for SsrB-mediated regulation of bio-films , we compared them to ssrB null mutants ."
5122,5123,69.txt,1,0,,,,"SoxS protein , activates sodA , glucose-6-phosphate dehydrogenase .
"
5123,5124,69.txt,2,0,,,,"SoxS protein , activates sodA , zwf .
"
5124,5125,69.txt,3,0,,,,"SoxS protein , activates sodA , antisense RNA to the porin OmpF mRNA .
"
5125,5126,69.txt,4,0,,,,"SoxS protein , activates sodA , micF .
"
5126,5127,69.txt,5,0,,,,"SoxS protein , activates sodA , DNA repair endonuclease IV .
"
5127,5128,69.txt,6,0,,,,"SoxS protein , activates sodA , nfo .
"
5128,5129,69.txt,7,0,,,,"SoxS protein , activates sodA , fpr .
"
5129,5130,69.txt,8,0,,,,"SoxS protein , activates sodA , ferrodoxin oxidoreductase .
"
5130,5131,69.txt,9,0,,,,"SoxS protein , activates sodA , NADPH .
"
5131,5132,69.txt,10,0,,,,"SoxS protein , activates sodA , efflux pump .
"
5132,5133,69.txt,11,0,,,,"SoxS protein , activates sodA , acrAB .
"
5133,5134,69.txt,12,0,,,,"SoxS protein , activates sodA , aconitase .
"
5134,5135,69.txt,13,0,,,,"SoxS protein , activates sodA , acnA .
"
5135,5136,69.txt,14,0,,,,"SoxS protein , activates sodA , heat-resistant fumarase .
"
5136,5137,69.txt,15,0,,,,"SoxS protein , activates sodA , fumC .
"
5137,5138,69.txt,16,0,,,,"SoxS protein , activates sodA , nitroreductase A .
"
5138,5139,69.txt,17,0,,,,"SoxS protein , activates sodA , nfsA ."
5139,5140,1371.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
5140,5141,183.txt,1,0,,,,"It has been demonstrated that co-regulation of pur genes by purR is the result of interaction between PurR bp consensus sequence of 5 ′ control region ( expect d pu
"
5141,5142,183.txt,2,0,,,,"It has been demonstrated that co-regulation of pur genes by purR is the result of interaction between PurR bp consensus sequence of 5 ′ control region ( expect , pu
"
5142,5143,183.txt,3,0,,,,It has been demonstrated that co-regulation of pur genes by purR is the result of interaction between PurR bp consensus sequence of 5 ′ control region ( expect t pu
5143,5144,1417.txt,1,0,,,,"that HilC are each capable of independently inducing expression of the hilC genes
"
5144,5145,1417.txt,2,0,,,,"We demonstrate that HilC are each capable of inducing expression of hilC .
"
5145,5146,1417.txt,3,0,,,,"We wanted to determine if HilC could induce expression of hilC in the absence of the other regulators .
"
5146,5147,1417.txt,4,0,,,,"HilC also induced expression of hilC .
"
5147,5148,1417.txt,5,0,,,,"HilC induced expression of hilC approximately threeto fourfold .
"
5148,5149,1417.txt,6,0,,,,"These data show that HilC are each capable of independently inducing expression of hilC , consistent with our model that HilC constitute a feed forward regulatory loop .
"
5149,5150,1417.txt,7,0,,,,"We show that HilC can each independently activate expression of the hilC genes .
"
5150,5151,1417.txt,8,0,,,,HilC are all also capable of activating expression of hilC independent of each other and comprise a complex feed forward regulatory loop .
5151,5152,1588.txt,1,0,,,,"Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays .
"
5152,5153,1588.txt,2,0,,,,"In addition , the lack of consensus PmrA-binding sites in the promoters of STM0459 suggested that these genes may be indirectly activated by PmrA ."
5153,5154,2081.txt,1,0,,,,"Under conditions of low-osmolarity , TviA is represses flhDC transcription , thereby negatively regulating flagella biosynthesis .
"
5154,5155,2081.txt,2,0,,,,TviA exerts its effect on flagellar gene regulation in conjunction with RcsB by repressing transcription of the flagellar master regulators flhDC .
5155,5156,2095.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both csiD genes in E. coli is stimulated by H-NS ."
5156,5157,746.txt,1,0,,,,"The OmpR protein regulates the transcription of the spiR genes , partly by acting there as a conventional TF .
"
5157,5158,746.txt,2,0,,,,"The OmpR protein regulates the transcription of the spiR genes , partly by acting there by acting as an anti-repressor ."
5158,5159,752.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) .
"
5159,5160,752.txt,2,0,,,,"Thus , we concluded that CRP all contribute towards the regulation of hlyE expression .
"
5160,5161,752.txt,3,0,,,,"In summary , the data suggest that CRP are positive regulators of hlyE expression in liquid culture in response to glucose-starvation , respectively .
"
5161,5162,752.txt,4,0,,,,"In summary , the data suggest that CRP are positive regulators of hlyE expression in liquid culture in response to oxygen , respectively .
"
5162,5163,752.txt,5,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
5163,5164,752.txt,6,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
5164,5165,752.txt,7,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
5165,5166,752.txt,8,0,,,,"This reciprocity of transcriptional efficiency provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
5166,5167,752.txt,9,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to glucose-starvation rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
5167,5168,752.txt,10,0,,,,"This reciprocity of binding site recognition provides a mechanism for the moderate upregulation of hlyE expression in response to oxygen rather than , for the much larger degree of upregulation when CRP act synergistically by binding at different sites within the ansB promoter .
"
5168,5169,752.txt,11,1,Salmonella,Salmonella,Salmonella,"Research in Crp-dependent transcriptional control of hlyE genes : role of environmental conditions Juan A. Fuentes , Matıas R. Jofré , Nicolás A. Villagra , Guido C. Mora * Laboratorio de Microbiologıa , Facultad de Ciencias Biológicas y Facultad de Medicina , Universidad Andres Bello , República 217 , Santiago de Chile , Chile Abstract A novel pathogenicity island , SPI-18 , carries ron , encoding virulence-factors in Salmonella .
"
5169,5170,752.txt,12,0,,,,"Research in Crp-dependent transcriptional control of hlyE genes : role of environmental conditions Juan A. Fuentes , Matıas R. Jofré , Nicolás A. Villagra , Guido C. Mora * Laboratorio de Microbiologıa , Facultad de Ciencias Biológicas y Facultad de Medicina , Universidad Andres Bello , República 217 , Santiago de Chile , Chile Abstract A novel pathogenicity island , SPI-18 , carries rries the taiA-hlyE .
"
5170,5171,752.txt,13,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Research in Crp-dependent transcriptional control of Salmonella Typhi taiA : role of environmental conditions Juan A. Fuentes , Matıas R. Jofré , Nicolás A. Villagra , Guido C. Mora * Laboratorio de Microbiologıa , Facultad de Ciencias Biológicas y Facultad de Medicina , Universidad Andres Bello , República 217 , Santiago de Chile , Chile Abstract A novel pathogenicity island , SPI-18 , carries rries the taiA-hlyE .
"
5171,5172,752.txt,14,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Nevertheless , genetic experiments showed that CRP participates in the negative regulation of hlyE in S. Typhi since crp deletion led to increased β-galactosidase activit .
"
5172,5173,752.txt,15,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Altogether , these results suggest that CRP are able to repress the rpoS expression by direct binding , thereby regulating hlyE expression in S. Typhi .
"
5173,5174,752.txt,16,0,,,,"Fuentes JA , Jofre MR , Villagra NA , Mora GC : RpoS-and Crp-dependent transcriptional control of hlyE genes : role of environmental conditions .
"
5174,5175,752.txt,17,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"RpoS integrates CRP to control Salmonella Typhi hlyE expression .
"
5175,5176,752.txt,18,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,RpoS integrates CRP to control Salmonella Typhi hlyE expression .
5176,5177,2042.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
5177,5178,961.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
5178,5179,1239.txt,1,0,,,,Both cadC and dsrA are repressed by H-NS .
5179,5180,975.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"YncC/McbR are also able to bind to the promoter region of the E. coli K-12 yciGFE genes .
"
5180,5181,975.txt,2,1,Salmonella,Salmonella,Salmonella,"However , the sequence , the length , , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC/McbR .
"
5181,5182,975.txt,3,1,Salmonella,Salmonella,Salmonella,"However , the position of H-NS binding regions , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC/McbR .
"
5182,5183,975.txt,4,1,Salmonella,Salmonella,Salmonella,"However , the position of the McbR/YncC , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by YncC/McbR ."
5183,5184,2056.txt,1,0,,,,"To examine whether ClpXP are involved in the regulation of pagC transcription , pagC expression were measured by using lacZ-fusions in strains with different genetic backgrounds ."
5184,5185,1577.txt,1,0,,,,"Fur repressed ssrB expression both under acidic conditions , which we ascribe to the direct binding of Fur to the ssrB promoter .
"
5185,5186,1577.txt,2,0,,,,"Fur repressed ssrB expression both inside macrophages , which we ascribe to the direct binding of Fur to the ssrB promoter .
"
5186,5187,1577.txt,3,0,,,,"We reveal that Fur provide evidence that Fur represses SsrB production by binding to the ssrB promoter .
"
5187,5188,1577.txt,4,0,,,,"The Fur regulator directly binds to the ssrB promoter .
"
5188,5189,1577.txt,5,0,,,,"Based on this finding , we explored whether the Fur regulator could directly bind to the ssrB promoter .
"
5189,5190,1577.txt,6,0,,,,"We further reasoned that if Fur controls SPI-2 genes via the repression of ssrB transcription , Fur repression of SPI-2 expression would be impaired when the ssrB gene is ectopically expressed from a heterologous promoter .
"
5190,5191,1577.txt,7,0,,,,"FIG 4 The Fur regulator directly binds to the ssrB promoter .
"
5191,5192,1577.txt,8,0,,,,"We determined that Fur represses ssrB transcription by directly binding to the ssrB promoter .
"
5192,5193,1577.txt,9,0,,,,"Because the putative 19-bp Fur box is located only 5 bp because Fur binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .
"
5193,5194,1577.txt,10,0,,,,"Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site on Fig. 4A binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter .
"
5194,5195,1577.txt,11,0,,,,"Because the putative 19-bp Fur box is located only 5 bp upstream of the SsrB binding site on the ssrB promoter binds to regions larger than the Fur box , it is possible that the Fur repressor competes with the SsrB activator for binding to the ssrB promoter ."
5195,5196,1211.txt,1,0,,,,"In vitro analyses by DNase I footprinting show that LeuO binds the hilE promoter region .
"
5196,5197,1211.txt,2,0,,,,"In vitro analyses by electrophoretic-mobility-shift analysis show that LeuO binds the hilE promoter region .
"
5197,5198,1211.txt,3,0,,,,"In vitro analyses by slot blotting show that LeuO binds the hilE promoter region .
"
5198,5199,1211.txt,4,1,unidentified plasmid,plasmid,unidentified plasmid,"Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in Fig. 4 .
"
5199,5200,1211.txt,5,1,unidentified plasmid,plasmid,unidentified plasmid,"Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in an independent manne .
"
5200,5201,1211.txt,6,1,unidentified plasmid,plasmid,unidentified plasmid,"Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in Fig. 4 .
"
5201,5202,1211.txt,7,1,unidentified plasmid,plasmid,unidentified plasmid,"Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in an independent manne .
"
5202,5203,1211.txt,8,1,unidentified plasmid,plasmid,unidentified plasmid,"Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in Fig. 4 .
"
5203,5204,1211.txt,9,1,unidentified plasmid,plasmid,unidentified plasmid,"Measurements of β-galactosidase activities of the plasmid-borne lac fusions showed that LeuO regulates expression of the P hilE promoters in an independent manne .
"
5204,5205,1211.txt,10,0,,,,"Binding of LeuO to the hilE promoter region To test whether LeuO is able to bind the hilE promoter region , a slot blot binding assay was performed .
"
5205,5206,1211.txt,11,0,,,,"Binding of LeuO to the hilE promoter region To test whether LeuO is able to bind the hilE promoter region , a slot blot binding assay was performed .
"
5206,5207,1211.txt,12,0,,,,"Quantitative analysis of Fig. 6B indicated that , under the conditions of the assay , LeuO bound the hilE DNA fragment with an approximate Kd of 0.37 μM .
"
5207,5208,1211.txt,13,0,,,,"Quantitative analysis of binding indicated that , under the conditions of the assay , LeuO bound the hilE DNA fragment with an approximate Kd of 0.37 μM ."
5208,5209,785.txt,1,0,,,,"Other genes varied in prevalence , including trhH ( encoding pilus assembly protein ) , sirA ( two-component system with barA ) , pagK ( PhoPQ-activated protein ) , and sseK1 ( encoding putative-secreted effector protein ) ."
5209,5210,791.txt,1,0,,,,"protein-DNA interaction assays showed regulation by HilD for six of these genes : gtgE , phoH , sinR , SL1263 -LRB- lpxR -RRB- were regulated directly , whereas SL1896 was regulated indirectly .
"
5210,5211,791.txt,2,0,,,,"Expression analyses showed regulation by HilD for six of these genes : gtgE , phoH , sinR , SL1263 -LRB- lpxR -RRB- were regulated directly , whereas SL1896 was regulated indirectly .
"
5211,5212,791.txt,3,0,,,,"HilD , regulates the expression of gtgE .
"
5212,5213,791.txt,4,0,,,,"that HilD directly controls the expression of the gtgE genes
"
5213,5214,791.txt,5,0,,,,"HilD binds to the regulatory regions of gtgE .
"
5214,5215,791.txt,6,0,,,,"To further define whether the HilD-mediated regulation of gtgE is indirect , we analyzed the interaction of HilD with the regulatory region of these genes .
"
5215,5216,791.txt,7,0,,,,"To further define whether the HilD-mediated regulation of gtgE is direct , we analyzed the interaction of HilD with the regulatory region of these genes .
"
5216,5217,791.txt,8,0,,,,"Together with the expression analyses , these binding assays demonstrate that HilD directly regulates the expression of the gtgE genes .
"
5217,5218,791.txt,9,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,S. Typhimurium;S. Typhimurium SL1344;Typhimurium;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium,"In this work , by applying a clustering method to S. Typhimurium SL1344 global expression data from the COLOMBOS database , we show that most of the known genes regulated by HilD , including the flagellar/chemot-axis genes , are indeed co-expressed with SPI-1 ; moreover , nine novel genes were identified : gtgE .
"
5218,5219,791.txt,10,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL4247-cat ; consistently , HilD bound to the regulatory regions of gtgE .
"
5219,5220,791.txt,11,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of SL3812-cat ; consistently , HilD bound to the regulatory regions of gtgE .
"
5220,5221,791.txt,12,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of lpxR-cat ; consistently , HilD bound to the regulatory regions of gtgE .
"
5221,5222,791.txt,13,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of sinR-cat ; consistently , HilD bound to the regulatory regions of gtgE .
"
5222,5223,791.txt,14,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of phoH-cat ; consistently , HilD bound to the regulatory regions of gtgE .
"
5223,5224,791.txt,15,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce the expression of gtgE-cat ; consistently , HilD bound to the regulatory regions of gtgE .
"
5224,5225,791.txt,16,2,Felis catus;Escherichia coli,cat;E. coli,Felis catus;Escherichia coli,"Additionally , we show that HilD can induce SL1896-cat , transcriptional-fusions , in the E. coli MC4100 strain ; consistently , HilD bound to the regulatory regions of gtgE .
"
5225,5226,791.txt,17,1,Felis catus,cat,Felis catus,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of FlhDC ; consistently , HilD bound to the regulatory regions of gtgE .
"
5226,5227,791.txt,18,2,Felis catus;Salmonella;Salmonella,cat;Salmonella;Salmonella-specific,Felis catus;Salmonella,"Additionally , we show that HilD can induce SL1896-cat , thus in the absence of other Salmonella-specific regulators ; consistently , HilD bound to the regulatory regions of gtgE .
"
5227,5228,791.txt,19,0,,,,"Thus , HilD directly regulates the expression of the gtgE genes , and positively .
"
5228,5229,791.txt,20,0,,,,"Therefore , the expression of gtgE is controlled by HilD in SPI-1-inducing conditions .
"
5229,5230,791.txt,21,0,,,,"Therefore , the expression of gtgE is controlled by HilD by another regulator in SPI-2-inducing conditions .
"
5230,5231,791.txt,22,0,,,,"Whether the regulation by HilD implies that the gtgE genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .
"
5231,5232,791.txt,23,0,,,,"Whether the regulation by HilD implies that the gtgE genes also have a role in the intestinal infection , as for most other genes regulated by HilD , needs to be investigated .
"
5232,5233,791.txt,24,1,Salmonella,Salmonella,Salmonella,"Whether the regulation by HilD implies that the gtgE genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .
"
5233,5234,791.txt,25,1,Salmonella,Salmonella,Salmonella,"Whether the regulation by HilD implies that the gtgE genes also have a role in the Salmonella invasion of host cells , as for most other genes regulated by HilD , needs to be investigated .
"
5234,5235,791.txt,26,0,,,,HilD binds to the regulatory region of gtgE .
5235,5236,1205.txt,1,0,,,,"A positive regulator , TviA ( VipR ) , activates its own synthesis by binding upstream of the tviA promoter [ 27 ] and interacts with RcsB to promote optimal transcription of genes involved in Vi antigen synthesis [ 24 , 25 , 28 , 29 ] .
"
5236,5237,1205.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Gallus gallus,S. Typhimurium;Typhimurium;chicken,Gallus gallus;Salmonella enterica subsp. enterica serovar Typhimurium,"a DphoN : : tviA mutant were grown in tryptone yeast extract broth containing 0.3 M NaCl and subsequently transferred into tissue culture medium Expression of tviA in S. Typhimurium results in increased translocation to the spleen in a chicken model By evading detection through sentinels of the intestinal immune system , TviA-mediated flagellin repression might prevent induction of mucosal barrier functions orchestrated by proinflammatory signals .
"
5237,5238,1205.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Gallus gallus,S. Typhimurium;Typhimurium;S. Typhimurium;Typhimurium;chicken,Gallus gallus;Salmonella enterica subsp. enterica serovar Typhimurium,"A S. Typhimurium DphoN mutant : : tviA mutant were grown in tryptone yeast extract broth containing 0.3 M NaCl and subsequently transferred into tissue culture medium Expression of tviA in S. Typhimurium results in increased translocation to the spleen in a chicken model By evading detection through sentinels of the intestinal immune system , TviA-mediated flagellin repression might prevent induction of mucosal barrier functions orchestrated by proinflammatory signals .
"
5238,5239,1205.txt,4,0,,,,"We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi fliC expression simultaneously .
"
5239,5240,1205.txt,5,0,,,,"We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi fliC expression simultaneously .
"
5240,5241,1205.txt,6,0,,,,"We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi capsular polysaccharide expression simultaneously .
"
5241,5242,1205.txt,7,0,,,,"We reasoned that this comparison would allow us to disentangle the contribution of the Vi capsular polysaccharide from the contribution of TviA , since a simple deletion of tviA is pleiotropic and would affect Vi capsular polysaccharide expression simultaneously ."
5242,5243,949.txt,1,0,,,,"It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators ."
5243,5244,1563.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
5244,5245,1563.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
5245,5246,578.txt,1,0,,,,The binding of YncC upstream of the yciG promoter were investigated .
5246,5247,2283.txt,1,0,,,,Fis might participate in downregulation of hlyE via RpoS
5247,5248,1952.txt,1,0,,,,"Figure 8 illustrates that H-NS is , indeed , a negative regulator of ompR .
"
5248,5249,1952.txt,2,0,,,,"Acid shock control of ompR expression The evidence suggested that H-NS bound to the ompR promoter represses transcription .
"
5249,5250,1952.txt,3,0,,,,"Acid shock control of ompR expression The evidence suggested that H-NS bound to the ompR promoter represses transcription .
"
5250,5251,1952.txt,4,0,,,,"Figure 8 illustrates that H-NS is , indeed , a negative regulator of ompR .
"
5251,5252,1952.txt,5,0,,,,"Acid shock control of ompR expression The evidence suggested that H-NS bound to the ompR promoter represses transcription .
"
5252,5253,1952.txt,6,0,,,,Acid shock control of ompR expression The evidence suggested that H-NS bound to the ompR promoter represses transcription .
5253,5254,1946.txt,1,0,,,,hilC whose products are both AraC/XylS-type transcription activators for unpublished results
5254,5255,2297.txt,1,1,unidentified,unidentified,unidentified,"Mutations in ams , hha and a previously unidentified PhoP-activated gene ( pag ) lead to increased hilA expression ( Fahlen et al. , 2000 , 2001 ) ."
5255,5256,544.txt,1,0,,,,"Like marRAB , acrAB are positively regulated by MarA .
"
5256,5257,544.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"In S. enterica the global regu-2 MarA regulate the acrAB operon by binding to mar/sox boxes .
"
5257,5258,544.txt,3,0,,,,"Expression of acrAB-tolC is regulated by the global regulator , MarA .
"
5258,5259,544.txt,4,1,Salmonella,Salmonella,Salmonella,"Other regulators of MarA did not contrib-ute to acrAB induction by indole in Salmonella .
"
5259,5260,544.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcription of acrAB is controlled by the homologous proteins MarA .
"
5260,5261,544.txt,6,0,,,,"In particular , the expression of acrAB is regulated by MarA .
"
5261,5262,544.txt,7,1,Salmonella,Salmonella,Salmonella,"For example , acrAB transcription in Salmonella is controlled by MarA .
"
5262,5263,544.txt,8,0,,,,"At a global level , acrAB expression is regulated by MarA ."
5263,5264,222.txt,1,0,,,,"InvF , regulates the expression of sinR ."
5264,5265,236.txt,1,0,,,,RcsA-independent genes consists of the small RNA activator of rpoS translation rprA .
5265,5266,550.txt,1,0,,,,"STM3120 encodes a possible citrate lyase and STM3121 , is a putative transcriptional regulators of the LysR family ."
5266,5267,1749.txt,1,0,,,,Expression of pmrAB is also indirectly regulated by the PhoPQ system
5267,5268,1991.txt,1,0,,,,"Induction of heme synthesis during oxidative-stress seems reasonable because OxyR also induces the synthesis of hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative-stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .
"
5268,5269,1991.txt,2,0,,,,"Induction of heme synthesis during oxidative-stress seems reasonable because OxyR also induces the synthesis of hydroperoxidase I. Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative-stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme .
"
5269,5270,1991.txt,3,0,,,,"Induction of heme synthesis during oxidative-stress seems reasonable because OxyR also induces the synthesis of a major heme-requir-ing enzyme Nevertheless , the reduction in hemA mRNA levels while the hemH mutant is activated suggests that during oxidative-stress it may be important to simultaneously shut off the heme synthesis pathway at its first step , while completing the conversion of potentially toxic intermediate products into heme ."
5270,5271,2240.txt,1,0,,,,"Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we therefore regulate spvRABCD .
"
5271,5272,2240.txt,2,0,,,,"Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we postulate that the RstA/RstB systems might coregulate iraP to control RpoS .
"
5272,5273,2240.txt,3,0,,,,"Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we postulate that the PhoP/PhoQ systems might coregulate iraP to control RpoS ."
5273,5274,2254.txt,1,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5274,5275,2254.txt,2,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5275,5276,2254.txt,3,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5276,5277,2254.txt,4,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5277,5278,2254.txt,5,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5278,5279,2254.txt,6,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5279,5280,2254.txt,7,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
5280,5281,2254.txt,8,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg sipB ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many ."
5281,5282,1985.txt,1,1,Salmonella,Salmonella,Salmonella,"Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates accessory factors -LRB- rck , pefI , srgA -RRB- ."
5282,5283,587.txt,1,0,,,,"In the previous report , H-NS acted as a strong repressor of hlyE expression , whereas here H-NS appears to have a positive effect on hlyE expression in the absence of glucose but an negative effect on hlyE expression in the presence of glucose .
"
5283,5284,587.txt,2,0,,,,"In the previous report , H-NS acted as a strong repressor of hlyE expression , whereas here H-NS appears to have a positive effect on hlyE expression in the absence of glucose but an attenuated effect on hlyE expression in the presence of glucose .
"
5284,5285,587.txt,3,0,,,,"This suggests that , in general , H-NS inhibits FNR-driven hlyE expression .
"
5285,5286,587.txt,4,0,,,,In hlyE are transcriptionally repressed by the nucleoid-associated protein H-NS .
5286,5287,1013.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In summary , we have shown that the H-NS-mediated regulation of hlyE expression in E. coli K-12 is more complex than was previously suggested because H-NS can negatively to hlyE expression .
"
5287,5288,1013.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In summary , we have shown that the H-NS-mediated regulation of hlyE expression in E. coli K-12 is more complex than was previously suggested because H-NS can contribute positively ."
5288,5289,1775.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,Putative regulation by ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of argR .
5289,5290,1761.txt,1,0,,,,"One of the interesting features of autonomous gogB expression was its co-regulation with other SPI-2 virulence genes by SsrB , the transcriptional activator of the SsrA/SsrB two-component regulatory system ."
5290,5291,2268.txt,1,0,,,,Candidate genes for this activity include mig-14 because inactivation of these PhoP-activated genes results in strains .
5291,5292,1007.txt,1,0,,,,"For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated ."
5292,5293,593.txt,1,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : ompR .
"
5293,5294,593.txt,2,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : ompR ."
5294,5295,1981.txt,1,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"Transcription of E. coli topA is driven by the interplay of at least four transcription start sites , allowing FIS to be both a repressor of E. coli topA expression .
"
5295,5296,1981.txt,2,2,unidentified plasmid;Escherichia coli;unidentified plasmid,plasmid;E. coli;plasmid,Escherichia coli;unidentified plasmid,"Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare 4A -RRB- .
"
5296,5297,1981.txt,3,2,unidentified plasmid;Escherichia coli;unidentified plasmid,plasmid;E. coli;plasmid,Escherichia coli;unidentified plasmid,"Although topA promoter function has routinely been studied using plasmid-based systems , our results indicate that in E. coli the expression of plasmid-borne PtopAEc is enhanced by FIS whereas the chromosomal copy of the promoter is repressed by FIS -LRB- compare Figs 3A -RRB- ."
5297,5298,1759.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) ."
5298,5299,2250.txt,1,0,,,,"H-NS , negatively regulates ompS1 expression by binding upstream of position -88 .
"
5299,5300,2250.txt,2,0,,,,"Expression of ompS1 was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .
"
5300,5301,2250.txt,3,0,,,,"The transcriptional profile was consistent with the hypothesis that H-NS represses the expression of ompS1 , .
"
5301,5302,2250.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"The results of our experiments concur with the concept that H-NS represses the expression of ompS1 in Salmonella serovar Typhi .
"
5302,5303,2250.txt,5,6,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmo;Salmo;Salmo;Salmo;Salmo-nella;Typhimurium,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris;Salmonella enterica subsp. enterica serovar Typhimurium,Previous studies also showed that ompS1 are repressed by H-NS in Salmo-nella serovar Typhimurium .
5303,5304,2244.txt,1,0,,,,"Among others , hilA are downregulated in both ihfB mutant H-NSTEPEC protein .
"
5304,5305,2244.txt,2,0,,,,"Among others , hilA are downregulated in both ihfA mutant H-NSTEPEC protein ."
5305,5306,1995.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"In Escherichia coli , sbp is positively regulated by Cbl , a transcriptional regulator with 60 % amino-acid similarity to CysB , involved in the regulation of cysteine biosynthesis from organic sulfur sources ."
5306,5307,597.txt,1,0,,,,"Our previous study showed that OmpR activates the transcription of fljB by promoting fliA expression , and indirectly increases the secretion of FljB : z66 by repressing Vi capsular antigen at high-osmolarity .
"
5307,5308,597.txt,2,0,,,,"Our previous study showed that OmpR activates the transcription of fljB by promoting flhDC expression , and indirectly increases the secretion of FljB : z66 by repressing Vi capsular antigen at high-osmolarity ."
5308,5309,1003.txt,1,0,,,,"Although not significantly enriched within the set of directly PhoPQ-regulated genes , the functional class related to pathogenicity and virulence also contained potential PhoPQ-dependent targets ( pagC , mgtC , virK , and STM0306 ) .
"
5309,5310,1003.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"STM0306 , a fourth PhoPQ-regulated gene that is involved in pathogenicity , is a paralog of the S. typhimurium SapA protein , which was shown to play a role in virulence ( Parra-Lopez et al. 1993 ) ."
5310,5311,1765.txt,1,0,,,,"Using a genetic approach , Fis was shown to be necessary for the induction of invF expression , genes .
"
5311,5312,1765.txt,2,0,,,,Fis activates a chromosomal invF : : Tn5lacZY reporter in the absence of HilA .
5312,5313,1771.txt,1,6,Escherichia coli;Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,E. coli;Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris;Escherichia coli,"This result is surprising because : ( i ) E. coli encodes homologues of the PhoP PhoQ and PmrA PmrB systems , the PmrD protein , as well as the PmrA-regulated genes mediating the LPS modifications required for polymyxin B resistance ( 24 ) ; ( ii ) its PhoP PhoQ system also responds to Mg2 ( 25 ) ; and ( iii ) mutations in its pmrA gene produce strains with the same phenotypes as Salmo-nella pmrA mutants ( 8 , 12 ) ."
5313,5314,2278.txt,1,0,,,,"A ugtL pagP double mutant was more sensitive than either the ugtL or pagP single mutants but still more resistant than the phoP mutant ( Fig. 2C ) , indicating that the ugtL and pagP genes participate in different pathways of magainin 2 resistance and that additional PhoP-regulated genes contribute to magainin 2 resistance .
"
5314,5315,2278.txt,2,0,,,,"In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .
"
5315,5316,2278.txt,3,0,,,,"The PhoP-regulated genes described and the modifications their products mediate are : pagP , palmitoyl transferase ; lpxO , formation of 2-hydroxy myristate ; pagL , 3-O-deacylase .
"
5316,5317,2278.txt,4,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .
"
5317,5318,2278.txt,5,0,,,,"The overlap in genes either downregulated or upregulated in bile between all strains was small ; only one gene ( pagP ) , a PhoP-PhoQ-regulated gene involved in modifying lipid-A ( 24 ) , was downregulated in all strains ( Fig. 2 ) ."
5318,5319,1017.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
5319,5320,583.txt,1,0,,,,"The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) ."
5320,5321,568.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhimurium;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"3 4 5 12 Salmonella serovar Typhi gi 16761966 6.59 65.66 351.3 / 0 6 848.4 / 0 Salmonella serovar Typhi Salmonella serovar Typhimurium Salmonella serovar Typhi Salmonella serovar Typhi 32 44 gi 16759110 gi 16764195 7.20 5.17 47.51 19.80 7 57.7 / 261.2 54 8 123.8 / 287.5 38/222 .4 gi 16502500 gi 16503032 5.17 5.15 21.50 23.2 7.21 e 20 13 20 35 49.6 / 0 103.1 / 0 123.2 / 0-66/0 Salmonella serovar Typhi Salmonella serovar Typhi Salmonella serovar Typhi Salmonella serovar Typhi gi 16760937 gi 16760937 gi 16760937 gi 16504014 5.09 5.06 5.03 6.12 51.89 52.45 52.47 51.89 SS-III -RRB- / OD of Salmonella serovar Typhi leuO FIG. 2 166 FIG. 2 -- Continued 166 The proteomic data revealed that LeuO represses the expression of tpx .
"
5321,5322,568.txt,2,0,,,,"The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code during biofilm formation .
"
5322,5323,568.txt,3,0,,,,"The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code in the exponential-growth-phase .
"
5323,5324,568.txt,4,0,,,,The tpx gene was also negatively regulated by LeuO ; this gene is proposed to code for a periplasmic antioxidant enzyme .
5324,5325,2293.txt,1,0,,,,"A novel NsrR-regulated gene designated STM1808 has been identified , along with hmp , hcp-hcr , yeaR-yoaG , ygbA and ytfE .
"
5325,5326,2293.txt,2,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in hcp , ygbA , ytfE , STM1808 and yeaR ( Experimental Procedures ) .
"
5326,5327,2293.txt,3,1,Salmonella,Salmonella,Salmonella,"These data confirm previous findings with regard to hmp , and additionally demonstrate that the NsrR-regulated ytfE and STM1808 genes contribute to Salmonella virulence .
"
5327,5328,2293.txt,4,1,Mus sp.,mice,Mus sp.,"We have identified a novel NsrR-regulated gene designated STM1808 , and demonstrated a role for specific NsrR-regulated genes in promoting growth during nitrosative-stress in-vitro ( hmp , STM1808 , ygbA and hcp ) and during systemic infection of mice in-vivo ( hmp , STM1808 , ytfE ) .
"
5328,5329,2293.txt,5,1,Mus sp.,mice,Mus sp.,"We have identified a novel NsrR-regulated gene designated STM1808 , and demonstrated a role for specific NsrR-regulated genes in promoting growth during nitrosative-stress in-vitro ( hmp , STM1808 , ygbA and hcp ) and during systemic infection of mice in-vivo ( hmp , STM1808 , ytfE ) .
"
5329,5330,2293.txt,6,1,Salmonella,Salmonella,Salmonella,"STM1808 and ytfE can be added to hmp as NsrR-regulated loci that contribute to Salmonella virulence ( Fig. 6 ) .
"
5330,5331,2293.txt,7,1,Mus sp.,mice,Mus sp.,"Our findings include the identification of a novel NsrR-regulated gene ( STM1808 ) that is important for nitrosative-stress resistance and virulence in mice .
"
5331,5332,2293.txt,8,0,,,,"These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) .
"
5332,5333,2293.txt,9,0,,,,"STM1808 is regulated by NsrR , whilst STM1808 mutants have a growth impairment upon exposure to NO ."
5333,5334,1942.txt,1,1,unidentified,unknown,unidentified,A tentative hypothesis is that asmA mutations might activate a MarA-regulated efflux pump hitherto unknown to transport bile-salts .
5334,5335,1956.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of adrA gene the upregulation of expression of lpfE genes
"
5335,5336,1956.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Typhimurium cells _ treated with polyphenol , suggesting that the CsgD can regulate the transcription of csgDEFG , csgBA operons the upregulation of expression of lpfE genes"
5336,5337,2287.txt,1,0,,,,"Cra protein activates ppsA , pckA , fbp"
5337,5338,554.txt,1,0,,,,"Finally , the identification of a SlyA binding site suggests a mechanism to explain how SlyA overproduction enhances hlyE expression by antagonizing the negative effects of H-NS .
"
5338,5339,554.txt,2,0,,,,"In contrast , in the absence of hns , SlyA overproduction did not enhance hlyE expression .
"
5339,5340,554.txt,3,0,,,,"indirectly , SlyA activates hlyE expression ultimately by counteracting the negative effects of H-NS
"
5340,5341,554.txt,4,0,,,,"indirectly , SlyA activates hlyE expression by modulating H-NS binding
"
5341,5342,554.txt,5,0,,,,"directly , SlyA activates hlyE expression ultimately by counteracting the negative effects of H-NS
"
5342,5343,554.txt,6,0,,,,"directly , SlyA activates hlyE expression by modulating H-NS binding
"
5343,5344,554.txt,7,0,,,,"in-vitro evidence suggests that SlyA activates hlyE expression by antagonizing H-NS-mediated repression .
"
5344,5345,554.txt,8,0,,,,"In vivo suggests that SlyA activates hlyE expression by antagonizing H-NS-mediated repression .
"
5345,5346,554.txt,9,0,,,,"that SlyA does not enhance hlyE expression in hns cultures
"
5346,5347,554.txt,10,0,,,,"SlyA activates hlyE expression by antagonising H-NS-mediated repression .
"
5347,5348,554.txt,11,1,Salmonella,Salmonella,Salmonella,"It was reported that hlyE could be activated by SlyA , an important regulator of virulence genes in Salmonella ."
5348,5349,232.txt,1,0,,,,"Cra protein activates ppsA , pckA , fbp"
5349,5350,226.txt,1,0,,,,"One HilD-activated gene product , RtsB , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon ( 49 ) .
"
5350,5351,226.txt,2,0,,,,"Recent work has demonstrated that HilD activates flhDC transcription late in the cell 
"
5351,5352,226.txt,3,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5352,5353,226.txt,4,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5353,5354,226.txt,5,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5354,5355,226.txt,6,0,,,,"Additional work has demonstrated that the flhDC genes , the master operon of the flagellar hierarchy , activate transcription of the hilD gene at early stages of growth , while the HilD regulator activates promoter 5 of the flhDC genes at later stages of growth .
"
5355,5356,226.txt,7,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5356,5357,226.txt,8,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5357,5358,226.txt,9,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5358,5359,226.txt,10,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5359,5360,226.txt,11,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5360,5361,226.txt,12,1,Salmonella,Salmonella,Salmonella,"Singer , H.M. , Ku C. , Deditius , J.A. , Hughes , K.T. , The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5361,5362,226.txt,13,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5362,5363,226.txt,14,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5363,5364,226.txt,15,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5364,5365,226.txt,16,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5365,5366,226.txt,17,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium,"Previously , by using ChIP-qPCR , it was found that HilD binds in-vivo to DNA regions -RRB- S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in flhDC + 31 .
"
5366,5367,226.txt,18,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium,"Previously , by using ChIP-seq , it was found that HilD binds in-vivo to DNA regions -RRB- S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in flhDC + 31 .
"
5367,5368,226.txt,19,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,S. Typhimurium;S. Typhimurium 14028s;Typhimurium;14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Salmonella enterica subsp. enterica serovar Typhimurium,"Previously , by using chromatin immunoprecipitation-sequencing , it was found that HilD binds in-vivo to DNA regions -RRB- S. Typhimurium 14028s genes ; furthermore , it was shown that HilD can induce the expression of a lpxR-lacZ translational fusion in flhDC + 31 .
"
5368,5369,226.txt,20,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5369,5370,226.txt,21,1,Salmonella,Salmonella,Salmonella,"The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC .
"
5370,5371,226.txt,22,1,Salmonella,Salmonella,Salmonella,"Furthermore , HilD acts as a direct activator of flhDC expression , strengthening the transcriptional cross talk between the SPI-1 regulons in Salmonella .
"
5371,5372,226.txt,23,1,Salmonella,Salmonella,Salmonella,"Furthermore , HilD acts as a direct activator of flhDC expression , strengthening the transcriptional cross talk between the flagellar regulons in Salmonella ."
5372,5373,540.txt,1,0,,,,"These results suggest that kgtP is downregulated by SlyA under evaluated conditions .
"
5373,5374,540.txt,2,0,,,,SlyA thus seems to downregulate kgtP expression by direct binding to the promoter region .
5374,5375,2052.txt,1,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR may come into play ."
5375,5376,971.txt,1,0,,,,"In accordance with apparent phosphod-iesterase activity in-vivo , the absence of STM1703 significantly activated CsgD expression whereby 361 STM1703 particularly was also required for temperature regulation of the rdar morphotype .
"
5376,5377,971.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Overcoming the temperature regulation of Salmonella serovar Typhimurium UMR1 by mutations in STM1703 demonstrated that both gene products act as suppressors of the rdar morphotype expression upstream of CsgD at 37 °C .
"
5377,5378,971.txt,3,0,,,,"Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .
"
5378,5379,971.txt,4,0,,,,"Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM1827 .
"
5379,5380,971.txt,5,0,,,,"Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .
"
5380,5381,971.txt,6,0,,,,"Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is part of an independent pathway overriding CsgD regulation by STM4264 .
"
5381,5382,971.txt,7,0,,,,"Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is either located downstream of STM1827 ."
5382,5383,965.txt,1,0,,,,"The expression of rcnA is specifically induced by cobalt via the derepressor RcnR .
"
5383,5384,965.txt,2,0,,,,The expression of rcnA is specifically induced by nickel via the derepressor RcnR .
5384,5385,1229.txt,1,0,,,,pagK are known to be regulated by SlyA
5385,5386,2046.txt,1,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .
"
5386,5387,2046.txt,2,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .
"
5387,5388,2046.txt,3,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .
"
5388,5389,2046.txt,4,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .
"
5389,5390,2046.txt,5,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Grob , P. , and Guiney , D. G. In Vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA , J. Bacteriol .
"
5390,5391,2046.txt,6,1,Starmerella aceti,to 125,Starmerella aceti,"Gel mobility-shift assays revealed that the SpvR fusion proteins were able to bind to 125-and 147-bp DNA fragments of the spvA , respectively .
"
5391,5392,2046.txt,7,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvA .
"
5392,5393,2046.txt,8,0,,,,"The SpvR protein is a positive transcriptional regulator of the LysR family and binds to inverted repeat recognition sequences upstream of the spvA promoter .
"
5393,5394,2046.txt,9,0,,,,"SpvR binds to both spvA promoters .
"
5394,5395,2046.txt,10,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Grob P , Guiney DG In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter region of spvA .
"
5395,5396,2046.txt,11,0,,,,SpvR is recognized as a positive regulator of the spv operon via transcription of spvA .
5396,5397,1567.txt,1,0,,,,"the former _ being regulated by a promoter located upstream of the pstS gene regulated by RpoS
"
5397,5398,1567.txt,2,0,,,,the former _ being regulated by a promoter located upstream of the pstS gene regulated by RpoS
5398,5399,1201.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"the E. coli asr gene where the RstA protein bound at a site between 68 upstream of the asr promoter
"
5399,5400,1201.txt,2,1,Escherichia coli,E. coli,Escherichia coli,the E. coli asr gene where the RstA protein bound at a site between 55 upstream of the asr promoter
5400,5401,795.txt,1,1,Escherichia coli;Escherichia coli,Escherichia coli;Escherichia coli,Escherichia coli,"The cellular concentration of the rs subunit of RNA polymerase in Escherichia coli is controlled at Hu , R. Regulation in the rpoS regulon of Escherichia coli .
"
5401,5402,795.txt,2,1,Escherichia coli;Escherichia coli,Escherichia coli;Escherichia coli,Escherichia coli,"The cellular concentration of the rs subunit of RNA polymerase in Escherichia coli is controlled at Hu , R. Regulation in the rpoS regulon of Escherichia coli ."
5402,5403,959.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
5403,5404,959.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
5404,5405,781.txt,1,0,,,,"Binding of H-NS to the intergenic region caused moderate activation of the regulated csgD promoter .
"
5405,5406,781.txt,2,0,,,,"In the absence of SsrA , unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD ( agfD ) , the master biofilm regulator by disrupting the silenced , H-NS-bound promoter .
"
5406,5407,781.txt,3,0,,,,"Similar binding behavior with D56A SsrB and SsrBc at the H-NS-bound csgD regulatory region was also Figure 5 .
"
5407,5408,781.txt,4,0,,,,"SsrB D56A and SsrBc condense H-NS-bound csgD DNA .
"
5408,5409,781.txt,5,0,,,,"factors _ required for biofilm formation specifically by activating csgD , the master biofilm regulator by disrupting the silenced , H-NS-bound promoter
"
5409,5410,781.txt,6,0,,,,"We further showed that H-NS was a negative regulator of csgD .
"
5410,5411,781.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5411,5412,781.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5412,5413,781.txt,9,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5413,5414,781.txt,10,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to various environmental stimuli due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5414,5415,781.txt,11,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5415,5416,781.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5416,5417,781.txt,13,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5417,5418,781.txt,14,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5418,5419,781.txt,15,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5419,5420,781.txt,16,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5420,5421,781.txt,17,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5421,5422,781.txt,18,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in S. Typhimurium , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5422,5423,781.txt,19,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5423,5424,781.txt,20,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to osmolality due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5424,5425,781.txt,21,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5425,5426,781.txt,22,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to pH due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5426,5427,781.txt,23,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5427,5428,781.txt,24,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to temperature due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5428,5429,781.txt,25,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgBAC operons .
"
5429,5430,781.txt,26,1,Escherichia coli,E. coli,Escherichia coli,"CsgD levels were undetected H-NS differentially regulate csgD expression Both in E. coli , the expression of csgD is sensitive to starvation due to the action of upstream global regulators at the intergenic region of the csgDEFG operons .
"
5430,5431,781.txt,27,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Furthermore , H-NS , was also known to regulate the expression of csgD in S. Typhimurium .
"
5431,5432,781.txt,28,1,Escherichia coli,E. coli,Escherichia coli,"Furthermore , H-NS , was also known to regulate the expression of csgD in E. coli .
"
5432,5433,781.txt,29,0,,,,"SsrB condenses H-NS bound csgD DNA .
"
5433,5434,781.txt,30,0,,,,"It is worth mentioning here that in our AFM images , it was apparent that H-NS was still bound to some regions of the csgD promoter when SsrB condensed the DNA ."
5434,5435,1215.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Cloning and nucleotide sequence of the cyclic-AMP-receptor-protein-regulated Salmonella typhimurium pepE gene and crystallization of its product , an α-aspartyl dipeptidase ."
5435,5436,1573.txt,1,0,,,,"Since PhoP is a transcriptional activator of the iraP -LRB- yaiB -RRB- gene , we postulate that the PhoP/PhoQ systems might coregulate iraP to control RpoS ."
5436,5437,1598.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,RpoS stabilization where PhoPQ participates by serving as a transcriptional activator of yaiB gene in S. Typhimurium
5437,5438,2091.txt,1,0,,,,"Our present model for ompS2 expression implies that LeuO relieves repression by disrupting either a structure in the region from 413 to 97 .
"
5438,5439,2091.txt,2,1,unidentified,unknown,unidentified,"Our present model for ompS2 expression implies that LeuO relieves repression by antagonizing the effect of an unknown repressor .
"
5439,5440,2091.txt,3,0,,,,"The repression of ompS2 could be due to the competition of LeuO for the binding site of the OmpR transcriptional activator as ompS2 expression is dependent of OmpR .
"
5440,5441,2091.txt,4,0,,,,"The repression of ompS2 could be due to the competition of LeuO for the binding site of the OmpR transcriptional activator as ompS2 expression is dependent of LeuO .
"
5441,5442,2091.txt,5,0,,,,"The ompS2 gene is expressed at lower concentrations of LeuO , whereas ompS1 is expressed at higher concentrations ."
5442,5443,2085.txt,1,0,,,,"Results Fis participates in the repression of hlyE at transcriptional level CRP is a regulator .
"
5443,5444,2085.txt,2,0,,,,"Fis participate in the repression of hlyE transcription by repressing rpoS transcription To find out whether CRP is repressing hlyE expression through a direct binding to the respective promoter region , we performed a shift mobility assay ."
5444,5445,756.txt,1,0,,,,The MetR protein acts as an activator for the transcription of metA .
5445,5446,742.txt,1,0,,,,"It has been demonstrated that ugd gene , are induced by PmrAB activation ."
5446,5447,2126.txt,1,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,Salmonella;Typhi;plasmid;Salmonella;Typhi;plasmid,unidentified plasmid;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Bacterial strains IMSS-II ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrc12 ) and IMSS-III ( Salmonella serovar Typhi IMSS-1 harboring plasmid pFMTrcleuO-50 ) were independently transformed with fusions of each of the LeuO-regulated genes ( pKK232-9 [ STY3070 ] , pKK232-9 [ assT ] , pKK232-9 [ ompS1 ] , pKK232-9 [ ompS2 ] , pKK232-9 [ tpx ] , pKK232-9 [ ompX ] , and pKK232-9 [ STY1978 ] ) to generate individual strains containing the LeuO regulator , as well as the promoter region of the LeuO-dependent gene ."
5447,5448,1349.txt,1,0,,,,"The observation that phoPQ and pmrAB mutants showed an increased susceptibility to colistin and polymyxin B , in the presence of eDNA , indicated a role for PhoPQ/PmrAB-regulated phenotypes in resistance to membrane acting antimicrobial peptides , likely through the aminoarabinose modification of LPS via the pmr operon ."
5448,5449,45.txt,1,0,,,,"In addition , hfq transcription was also induced by OmpR , while Hfq inhibited OmpR expression as a feedback ."
5449,5450,805.txt,1,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
5450,5451,805.txt,2,1,unidentified,not shown,unidentified,The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
5451,5452,51.txt,1,0,,,,"Of these genes , a master regulator of the flagellar operon , aer are known to bind CRP .
"
5452,5453,51.txt,2,0,,,,"Of these genes , flhD , aer are known to bind CRP .
"
5453,5454,51.txt,3,0,,,,"Of these genes , a master regulator of the flagellar operon , aer are predicted to have CRP ."
5454,5455,811.txt,1,0,,,,"The expression of ssrAB is , in turn , regulated by SlyA .
"
5455,5456,811.txt,2,0,,,,"SlyA cooperate to directly control the expression of ssrAB in our unpublished results .
"
5456,5457,811.txt,3,0,,,,"SlyA cooperate to directly control the expression of ssrAB in SPI-1-inducing conditions .
"
5457,5458,811.txt,4,0,,,,"SlyA involvement in TCS regulation has been previously discussed , suggesting that SlyA regulates the locus of ssrAB in SPI-2 .
"
5458,5459,811.txt,5,0,,,,"SlyA involvement in two-component system regulation has been previously discussed , suggesting that SlyA regulates the locus of ssrAB in SPI-2 ."
5459,5460,2132.txt,1,0,,,,"In the present study , the expression from lac fusion was retained after disruption in hilD in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
5460,5461,2132.txt,2,0,,,,"In the present study , the expression from the hilA was retained after disruption in hilD in cells , suggesting the contribution of RtsA on the expression from the hilA promoter in these mutants .
"
5461,5462,2132.txt,3,0,,,,"that RtsA are each capable of independently inducing expression of the hilD genes
"
5462,5463,2132.txt,4,0,,,,"We demonstrate that RtsA are each capable of inducing expression of hilD .
"
5463,5464,2132.txt,5,0,,,,"We had previously demonstrated that RtsA increased expression of hilD .
"
5464,5465,2132.txt,6,0,,,,"We wanted to determine if RtsA could induce expression of hilD in the absence of the other regulators .
"
5465,5466,2132.txt,7,0,,,,"RtsA also induced expression of hilD .
"
5466,5467,2132.txt,8,0,,,,"RtsA induced expression of hilD ~ 10-to 12-fold .
"
5467,5468,2132.txt,9,0,,,,"These data show that RtsA are each capable of independently inducing expression of hilD , consistent with our model that RtsA constitute a feed forward regulatory loop .
"
5468,5469,2132.txt,10,0,,,,"We show that RtsA can each independently activate expression of the hilD genes .
"
5469,5470,2132.txt,11,0,,,,"RtsA are clearly able to induce hilD transcription .
"
5470,5471,2132.txt,12,0,,,,RtsA are all also capable of activating expression of hilD independent of each other and comprise a complex feed forward regulatory loop .
5471,5472,3.txt,1,0,,,,Both cadC and dsrA are repressed by H-NS .
5472,5473,1413.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
5473,5474,187.txt,1,0,,,,"In vitro characterization of transcriptional-fusions to virulence genes As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) ."
5474,5475,1375.txt,1,0,,,,increased ferrous iron uptake associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein
5475,5476,79.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"A.H. Yoo , S.W. Kim , J.E. Yu , Y.H. Kim , J. Cha , J. Oh , S.K. Eo , J.H. Lee , H.Y. Kang , Requirement of Fur for full induction of dps expression in Salmonella enterica serovar typhimurium , J. Microbiol .
"
5476,5477,79.txt,2,0,,,,"Then , in the transition to stationary-phase growth , Fur , contribute to increase dps transcription to up to 200 000 molecules per cell ."
5477,5478,839.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"A. Olsen , A. Arnqvist , M. Hammar , S. Sukupolvi , S. Normark , The RpoS sigma factor relieves HNS-mediated transcriptional repression of csgA , the subunit gene of fibronectin-binding curli in Escherichia coli , Mol ."
5478,5479,1361.txt,1,0,,,,"In turn , fliA is positively controlled by FlhC .
"
5479,5480,1361.txt,2,0,,,,The FlhC proteins act together in an FlhD2C2 hetero-tetramer to activate the σ70 promoter of fliA gene .
5480,5481,193.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resistance phenotype .
"
5481,5482,193.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resistance phenotype .
"
5482,5483,193.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Identification of the CysB-regulated gene , hslJ , related to the Escherichia coli novobiocin resist-ance phenotype ."
5483,5484,1407.txt,1,0,,,,"AraC requires arabinose for the expression of AraC-activated promoters ( Gallegos et al. , 1997 ; Soisson et al. , 1997 ) , therefore we hypothesized that InvF also required a cofactor for transcriptional activation of sigD and sicA ."
5484,5485,178.txt,1,0,,,,"Further , this study showed that yqhD activation was induced by direct binding of YqhC to the promoter region of the yqhD gene ."
5485,5486,86.txt,1,0,,,,"Radiolabelled gyrA was incubated with increasing concentrations of Fis protein prior to digestion with DNase I .
"
5486,5487,86.txt,2,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS 
"
5487,5488,86.txt,3,0,,,,"Thus , global supercoiling homeostasis is maintained in part by FIS "
5488,5489,92.txt,1,0,,,,"The involvement of several Fur-regulated , iron response genes ( entE , entF , fes and gpmA ) in NE-enhanced growth and the altered expression of the hfq gene , encoding an RNA chaperone required for stability of several small antisense regulatory RNAs including RyhB [ 23 ] suggested that the ryhB gene may also be differentially expressed in the presence versus absence of norepinephrine : a 13-fold decrease in transcription was observed for the small regulatory RNA during norepinephrine exposure ."
5489,5490,144.txt,1,0,,,,"Purified RcsB-RflM complex binds with high affinity to the flhDC promoter .
"
5490,5491,144.txt,2,0,,,,"We next analyzed binding of RcsB-RflM complex to the flhDC promoter in detail .
"
5491,5492,144.txt,3,0,,,,"We further demonstrated that efficient binding of the RcsB-RflM complex to the flhDC promoter required the DNA-binding domain of RflM .
"
5492,5493,144.txt,4,0,,,,"We thus propose that RflM enables a stable binding of a RcsB-RflM heterodimer to the flhDC promoter .
"
5493,5494,144.txt,5,0,,,,"We thus propose that RflM enables a fast binding of a RcsB-RflM heterodimer to the flhDC promoter .
"
5494,5495,144.txt,6,0,,,,Schematic model of RcsB-RflM-dependent regulation of flhDC transcription .
5495,5496,622.txt,1,0,,,,The simplest hypothesis is that SirA represses the master regulator of the flagellar regulon flhDC gene fusions .
5496,5497,636.txt,1,0,,,,"Moreover , the LeuO activator of the LysR family was identified as a regulator for ompS2 ."
5497,5498,150.txt,1,0,,,,"In the resulting YB1 strain , the FNR related anaerobic capable promoter PpepT controls asd transcription while PsodA , facilitates transcription of antisense asd .
"
5498,5499,150.txt,2,0,,,,"In the resulting YB1 strain , the FNR related anaerobic capable promoter PpepT controls asd transcription while an aerobic promoter , facilitates transcription of antisense asd ."
5499,5500,1639.txt,1,0,,,,"It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .
"
5500,5501,1639.txt,2,1,Salmonella,Salmonella,Salmonella,"Therefore , SirA appears to be a major regulator of Salmonella intestinal virulence , whereas SdiA regulates other genes of srgB .
"
5501,5502,1639.txt,3,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
5502,5503,1177.txt,1,0,,,,These results indicate that both ArcA are involved in the regulation of hilD in response to low O2 conditions
5503,5504,385.txt,1,0,,,,"Because HilE is a negative regulator of hilD , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level .
"
5504,5505,385.txt,2,0,,,,post-translational repression by HilE dampens hilD activation
5505,5506,1611.txt,1,0,,,,"To confirm the involvement of HilD in bile-mediated repression of SPI-1 , we assessed chromosomal sipC : ."
5506,5507,1605.txt,1,0,,,,"mRNA levels of other PhoP-regulated genes ( mig-14 , pagC , and pagD ) also asymptotically reached the steady-state levels in the EG14943 strain , which is shown in fig .
"
5507,5508,1605.txt,2,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) ."
5508,5509,391.txt,1,0,,,,"Therefore , under these conditions , the activity of SirA appears to be minimal , although the magnitude of repression of the flagellar genes mirrors the magnitude of activation of sopB ."
5509,5510,1163.txt,1,0,,,,"FliZ are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 .
"
5510,5511,1163.txt,2,0,,,,"YdiV are known to repress each other , with FliZ directly repressing ydiV transcription and YdiV indirectly repressing fliZ transcription via FlhD4C2 ."
5511,5512,1188.txt,1,0,,,,"Also , when hilD is under the control of the lac promoter , hilA is still regulated by HilE .
"
5512,5513,1188.txt,2,0,,,,"Because HilE is a negative regulator of hilD , a tentative interpretation for the occurrence of HilE-dependent SPI-1 repression was that LeuO might increase the HilE level ."
5513,5514,1836.txt,1,0,,,,"Thus , the OmpR regulators positively regulate ompS2 .
"
5514,5515,1836.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva , E. OmpR and Leu positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5515,5516,1836.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5516,5517,1836.txt,4,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva E. OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5517,5518,1836.txt,5,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5518,5519,1836.txt,6,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5519,5520,1836.txt,7,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5520,5521,1836.txt,8,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva , E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5521,5522,1836.txt,9,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva , E. OmpR and LeuO positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5522,5523,1836.txt,10,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5523,5524,1836.txt,11,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Calva , E. OmpR and Leu positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
"
5524,5525,1836.txt,12,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Calva E. OmpR positively regulate the Salmonella enterica serovar Typhi ompS2 porin gene .
5525,5526,1822.txt,1,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , osmolarity , DNA structure , RpoS , DnaJ , DnaK , GrpE .
"
5526,5527,1822.txt,2,0,,,,"The flhDC master operon is influenced by c-AMP , CAP , osmolarity , DNA structure , RpoS , heat-shock .
"
5527,5528,1822.txt,3,0,,,,"The flhDC master operon is influenced by catabolite-repression , osmolarity , DNA structure , RpoS , DnaJ , DnaK , GrpE .
"
5528,5529,1822.txt,4,0,,,,"The flhDC master operon is influenced by catabolite-repression , osmolarity , DNA structure , RpoS , heat-shock ."
5529,5530,408.txt,1,0,,,,"-RRB- b-galactosidase Activity b-galactosidase Activit SirA induction of invF requires HilD Previous evidence suggested that SirA required the HilC/HilD/RtsA binding sites in the hilA promoter to induce thus the entire SPI1 TTSS b-galactosidase Activity b-galactosidase Activit Fig. 5 .
"
5530,5531,408.txt,2,0,,,,"-RRB- b-galactosidase Activity b-galactosidase Activit SirA induction of invF requires HilD Previous evidence suggested that SirA required the HilC/HilD/RtsA binding sites in the hilA promoter to induce expression of hilA .
"
5531,5532,408.txt,3,0,,,,"In support of our model , we demonstrate that SirA induction of invF requires the presence of HilD ."
5532,5533,420.txt,1,0,,,,expression of activity of FlhC proteins in initiating the transcription of fliA-fused lacZ gene after induction of IPTG-controlled flhDC genes in cells depleted either of DnaK or of both DnaK and ClpP .
5533,5534,346.txt,1,0,,,,"However , adrA transcription was also diminished when AdrA was overexpressed , suggesting that elevated CsgD expression far above wild-type levels inhibited the transcription of adrA ."
5534,5535,352.txt,1,0,,,,"plasmids _ expressing HhaR14A/R17A under control of the native hha promoter
"
5535,5536,352.txt,2,0,,,,"plasmids _ expressing HhaR14A/R17A under control of the native hha promoter
"
5536,5537,352.txt,3,0,,,,plasmids _ expressing HhaR14A/R17A under control of the native hha promoter
5537,5538,434.txt,1,0,,,,"OxyR regulation of fur .
"
5538,5539,434.txt,2,0,,,,"OxyR regulation of fur .
"
5539,5540,434.txt,3,0,,,,"OxyR regulation of fur .
"
5540,5541,434.txt,4,0,,,,OxyR regulation of fur .
5541,5542,353.txt,1,0,,,,"The tum homologue of Fels-2 was responsible for lexA lethality and had a LexA-repressed promoter .
"
5542,5543,353.txt,2,0,,,,Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a lexA mutant with a concomitant 50-fold reduction in deletion rate .
5543,5544,435.txt,1,0,,,,"The expression of pgtE in the presence of PhoP/Q-inducing N-minimal-medium with a low Mg concen-21 tration was shown in some studies , although Guina et al. reported that the PhoP/PhoQ regulatory system does not account for the regulation of transport of pgtE .
"
5544,5545,435.txt,2,0,,,,"The expression of pgtE in the presence of PhoP/Q-inducing N-minimal-medium with a low Mg concen-21 tration was shown in some studies , although Guina et al. reported that the PhoP/PhoQ regulatory system does not account for the regulation of transcription of pgtE ."
5545,5546,421.txt,1,0,,,,"To understand the function of TdcA in pathogenesis , we performed two-dimensional gel electrophoresis and found that flagellar and PhoP-regulated proteins were affected by the tdcA mutation .
"
5546,5547,421.txt,2,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) ."
5547,5548,347.txt,1,0,,,,"OmpR-P binds to sites downstream of the ssrA transcriptional start site , activating ssrA .
"
5548,5549,347.txt,2,0,,,,"OmpR-P binds to sites upstream of the ssrA transcriptional start site , activating ssrA .
"
5549,5550,347.txt,3,0,,,,"OmpR-P binds to sites downstream of the ssrA transcriptional start site , activating ssrA .
"
5550,5551,347.txt,4,0,,,,"OmpR-P binds to sites upstream of the ssrA transcriptional start site , activating ssrA ."
5551,5552,1823.txt,1,0,,,,"Inhibition of CysB protein binding to a cysJIH promoter fragment by sulfide .
"
5552,5553,1823.txt,2,0,,,,"Unexpectedly , CysB downregulated cysJIH operon ."
5553,5554,409.txt,1,0,,,,"H-NS _ required for normal repression of the proV locus
"
5554,5555,409.txt,2,0,,,,"H-NS _ required for normal repression of the proV locus
"
5555,5556,409.txt,3,0,,,,"The proV promoter were used as negative control regions , respectively , as H-NS binds to the proV promoter ."
5556,5557,1189.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5-to 2-fold increase of hilA expression under in-vitro SPI-1-inducing conditions .
"
5557,5558,1189.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5-to 2-fold increase of hilA expression under in-vitro high salt .
"
5558,5559,1189.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fnr has been previously reported to be a negative regulator of hilA in S. Typhimurium , as loss of Fnr caused a 1.5-to 2-fold increase of hilA expression under in-vitro low O2 .
"
5559,5560,1189.txt,4,0,,,,"However , whether the repression of hilA by Fnr was induced by low O2 was not clarified in those studies ."
5560,5561,1837.txt,1,1,Salmonella,Salmonella,Salmonella,"Dual control by a s32 promoter in concert with a ROSE-like RNA thermometer was also shown for the ibpA genes of Salmonella .
"
5561,5562,1837.txt,2,1,Escherichia coli,E. coli,Escherichia coli,Dual control by a s32 promoter in concert with a ROSE-like RNA thermometer was also shown for the ibpA genes of E. coli .
5562,5563,390.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
5563,5564,390.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
5564,5565,1604.txt,1,0,,,,"Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is LexA .
"
5565,5566,1604.txt,2,0,,,,"Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is LexA .
"
5566,5567,1604.txt,3,0,,,,"Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS .
"
5567,5568,1604.txt,4,0,,,,"Induction of sbmC by DNA damage is positively regulated by H-NS binding ,12 suggesting sbmC induction by FQs is H-NS ."
5568,5569,1162.txt,1,0,,,,"As demonstrated in Figure 6A , zirTS : : lacZ expression was found to be about 2.3 fold higher in the DoxyR background than P ,0.0001 , suggesting that OxyR is involved in the regulation of these genes .
"
5569,5570,1162.txt,2,0,,,,"As demonstrated in Figure 6A , zirTS : : lacZ expression was found to be about 2.3 fold higher in the DoxyR background than the wild-type strain , suggesting that OxyR is involved in the regulation of these genes ."
5570,5571,1176.txt,1,0,,,,The biofilm master regulatory gene csgD is activated by unphosphorylated RcsB .
5571,5572,1610.txt,1,0,,,,These studies are in agreement with our results that gene nmpC -LRB- -RRB- is regulated by SlyA .
5572,5573,384.txt,1,0,,,,"Activation of tolC gene transcription is achieved through the direct binding of a positive regulator of the AraC/XylS family , to the operator regions of these genes .
"
5573,5574,384.txt,2,0,,,,"Activation of tolC gene transcription is achieved through the direct binding of a positive regulator of the AraC/XylS family , to the operator regions of these genes ."
5574,5575,1638.txt,1,0,,,,"Since FimY are both required to activate fimA , it is possible that these two proteins form a complex to bind the promoter of fimA ."
5575,5576,637.txt,1,0,,,,"STM3611 , as a class III flagellar gene , is indirectly regulated by STM1697 via FliA .
"
5576,5577,637.txt,2,0,,,,"STM3611 , as a class III flagellar gene , is indirectly regulated by STM1344 via FliA .
"
5577,5578,637.txt,3,0,,,,"STM3611 , as a class III flagellar gene , is indirectly regulated by FlhDC via FliA ."
5578,5579,151.txt,1,0,,,,"The aim of the present study was to identify the molecular mechanisms of CadC-mediated transcriptional repression of ompR .
"
5579,5580,151.txt,2,0,,,,"These findings reveal a previously un recognized regulatory mechanism by which CadC represses autoinduction of the ompR gene .
"
5580,5581,151.txt,3,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Discussion Inverse correlation between the response regulator OmpR S. enterica serovar Typhimurium CadC is known to act as a repressor of ompR transcription during acid adaptation .
"
5581,5582,151.txt,4,0,,,,"Discussion Inverse correlation between the acid-sensing regulator CadC CadC is known to act as a repressor of ompR transcription during acid adaptation .
"
5582,5583,151.txt,5,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"CadC interacts directly with OmpR Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to RNA polymerase .
"
5583,5584,151.txt,6,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"CadC interacts directly with OmpR Since S. enterica serovar Typhimurium OmpR response re-gulator was shown to induce its own synthesis by binding to its promoter , we hypothesized that CadC could mediate the repression of ompR gene expression by direct interaction with OmpR , sterically hindering binding of OmpR to its own promoter .
"
5584,5585,151.txt,7,0,,,,"Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of motility , at least during acid adaptation .
"
5585,5586,151.txt,8,0,,,,"Since our data clearly demonstrated CadCmediated repression of ompR gene expression , we speculated that CadC may be involved in the control of fla-gellation , at least during acid adaptation .
"
5586,5587,151.txt,9,0,,,,"a possible mechanism _ underlying the CadC-mediated repression of ompR autoinduction
"
5587,5588,151.txt,10,0,,,,a possible mechanism _ underlying the CadC-mediated repression of ompR autoinduction
5588,5589,145.txt,1,0,,,,"Transcription initiation of the mgtC gene is regulated by the PhoP/PhoQ system , a major regulator of intramacrophage survival and virulence .
"
5589,5590,145.txt,2,0,,,,"Transcription initiation of the mgtC gene is regulated by the PhoP/PhoQ system , a major regulator of intramacrophage survival and virulence .
"
5590,5591,145.txt,3,3,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Plasmid;S. Typhi;Typhi;GIFU 10007;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,"Plasmid Description Source Strains S. Typhi GIFU 10007 WT-pBAD addition , virulence genes mgtC locus is regulated by the PhoP/PhoQ two-component regulatory system in S. Typhimurium .
"
5591,5592,145.txt,4,12,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;bacterium IFAM-2074;Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium;bacterium IFAM-1493;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-3215;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Plasmid;S. Typhi;Typhi;GIFU 10007;bacterium;bacterium;bacterium;bacterium;bacterium;bacterium;bacterium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-3215;bacterium IFAM-2074;bacterium;bacterium IFAM-1493;Salmonella;bacterium IFAM-3211;Salmonella enterica;bacterium IFAM-3359;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,"Plasmid Description Source Strains S. Typhi GIFU 10007 WT-pBAD addition , virulence genes mgtC locus is regulated by the PhoP/PhoQ two-component regulatory system in the facultative intracellular bacterium Salmonella enterica serovar Typhimurium .
"
5592,5593,145.txt,5,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi;GIFU 10007;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Salmonella enterica subsp. enterica serovar Typhimurium,"Strain Description Source Strains S. Typhi GIFU 10007 WT-pBAD addition , virulence genes mgtC locus is regulated by the PhoP/PhoQ two-component regulatory system in S. Typhimurium .
"
5593,5594,145.txt,6,11,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;bacterium IFAM-2074;Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium;bacterium IFAM-1493;bacterium IFAM-3211;bacterium IFAM-3359;bacterium IFAM-3215;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi;GIFU 10007;bacterium;bacterium;bacterium;bacterium;bacterium;bacterium;bacterium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007;Candidatus Saganbacteria bacterium CG08_land_8_20_14_0_20_45_16;bacterium IFAM-3215;bacterium IFAM-2074;bacterium;bacterium IFAM-1493;Salmonella;bacterium IFAM-3211;Salmonella enterica;bacterium IFAM-3359;Salmonella enterica subsp. enterica serovar Typhimurium,"Strain Description Source Strains S. Typhi GIFU 10007 WT-pBAD addition , virulence genes mgtC locus is regulated by the PhoP/PhoQ two-component regulatory system in the facultative intracellular bacterium Salmonella enterica serovar Typhimurium .
"
5594,5595,145.txt,7,0,,,,"In addition , the mgtC locus , are regulated by the PhoP/PhoQ two-component regulatory ¬ − 1.9-226 ¬ Fig. 2 .
"
5595,5596,145.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In addition , the mgtC locus , are regulated by the PhoP/PhoQ two-component regulatory system in S. Typhimurium ."
5596,5597,623.txt,1,0,,,,"While crp increases the expression of this report , the regulatory RNAs csrB and csrC inhibit the activity of CsrA protein ."
5597,5598,93.txt,1,0,,,,"Thus OmpR/EnvZ , seem to convert pH decreases into the regulation of different virulence-factors while the primary role of fur appears to be protection against acid stress itself ."
5598,5599,179.txt,1,0,,,,"An increase in OmpR-P levels would enable OmpR-P to bind to lower affinity sites , repressing ssrA ."
5599,5600,87.txt,1,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
5600,5601,87.txt,2,0,,,,"With the exception of xylA , the last AraC-regulated gene to be identified was araJ , more than 30 years ago ( 27 ) ."
5601,5602,1360.txt,1,0,,,,ArcA Bind to the lpxO Promoter Region Our results indicate that ArcA have a role .
5602,5603,1406.txt,1,0,,,,"Interestingly , lacZ fusion was also positively regulated by LeuO ."
5603,5604,192.txt,1,0,,,,These data indicate that CRP represses expression of parE .
5604,5605,186.txt,1,0,,,,"a putative RcsB binding site in the promoter region of the hilA gene _ suggesting that the transcriptional repression of the sipC genes observed in the rcsC11 mutant might result from reduced levels of hilA expression
"
5605,5606,186.txt,2,0,,,,"a putative RcsB binding site in the promoter region of the hilA gene _ suggesting that the transcriptional repression of the invF genes observed in the rcsC11 mutant might result from reduced levels of hilA expression
"
5606,5607,186.txt,3,0,,,,a putative RcsB binding site in the promoter region of the hilA gene _ suggesting that the transcriptional repression of the invG genes observed in the rcsC11 mutant might result from reduced levels of hilA expression
5607,5608,1412.txt,1,2,Salmonella;Salmonella;Escherichia coli,S. enterica;enterica;E. coli,Escherichia coli;Salmonella,"In electro-phoretic mobility-shift assays , Fis was found to bind to both gyrB promoters of S. enterica , despite the strong divergence from the E. coli sequence on the part of the former .
"
5608,5609,1412.txt,2,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. Typhimurium;Typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Fis also binds to and represses the promoters of the gyrB genes in both E. coli and S. Typhimurium , resulting in reduced levels of DNA supercoiling .
"
5609,5610,1412.txt,3,2,Escherichia coli;Salmonella;Salmonella,E. coli;S. enterica;enterica,Escherichia coli;Salmonella,"In E. coli , FIS binds the gyrB promoters to repress their expression ; similarly , FIS has been found to repress S. enterica gyrB .
"
5610,5611,1412.txt,4,0,,,,"Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrB might differ between the two species .
"
5611,5612,1412.txt,5,0,,,,"Therefore the observed differences in FIS control of DNA supercoiling suggested that the role of FIS in the regulation of gyrB might differ between the two species .
"
5612,5613,1412.txt,6,0,,,,FIS control of gyrB .
5613,5614,838.txt,1,0,,,,SoxS is involved in the LsrR-mediated regulation of the sodA gene .
5614,5615,78.txt,1,0,,,,"The transcriptional expression of prpBCDE from PprpB is regulated by IHF , cAMP-CRP complex , a transcriptional regulator , .
"
5615,5616,78.txt,2,0,,,,"The transcriptional expression of prpBCDE from PprpB is regulated by IHF , cAMP-CRP complex , PrpR , .
"
5616,5617,78.txt,3,0,,,,"The transcriptional expression of prpBCDE from the prpBCDE promoter is regulated by IHF , cAMP-CRP complex , a transcriptional regulator , .
"
5617,5618,78.txt,4,0,,,,"The transcriptional expression of prpBCDE from the prpBCDE promoter is regulated by IHF , cAMP-CRP complex , PrpR , ."
5618,5619,1374.txt,1,1,Salmonella,Salmonella,Salmonella,Other regulators of SdiA did not contrib-ute to acrAB induction by indole in Salmonella .
5619,5620,810.txt,1,0,,,,"The role of the alternative cf factor RpoS in the regulation of the starvation survival loci , stiC , has been characterized .
"
5620,5621,810.txt,2,0,,,,"Since stiC loci are regulated by RpoS , we wanted to examine the combined effects of sti mutations on starvation survival .
"
5621,5622,810.txt,3,0,,,,"Since stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .
"
5622,5623,810.txt,4,0,,,,"On the basis of the fact that stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiC are not induced and/or because stiB is overexpressed in an rpoS mutant .
"
5623,5624,810.txt,5,0,,,,"On the basis of the fact that stiC are all regulated by RpoS , one might predict that rpoS mutants exhibit increased sensitivity to the effects of C starvation because stiA are not induced and/or because stiB is overexpressed in an rpoS mutant ."
5624,5625,50.txt,1,0,,,,"These results showed that , whereas OmpR-mediated regulation of hilA expression was dampened in a DhilC DrtsA background , regulation was blocked only in strains missing HilD , suggesting that OmpR controls SPI1 expression by regulating hilD expression .
"
5625,5626,50.txt,2,0,,,,"Increased OmpR can be recruited to bind to hilD promoters , in a process .
"
5626,5627,50.txt,3,0,,,,"The OmpR protein also controls the transcription of key regulatory genes in hilD , allowing OmpR to contribute to the coordination of expression of these major virulence genetic elements ."
5627,5628,2.txt,1,0,,,,"Since swarming motility in both cysB and cysE is restored by the inclusion of cysteine in the swarm medium , a CysB-regulated gene outside of the cysteine biosynthetic genes is not the reason that these strains are incapable of swarming on standard swarm medium .
"
5628,5629,2.txt,2,1,Salmonella,Salmonella,Salmonella,"CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .
"
5629,5630,2.txt,3,1,Salmonella,Salmonella,Salmonella,"CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .
"
5630,5631,2.txt,4,1,Salmonella,Salmonella,Salmonella,"CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB .
"
5631,5632,2.txt,5,1,Salmonella,Salmonella,Salmonella,"CysB protein also autoregulates its own synthesis by binding to the cysB promoter as a In Salmonella , amino-acid biosynthesis is tightly regulated by The cys regulon is under the positive control of CysB ."
5632,5633,2133.txt,1,0,,,,"The transcription of csrB is regulated by UvrY .
"
5633,5634,2133.txt,2,1,Escherichia coli,E. coli,Escherichia coli,UvrY of E. coli both control the csr system by directly binding the csrB gene .
5634,5635,2127.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) ."
5635,5636,804.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Freundlich , M. negative control of ompB transcription in Escherichia coli by the cyclic-AMP-receptor-protein .
"
5636,5637,804.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Freundlich , M. Positive control of ompB transcription in Escherichia coli by the cyclic-AMP-receptor-protein .
"
5637,5638,804.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Freundlich , M. negative control of ompB transcription in Escherichia coli by the cyclic-AMP-receptor-protein .
"
5638,5639,804.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Freundlich , M. Positive control of ompB transcription in Escherichia coli by the cyclic-AMP-receptor-protein .
"
5639,5640,804.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"Freundlich , M. negative control of ompB transcription in Escherichia coli by the cyclic-AMP-receptor-protein .
"
5640,5641,804.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"Freundlich , M. Positive control of ompB transcription in Escherichia coli by the cyclic-AMP-receptor-protein ."
5641,5642,44.txt,1,0,,,,"Initially , it was proposed as a putative effector because the gene srfJ is positively regulated by SsrB .
"
5642,5643,44.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by the repressor of the myo-inositol utilization genes in S. Typhimurium .
"
5643,5644,44.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by the repressor of the myo-inositol utilization genes in S. Typhimurium .
"
5644,5645,44.txt,4,0,,,,"Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR .
"
5645,5646,44.txt,5,0,,,,"Surprisingly , we found that , in addition to the regulation by SsrB , srfJ is also negatively regulated by IolR .
"
5646,5647,44.txt,6,0,,,,"Interestingly , a transcriptional lux fusion with 2357 bp upstream of srfJ is regulated by SsrB , recapitulating the regulation patterns ."
5647,5648,1348.txt,1,0,,,,"GlcNAc6P inactivates NagC leading to full-scale induction of both the chiP
"
5648,5649,1348.txt,2,0,,,,GlcNAc6P inactivates NagC leading to full-scale induction of both the chiP
5649,5650,743.txt,1,1,unidentified plasmid;unidentified plasmid,plasmid;plasmid,unidentified plasmid,"CsrA induces expression of plasmid-encoded fimbriae by binding the pefA 50-UTR Since the substantial PefA expression was CsrA dependent , we wanted to study the mechanism by which CsrA activates expression of plasmid-encoded fimbriae .
"
5650,5651,743.txt,2,0,,,,"These data suggested that CsrA bound specifically to a single GGA binding site in the pefA 50-UTR .
"
5651,5652,743.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"To further investigate whether binding of CsrA to the GGA motif in the pefA 50-UTR was required for expression of plasmid-encoded fimbriae , we introduced point mutations into the Figure 3 CsrA regulates expression of PefA .
"
5652,5653,743.txt,4,2,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,plasmid;S. typhimurium;typhimurium;plasmid,Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,The CsrA-binding site in the pefA 50-UTR controls expression of plasmid-encoded fimbriae in-vivo A possible biological-function for the hierarchical control of fimbrial expression would be to ensure that S. typhimurium does not express plasmid-encoded fimbriae while residing outside a host .
5653,5654,757.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , five transcription factors have been implicated : hmp transcription is repressed by NsrR .
"
5654,5655,757.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , five transcription factors have been implicated : hmp transcription is repressed by NsrR .
"
5655,5656,757.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , previous studies have determined that NsrR negatively regulates the expression of the hmp genes .
"
5656,5657,757.txt,4,0,,,,"NsrR inhibits hmp expression .
"
5657,5658,757.txt,5,0,,,,NsrR inhibits hmp transcription .
5658,5659,2084.txt,1,0,,,,"a 1.1 1.1 a a rbsA 1.1 ABC superfamily -LRB- -RRB- , -- D-ribose high-affinity transport protein ABC superfamily -LRB- -RRB- , D-ribose transport protein ABC superfamil , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant
"
5659,5660,2084.txt,2,0,,,,"rbs Operon That Are Regulated by luxS = Autoinducer-2 at Mid-Log Phase a 1.1 1.1 a a rbsA 1.1 ABC superfamily -LRB- -RRB- , -- D-ribose high-affinity transport protein ABC superfamily -LRB- -RRB- , D-ribose transport protein ABC superfamil , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant"
5660,5661,2090.txt,1,0,,,,These included the cold-shock-responsive hns gene previously shown to be activated by the hha gene and -LRB- like H-NS -RRB- regulates several virulence genes in response to temperature .
5661,5662,1599.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,In S. Typhimurium the principal regulator of hmp expression during nitrosative-stress is the transcriptional repressor NsrR .
5662,5663,1214.txt,1,2,Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;Salmonella;Salmonella-specific;plasmid,Salmonella;unidentified plasmid,"Evaluation of the specificity o Salmonella P using various intestinal bacterial species * f CR primers virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .
"
5663,5664,1214.txt,2,2,Salmonella;Salmonella;Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;Salmonella;Salmonella-specific;plasmid,Salmonella;unidentified plasmid,"Evaluation of the specificity o Salmonella P using various intestinal bacterial species * f CR primers virulence gene , Salmonella enterotoxin gene ( stn ) , invA gene , Fur-regulated gene , histidine transport operon , junction between SipB and SipC virulence genes , Salmonella-specific repetitive DNA fragment , and multiplex targeting invA gene and spvC gene of the virulence plasmid .
"
5664,5665,1214.txt,3,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .
"
5665,5666,1214.txt,4,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) ."
5666,5667,780.txt,1,0,,,,These data suggest that CRP activates ompA expression during stationary-phase .
5667,5668,958.txt,1,0,,,,"A similar promoter induction pattern was observed when a mutant was grown in MM with glucose , indicating a STM4417-medi-ated negative regulation of the genes ."
5668,5669,1572.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , ansB is positively coregulated by cyclic-AMP-receptor-protein .
"
5669,5670,1572.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , ansB is positively coregulated by CRP .
"
5670,5671,1572.txt,3,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"In S. enterica , the anaerobic regulation of ansB may require only CRP ."
5671,5672,1566.txt,1,0,,,,"Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner .
"
5672,5673,1566.txt,2,0,,,,"This resulting low level of OmpR was adequate to enable the acid induction of ompC in Fig. 3C .
"
5673,5674,1566.txt,3,0,,,,"This resulting low level of OmpR was adequate to enable the acid induction of ompC in log phase cells .
"
5674,5675,1566.txt,4,0,,,,"Nevertheless , the ompC genes in both organisms are induced by acid in an OmpR-dependent manner .
"
5675,5676,1566.txt,5,0,,,,"This resulting low level of OmpR was adequate to enable the acid induction of ompC in Fig. 3C .
"
5676,5677,1566.txt,6,0,,,,"This resulting low level of OmpR was adequate to enable the acid induction of ompC in log phase cells .
"
5677,5678,1566.txt,7,0,,,,"Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompC suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .
"
5678,5679,1566.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,"Forst S , Delgado J , Rampersaud A et al In vivo phosphorylation of OmpR , the transcription activator of the ompC genes in Escherichia coli ."
5679,5680,794.txt,1,0,,,,"It is interesting to note that several regulators of HilC , were found in significantly lower levels in the dam mutant ."
5680,5681,1200.txt,1,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
5681,5682,1200.txt,2,0,,,,"Together with a bioinformatic analysis of other Enterobacteriaceae species , these data identify a conserved AraC regulon that includes 7 previously described AraC-regulated genes ( araB , araA , araD , araE , araF , araG , and araH ) as well as three novel targets identified in this work ( ytfQ , araT , and araU ) ."
5682,5683,1228.txt,1,1,Salmonella,Salmonella,Salmonella,"Summary The Salmonella ugd gene is required for the incorporation of 4-aminoarabinose in the lipopolysaccharide and resistance to the antibiotic polymyxin B. Transcription of the ugd gene is induced by Fe3 + via the PmrA -- PmrB two-component system and by low Mg2 + in a process that requires the PhoP -- PhoQ two-component system , the PhoP-activated PmrD protein and the PmrA -- PmrB system .
"
5683,5684,1228.txt,2,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
5684,5685,1228.txt,3,0,,,,"b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .
"
5685,5686,1228.txt,4,0,,,,"b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .
"
5686,5687,1228.txt,5,0,,,,"D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .
"
5687,5688,1228.txt,6,1,Salmonella,Salmonella,Salmonella,"the PhoP-dependent conditions activate ugd expression in Salmonella
"
5688,5689,1228.txt,7,1,Salmonella,Salmonella,Salmonella,"the PhoP-dependent conditions activate ugd expression in Salmonella
"
5689,5690,1228.txt,8,1,Salmonella,Salmonella,Salmonella,"the PhoP-dependent conditions activate ugd expression in Salmonella
"
5690,5691,1228.txt,9,1,Salmonella,Salmonella,Salmonella,the PhoP-dependent conditions activate ugd expression in Salmonella
5691,5692,964.txt,1,0,,,,"Mutations in the phoPQ operon affect the expression of two sets of genes , the PhoP-activated genes ( pag ) and the PhoP-repressed genes ( prg ) ."
5692,5693,2047.txt,1,0,,,,"RamA binds to the upstream region of tolC .
"
5693,5694,2047.txt,2,0,,,,"Bile RamA directly controls the expression of tolC .
"
5694,5695,2047.txt,3,0,,,,"It has been confirmed that RamA can bind to the upstream promoter region of tolC .
"
5695,5696,2047.txt,4,0,,,,"Activation of tolC gene transcription is achieved through the direct binding of RamA , to the operator regions of these genes ."
5696,5697,2053.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"SlyA , antagonizes H-NS-medi-ated repression of hlyE transcription in E. coli ."
5697,5698,970.txt,1,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag ; examples include mgtBC and genes encoded by SPI2 ) and PhoP-repressed genes ( prg ; examples include genes encoded by SPI1 ) .
"
5698,5699,970.txt,2,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK ."
5699,5700,227.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"H-NS may directly repress PhilA because repression of hilA in E. coli requires both the upstream .
"
5700,5701,227.txt,2,0,,,,"Thus , H-NS appears to be important for hilA repression by osmolarity .
"
5701,5702,227.txt,3,0,,,,"The small nucleoid-bind-ing protein H-NS represses hilA in response to low-osmolarity .
"
5702,5703,227.txt,4,0,,,,"In exponential phase cells , the results provided evidence that H-NS repress hilA expression .
"
5703,5704,227.txt,5,0,,,,"Interestingly , a partial inhibition of H-NS activity in cells resulted in a signi-ficant induction of hilA expression , up to about 50 % of the expression .
"
5704,5705,227.txt,6,0,,,,"Our work shows that H-NS repress hilA under account for SPI1 gene silencing .
"
5705,5706,227.txt,7,0,,,,"Our work shows that H-NS repress hilA under a set of physiological conditions .
"
5706,5707,227.txt,8,0,,,,"Our work shows that H-NS repress hilA under a set of well-defined environmental .
"
5707,5708,227.txt,9,0,,,,"Finally , in-vitro-transcription data show that IHF interferes with H-NS repression of hilA ."
5708,5709,541.txt,1,0,,,,"Two reports have shown that prgH expression , can be upregulated by artificially expressing high levels of HilC even in the absence of hilA .
"
5709,5710,541.txt,2,0,,,,"Two reports have shown that invF expression , can be upregulated by artificially expressing high levels of HilC even in the absence of hilA .
"
5710,5711,541.txt,3,0,,,,"the key regulator hilA , we have focused on two activators of HilC .
"
5711,5712,541.txt,4,0,,,,"HilC can independently activate the hilA promoter .
"
5712,5713,541.txt,5,0,,,,"These data suggest that HilC may activate hilA expression in response to a set of signals .
"
5713,5714,541.txt,6,0,,,,"We wanted to determine if HilC could induce expression of hilA in the absence of the other regulators .
"
5714,5715,541.txt,7,0,,,,"The data in Fig. 2 demonstrate that HilC are able to induce expression of hilA in the absence of the other regulators .
"
5715,5716,541.txt,8,0,,,,"We show that HilC can each independently activate expression of the hilA genes .
"
5716,5717,541.txt,9,0,,,,"However , HilC normally act in concert to activate hilA .
"
5717,5718,541.txt,10,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella;enterica,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC .
"
5718,5719,541.txt,11,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella;enterica,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Olekhnovich , I.N. , and Kadner , R.J. Contribution of the RpoA C-terminal domain to stimulation of the Salmo-nella enterica hilA promoter by HilC .
"
5719,5720,541.txt,12,0,,,,"8,13,14 HilC can activate expression of hilA .
"
5720,5721,541.txt,13,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .
"
5721,5722,541.txt,14,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .
"
5722,5723,541.txt,15,0,,,,"The mechanism by which HilC activate expression of hilA
"
5723,5724,541.txt,16,0,,,,"That means that at least hilA are induced by HilC .
"
5724,5725,541.txt,17,0,,,,"Under high-osmolarity conditions , HilC activate SPI1 genes indirectly through hilA .
"
5725,5726,541.txt,18,0,,,,"Under high-osmolarity conditions , HilC activate SPI1 genes directly through hilA .
"
5726,5727,541.txt,19,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .
"
5727,5728,541.txt,20,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC .
"
5728,5729,541.txt,21,0,,,,"HilC are each capable of activating hilA transcription .
"
5729,5730,541.txt,22,0,,,,"Earlier work on mathematical modeling of regulation of expression of hilA by HilC was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .
"
5730,5731,541.txt,23,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; 2001 ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
5731,5732,541.txt,24,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lee ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
5732,5733,541.txt,25,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilC are central activators of hilA expression ( Ellermeier et al. , 2005 ; Lucas ; Schechter et al. , Abbreviations : Cy , Cyanine ; SSC , saline sodium citrate ; SPI1 , Salmonella pathogenicity island 1 ; S. Typhimurium , Salmonella enterica serovar Typhimurium ; TTSS , type III secretion system .
"
5733,5734,541.txt,26,0,,,,"hilA expression is induced by three transcriptional activators , HilC .
"
5734,5735,541.txt,27,0,,,,"Transcription of hilA is directly activated by HilC .
"
5735,5736,541.txt,28,0,,,,"Inducible expression HilC protein was sufficient to activate hilA following growth at 42 °C .
"
5736,5737,541.txt,29,0,,,,"HilC , activate directly the expression of hilA , independently of HilA ."
5737,5738,555.txt,1,0,,,,"Although the SlyA protein is a transcriptional activator of the ugtL gene , it footprinted the ugtL promoter at a region located downstream of the transcription start site .
"
5738,5739,555.txt,2,0,,,,"the ugtL promoter _ performed with increasing amounts of SlyA proteins
"
5739,5740,555.txt,3,0,,,,"To activate transcription of ugtL , both SlyA must bind to its promoter simultaneously ."
5740,5741,233.txt,1,3,Escherichia coli;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,E. coli;E. coli;S. Typhimurium;Typhimurium;plasmid,unidentified plasmid;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In contrast , consistent with the hypothesis that zupT is constitutively expressed in E. coli , this putative consensus sequence was found to be absent in the E. coli zupT promoter .31 To test whether S. Typhimurium zupT is regulated by Zur , we electroporated plasmid pMCPzupT-lacZ in a strain lacking PP127 , obtaining pMCPzupT-lacZ zur .
"
5741,5742,233.txt,2,3,Escherichia coli;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,E. coli;E. coli;S. Typhimurium;Typhimurium;plasmid,unidentified plasmid;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In contrast , consistent with the hypothesis that zupT is constitutively expressed in E. coli , this putative consensus sequence was found to be absent in the E. coli zupT promoter .31 To test whether S. Typhimurium zupT is regulated by Zur , we electroporated plasmid pMCPzupT-lacZ in a strain lacking zur , obtaining pMCPzupT-lacZ zur .
"
5742,5743,233.txt,3,3,Escherichia coli;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,E. coli;E. coli;S. Typhimurium;Typhimurium;plasmid,unidentified plasmid;Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In contrast , consistent with the hypothesis that zupT is constitutively expressed in E. coli , this putative consensus sequence was found to be absent in the E. coli zupT promoter .31 To test whether S. Typhimurium zupT is regulated by Zur , we electroporated plasmid pMCPzupT-lacZ in a strain lacking zur , obtaining the strain PP153 ."
5743,5744,2286.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth , followed by a burst of expression in late exponential-growth and a decrease in expression during stationary-phase ( Xu and Johnson , 1995 ) .
"
5744,5745,2286.txt,2,0,,,,"In our model , we propose that Fis acts as a positive regulator of hilA .
"
5745,5746,2286.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"However , the Fis-regulated E. coli proP gene seems to be regulated in a manner similar to that of hilA , in that levels are low during early exponential phase growth .
"
5746,5747,2286.txt,4,0,,,,"Fis is involved in SPI expression Positive regulation of SPI-1 genes by Fis was expected considering the fact that hilA , is upregulated by Fis .
"
5747,5748,2286.txt,5,0,,,,The hilA promoter is directly controlled by Fis .
5748,5749,1957.txt,1,0,,,,"However , there are indications that CRP-cAMP also plays a different role as an activator of rpoS expression during the late stages of growth .
"
5749,5750,1957.txt,2,0,,,,"further _ suggesting that cAMP-CRP upregulated rpoS expression
"
5750,5751,1957.txt,3,0,,,,"further _ suggesting that cAMP-CRP upregulated rpoS expression
"
5751,5752,1957.txt,4,0,,,,"cAMP-CRP stimulated transcription of rpoS .
"
5752,5753,1957.txt,5,0,,,,"Interestingly , in the stationary-phase , we still observed a slight increase of rpoS transcription in the ppk mutant compared with WT , although both of the cAMP-CRP-binding sites were mutated ( Fig. 6B ) ."
5753,5754,569.txt,1,0,,,,"moreover , we demonstrate that CpxR-P negatively affects the stability of HilD and thus decreases the expression of hilD hilA , located in SPI-1 .
"
5754,5755,569.txt,2,0,,,,"moreover , we demonstrate that CpxR-P negatively affects the stability of HilD and thus decreases the expression of hilD itself , located in SPI-1 ."
5755,5756,1943.txt,1,0,,,,"However , no significant differences were observed in fliN mRNA levels between isolates , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected .
"
5756,5757,1943.txt,2,0,,,,"However , no significant differences were observed in fliN mRNA levels between the two classes , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected ."
5757,5758,2292.txt,1,0,,,,"To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured-galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM .
"
5758,5759,2292.txt,2,0,,,,"an allosteric change enables AraC to activate the expression of araE
"
5759,5760,2292.txt,3,0,,,,"As AraC activates araE transcription , suppression in an AraCˉ background might be caused by a decrease of intracellular L-arabinose due to lack of AraE permease ."
5760,5761,2279.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli , although the galP gene is controlled via a single operator with high affinity .
"
5761,5762,2279.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in E. coli , although the galP gene is controlled via a single operator with high affinity ."
5762,5763,1770.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
5763,5764,582.txt,1,0,,,,"Surprisingly , the SsrB response regulator positively regulated the formation of biofilms by activating csgD expression in the absence of any phos-pho-donors .
"
5764,5765,582.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Unphosphorylated SsrB activates csgD expression Biofilm formation in Salmonella Typhimurium is governed by the master regulator , CsgD .
"
5765,5766,582.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Unphosphorylated SsrB activates csgD expression Biofilm formation in Escherichia coli is governed by the master regulator , CsgD .
"
5766,5767,582.txt,4,0,,,,"An obvious null hypothesis was therefore to test whether SsrB -LRB- in its unphosphorylated state -RRB- , activated the expression of csgD .
"
5767,5768,582.txt,5,0,,,,"We show that under biofilm-inducing conditions , unphosphorylated SsrB is sufficient to activate the expression of csgD ."
5768,5769,1016.txt,1,0,,,,sifB is regulated by SprB
5769,5770,1002.txt,1,0,,,,"RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) ."
5770,5771,596.txt,1,0,,,,"In agreement with that , at logarithmic phase , higher expression of tlpA : : lacZ was found in the rpoS background vs. the wild-type , suggesting a possible role for RpoS in the regulation of tlpA .
"
5771,5772,596.txt,2,0,,,,"In agreement with that , during stationary-phase , higher expression of tlpA : : lacZ was found in the rpoS background vs. the wild-type , suggesting a possible role for RpoS in the regulation of tlpA .
"
5772,5773,596.txt,3,0,,,,"In agreement with this , higher expression levels of tlpA : : lacZ were found in stationary-phased culture , in the absence of the alternative stationary-phase sigma factor RpoS , indicating that RpoS plays a role in the regulation of tlpA ."
5773,5774,1764.txt,1,0,,,,"DksA Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether HF-I , two potent regulators of rpoS translation , were required for acid shock control .
"
5774,5775,1764.txt,2,0,,,,"DksA Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether HF-I , two potent regulators of rpoS translation , were required for acid shock control .
"
5775,5776,1764.txt,3,0,,,,"Hfq Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .
"
5776,5777,1764.txt,4,0,,,,"Hfq Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .
"
5777,5778,1764.txt,5,0,,,,"DksA Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether Hfq , two potent regulators of rpoS translation , were required for acid shock control .
"
5778,5779,1764.txt,6,0,,,,"DksA Are Required for Acid Shock Induction Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .
"
5779,5780,1764.txt,7,0,,,,"DksA Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether Hfq , two potent regulators of rpoS translation , were required for acid shock control .
"
5780,5781,1764.txt,8,0,,,,"DksA Are Required for Maximal Expression of rpoS Establishing that acid shock induces rpoS translation raised the question of whether DksA , two potent regulators of rpoS translation , were required for acid shock control .
"
5781,5782,1764.txt,9,0,,,,"Since DksA , two potent regulators of rpoS translation , were not absolutely required for acid shock induction , other factors must be involved in resolving the secondary structure ."
5782,5783,1994.txt,1,0,,,,"Results Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the absence of LeuO .
"
5783,5784,1994.txt,2,0,,,,"Results Activation of leuO transcription represses SPI-1 To confirm previous evidence indicating that SPI-1 might be repressed by LeuO , we compared the expression of selected SPI-1 genes in the presence .
"
5784,5785,1994.txt,3,0,,,,"Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of OFF subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -
"
5785,5786,1994.txt,4,0,,,,"Single cell analysis of gene expression by flow cytometry confirmed that HilE plays a role in LeuO-mediated repression of SPI-1 : activation of leuO expression decreased the activity of a sipB : : GFP fusion : GFP expression ; a hilE null mutation increased sipB : : GFP expression and reduced the size of the SPI-1 subpopulation , in agreement with the role of HilE as a SPI-1 repressor ; activation of leuO expression in a HilE − background yielded a small subpopulation of sipB -
"
5786,5787,1994.txt,5,0,,,,"In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion Fig. 7B , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO .
"
5787,5788,1994.txt,6,0,,,,"In the absence of HilE , activation of leuO transcription reduced epithelial cell invasion three-to fourfold , thereby providing further evidence for HilE-independent downregulation of SPI-1 by LeuO ."
5788,5789,2245.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Escherichia coli where inactivation of RpoS reduced Pol IV protein levels three-to fivefold in the wild-type background , indicating that regulation of dinB expression is different in these two species"
5789,5790,2251.txt,1,0,,,,"( tldD ) transcripts _ suggesting that MntR may also act upstream of tldD in the control of cdtB gene expression
"
5790,5791,2251.txt,2,0,,,,"( tldD ) transcripts _ suggesting that MntR may also act upstream of sty3548 in the control of cdtB gene expression
"
5791,5792,2251.txt,3,0,,,,"( tldD ) transcripts _ suggesting that MntR may also act upstream of tldD in the control of cdtB gene expression
"
5792,5793,2251.txt,4,0,,,,( tldD ) transcripts _ suggesting that MntR may also act upstream of sty3548 in the control of cdtB gene expression
5793,5794,1758.txt,1,0,,,,"Alternatively , the LeuO protein stimulate transcription of the ilvIH operon to leucine limitation ."
5794,5795,1980.txt,1,0,,,,"The next question addressed was whether acid shock might control ompR expression by changing the phosphorylation level of OmpR or , perhaps , by modulating ompR P2 repression by H-NS .
"
5795,5796,1980.txt,2,0,,,,"H-NS represses ompR expression .
"
5796,5797,1980.txt,3,0,,,,"An alternative model states acid regulates ompR by modulating repression by H-NS
"
5797,5798,1980.txt,4,0,,,,"that H-NS represses ompR
"
5798,5799,1980.txt,5,0,,,,"autoinduction in which OmpR-P overcomes H-NS repression of ompR on OmpR-P-dependent ATR gene promoters
"
5799,5800,1980.txt,6,0,,,,"The next question addressed was whether acid shock might control ompR expression by changing the phosphorylation level of OmpR or , perhaps , by modulating ompR P2 repression by H-NS .
"
5800,5801,1980.txt,7,0,,,,"H-NS represses ompR expression .
"
5801,5802,1980.txt,8,0,,,,"An alternative model states acid regulates ompR by modulating repression by H-NS
"
5802,5803,1980.txt,9,0,,,,"that H-NS represses ompR
"
5803,5804,1980.txt,10,0,,,,autoinduction in which OmpR-P overcomes H-NS repression of ompR on OmpR-P-dependent ATR gene promoters
5804,5805,1028.txt,1,0,,,,"Inactivation of LsrR by the presence of phosphorylated AI-2 allows invF , sicA , sopB , sopE and fliC , fliD gene transcription .
"
5805,5806,1028.txt,2,0,,,,"Inactivation of LsrR by the presence of phosphorylated AI-2 allows invF , sicA , sopB , sopE and flagella gene transcription ."
5806,5807,2247.txt,1,0,,,,"Besides overall transcriptional decreases for genes , lower transcript abundances were observed in rpoA ( encoding DNA-directed RNA polymerase subunit alpha ) , DNA-binding protein Fis ."
5807,5808,1996.txt,1,0,,,,"Because PhoP/PhoQ regulates more than 40 genes , additional PhoP/PhoQ-activated genes , including pmrD and pagD , were examined to determine if bile specifically regulated pagC , or if it has a general effect on PhoP/PhoQ-regulated genes ."
5808,5809,1982.txt,1,0,,,,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5809,5810,1982.txt,2,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5810,5811,1982.txt,3,0,,,,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5811,5812,1982.txt,4,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5812,5813,1982.txt,5,0,,,,"SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , that of the spvABCD operon .
"
5813,5814,1982.txt,6,0,,,,"SpvR binds to regulatory sequences upstream of both the spvR and spvA promoters , inducing its own expression of the spvABCD operon .
"
5814,5815,1982.txt,7,0,,,,"Norel , F. Relationships between SpvR S phase in the control of spvR , the regulatory gene of operon .
"
5815,5816,1982.txt,8,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Norel , F. Relationships between SpvR S phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5816,5817,1982.txt,9,0,,,,"Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5817,5818,1982.txt,10,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5818,5819,1982.txt,11,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .
"
5819,5820,1982.txt,12,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .
"
5820,5821,1982.txt,13,0,,,,"Relationships between SpvR phase in the control of spvR , the regulatory gene of operon .
"
5821,5822,1982.txt,14,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5822,5823,1982.txt,15,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .
"
5823,5824,1982.txt,16,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .
"
5824,5825,1982.txt,17,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Grob , P. , and Guiney , D. G. In Vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR , J. Bacteriol .
"
5825,5826,1982.txt,18,0,,,,"Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5826,5827,1982.txt,19,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5827,5828,1982.txt,20,0,,,,"Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5828,5829,1982.txt,21,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5829,5830,1982.txt,22,1,Starmerella aceti,to 125,Starmerella aceti,"Gel mobility-shift assays revealed that the SpvR fusion proteins were able to bind to 125-and 147-bp DNA fragments of spvR promoter regions , respectively .
"
5830,5831,1982.txt,23,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter regions of spvR .
"
5831,5832,1982.txt,24,0,,,,"SpvR binds to both the spvR .
"
5832,5833,1982.txt,25,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Grob P , Guiney DG In vitro binding of the Salmonella dublin virulence plasmid regulatory protein SpvR to the promoter region of spvR .
"
5833,5834,1982.txt,26,0,,,,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5834,5835,1982.txt,27,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , Norel , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence .
"
5835,5836,1982.txt,28,0,,,,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of operon .
"
5836,5837,1982.txt,29,2,Salmonella;unidentified plasmid,Salmonella;plasmid,Salmonella;unidentified plasmid,"Robbe-Saule , V. , Schaeffer , F. , Kowarz , L. , , F. Relationships between H-NS , sigma S , SpvR phase in the control of spvR , the regulatory gene of the Salmonella plasmid virulence ."
5837,5838,2253.txt,1,0,,,,"pagC are known to be repressed , respectively , by the active form of PhoP ."
5838,5839,1014.txt,1,0,,,,"Expression of ptsG , is repressed by Mlc ."
5839,5840,580.txt,1,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
5840,5841,580.txt,2,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA ."
5841,5842,1772.txt,1,0,,,,"The data show that all three genes , hilC , were repressed by H-NS and/or Hha ."
5842,5843,1766.txt,1,0,,,,"The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of carbon storage .
"
5843,5844,1766.txt,2,0,,,,"The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of biofilm formation .
"
5844,5845,1766.txt,3,0,,,,"The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of motility .
"
5845,5846,1766.txt,4,0,,,,The negative selection of the barA mutant at all sites after oral dosing of calves is consistent with the role of SirA TCS in control of T3SS-1 .
5846,5847,594.txt,1,0,,,,"the osmY genes were repressed by StpA at LEP
"
5847,5848,594.txt,2,0,,,,the osmY genes were repressed by StpA at the MEP stage of growth
5848,5849,1000.txt,1,0,,,,"In addition to HilD , the expression of lpxR in SPI-1-inducing conditions is positively regulated by a MarR-like regulator63 ."
5849,5850,219.txt,1,0,,,,"Our results show that CpxR , induces the transcription of clpP neighbor genes encoding the ClpXP protease ."
5850,5851,1955.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
5851,5852,2284.txt,1,0,,,,"Although HilC regulate two promoters upstream of hilC , they activate one and repress the other , such that overall HilC appear to have no effect on hilC expression .
"
5852,5853,2284.txt,2,0,,,,"These results indicate that Lon is involved in the autoregulation of hilC transcription by modulating amounts of HilC .
"
5853,5854,2284.txt,3,0,,,,"This work demonstrates the regulation of hilC by HilC .
"
5854,5855,2284.txt,4,0,,,,The HilC proteins bind to the common DNA sites at hilC promoters .
5855,5856,2290.txt,1,0,,,,"As PhoP is a negative regulator of the hilA expression , this decreased expression can not account for the downregulation of the hilA gene by the fliZ mutation ."
5856,5857,1799.txt,1,0,,,,To the functional category related to the `` cell envelope 
5857,5858,1941.txt,1,0,,,,The cAMP-CRP complex positively regulates the transcription of the flhDC operon .
5858,5859,543.txt,1,0,,,,sufC was not regulated by either RpoS alone
5859,5860,225.txt,1,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
5860,5861,1969.txt,1,0,,,,"The effect of OmpR appears to be direct , based on our observation that OmpR-P binds to the intergenic region between ssrA .
"
5861,5862,1969.txt,2,0,,,,"Altogether , our data indicate that OmpR-P binds to the upstream region of ssrA .
"
5862,5863,1969.txt,3,0,,,,"Altogether , our data indicate that OmpR-P binds around the intergenic region between ssrA .
"
5863,5864,1969.txt,4,0,,,,"OmpR-P binds to sites downstream of the ssrA transcriptional start site , activating ssrA .
"
5864,5865,1969.txt,5,0,,,,"OmpR-P binds to sites upstream of the ssrA transcriptional start site , activating ssrA .
"
5865,5866,1969.txt,6,0,,,,"OmpR-P binds to sites downstream of the ssrA transcriptional start site , activating ssrA .
"
5866,5867,1969.txt,7,0,,,,"OmpR-P binds to sites upstream of the ssrA transcriptional start site , activating ssrA .
"
5867,5868,1969.txt,8,0,,,,"In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrA genes ."
5868,5869,231.txt,1,0,,,,"In accord with these data , another group showed that dalS/STM1633 clustered into an SsrB-controlled regulatory network enriched in virulence genes including genes in SPI-2 and with srfN ( 19 ) , the latter of which we previously showed was required for in-vivo fitness ( 20 ) .
"
5869,5870,231.txt,2,0,,,,"SsrB controls srfN directly through binding to the srfN cis-regulatory element
"
5870,5871,231.txt,3,0,,,,"SsrB controls srfN directly through binding to the srfN cis-regulatory element
"
5871,5872,231.txt,4,0,,,,SsrB controls srfN directly through binding to the srfN cis-regulatory element
5872,5873,557.txt,1,0,,,,"Even a recent report in which the proteomes of wild type , hilA null ( a transcriptional regulator of SPI-1 genes ) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus ( Brown et al. , 2014 ) , as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation ."
5873,5874,2045.txt,1,0,,,,this effect was reflected by induction of cspD and proteins ( CspC ) in response to preadaptation to cold-stress
5874,5875,966.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Notably , our observation that deletion of all of the IS200 copies in S. Typhimurium impacted on the expression of an SPI-1 gene not under the control of InvF is consistent with tnpA producing either a multi-functional regulatory RNA or , as in the case of IS1341 , multiple regulatory sRNAs ."
5875,5876,972.txt,1,0,,,,FimZY have been shown to repress the expression of hilA by controlling expression of hilE .
5876,5877,2051.txt,1,0,,,,Transcription of ssrA genes is repressed by Lrp .
5877,5878,1558.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
5878,5879,2079.txt,1,0,,,,mlrA expression itself is positively regulated by RpoS .
5879,5880,1570.txt,1,0,,,,"Although not significantly enriched within the set of directly PhoPQ-regulated genes , the functional class related to pathogenicity and virulence also contained potential PhoPQ-dependent targets ( pagC , mgtC , virK , and STM0306 ) ."
5880,5881,782.txt,1,0,,,,"The FlhDC-regulated ycgR and yhjH genes ( Ko and Park , 2000 ) were also strongly repressed ( 0.08-and 0.18-fold at 45 min respectively ; Table 8 ) ."
5881,5882,1216.txt,1,0,,,,The ArcAB system can also act as a positive regulator by the induction of cydAB
5882,5883,1202.txt,1,0,,,,"Two reports have shown that prgH expression , can be upregulated by artificially expressing high levels of SirC , SprA even in the absence of hilA .
"
5883,5884,1202.txt,2,0,,,,"Two reports have shown that invF expression , can be upregulated by artificially expressing high levels of SirC , SprA even in the absence of hilA ."
5884,5885,796.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"orby , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5885,5886,796.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,".L. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5886,5887,796.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"rown , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5887,5888,796.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,".J. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5888,5889,796.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"arshall , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5889,5890,796.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,". , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5890,5891,796.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"lank , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5891,5892,796.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,". , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5892,5893,796.txt,9,1,Escherichia coli,Escherichia coli,Escherichia coli,"awley , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5893,5894,796.txt,10,1,Escherichia coli,Escherichia coli,Escherichia coli,".L. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5894,5895,796.txt,11,1,Escherichia coli,Escherichia coli,Escherichia coli,"obman , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5895,5896,796.txt,12,1,Escherichia coli,Escherichia coli,Escherichia coli,".R. , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5896,5897,796.txt,13,1,Escherichia coli,Escherichia coli,Escherichia coli,"rocklehurst , A.P. ZntR is espon-sive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5897,5898,796.txt,14,1,Escherichia coli,Escherichia coli,Escherichia coli,"ZntR is responsive MerR-like transcriptional regulator of zntA in Escherichia coli .
"
5898,5899,796.txt,15,0,,,,"The zntA gene is under the control of the transcriptional activator ZntR .
"
5899,5900,796.txt,16,1,Escherichia coli,Escherichia coli,Escherichia coli,"Toxicol Appl Pharmacol 204 : 274 -- 308 Brocklehurst KR , Hobman JL , Lawley B , Blank L , Marshall SJ , Brown NL , Morby AP ZntR is a Zn - responsive MerR-like transcriptional regulator of zntA in Escherichia coli ."
5900,5901,1564.txt,1,0,,,,"Plumbridge , the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon ."
5901,5902,2086.txt,1,0,,,,"As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) .
"
5902,5903,2086.txt,2,0,,,,"A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) ."
5903,5904,769.txt,1,0,,,,"As described previously , the microarray data showed repression of the PmrAB-regulated pmrF gene ."
5904,5905,741.txt,1,0,,,,"Candidate genes for this activity include mig-14 , virK and somA because inactivation of these PhoP-activated genes results in strains displaying increased susceptibility to polymyxin B ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) .
"
5905,5906,741.txt,2,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK .
"
5906,5907,741.txt,3,0,,,,"These regulated genes included induction of PhoP-activated genes -LRB- pags -RRB- virK .
"
5907,5908,741.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Methods -- The TLC plates were covered by a staining solution containing agar , Luria-Bertani medium , 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside ( X-gal ) , kanamycin and a S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to an archetypal PhoP-activated gene virK .
"
5908,5909,741.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"( a ) Bioautography carried out with the S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to a PhoP-activated gene virK .
"
5909,5910,741.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"After development the solvent was removed and the plate was revealed by bioautography with a S. Typhimurium strain that harbours a reporter transcriptional lacZ-fusion to a PhoP-activated gene virK as described in the Methods section .
"
5910,5911,741.txt,7,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Chryseobacterium gallinarum,S. typhimurium;typhimurium;strain ( 100,Chryseobacterium gallinarum;Salmonella enterica subsp. enterica serovar Typhimurium,"The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB-medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg/mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) .
"
5911,5912,741.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Inhibitory activity was detected by overlaying the plate with an aqueous solution of soft agar containing X-gal and a homogeneous suspension of the S. typhimurium strain that harbours a reporter transcriptional lacZ-fusion to an archetypal PhoP-activated gene virK .
"
5912,5913,741.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,of the S. typhimurium str in that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK or to a gene activated by the O
5913,5914,999.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Escherichia coli where inactivation of RpoS reduced Pol IV protein levels three-to fivefold in the wild-type background , indicating that regulation of dinB expression is different in these two species"
5914,5915,755.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , previous studies have determined that NsrR negatively regulates the expression of the ytfE genes .
"
5915,5916,755.txt,2,0,,,,Expression of ytfE is repressed by NsrR
5916,5917,1438.txt,1,1,Salmonella,Salmonella,Salmonella,"PhoP was reported to bind to the ssrB promoter when Salmonella are inside macrophages .
"
5917,5918,1438.txt,2,0,,,,"The role of SsrB in the regulation by PhoP was investigated in a double mutant phoQ24 ssrB .
"
5918,5919,1438.txt,3,0,,,,"PhoP also controls expression of Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .
"
5919,5920,1438.txt,4,0,,,,"PhoP also controls expression of Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .
"
5920,5921,1438.txt,5,1,Salmonella,Salmonella,Salmonella,"PhoP also controls expression of Salmonella pathogenicity island-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .
"
5921,5922,1438.txt,6,1,Salmonella,Salmonella,Salmonella,"PhoP also controls expression of Salmonella pathogenicity island-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .
"
5922,5923,1438.txt,7,0,,,,"The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .
"
5923,5924,1438.txt,8,0,,,,"The response regulator PhoP controls Spi-2 by binding to the ssrB promoter region ′ - UTR of the spiR transcript .
"
5924,5925,1438.txt,9,0,,,,"Under low osmolality , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
5925,5926,1438.txt,10,0,,,,"Under acidic pH , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
5926,5927,1438.txt,11,0,,,,"Since PhoP regulates expression of ssrB , it also regulates expression of genes in the SsrB regulon ."
5927,5928,2131.txt,1,0,,,,"CueR is known to be a copper-responsive transcriptional regulator of the copA gene .
"
5928,5929,2131.txt,2,0,,,,"copA is shown here to be transcriptionally controlled by CueR
"
5929,5930,2131.txt,3,2,Salmonella;Escherichia coli;Salmonella,Salmonella;E. coli;Salmonella,Escherichia coli;Salmonella,"Expression of copA in Salmonella is directly controlled by CueR Unlike in E. coli , in Salmonella copA are located adjacent in the genome .
"
5930,5931,2131.txt,4,2,Salmonella;Escherichia coli;Salmonella,Salmonella;E. coli;Salmonella,Escherichia coli;Salmonella,"Expression of copA in Salmonella is directly controlled by CueR Unlike in E. coli , in Salmonella cueR are located adjacent in the genome .
"
5931,5932,2131.txt,5,2,Salmonella;synthetic construct,Salmonella;primer,synthetic construct;Salmonella,"To confirm that copA transcription in Salmonella is controlled directly by the transcriptional regulator CueR , we first mapped the transcription start site of the gene by primer-extension analysis , using RNA .
"
5932,5933,2131.txt,6,0,,,,"CueR binds to the promoter region of copA .
"
5933,5934,2131.txt,7,0,,,,"Among these , we identified the GolS-target operators from the golTS operon and the golB gene ( Checa et al. , 2007 ) , as well as the CueR-controlled operators from cueO and copA genes ( Kim et al. , 2002 ; Espariz et al. , 2007 ) .
"
5934,5935,2131.txt,8,0,,,,CueR regulates copA .
5935,5936,0.txt,1,0,,,,"The dps promoter is activated by IHF S in stationary-phase .
"
5936,5937,0.txt,2,0,,,,"M , G. 1994 The dps promoter is activated by IHF and s in stationary-phase .
"
5937,5938,0.txt,3,0,,,,"The dps promoter is activated by IHF S in stationary-phase .
"
5938,5939,0.txt,4,0,,,,"The dps promoter is activated by IHF in stationary-phase .
"
5939,5940,0.txt,5,0,,,,"The dps promoter is activated by IHF S in stationary-phase .
"
5940,5941,0.txt,6,0,,,,The dps promoter is activated by IHF in stationary-phase .
5941,5942,52.txt,1,0,,,,FliA-dependent activation of FlgM ensures an effectiv `` off 
5942,5943,812.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Role of the MetR regulatory system in vitamin-B12-mediated repression of the Salmonella typhimurium metE gene .
5943,5944,46.txt,1,1,unidentified,unknown,unidentified,A tentative hypothesis is that asmA mutations might activate a MarA-regulated efflux pump hitherto unknown to transport bile-salts .
5944,5945,806.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
5945,5946,2125.txt,1,0,,,,"The transcription of csrB is regulated by SirA .
"
5946,5947,2125.txt,2,2,Salmonella;Escherichia coli,Salmonella;E. coli,Escherichia coli;Salmonella,"SirA regulates csrC In both Salmonella and E. coli , SirA directly regulates csrB .
"
5947,5948,2125.txt,3,0,,,,"To test the hypothesis that csrC is directly regulated by SirA , in-vitro gel mobility-shift assays were performed as previously described for csrB .
"
5948,5949,2125.txt,4,1,Salmonella,Salmonella,Salmonella,"SirA of Salmonella both control the csr system by directly binding the csrB gene .
"
5949,5950,2125.txt,5,0,,,,"These two reports suggest that in contrast to csrB , the regulation of csrC by SirA may be indirect .
"
5950,5951,2125.txt,6,0,,,,"No further increase in PefA expression was apparent in a sirA csrB csrC DfimAICDHF mutant ( TS133 ) ( Figure 2C ) , thus the lack of SirA or inactivation of the SirA-regulated genes csrB and csrC produced similar effects on PefA expression .
"
5951,5952,2125.txt,7,0,,,,"No further increase in PefA expression was apparent in a sirA csrB csrC DfimAICDHF mutant ( TS133 ) ( Figure 2C ) , thus the lack of SirA or inactivation of the SirA-regulated genes csrB and csrC produced similar effects on PefA expression .
"
5952,5953,2125.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. typhimurium , SirA is a positive regulator of csrB .
"
5953,5954,2125.txt,9,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , SirA is a positive regulator of csrB ."
5954,5955,190.txt,1,0,,,,"The genes slrP and dsbA are also induced by HilD independently of InvF .
"
5955,5956,190.txt,2,0,,,,The genes slrP and dsbA are also induced by HilD independently of both HilA .
5956,5957,1404.txt,1,0,,,,"These data demonstrated that the expression of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C ."
5957,5958,1362.txt,1,0,,,,"The interpretation of these data was that OmpR controls hilC transcription .
"
5958,5959,1362.txt,2,0,,,,"Increased OmpR can be recruited to bind to hilC promoters , in a process .
"
5959,5960,1362.txt,3,0,,,,"The OmpR protein also controls the transcription of key regulatory genes in hilC , allowing OmpR to contribute to the coordination of expression of these major virulence genetic elements ."
5960,5961,1376.txt,1,0,,,,"Additive effect of STM1697 on virulence As STM1344 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
5961,5962,1376.txt,2,0,,,,"Additive effect of STM1697 on virulence As STM1697 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
5962,5963,1376.txt,3,0,,,,"Additive effect of STM1697 on rdar biofilm formation As STM1344 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
5963,5964,1376.txt,4,0,,,,"Additive effect of STM1697 on rdar biofilm formation As STM1697 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
5964,5965,1376.txt,5,0,,,,"Additive effect of STM1697 on motility As STM1344 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
5965,5966,1376.txt,6,0,,,,"Additive effect of STM1697 on motility As STM1697 both work through inhibition of FlhD4C2 functionality , we investigated whether they act additively .
"
5966,5967,1376.txt,7,0,,,,"D. Electro mobility-shift assay _ elucidating a role of STM1697 in inhibition of FlhD4C2 interaction with its target DNA
"
5967,5968,1376.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. typhimurium UMR1 _ Having demonstrated that STM1697 inhibits motility by interacting with FlhD4C2
"
5968,5969,1376.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. typhimurium UMR1 _ Having demonstrated that STM1697 inhibits motility by interacting with FlhD4C2
"
5969,5970,1376.txt,10,0,,,,"S5B ) , suggesting that STM1697 affects rdar morphotype solely through inhibition of FlhD4C2 .
"
5970,5971,1376.txt,11,0,,,,"As FlhD4C2 is a highly conserved protein , we hypothesize that STM1697 homologues affect motility through inhibition of FlhD4C2 functionality also in other bacteria .
"
5971,5972,1376.txt,12,0,,,,"Most importantly , our studies suggested that STM1697 regulates flagellar formation by inhibiting FlhD4C2 from recruiting RNA polymerase to the promoters of class II flagellar genes .
"
5972,5973,1376.txt,13,0,,,,"Most importantly , our studies suggested that STM1697 regulates flagellar formation by inhibiting FlhD4C2 by disturbing the interaction between DNA .
"
5973,5974,1376.txt,14,0,,,,"Most importantly , our studies suggested that STM1697 regulates flagellar formation by inhibiting FlhD4C2 by disturbing the interaction between FlhD4C2 .
"
5974,5975,1376.txt,15,0,,,,"To determine whether STM1697 inhibits the DNA-binding activity of FlhD4C2 , we performed a series of EM-SAs .
"
5975,5976,1376.txt,16,0,,,,"Interestingly the purified STM1697 protein did not effectively inhibit the DNA binding activity of FlhD4C2 even if the molar ratio of FlhDC was as high as 18:1 .
"
5976,5977,1376.txt,17,0,,,,Interestingly the purified STM1697 protein did not effectively inhibit the DNA binding activity of FlhD4C2 even if the molar ratio of STM1697 was as high as 18:1 .
5977,5978,1410.txt,1,1,Escherichia coli,E. coli,Escherichia coli,Prigent-Combaret et al. suggested that 51 52 E. coli OmpR is also a regulator of the csgD regulator .
5978,5979,184.txt,1,0,,,,"The StpAA77D variant provided even greater repression of proV by reducing their transcript levels by 20-fold relative to StpAWT .
"
5979,5980,184.txt,2,0,,,,The StpAA77D variant provided even greater repression of proV by reducing their transcript levels by 4-fold relative to StpAWT .
5980,5981,2119.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Previously in E. coli , YdcI was shown to regulate the expression of gltA carbon flux to the TCA cycle ."
5981,5982,609.txt,1,0,,,,The most likely hypothesis to explain the repression of Rck expression at 25 °C would be a regulation by the nucleoprotein H-NS since two previous transcriptomic studies suggested a downregulation of rck by H-NS .
5982,5983,91.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
5983,5984,1389.txt,1,0,,,,"To determine whether the PmrA-regulated genes identified herein affect lipid-A structure ( particularly for STM4118 , which demonstrated somewhat decreased PM resistance ) , purified lipid-A from each mutant ( PmrA background ) was compared to that of the C parental strain for the presence of Ara4N .
"
5984,5985,1389.txt,2,0,,,,"Using site directed mutagenesis , Marchal et al. demonstrated that the fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM4118 promoters .
"
5985,5986,1389.txt,3,0,,,,"Using site directed mutagenesis , Marchal et al. demonstrated that the third positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM4118 promoters .
"
5986,5987,1389.txt,4,0,,,,Here we demonstrate that the PmrA-regulated STM4118 ( cptA ) gene is necessary for the addition of pEtN to the LPS core .
5987,5988,85.txt,1,1,Salmonella,Enteritidis,Salmonella,"The same behavior has been described for other ArcA-controlled promoters in 6 Time : 14:6 # lpxO Expression Is Regulated by Fnr and ArcA in Response to Oxygen Availability FIGURE 2  Main lipid-A species produced by S. Enteritidis .
"
5988,5989,85.txt,2,0,,,,"genetic analyses indicate that this process is regulated by ArcA controlling the expression of lpxO .
"
5989,5990,85.txt,3,0,,,,"Biochemical analyses indicate that this process is regulated by ArcA controlling the expression of lpxO .
"
5990,5991,85.txt,4,0,,,,"The above results led us to hypothesize that lpxO expression is regulated by oxygen availability through the activity of transcription regulators ArcA and/or Fnr .
"
5991,5992,85.txt,5,0,,,,"These observations suggest that ArcA is a negative regulator of lpxO expression under anaerobic conditions .
"
5992,5993,85.txt,6,0,,,,"On the other hand , both ArcA bound to the lpxO promoter .
"
5993,5994,85.txt,7,0,,,,"These results indicate that ArcA regulate lpxO expression through direct binding to its promoter region .
"
5994,5995,85.txt,8,0,,,,"In addition , we also demonstrate that ArcA control the oxygen-dependent lipid-A hydroxylation by directly regulating the expression of lpxO .
"
5995,5996,85.txt,9,0,,,,"Our results also showed that both ArcA are able to bind in-vitro to the promoter regions of lpxO , strongly suggesting a direct role for these regulators in the control of lpxO transcription .
"
5996,5997,85.txt,10,0,,,,"Our results also showed that both ArcA are able to bind in-vitro to the promoter regions of lpxO , strongly suggesting a direct role for these regulators in the control of lpxO transcription .
"
5997,5998,85.txt,11,1,Salmonella,Enteritidis,Salmonella,a model in which ArcA control the expression of lpxO in S. Enteritidis to achieve a fine-tuning of lipid-A hydroxylation levels
5998,5999,153.txt,1,0,,,,"The dps promoter is activated by OxyR during-growth in stationary-phase .
"
5999,6000,153.txt,2,0,,,,"M , G. 1994 The dps promoter is activated by OxyR during-growt in stationary-phase .
"
6000,6001,153.txt,3,0,,,,"The dps promoter is activated by OxyR during-growth in stationary-phase .
"
6001,6002,153.txt,4,0,,,,"The dps promoter is activated by OxyR during-growth in stationary-phase .
"
6002,6003,153.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"Moreover , while in E. coli the expression of dps in logarithmic phase is modulated by the exposition to sources of hydrogen-peroxide -LRB- mediated by OxyR -RRB- , in the stationary-phase its expression is not induced by this reactive oxygen specie .
"
6003,6004,153.txt,6,0,,,,"The dps promoter is activated by OxyR during-growth in stationary-phase .
"
6004,6005,153.txt,7,0,,,,"Activated OxyR induces H2O2 breakdown , dps lipids .
"
6005,6006,153.txt,8,0,,,,The dps promoter is activated by OxyR during-growth in stationary-phase .
6006,6007,635.txt,1,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rcsC .
"
6007,6008,635.txt,2,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rcsC ."
6008,6009,621.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007,GIFU10007,Salmonella enterica subsp. enterica serovar Typhimurium GIFU10007,Purified recombinant protein OmpRHis6 of GIFU10007 was shown to bind the upstream region of the yehU gene by the gel-shift assay .
6009,6010,147.txt,1,0,,,,"InvF production indirectly increases transcription of the sipC genes
"
6010,6011,147.txt,2,0,,,,"InvF production directly increases transcription of the sipC genes
"
6011,6012,147.txt,3,0,,,,"InvF production indirectly increases transcription of the sipC genes
"
6012,6013,147.txt,4,0,,,,"InvF production directly increases transcription of the sipC genes
"
6013,6014,147.txt,5,0,,,,"InvF positively regulates effector proteins within sipC and located outside -LRB- sopE -RRB- with the help of chaperone SicA .
"
6014,6015,147.txt,6,0,,,,"InvF positively regulates effector proteins within sipC and located outside -LRB- sopD -RRB- with the help of chaperone SicA .
"
6015,6016,147.txt,7,0,,,,"InvF positively regulates effector proteins within sipC and located outside -LRB- sopB -RRB- with the help of chaperone SicA .
"
6016,6017,147.txt,8,0,,,,InvF induces the expression of sipC -LSB- 14e16 -RSB- .
6017,6018,1148.txt,1,1,Salmonella,Salmonella,Salmonella,"In support of this evolutionary confinement among Salmonella , Navarre et al. suggested potential negative regulation of srfN by the histone-like nucleoid structuring protein H-NS ."
6018,6019,1160.txt,1,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6019,6020,1160.txt,2,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6020,6021,1160.txt,3,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6021,6022,1160.txt,4,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , Vi-antigen expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6022,6023,1160.txt,5,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6023,6024,1160.txt,6,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased growth Others H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6024,6025,1160.txt,7,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , co regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many .
"
6025,6026,1160.txt,8,2,Sus scrofa;unidentified,pig;Unknown,Sus scrofa;unidentified,"Alteration in SPI-1 , flagellin expression Multiple , ( egpag , pig , SPV , SP12 genes ) Multiple , ( eg invF ) Osmolarity RcsB/RcsC Alternative ( T factors RpoS Starvation Multiple , ( eg spv ) Many , induction of stress tolerance , inreased intracellular survival H-NS Temperature , ( DNAtopology ) Temperature Iron , pH Many Global gene regulator TlpA Fur Unknown flpA Multiple , ( eg sitABCD ) Many ."
6026,6027,1606.txt,1,0,,,,"In minimal M9 medium , a striking 80-fold increase in pdxK expression was observed in the ptsJ knockout mutant strain with respect to Fig. 1A , clearly indicating that PtsJ is a transcriptional repressor of this gene .
"
6027,6028,1606.txt,2,0,,,,"In minimal M9 medium , a striking 80-fold increase in pdxK expression was observed in the ptsJ knockout mutant strain with respect to wild-type , clearly indicating that PtsJ is a transcriptional repressor of this gene ."
6028,6029,392.txt,1,0,,,,"the ssaG genes are controlled by HilD indirectly , respectively
"
6029,6030,392.txt,2,0,,,,"the ssaG genes are controlled by HilD directly , respectively"
6030,6031,386.txt,1,0,,,,"SprB , regulates the expression of sipC ."
6031,6032,1612.txt,1,0,,,,turn _ regulated by the OmpR/EnvZ two-component system by direct binding to the ssrAB promoter
6032,6033,1174.txt,1,0,,,,"In vitro characterization of transcriptional-fusions to virulence genes As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) ."
6033,6034,1821.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
6034,6035,1835.txt,1,0,,,,"In light of the role for SPI-2 in adaptation to the macrophage , it was interesting to observe that the macrophage-induced genes mig-3 and mig-14 , and a number of PhoP-PhoQ-activated genes also showed a dependency on Fis ( Table 3 ) ."
6035,6036,379.txt,1,1,Salmonella,Salmonella,Salmonella,"To confirm CRP control , CyaR RNA levels were determined in Salmonella strains inactivated for crp in early stationary-phase .
"
6036,6037,379.txt,2,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6037,6038,379.txt,3,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6038,6039,379.txt,4,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6039,6040,379.txt,5,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6040,6041,379.txt,6,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6041,6042,379.txt,7,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6042,6043,379.txt,8,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6043,6044,379.txt,9,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6044,6045,379.txt,10,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6045,6046,379.txt,11,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6046,6047,379.txt,12,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6047,6048,379.txt,13,0,,,,"THE observation that crp mutantsoverproduce adenosine-3 
"
6048,6049,379.txt,14,0,,,,"Hence , combined repression of crp mRNAs by SdsR endorses down-regulation of the CRP regulon ."
6049,6050,437.txt,1,0,,,,"In addition to controlling SPI1 expression , HilA represses expression of flhD expression ."
6050,6051,351.txt,1,0,,,,"the hemX gene were used as negative control regions , respectively , as H-NS does not bind to the hemX gene .
"
6051,6052,351.txt,2,0,,,,"the hemX gene were used as positive control regions , respectively , as H-NS does not bind to the hemX gene .
"
6052,6053,351.txt,3,0,,,,"The proV promoter were used as negative control regions , respectively , as H-NS does not bind to the hemX gene .
"
6053,6054,351.txt,4,0,,,,"The proV promoter were used as positive control regions , respectively , as H-NS does not bind to the hemX gene ."
6054,6055,1809.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Interplay between global regulators of Escherichia coli : effect of RpoS on the transcription of the gene osmC .
"
6055,6056,1809.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Gutierrez , C. Interplay between global regulators of Escherichia coli : effect of RpoS on transcription of the gene osmC .
"
6056,6057,1809.txt,3,0,,,,"Among the 38 genes , osmC were previously reported to be regulated by RpoS ."
6057,6058,345.txt,1,0,,,,"The expression of hilA is itself controlled by two additional SPI-1 regulators : HilC .
"
6058,6059,345.txt,2,0,,,,"HilC bind the same regions upstream of hilA .
"
6059,6060,345.txt,3,0,,,,"In addition to binding upstream of hilA , HilC also bind to sites upstream of hilC .
"
6060,6061,345.txt,4,0,,,,"In addition to binding upstream of hilA , HilC also bind within S. Akbar , unpublished results .
"
6061,6062,345.txt,5,0,,,,"In addition to binding upstream of hilA , HilC also bind within the prgH-hilD intergenic region .
"
6062,6063,345.txt,6,0,,,,"HilC are positive regulators of hilA expression
"
6063,6064,345.txt,7,0,,,,"HilC have been shown to bind to URS of hilA .
"
6064,6065,345.txt,8,0,,,,"HilC have been shown to bind to the upstream repressing sequence of hilA .
"
6065,6066,345.txt,9,0,,,,"HilC bind directly to the upstream sequence of hilA .
"
6066,6067,345.txt,10,0,,,,"HilC can independently bind the hilA promoter .
"
6067,6068,345.txt,11,0,,,,"a model in which expression of hilA is controlled by the combined action of HilC
"
6068,6069,345.txt,12,0,,,,"a model in which expression of hilA is controlled by the combined action of HilC
"
6069,6070,345.txt,13,0,,,,"This is consistent with the feedforward loop model ; when neither HilC are present , regulation of hilA is dampened , even though the primary signal is mediated through HilD .
"
6070,6071,345.txt,14,0,,,,"HilC bind to overlapping sites in the hilA promoter .
"
6071,6072,345.txt,15,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lee , C.A. Roles of HilC in regulation of hilA expression in Salmonella enterica sero-var Typhimurium .
"
6072,6073,345.txt,16,0,,,,"Studies have shown PheU that HilC can each individually bind to the hilA promoter
"
6073,6074,345.txt,17,0,,,,"HilC , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by the sic/sip operon -- in a fashion independent of HilA .
"
6074,6075,345.txt,18,0,,,,"HilC , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through -- in a fashion independent of HilA .
"
6075,6076,345.txt,19,0,,,,"This work demonstrates the regulation of hilA by HilC .
"
6076,6077,345.txt,20,0,,,,"HilC were described to influence the expression of hilA .
"
6077,6078,345.txt,21,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SCHECHTER L.M. , LEE C.A. : HilC , directly bind the Salmonella typhimurium hilA promoter .
"
6078,6079,345.txt,22,0,,,,"Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilC .
"
6079,6080,345.txt,23,0,,,,"Earlier work on mathematical modeling of regulation of expression of hilA by HilC was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .
"
6080,6081,345.txt,24,0,,,,"The results of these surveys can be summarized as follows : i. Dam-dependent regulation of hilA was not abolished in the absence of HilC .
"
6081,6082,345.txt,25,0,,,,"The results of these surveys are shown in Figure 3 : i. Dam-dependent regulation of hilA was not abolished in the absence of HilC .
"
6082,6083,345.txt,26,0,,,,"In turn , hilA is regulated by HilC .
"
6083,6084,345.txt,27,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Schechter LM , Lee CA : HilC , directly bind the Salmonella typhimurium hilA promoter .
"
6084,6085,345.txt,28,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilC mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , SgJ-4 , and SgJ-5 for 30 min in InT-407 cells .
"
6085,6086,345.txt,29,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilC mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , SgJ-4 , and pH 5 for 30 min in InT-407 cells .
"
6086,6087,345.txt,30,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilC mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , pH 4 , and SgJ-5 for 30 min in InT-407 cells .
"
6087,6088,345.txt,31,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilC mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , pH 4 , and pH 5 for 30 min in InT-407 cells .
"
6088,6089,345.txt,32,0,,,,"Differential expression of hilA , is influenced by HilC
"
6089,6090,345.txt,33,0,,,,"Expression of hilA is directly controlled by SPI-1-encoded HilC and HilD
"
6090,6091,345.txt,34,0,,,,"LoiA activates expression of hilA gene through activating hilD As the expression of hilA is directly controlled by HilC , we tested whether LoiA regulates HilA through any of these three regulators ."
6091,6092,423.txt,1,0,,,,"Relative luminescence in all the figures stands for the absolute 10-s luminescence Because the Fur protein is a repressor of transcription , it was expected that deletion of the fur box from the sdiA promoter would increase sdiA transcription .
"
6092,6093,423.txt,2,1,unidentified plasmid;unidentified plasmid,plasmid;plasmid,unidentified plasmid,"We next examined transcription of the two Fur-repressed genes in the strain that carried deletions of the rstA and fur genes and harbored either the RstA expression plasmid or the plasmid vector ; analysis determined that the mRNA levels of fhuA and fhuF were similar to those in the fur deletion strain regardless of RstA expression ( Fig. 1B ) .
"
6093,6094,423.txt,3,0,,,,"Iron depletion also eliminated the regulatory effect of RstA on the Fur-repressed genes : in bacterial cells grown in LB-medium containing the iron-specific chelator dipyridyl , the transcription levels of the fhuA and fhuF genes were increased to the levels observed in the fur deletion strain even when the RstA protein was overexpressed ( Fig. 1B ) .
"
6094,6095,423.txt,4,0,,,,"We also determined that the Fur protein was acting as a transcriptional repressor of the feoAB operon because deletion of the fur gene resulted in a twofold increase of Fig. 2A .
"
6095,6096,423.txt,5,0,,,,"We also determined that the Fur protein was acting as a transcriptional repressor of the feoAB operon because deletion of the fur gene resulted in a twofold increase of the wild-type feoAB transcripts .
"
6096,6097,423.txt,6,0,,,,"Expression of each sRNA was also induced when fur was deleted , confirming the role of Fur as a repressor for both of these sRNAs .
"
6097,6098,423.txt,7,1,unidentified plasmid,plasmid,unidentified plasmid,"Fur ( H90R ) production from the plasmid-linked lac promoter could no longer complement ssaG expression in the fur deletion strain under pH Fig. 2B , further that Fur repression of SPI-2 expression under acidic conditions is dependent on iron .
"
6098,6099,423.txt,8,1,unidentified plasmid,plasmid,unidentified plasmid,"Fur ( H90R ) production from the plasmid-linked lac promoter could no longer complement ssaG expression in the fur deletion strain under pH 6.0 conditions , further that Fur repression of SPI-2 expression under acidic conditions is dependent on iron .
"
6099,6100,423.txt,9,0,,,,"Therefore , Fur might indirectly repress tcf expression by repressing these sRNAs , as loss of fur in low iron concomitantly increases expression of both sRNAs ."
6100,6101,344.txt,1,2,Escherichia coli;Salmonella;Salmonella;Salmonella,Escherichia coli;S. enterica;enterica;Salmonella,Escherichia coli;Salmonella,"We used the model to analyze the intergenic regions of the Escherichia coli ( 40 ) and S. enterica ( 41 ) genomes by using relaxed thresholds ( 25 ) , which allowed the recovery of PhoP-regulated promoters with weak matching to the PhoP box consensus , such as the Salmonella pmrD promoter , that could not be detected by using consensus cutoffs ( 2 , 25 ) despite being regulated and footprinted by the PhoP protein ( 18 , 26 ) .
"
6101,6102,344.txt,2,1,Salmonella,Salmonella,Salmonella,"the Salmonella pmrD promoter could not be detected by using consensus cutoffs despite being regulated by the PhoP protein
"
6102,6103,344.txt,3,1,Salmonella,Salmonella,Salmonella,"the Salmonella pmrD promoter could not be detected by using consensus cutoffs despite being regulated by the PhoP protein
"
6103,6104,344.txt,4,0,,,,"the pmrD promoter harbors binding sites for both the PhoP
"
6104,6105,344.txt,5,0,,,,"When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the pmrD promoters increased during the first 10 min .
"
6105,6106,344.txt,6,0,,,,"When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the pmrD promoters increased during the first 10 min .
"
6106,6107,344.txt,7,0,,,,"When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the pmrD promoters then asymptotically reached the steady-state levels .
"
6107,6108,344.txt,8,0,,,,"When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the pmrD promoters then asymptotically reached the steady-state levels .
"
6108,6109,344.txt,9,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
6109,6110,1808.txt,1,1,Salmonella,Salmonella,Salmonella,Other regulators of AcrR did not contrib-ute to acrAB induction by indole in Salmonella .
6110,6111,422.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Consistent with the role of FimZ as an activator of S. typhimurium fimA expression , fimZ mutants exhibit only low levels of fimA expression .
"
6111,6112,422.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Consistent with the role of FimZ as an activator of S. typhimurium fimA expression , fimZ mutants are non-fimbriate .
"
6112,6113,422.txt,3,0,,,,"Since FimZ are both required to activate fimA , it is possible that these two proteins form a complex to bind the promoter of fimA .
"
6113,6114,422.txt,4,0,,,,We demonstrated that FimZ is a transcriptional activator of fimA .
6114,6115,436.txt,1,0,,,,"Expression of hilA is increased by PhoPQ for Inversion Stimulation , Fis .
"
6115,6116,436.txt,2,0,,,,Induction of the SPI-1 transcriptional activator hilA further support a model in which RNS target PhoPQ signaling .
6116,6117,350.txt,1,0,,,,"Nevertheless , this effect was abolished in the rpoS mutant , indicating that induction of hlyE transcription is dependent on RpoS under these conditions .
"
6117,6118,350.txt,2,0,,,,"These results show that hlyE transcription is increased by low pH and high-osmolarity in an RpoS-dependent manner .
"
6118,6119,350.txt,3,0,,,,"hlyE gene transcription is induced by low pH in an RpoS-dependent manner .
"
6119,6120,350.txt,4,0,,,,"hlyE gene transcription is induced by high-osmolarity in an RpoSdependent manner .
"
6120,6121,350.txt,5,0,,,,"Discussion In this work , we showed that hlyE genes found in SPI-18 present RpoS-dependent induction at low pH or high-osmolarity .
"
6121,6122,350.txt,6,0,,,,"In this work , we showed that the hlyE is upregulated in low pH and high-osmolarity in an RpoSdependent manner .
"
6122,6123,350.txt,7,0,,,,"Finally , rpoS is epistatic over phoPQ , reinforcing the fact that the induction of the hlyE expression under low concentration of Mg2 + occurs via RpoS .
"
6123,6124,350.txt,8,0,,,,"In this paper we showed that RpoS is the most import-ant activator of hlyE expression .
"
6124,6125,350.txt,9,0,,,,"Furthermore , hlyE induction by high-osmolarity is RpoS dependent ."
6125,6126,378.txt,1,0,,,,RhaS activates the rhaBAD genes via binding to another inverted repeat of two sites .
6126,6127,1834.txt,1,0,,,,"In order to test this possibility , pKKOPA99C was introduced into the flhD : : TnlO derivatives of the expression of respective flagellar operons in FlhDC-depletion background was examined after the tac-fliA gene was induced for 2 h with IPTG ."
6127,6128,1820.txt,1,0,,,,"rbs Operon That Are Regulated by luxS = Autoinducer-2 at Mid-Log Phase a 1.1 1.1 a membran , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant
"
6128,6129,1820.txt,2,0,,,,"rbs Operon That Are Regulated by luxS = Autoinducer-2 at Mid-Log Phase a 1.1 1.1 a a rbsA 1.1 ABC superfamily -LRB- -RRB- , -- D-ribose high-affinity transport protein ABC superfamily -LRB- -RRB- , D-ribose transport protein ABC superfamil , D-ribose high-affinity transport protein D-ribose high-affinity transport system membrane-associated protein Ribokinase Transcriptional repressor for GalR = LacI famil -- 1.1 -- -- rbsB 2.0 1.1 a 1.2 a 1.2 a 1.0 -- rbsC 1.1 a 1.3 a -- 1.2 -- rbsD 1.1 a -- -- -- 1.2 1.1 a rbsK rbsR 2.2 2.5 -- -- Differentially regulated genes between wild type -LRB- W mutant cell-free supernatant"
6129,6130,1613.txt,1,0,,,,"Shaded in light gray are the genes of CysB -LRB- as an activator of the cbl gene -RRB- according to a scheme down-regulated genes , 3.25-fold decrease was observed for treC ."
6130,6131,387.txt,1,0,,,,"Deletion of the fur box resulted in a twofold increase of sdiA transcription , consistent with a repressive function of the Fur protein ."
6131,6132,1175.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"The S. Typhimurium ferritins are differentially regulated Previous studies in E. coli have shown that Fur positively regulates bfr expression under Fe-replete conditions .
"
6132,6133,1175.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimu,Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , the S. Typhimu-rium bfr are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .
"
6133,6134,1175.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .
"
6134,6135,1175.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar to the S. Typhimurium bfr are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA ."
6135,6136,1161.txt,1,0,,,,"In the comparison of tolC strains in an Mg2-free buffer , the PhoPQ-activated modifica tions resulted in a more-than-fourfold increase in the barrier function against the penetration of a cationic dye , ethidium , in comparison with the phoP null mutant , in which the modification was absent ( Fig. 2 , left panel ) ."
6136,6137,393.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
6137,6138,393.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6138,6139,1607.txt,1,0,,,,"In contrast , the H-NSI11A mutant main-Disruption of the Hha/H-NS Interaction in Vivo Results in tained wild type levels of proV transcript but derepressed hilA Misregulation of Select H-NS-repressed Genes -- To clarify and ssrA by 145-and 9.5-fold compared with H-NSWT levels ."
6139,6140,1149.txt,1,0,,,,"First , HilD , binds directly to several sites within de-represses hilA expression .
"
6140,6141,1149.txt,2,0,,,,"First , HilD , binds directly to several sites within PhilA hilA expression .
"
6141,6142,1149.txt,3,0,,,,"The expression of hilA is itself controlled by two additional SPI-1 regulators : HilD .
"
6142,6143,1149.txt,4,0,,,,"HilD bind the same regions upstream of hilA .
"
6143,6144,1149.txt,5,0,,,,"Both HilC and HilD are positive regulators of hilA expression .
"
6144,6145,1149.txt,6,0,,,,"HilD are positive regulators of hilA expression
"
6145,6146,1149.txt,7,0,,,,"HilD have been shown to bind to URS of hilA .
"
6146,6147,1149.txt,8,0,,,,"HilD have been shown to bind to the upstream repressing sequence of hilA .
"
6147,6148,1149.txt,9,0,,,,"HilD bind directly to the upstream sequence of hilA .
"
6148,6149,1149.txt,10,0,,,,"As shown in Fig. 8 , the increased effect of Lon depletion on hilA expression was abolished by depletion of both HilC and HilD , suggesting that both proteins are also involved in regulation of SPI1 by Lon under SPI1-repressing conditions .
"
6149,6150,1149.txt,11,0,,,,"HilD can independently bind the hilA promoter .
"
6150,6151,1149.txt,12,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"HilD , directly bind the Salmonella typhimurium hilA promoter .
"
6151,6152,1149.txt,13,0,,,,"a model in which expression of hilA is controlled by the combined action of HilD
"
6152,6153,1149.txt,14,0,,,,"a model in which expression of hilA is controlled by the combined action of HilD
"
6153,6154,1149.txt,15,0,,,,"HilD is required for EnvZ/OmpR regulation of hilA It was previously concluded that the EnvZ/OmpR two-component system functioned through hilC to regulate expression of invasion genes .
"
6154,6155,1149.txt,16,0,,,,"HilD bind to overlapping sites in the hilA promoter .
"
6155,6156,1149.txt,17,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lee , C.A. Roles of HilD in regulation of hilA expression in Salmonella enterica sero-var Typhimurium .
"
6156,6157,1149.txt,18,0,,,,"Studies have shown PheU that HilD can each individually bind to the hilA promoter
"
6157,6158,1149.txt,19,0,,,,"HilD , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by the sic/sip operon -- in a fashion independent of HilA .
"
6158,6159,1149.txt,20,0,,,,"HilD , in addition to regulation of hilA , are all capable of inducing expression of the inv/spa operon -- and by read-through -- in a fashion independent of HilA .
"
6159,6160,1149.txt,21,0,,,,"This work demonstrates the regulation of hilA by HilD .
"
6160,6161,1149.txt,22,0,,,,"It also demonstrates EnvZ/OmpR control of hilA through HilD .
"
6161,6162,1149.txt,23,0,,,,"It also demonstrates BarA/SirA control of hilA through HilD .
"
6162,6163,1149.txt,24,0,,,,"HilD were described to influence the expression of hilA .
"
6163,6164,1149.txt,25,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"SCHECHTER L.M. , LEE C.A. : HilD , directly bind the Salmonella typhimurium hilA promoter .
"
6164,6165,1149.txt,26,0,,,,"To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilD-lac chromosomal fusions .
"
6165,6166,1149.txt,27,0,,,,"To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of hilC-lac .
"
6166,6167,1149.txt,28,0,,,,"To test whether HilD activators of hilA are also regulated by these proteins , we investigated the transcription of rtsA-lac .
"
6167,6168,1149.txt,29,0,,,,"In this work , we demonstrated that Fur regulates expression of hilA via control of HilD .
"
6168,6169,1149.txt,30,0,,,,"Transcription from the hilA promoter is in turn mainly regulated by three transcription factors ; HilD .
"
6169,6170,1149.txt,31,0,,,,"Of these regulators , HilD can be considered as the most important single regulator of the hilA promoter since the hilD knockout strain shows nearly basal levels of HilA under inducing conditions .
"
6170,6171,1149.txt,32,0,,,,"Model 4 : Two feedforward loops with OR gate model of regulation of PhilA by heterodimers of HilC-HilD , HilC-RtsA and HilD-RtsA In this case functions s3 , s4 and s are m 5-1/4 : ð 1/2 HilD 1/2 HilC ÞH3 kH3 þ ð 1/2 HilD 1/2 HilC ÞH3 3 odified as follows : s 3 s 4 Model 2 : Two feedforward loops with OR gate logic for regulation of P by HilD , HilC and RtsA -LRB- monomer hilA activation -RRB- ðModel 4Þ s 5 In this case , the rate of change of HilA concentration is a additive function of the three input transactivators via the functions s3 , s4 and s5 corresponding to HilD , HilC and RtsA respectively and is represented as : d 1/2 HilA 1/4 1/2 þ 1/2 þ þ b3 b3 s3 s4 s5 s dt Model 3 : Two feedforward loops with OR gate model for regulation of PhilA by monomers of HilD , HilC and RtsA and addition of positive feedback on RtsA and HilC as well as cross activations of RtsA on HilC and vice versa where functions s7 and s9 represent the auto-activation of HilC and RtsA respectively and functions s8 and s10 represent the cross activation of HilC by RtsA and vice versa respectively .
"
6171,6172,1149.txt,33,0,,,,"Model 4 : Two feedforward loops with OR gate model of regulation of PhilA by heterodimers of HilC-HilD , HilC-RtsA and HilD-RtsA In this case functions s3 , s4 and s are m 5-1/4 : ð 1/2 HilD 1/2 HilC ÞH3 kH3 þ ð 1/2 HilD 1/2 HilC ÞH3 3 odified as follows : s 3 s 4 Model 2 : Two feedforward loops with OR gate logic for regulation of P by HilD , HilC and RtsA -LRB- monomer hilA activation -RRB- ðModel 4Þ s 5 In this case , the rate of change of HilA concentration is a additive function of the three input transactivators via the functions s3 , s4 and s5 corresponding to HilD , HilC and RtsA respectively and is represented as : d 1/2 HilA 1/4 1/2 þ 1/2 þ þ b3 b3 s3 s4 s5 s dt Model 3 : Two feedforward loops with OR gate model for regulation of PhilA by monomers of HilD , HilC and RtsA and addition of positive feedback on RtsA and HilC as well as cross activations of RtsA on HilC and vice versa where functions s7 and s9 represent the auto-activation of HilC and RtsA respectively and functions s8 and s10 represent the cross activation of HilC by RtsA and vice versa respectively .
"
6172,6173,1149.txt,34,0,,,,"Earlier work on mathematical modeling of regulation of expression of hilA by HilD was based on feed-forward architecture , considering HilD to be the primary activator of the feed-forward loop .
"
6173,6174,1149.txt,35,0,,,,"In turn , hilA is regulated by HilD .
"
6174,6175,1149.txt,36,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Schechter LM , Lee CA : HilD , directly bind the Salmonella typhimurium hilA promoter .
"
6175,6176,1149.txt,37,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , SgJ-4 , and SgJ-5 for 30 min in InT-407 cells .
"
6176,6177,1149.txt,38,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , SgJ-4 , and pH 5 for 30 min in InT-407 cells .
"
6177,6178,1149.txt,39,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , pH 4 , and SgJ-5 for 30 min in InT-407 cells .
"
6178,6179,1149.txt,40,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD mutually regulate the hilA gene expression 2 1 1 0 Control SGJ-3 SGJ-4 SGJ-5 0 SGJ-4 SGJ-3 Control SGJ-5 Fig. 3 Invasive ability of lysogenic S. Typhimurium , pH 4 , and pH 5 for 30 min in InT-407 cells .
"
6179,6180,1149.txt,41,0,,,,"These results suggest that CpxR represses hilA by affecting the autoregulation of HilD .
"
6180,6181,1149.txt,42,0,,,,"HilD directly regulates hilA
"
6181,6182,1149.txt,43,0,,,,"The transcription of hilA is regulated by HilD .
"
6182,6183,1149.txt,44,0,,,,"HilD plays a major role in the regulation of hilA
"
6183,6184,1149.txt,45,0,,,,"The C-terminal domain of RNAPa has been shown to be important for transcription of HilD-regulated genes in-vivo , as the mutation of leucine 289 to phenylalanine within this domain fails to induced hilA expression , similarly to a hilD null mutant ( Boddicker et al. , 2003 ) .
"
6184,6185,1149.txt,46,0,,,,"Additionally , this strain harbored a HilD-regulated hilA 
"
6185,6186,1149.txt,47,0,,,,"Differential expression of hilA , is influenced by HilD
"
6186,6187,1149.txt,48,0,,,,"the hilA genes are controlled by HilD indirectly , respectively
"
6187,6188,1149.txt,49,0,,,,"the hilA genes are controlled by HilD directly , respectively
"
6188,6189,1149.txt,50,0,,,,"EMSA was used to test the binding of the indicated concentrations of HilD to 6 
"
6189,6190,1149.txt,51,0,,,,"HilD is a dominant regulator of hilA transcription
"
6190,6191,1149.txt,52,0,,,,"HilD plays a major role in regulating hilA expression .
"
6191,6192,1149.txt,53,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6192,6193,1149.txt,54,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6193,6194,1149.txt,55,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6194,6195,1149.txt,56,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6195,6196,1149.txt,57,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6196,6197,1149.txt,58,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6197,6198,1149.txt,59,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .
"
6198,6199,1149.txt,60,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .
"
6199,6200,1149.txt,61,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6200,6201,1149.txt,62,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6201,6202,1149.txt,63,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6202,6203,1149.txt,64,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6203,6204,1149.txt,65,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6204,6205,1149.txt,66,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6205,6206,1149.txt,67,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .
"
6206,6207,1149.txt,68,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .
"
6207,6208,1149.txt,69,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6208,6209,1149.txt,70,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6209,6210,1149.txt,71,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6210,6211,1149.txt,72,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , activation of hilA via HilD , CpxA/R , BarA/SirA .
"
6211,6212,1149.txt,73,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6212,6213,1149.txt,74,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6213,6214,1149.txt,75,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6214,6215,1149.txt,76,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via posttranslational regulation of HilD , DNA adenine methylase , EnvZ-OmpR , CpxA/R , BarA/SirA .
"
6215,6216,1149.txt,77,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6216,6217,1149.txt,78,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6217,6218,1149.txt,79,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6218,6219,1149.txt,80,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , activation of hilA via HilD , CpxA/R , BarA/SirA .
"
6219,6220,1149.txt,81,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6220,6221,1149.txt,82,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , repression of hilA by decreasing the stability of HilD , BarA/SirA .
"
6221,6222,1149.txt,83,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , activation of hilA via activation of csrB/csrC to block CsrA repression of hilD .
"
6222,6223,1149.txt,84,0,,,,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including FliZ , activation of hilA via posttranslational regulation of HilD , EnvZ-OmpR , CpxA/R , BarA/SirA .
"
6223,6224,1149.txt,85,1,unidentified,unknown,unidentified,"Many other regulators affect SPI-1 genes and/or HilA expression through HilD , including activation of hilA via an unknown regulation of HilD .
"
6224,6225,1149.txt,86,0,,,,"LoiA activates expression of hilA gene through activating hilD As the expression of hilA is directly controlled by HilD , we tested whether LoiA regulates HilA through any of these three regulators .
"
6225,6226,1149.txt,87,0,,,,"HilD , binds directly to several sites within the hilA promoter .
"
6226,6227,1149.txt,88,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Given that expression of hilA , significantly increases in bile , we investigated if HilD is posttranscriptionally regulated by bile in S. Typhi .
"
6227,6228,1149.txt,89,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In terms of understanding how S. Typhimurium differ with regard to SPI-1 expression in bile , our results , in combination with previous findings , dem-onstrate that HilD is differentially regulated by hilA .
"
6228,6229,1149.txt,90,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"In terms of understanding how S. Typhi differ with regard to SPI-1 expression in bile , our results , in combination with previous findings , dem-onstrate that HilD is differentially regulated by hilA ."
6229,6230,620.txt,1,0,,,,"Expression of hilA is increased by the pleiotropic activator proteins OmpR for Inversion Stimulation , Fis ."
6230,6231,146.txt,1,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in yeaR ."
6231,6232,152.txt,1,2,Escherichia coli;Salmonella;Escherichia coli,Escherichia coli;Salmonella;Escherichia coli,Escherichia coli;Salmonella,"We hypothesized that the PhoP-activated yrbL gene of Escherichia coli might participate in an analogous loop with the PmrA protein because both the Salmonella pmrD and Escherichia coli yrbL promoters can be found in the same promoter profile and harbor similarly arranged PhoP and PmrA boxes ( Fig. 1 D and E ) .
"
6232,6233,152.txt,2,0,,,,"A possible multicomponent loop involving the PhoP-activated yrbL gene .
"
6233,6234,152.txt,3,0,,,,"As shown in Fig. 4C , this motif is also observed in a similar position and in the same orientation in a subset of PhoP-activated genes , including phoP , mgtA , pmrD , yrbL , slyB , and orgB ( 49 ) ."
6234,6235,634.txt,1,0,,,,We predicted the PmrAB-dependent regulation of four additional targets : aroQ .
6235,6236,84.txt,1,0,,,,"a regulatory circuit in which flgM negatively regulates FliA function in flagellar-mutant backgrounds
"
6236,6237,84.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In flagellum-defective strains , the flgM gene product of S. typhimurium negatively regulates flagellar genes by inhibiting the activity of FliA ."
6237,6238,1388.txt,1,0,,,,"SoxRS regulation of fur .
"
6238,6239,1388.txt,2,0,,,,"SoxRS regulation of fur .
"
6239,6240,1388.txt,3,0,,,,"SoxRS regulation of fur .
"
6240,6241,1388.txt,4,0,,,,SoxRS regulation of fur .
6241,6242,90.txt,1,4,Tetragenococcus koreensis;Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,strain JS;Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Tetragenococcus koreensis;Salmonella enterica subsp. enterica serovar Typhimurium,"Notably , after all strains were induced simultaneously by GEN Citation : to the 15th passage at subinhibitory concentrations , strain JS △ cpxR/pcpxR showed significant increases in d mdtA genes , Huang H , Sun Y , Yuan L , Pan Y , Gao Y , Ma C and Hu G Regulation of the Two-Component Regulator CpxR on Aminoglycosides and β-lactams Resista in Salmonella enterica serovar Typhimurium ."
6242,6243,608.txt,1,0,,,,"The ChIP-chip analysis identified binding of AraC upstream of ppa ( divergently transcribed genes ) .
"
6243,6244,608.txt,2,0,,,,"We did not detect significant regulation of ppa by AraC in the transcription profiling experiment ; however , ytfQ encodes a transporter ."
6244,6245,1377.txt,1,0,,,,"Like marRAB , tolC are positively regulated by Rob ."
6245,6246,2118.txt,1,0,,,,"Mutants defective in hns exhibited high , constitutive levels of OmpR not subject to further induction by acid shock .
"
6246,6247,2118.txt,2,0,,,,"Mutants defective in hns exhibited high , constitutive levels of OmpR not subject to further induction by acid shock .
"
6247,6248,2118.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Calva E OmpR positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Calva E Negative osmoregulation of gene independently of OmpR in an hns background .
"
6248,6249,2118.txt,4,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Puente JL OmpR positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Puente JL Negative osmoregulation of gene independently of OmpR in an hns background ."
6249,6250,185.txt,1,0,,,,"PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl .
"
6250,6251,185.txt,2,1,Salmonella,Salmonella,Salmonella,"Transcriptional regulation of Salmonella virulence -- a phoQ periplasmic domain mutation results in increased net phosphotransfer to PhoP .
"
6251,6252,185.txt,3,0,,,,"The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .
"
6252,6253,185.txt,4,1,unidentified plasmid,plasmid,unidentified plasmid,"that harbored a plasmid with the phoQ genes under the control of a derivative of the lac promoter because a strain with a chromosomal phoQ mutation would constitutively activate the PhoP protein
"
6253,6254,185.txt,5,1,unidentified plasmid,plasmid,unidentified plasmid,"that harbored a plasmid with the phoP-HA genes under the control of a derivative of the lac promoter because a strain with a chromosomal phoQ mutation would constitutively activate the PhoP protein
"
6254,6255,185.txt,6,0,,,,"This was true not only for a strain transcribing the phoP-HA phoQ genes from the wild-type ( i.e. , PhoP-autoregulated ) promoter ( Fig ."
6255,6256,1411.txt,1,0,,,,narH are positively regulated by SlyA
6256,6257,1405.txt,1,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
6257,6258,1405.txt,2,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .
"
6258,6259,1405.txt,3,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
6259,6260,1405.txt,4,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS .
"
6260,6261,1405.txt,5,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
6261,6262,1405.txt,6,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Sasakawa , C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by virF by H-NS .
"
6262,6263,1405.txt,7,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by repression by H-NS .
"
6263,6264,1405.txt,8,1,Shigella flexneri,Shigella flexneri,Shigella flexneri,"Tobe T , Yoshikawa M , Mizuno T , Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri : activation by VirF by H-NS ."
6264,6265,191.txt,1,0,,,,"A novel NsrR-regulated gene designated STM1808 has been identified , along with hmp , hcp-hcr , yeaR-yoaG , ygbA and ytfE .
"
6265,6266,191.txt,2,1,Salmonella,Salmonella,Salmonella,"Moreover , the operons of hcp-hcr , ytfE , ygbA , hmp , previously shown to be regulated by NsrR in Salmonella , were found to be induced 678.1 - , 314.5 - , 130.2 - , 123.7-and 15.9-fold , respectively , by the absence of NsrR .
"
6266,6267,191.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Moreover , the operons of hcp-hcr , ytfE , ygbA , hmp , previously shown to be regulated by NsrR in Escherichia coli - , 123.7-and 15.9-fold , respectively , by the absence of NsrR ."
6267,6268,1363.txt,1,0,,,,"that EutR influenced expression of ssrB targets
"
6268,6269,1363.txt,2,0,,,,"S8 Fig _ indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter
"
6269,6270,1363.txt,3,0,,,,"Fig 4B _ indicating that EutR may regulate SPI-2 expression by binding the ssrB promoter
"
6270,6271,1363.txt,4,0,,,,"EMSAs indicated that EutR directly binds the ssrB promoter to activate expression of Fig 4C .
"
6271,6272,1363.txt,5,0,,,,"EMSAs indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 .
"
6272,6273,1363.txt,6,0,,,,"Electrophoretic mobility-shift assays indicated that EutR directly binds the ssrB promoter to activate expression of Fig 4C .
"
6273,6274,1363.txt,7,0,,,,"Electrophoretic mobility-shift assays indicated that EutR directly binds the ssrB promoter to activate expression of SPI-2 .
"
6274,6275,1363.txt,8,0,,,,"To test our findings within the complexities of the in-vivo environment , we assessed EutR-dependent regulation of ssrB using single strain infections .
"
6275,6276,1363.txt,9,0,,,,In vitro assays revealed that EutR directly binds the ssrB promoter to activate SPI-2 expression .
6276,6277,807.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of NICHOLAS M. KREDICH * Departments of Biochemistry , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by the CysB protein .
"
6277,6278,807.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of NICHOLAS M. KREDICH * Departments of Medicine , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by the CysB protein .
"
6278,6279,807.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of Sulfide JACEK OSTROWSKI of Biochemistry , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by the CysB protein .
"
6279,6280,807.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of Sulfide JACEK OSTROWSKI of Medicine , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by the CysB protein .
"
6280,6281,807.txt,5,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of NICHOLAS M. KREDICH * Departments of Biochemistry , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by an inducer .
"
6281,6282,807.txt,6,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of NICHOLAS M. KREDICH * Departments of Medicine , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by an inducer .
"
6282,6283,807.txt,7,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of Sulfide JACEK OSTROWSKI of Biochemistry , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by an inducer .
"
6283,6284,807.txt,8,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium;Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"172 , No. 2 In Vitro Interactions of CysB Protein with the cysJIH Promoter of Salmonella typhimurium : Inhibitory Effects of Sulfide JACEK OSTROWSKI of Medicine , Dluke University Medical Center , Durham , North Carolina 27710 The cysteine regulon of Salmonella typhimurium is positively regulated by an inducer .
"
6284,6285,807.txt,9,0,,,,"L-Cysteine did not affect in-vitro-transcription initiation or binding of CysB protein to the cysJIH promoter region .
"
6285,6286,807.txt,10,0,,,,"CysB protein at concentrations as high as 25 jig/ml did bind a small contaminant of cysJIH promoter fragment .
"
6286,6287,807.txt,11,0,,,,"The gel mobility-shift assay was used to study in-vitro effects of L-cysteine on the binding of CysB protein to cysJIH promoter DNA .
"
6287,6288,807.txt,12,0,,,,"The gel mobility-shift assay was used to study in-vitro effects of sulfide on the binding of CysB protein to cysJIH promoter DNA .
"
6288,6289,807.txt,13,0,,,,"that CysB protein binds to the cysJIH promoter region in-vitro
"
6289,6290,807.txt,14,0,,,,"The ability of sulfide to inhibit binding of CysB protein to the cysJIH promoter is competitive with N-acetyl-L-serine .
"
6290,6291,807.txt,15,0,,,,"The ability of sulfide to inhibit binding of CysB protein to the cysJIH promoter parallels its effects on transcription initiation .
"
6291,6292,807.txt,16,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Hryniewicz , M.M. , and Kredich , N.M. Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium .
"
6292,6293,807.txt,17,0,,,,"Stoichiometry of binding of CysB to the cysJIH .
"
6293,6294,807.txt,18,0,,,,"CysB , in turn , is a positive regulator of cysJIH .
"
6294,6295,807.txt,19,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Taken together , our results suggests that CysB regulates expression of cysJIH operon to produce H2S as a cellular protector during oxidative-stress in S. Typhimurium .
"
6295,6296,807.txt,20,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .
"
6296,6297,807.txt,21,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .
"
6297,6298,807.txt,22,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .
"
6298,6299,807.txt,23,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .
"
6299,6300,807.txt,24,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .
"
6300,6301,807.txt,25,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .
"
6301,6302,807.txt,26,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .
"
6302,6303,807.txt,27,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .
"
6303,6304,807.txt,28,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .
"
6304,6305,807.txt,29,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .
"
6305,6306,807.txt,30,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .
"
6306,6307,807.txt,31,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .
"
6307,6308,807.txt,32,0,,,,"In this work , we propose a model and the presence of the transcriptional regulator of CysB , and the products of the cysJIH operon .
"
6308,6309,807.txt,33,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"olecular characterization of the cysJIH promoters of Salmonella typhimurium : regulation by CysB protein and N-acetyl-L-serine , J. Bacteriol .
"
6309,6310,807.txt,34,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"M.M. Hryniewicz , N.M. Kredich , Stoichiometry of binding of CysB to the cysJIH , cysK , and cysP promoter regions of Salmonella typhimurium , J. Bacteriol .
"
6310,6311,807.txt,35,0,,,,Stoichiometry of binding of CysB to the cysJIH .
6311,6312,47.txt,1,0,,,,"HilA , regulates the expression of gtgE ."
6312,6313,2124.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"the S. Typhi yncD gene indicates that the expression of the yncD gene may be regulated by the PmrAB system
"
6313,6314,2124.txt,2,0,,,,"Upstream of the yncD gene , cattttcttaacttaat , was found , which indicated that the expression of the yncD gene may be regulated by the PmrAB system .
"
6314,6315,2124.txt,3,0,,,,"Upstream of the yncD gene , a possible PmrAB-box sequence , was found , which indicated that the expression of the yncD gene may be regulated by the PmrAB system ."
6315,6316,1.txt,1,0,,,,"The fact that tnpA inhibited InvF protein expression at an early growth phase while not affecting invF mRNA levels suggests that translation inhibition is invF pairing .
"
6316,6317,1.txt,2,0,,,,The fact that tnpA inhibited InvF protein expression at an early growth phase while not affecting invF mRNA levels suggests that translation inhibition is at least one consequence of tnpA .
6317,6318,2130.txt,1,0,,,,"multiple genomes found that the only targets directly regulated by PhoP in all species were its negative regulator slyB
"
6318,6319,2130.txt,2,0,,,,"As seen in Fig. 5 , phosphorylated PhoP was able to bind to the promoter of slyB with similar kinetics , whereas no binding was detected to the promoter of phoN .
"
6319,6320,2130.txt,3,0,,,,"As seen in Fig. 7B , PhoP was able to bind to the promoters of slyB .
"
6320,6321,2130.txt,4,0,,,,"As seen in Figure 6A , PhoP was able to bind to the slyB promoters"
6321,6322,1439.txt,1,0,,,,"To understand the regulation of acrAB by RamA , EMSA with the RamA protein were performed .
"
6322,6323,1439.txt,2,0,,,,"To understand the regulation of acrAB by RamA , electrophoretic-mobility-shift assays with the RamA protein were performed .
"
6323,6324,1439.txt,3,0,,,,"Bile RamA directly controls the expression of acrAB .
"
6324,6325,1439.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"These authors describe that acrAB is 1 12 actually regulated by RamA in Salmonella Typhimurium .
"
6325,6326,1439.txt,5,1,Salmonella,Salmonella,Salmonella,"These results suggest that RamA is the major regulator of Salmonella may mask the contributions of any other acrAB regulators .
"
6326,6327,1439.txt,6,1,Salmonella,Salmonella,Salmonella,"These results suggest that RamA is the major regulator of Salmonella acrAB .
"
6327,6328,1439.txt,7,0,,,,"RamA controls the expression of acrAB in response to environmental signals
"
6328,6329,1439.txt,8,0,,,,"that RamA is a master regulator of acrAB
"
6329,6330,1439.txt,9,1,Salmonella,Salmonella,Salmonella,"A recent study suggests that RamA is 27 a master regulator of Salmonella acrAB .
"
6330,6331,1439.txt,10,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"According to analysis of the relationship between Salmonella AcrAB regulators , RamA is the most effective regulator of Salmonella acrAB .
"
6331,6332,1439.txt,11,1,Salmonella,Salmonella,Salmonella,"According to analysis of the relationship between tigecycline resistance , RamA is the most effective regulator of Salmonella acrAB .
"
6332,6333,1439.txt,12,0,,,,"It has been confirmed that RamA can bind to the upstream promoter region of acrAB .
"
6333,6334,1439.txt,13,0,,,,"Activation of the acrAB operon is achieved through the direct binding of RamA , to the operator regions of these genes .
"
6334,6335,1439.txt,14,0,,,,"In particular , the expression of acrAB is regulated by RamA .
"
6335,6336,1439.txt,15,0,,,,"In S. Haardt , RamA mainly regulates the expression of acrAB .
"
6336,6337,1439.txt,16,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , RamA mainly regulates the expression of acrAB .
"
6337,6338,1439.txt,17,1,Salmonella,Salmonella,Salmonella,"For example , acrAB transcription in Salmonella is controlled by the AraC/XylS-like regulators RamA ."
6338,6339,813.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
6339,6340,53.txt,1,1,Salmonella,Salmonella,Salmonella,"Expression of hmpA is repressed by Fur in Salmonella , making it responsive The SOS response Free radicals are potent inducers of bacterial SOS responses in-vitro .
"
6340,6341,53.txt,2,0,,,,"In addition , Fur is also linked in nitrosative-stress by repressing hmpA ."
6341,6342,754.txt,1,0,,,,"OmpR activates the expression of ssrB
"
6342,6343,754.txt,2,0,,,,"How does OmpR activate expression of ssrB ?
"
6343,6344,754.txt,3,0,,,,"Elimination of ompR on the srfH -- lacZ activity was comparable with elimination of ssrB , perhaps the apparent OmpR stimulation of srfH is via its effect on expression of SsrB .
"
6344,6345,754.txt,4,0,,,,"Under low osmolality , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .
"
6345,6346,754.txt,5,0,,,,"Under acidic pH , the ssrB genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn ."
6346,6347,998.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .
"
6347,6348,998.txt,2,0,,,,"PhoP binds to the promoter region of mgtC .
"
6348,6349,998.txt,3,1,Salmonella,Salmonella,Salmonella,"The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .
"
6349,6350,998.txt,4,1,unidentified,not shown,unidentified,"The experimental verification that the PhoP protein binds to promoters in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6350,6351,998.txt,5,0,,,,"The experimental verification that the PhoP protein binds to promoters in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6351,6352,998.txt,6,1,unidentified,not shown,unidentified,"The experimental verification that the PhoP protein binds to promoters in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6352,6353,998.txt,7,0,,,,"The experimental verification that the PhoP protein binds to promoters in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6353,6354,998.txt,8,1,unidentified,not shown,unidentified,"The experimental verification that the PhoP protein binds to different classes in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6354,6355,998.txt,9,0,,,,"The experimental verification that the PhoP protein binds to different classes in-vivo and Fig. 2C , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6355,6356,998.txt,10,1,unidentified,not shown,unidentified,"The experimental verification that the PhoP protein binds to different classes in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite data not shown , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6356,6357,998.txt,11,0,,,,"The experimental verification that the PhoP protein binds to different classes in-vivo and in-vitro , together with the demonstration that the PhoP box is necessary for mgtC transcription despite its unusual orientation , argues against proposals that atypical PhoP-dependent promoters are regulated by the PhoP protein only indirectly .
"
6357,6358,998.txt,12,1,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"The level of PagC protein is lowered in a mgtC null mutant : ( A ) , 1-D SDS-PAGE of outer-membrane proteins isolated from 14028s ( wild-type ) or NM14 ( DmgtC ) grown in low Mg2þ medium ( conditions that activate PhoP-regulated genes ) .
"
6358,6359,998.txt,13,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .
"
6359,6360,998.txt,14,0,,,,"This is because the PhoP protein , virulence , activates mgtC transcription directly by binding to the mgtC promoter .
"
6360,6361,998.txt,15,1,Salmonella,Salmonella,Salmonella,"This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to recruiting RNA polymerase .
"
6361,6362,998.txt,16,1,Salmonella,Salmonella,Salmonella,"This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .
"
6362,6363,998.txt,17,1,Salmonella,Salmonella,Salmonella,"This is because the PhoP protein , a major regulator of Salmonella , activates mgtC transcription directly by binding to the mgtC promoter .
"
6363,6364,998.txt,18,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .
"
6364,6365,998.txt,19,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , mgtC were selected to evaluate the role of Pat in the regulation of PhoP activity .
"
6365,6366,998.txt,20,0,,,,"efp enables differential expression of genes that Pro respond to proline-tRNA levels gene because , like mgtC , it is regulated by the PhoP/absence of supporting inforPhoQ two component system at the transcription initia-mation Fig .
"
6366,6367,998.txt,21,0,,,,"efp enables differential expression of genes that Pro respond to proline-tRNA levels gene because , like mgtC , it is regulated by the PhoP/absence of the efp gene -LRB- Fig. 2B ."
6367,6368,740.txt,1,0,,,,HilA represses the promoter of ssaH
6368,6369,768.txt,1,0,,,,"The suppressive effects of spermine NONOate on PhoP-dependent gene transcription appear to be directly related to the production of RNS because the polyamine base spermine did not suppress the acid-induced expression of the PhoP-activated loci lpxO , pqaA , and pcgE ( fig. 6B -- D ) .
"
6369,6370,768.txt,2,0,,,,"The acid-inducible expression of the PhoP-activated loci lpxO , pqaA and pcgE were monitored in the presence or absence of 250 mM spermine , 250 mM spermine NONOate or 500 mM NaNO2 ( B -- D ) ."
6370,6371,2093.txt,1,0,,,,"Five of the HilD/HilC/RtsA-bound regions associated with direct transcription activation of protein-coding genes outside SPI-1 overlap regions that are likely bound by H-NS ( HilD/HilC/RtsA binding sites associated with regulation of lpxR , , siiA , mcpC , and ssaG ) ."
6371,6372,2087.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6372,6373,797.txt,1,0,,,,"While the two single point mutations , significantly enhanced StpA 
"
6373,6374,797.txt,2,0,,,,"While the two single point mutations , significantly enhanced StpA 
"
6374,6375,797.txt,3,0,,,,"While the two single point mutations , significantly enhanced StpA 
"
6375,6376,797.txt,4,0,,,,"While A77D , significantly enhanced StpA 
"
6376,6377,797.txt,5,0,,,,"While A77D , significantly enhanced StpA 
"
6377,6378,797.txt,6,0,,,,"While A77D , significantly enhanced StpA 
"
6378,6379,797.txt,7,0,,,,"While M4T , significantly enhanced StpA 
"
6379,6380,797.txt,8,0,,,,"While M4T , significantly enhanced StpA 
"
6380,6381,797.txt,9,0,,,,"While M4T , significantly enhanced StpA "
6381,6382,1203.txt,1,0,,,,"Furthermore , STM1330 are regulated by PhoP ."
6382,6383,1565.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"However , in the presence of H2O2 , transcription of fur is also activated by OxyR in E. coli , resulting in repression of target mRNAs for iron-uptake proteins ."
6383,6384,1571.txt,1,0,,,,the sodA gene is negatively regulated by FNR44
6384,6385,2078.txt,1,0,,,,"that the transcriptional activator RamA , plays the dominant role in few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
6385,6386,2078.txt,2,0,,,,"that the transcriptional activator RamA , plays the dominant role in few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
6386,6387,2078.txt,3,0,,,,"that the transcriptional activator RamA , plays the dominant role in few inducers of RamA have been reported ; however , Nikaido et al. 18,19 demonstrated increased expression of ramA in response to the bacterial metabolite indole
"
6387,6388,2078.txt,4,1,Phaeoacremonium santali,a 28,Phaeoacremonium santali,"At the transcriptional level , the induction of ramA expression may be amplified by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .
"
6388,6389,2078.txt,5,0,,,,"At the transcriptional level , the induction of ramA expression may be amplified by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .
"
6389,6390,2078.txt,6,1,Phaeoacremonium santali,a 28,Phaeoacremonium santali,"At the transcriptional level , the induction of ramA expression may be relayed by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .
"
6390,6391,2078.txt,7,0,,,,"At the transcriptional level , the induction of ramA expression may be relayed by ncRNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .
"
6391,6392,2078.txt,8,1,Phaeoacremonium santali,a 28,Phaeoacremonium santali,"At the transcriptional level , the induction of ramA expression may be amplified by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .
"
6392,6393,2078.txt,9,0,,,,"At the transcriptional level , the induction of ramA expression may be amplified by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .
"
6393,6394,2078.txt,10,1,Phaeoacremonium santali,a 28,Phaeoacremonium santali,"At the transcriptional level , the induction of ramA expression may be amplified by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .
"
6394,6395,2078.txt,11,0,,,,"At the transcriptional level , the induction of ramA expression may be amplified by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .
"
6395,6396,2078.txt,12,1,Phaeoacremonium santali,a 28,Phaeoacremonium santali,"At the transcriptional level , the induction of ramA expression may be relayed by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .
"
6396,6397,2078.txt,13,0,,,,"At the transcriptional level , the induction of ramA expression may be relayed by a 144 bp non-coding RNA likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati .
"
6397,6398,2078.txt,14,1,Phaeoacremonium santali,a 28,Phaeoacremonium santali,"At the transcriptional level , the induction of ramA expression may be relayed by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At , Ricci et a 28 revealed a higher order of f RamA regulati .
"
6398,6399,2078.txt,15,0,,,,"At the transcriptional level , the induction of ramA expression may be relayed by StyR-3 likely processed from ′ the 5 untranslated region of the ramA mRNA , which was also shown to interfere with RamR -- DNA binding activity .35 At t the protein lev 28 revealed a higher order of f RamA regulati ."
6399,6400,1217.txt,1,0,,,,"This lack of an in-vitro phenotype agrees with the fact that RpoS positively regulates spvR expression .
"
6400,6401,1217.txt,2,0,,,,"Indeed , RpoS participates in the induction of spvR .
"
6401,6402,1217.txt,3,0,,,,"It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .
"
6402,6403,1217.txt,4,0,,,,"It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .
"
6403,6404,1217.txt,5,0,,,,"It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .
"
6404,6405,1217.txt,6,0,,,,It is possible that the upregulation of spvR may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .
6405,6406,783.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of ArcA in activation .
"
6406,6407,783.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of ArcA in repression .
"
6407,6408,783.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of ArcA in activation .
"
6408,6409,783.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of ArcA in repression .
"
6409,6410,783.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"Aerobic regulation of cydAB operon expression in Escherichia coli : roles of ArcA in activation .
"
6410,6411,783.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,Aerobic regulation of cydAB operon expression in Escherichia coli : roles of ArcA in repression .
6411,6412,973.txt,1,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .
"
6412,6413,973.txt,2,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE ."
6413,6414,1559.txt,1,0,,,,"In contrast , absence of H-NS showed 5.3-fold increase of hilA expression under low-osmolarity conditions .
"
6414,6415,1559.txt,2,0,,,,"in antagonizing H-NS silencing of hilA to promote its Stationary-phase induction of hilA in strain expression under permissive conditions .
"
6415,6416,1559.txt,3,0,,,,"Whereas hilA induction at antagonize H-NS hilA silencing account for hilA derepres-the onset of the stationary-phase should be abolished in sion in cells growing in LB-medium at 37 uC .
"
6416,6417,1559.txt,4,0,,,,"Whereas hilA induction at antagonize H-NS hilA silencing account for hilA derepres-the onset of the stationary-phase should be abolished in sion in cells entering mutants .
"
6417,6418,1559.txt,5,0,,,,"Interestingly , a partial inhibition of H-NS activity in cells resulted in a signi-ficant induction of hilA expression , up to about 50 % of the expression ."
6418,6419,2050.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
6419,6420,2050.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6420,6421,2044.txt,1,0,,,,"However , no significant differences were observed in flgB mRNA levels between isolates , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected .
"
6421,6422,2044.txt,2,0,,,,"However , no significant differences were observed in flgB mRNA levels between the two classes , suggesting that class 3 genes -LRB- controlled by FliA sigma factor -RRB- , but not class 2 genes , were affected ."
6422,6423,967.txt,1,0,,,,"It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a negative regulator of sefA expression .
"
6423,6424,967.txt,2,0,,,,It is possible that the downregulation of sefA in TSP-adapted cells may result from the upregulation of RpoS because RpoS is a positive regulator of spvR expression .
6424,6425,230.txt,1,0,,,,"Interestingly , a transcriptional lux fusion with 2357 bp upstream of srfJ is regulated by PhoP , recapitulating the regulation patterns ."
6425,6426,556.txt,1,0,,,,"PhoP -RCB- PhoQ activates transcription of pmrA -RCB- B .
"
6426,6427,556.txt,2,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
6427,6428,556.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,SL1344;14028s,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .
"
6428,6429,556.txt,4,0,,,,the regulatory gene pmrA is post-tran-scriptionally activated by the PhoP
6429,6430,542.txt,1,1,unidentified,none,unidentified,"Through the use of transcriptional-fusions , none of or tol-associated genes were shown to be regulated by PhoPQ ; however , all of orfX , orf1 , tolQRA are predicted to be cotranscribed .
"
6430,6431,542.txt,2,1,unidentified,none,unidentified,"Through the use of transcriptional-fusions , none of the putative tol genes were shown to be regulated by PhoPQ ; however , all of orfX , orf1 , tolQRA are predicted to be cotranscribed ."
6431,6432,1968.txt,1,0,,,,"The SoxRS-and MarRAB-regulated genes that contribute t broad antibiotic resistance include the acrAB operon encoding a multidrug efflux pump ( 22 , 25 , 30 ) and the micF gene encoding an antisense RNA that inhibits synthesis of the OmpF outer membrane porin ( 6 , 7 , 32 ) .
"
6432,6433,1968.txt,2,0,,,,"Altogether , these results indicated that lack of AsmA does not increase acrAB transcription and suggested that bile resistance mediated by asmA mutations may involve MarRAB-regulated genes other than acrAB .
"
6433,6434,1968.txt,3,0,,,,"Altogether , these results indicated that lack of AsmA does not increase acrAB transcription and suggested that bile resistance mediated by asmA mutations may involve MarRAB-regulated genes other than acrAB ."
6434,6435,224.txt,1,1,Salmonella,Salmonella,Salmonella,"Although a non-cytotoxic form of polymyxin B -- termed polymyxin B nonapeptide -- could partially protect a Salmonella pmrA mutant from Fe - mediated killing inactivation of the PmrA-activated loci responsible for the lipid-A modification with i.e. pbgP or phosphoethanolamine ( i.e. pmrC ) did not render the organism susceptible to Fe .
"
6435,6436,224.txt,2,1,Salmonella,Salmonella,Salmonella,"Although a non-cytotoxic form of polymyxin B -- termed polymyxin B nonapeptide -- could partially protect a Salmonella pmrA mutant from Fe - mediated killing inactivation of the PmrA-activated loci responsible for the lipid-A modification with 4-aminoarabinose or phosphoethanolamine ( i.e. pmrC ) did not render the organism susceptible to Fe .
"
6436,6437,224.txt,3,0,,,,"Further support for PmrA pathways is the observation that inactivation of pmrA does not completely abolish the DrpoN-mediated PM resistance .
"
6437,6438,224.txt,4,1,Salmonella,Salmonella,Salmonella,"We have now determined that the regulatory protein PmrA is an antivirulence factor because inactivation of the pmrA gene exacerbated Salmonella virulence in Fig. 1A .
"
6438,6439,224.txt,5,2,Salmonella;Mus sp.,Salmonella;mice,Mus sp.;Salmonella,We have now determined that the regulatory protein PmrA is an antivirulence factor because inactivation of the pmrA gene exacerbated Salmonella virulence in C3H/HeN mice .
6439,6440,1940.txt,1,0,,,,"Repression by CytR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .
"
6440,6441,1940.txt,2,0,,,,Repression by CytR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .
6441,6442,1798.txt,1,0,,,,"Our results show that PhoBR is capable of inducing fimZ expression , whereas PhoPQ does upregulate hilE in an FimZ-dependent manner .
"
6442,6443,1798.txt,2,0,,,,"the PhoPQ signal leads to induction of hilE expression
"
6443,6444,1798.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"Even in the absence of hilE , hilA : : lacZY plasmid reporter levels still showed a 25.9-fold reduction when the PhoPQ regulators were activated by magnesium .
"
6444,6445,1798.txt,4,0,,,,"Since our studies indicated that PhoPQ plays a role in inducing hilE expression , we examined whether the phoBR regulon also regulates hilA via HilE .
"
6445,6446,1798.txt,5,0,,,,"Under conditions of low magnesium concentration , the PhoPQ regulon is activated , leading to the phosphorylation of FimZ with the subsequent increase in hilE expression ."
6446,6447,2291.txt,1,0,,,,"This sRNA is encoded in an intergenic region and is transcribed divergently from the bfd gene , which encodes a Fur-regulated bacterioferritin-associated ferredoxin protein ."
6447,6448,2285.txt,1,0,,,,"In a starvation medium , the GGDEF domain protein STM1987 activated cellulose biosynthesis independent of CsgD ."
6448,6449,1954.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
6449,6450,218.txt,1,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in bacteria ; Fis has also been shown to bind to the ssrA promoter .
"
6450,6451,218.txt,2,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in bacteria ; Fis has also been shown to bind to the ssrA promoter .
"
6451,6452,218.txt,3,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in LB medium ; Fis has also been shown to bind to the ssrA promoter .
"
6452,6453,218.txt,4,0,,,,"ssrA promoter activity The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in Bertani medium ; Fis has also been shown to bind to the ssrA promoter .
"
6453,6454,218.txt,5,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in LB medium ; Fis has also been shown to bind to the ssrA promoter .
"
6454,6455,218.txt,6,0,,,,"Fis The Fis nucleoid-associated protein has been shown previously to be required for upregulation of other SPI-2 genes in Bertani medium ; Fis has also been shown to bind to the ssrA promoter .
"
6455,6456,218.txt,7,0,,,,"We wished to examine the contribution of Fis to ssrA gene expression in bacteria .
"
6456,6457,218.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,Our data establish a role for the Fis protein in the upregulation of the ssrA gene when S. Typhimurium grows in macrophage .
6457,6458,1767.txt,1,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
6458,6459,1001.txt,1,0,,,,"In contrast , H-NS positively regulates OmpF levels by transcriptionally repressing micF ."
6459,6460,595.txt,1,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , three homologous transcriptional activators , have been associated with increased acrB .
"
6460,6461,595.txt,2,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , MarA , have been associated with increased acrB .
"
6461,6462,595.txt,3,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , SoxS , have been associated with increased acrB .
"
6462,6463,595.txt,4,0,,,,"AcrR is the local repressor and mutations within its coding sequence have been associated with increased expression of the pump .14 In addition , RamA , have been associated with increased acrB ."
6463,6464,581.txt,1,0,,,,"Glucose and inositol metabolism phosphatase/inositol phosphatase -LRB- Agp -RRB- Required for the catalysis of the GTP-dependent translocation step during translation elongation 37 , 38 , Elongation factor G -LRB- FusA -RRB- Transcription , ribosomal structure and translation 1.54E-05 , 2.80E-05 , 1.11E-06 , 2.38E-04 , 9.20E-07 , 6.45 , 7.51 , 9.05 , 5.64 , 9.26 , gi 16762837 , gi 213586434 240 , 254 , 262 , Member of the aminoacyl-tRNA synthetases Prolyl-tRNA synthetase -LRB- ProS -RRB- Transcription , ribosomal 4.75E-05 4.79 structure and translation 425 gi 162139614 Prevents aggregation of denatured proteins , in association with dnaK , dnaJ Heat shock protein -LRB- GrpE -RRB- Stress response 8.48E-05 2.28 1127 gi 340000338 Cytoplasmic regulator of phoP/phoQ , controls the transcription of genes involved in virulence , transport and LPS modification 1115 DNA-binding transcriptional regulator -LRB- PhoP -RRB- Stress response , regulation 8.28E-04 3.02 gi 16764586 Peptidyl-prolyl cis-trans isomerase -LRB- SurA -RRB- Facilitate the proper folding of proteins in the periplasm 3.72 gi 16759087 1.34E-03 Stress response 732 Stress response Forms a complex with YfgL , YfiO , and NlpB ."
6464,6465,1015.txt,1,0,,,,"Activated OxyR induces katG , dps ahpCF .
"
6465,6466,1015.txt,2,0,,,,"Activated OxyR induces katG , dps lipids .
"
6466,6467,1015.txt,3,0,,,,"Activated OxyR induces katG , DNA-protection ahpCF .
"
6467,6468,1015.txt,4,0,,,,"Activated OxyR induces katG , DNA-protection lipids ."
6468,6469,1773.txt,1,0,,,,"the protease _ known to affect HilD , as in mutants of lon , sipC remained repressed by Fig. 4B
"
6469,6470,1773.txt,2,0,,,,"the protease _ known to affect HilD , as in mutants of lon , sipC remained repressed by Pat"
6470,6471,2252.txt,1,0,,,,"However , with the potential exception of FliZ , post-transcriptional regulators of hilD seem to affect either HilD protein activity .
"
6471,6472,2252.txt,2,0,,,,"However , with the potential exception of FliZ , post-transcriptional regulators of hilD seem to affect either the HilD protein level ."
6472,6473,1983.txt,1,1,Bacillus subtilis,Bacillus subtilis,Bacillus subtilis,Bacillus subtilis PhoP binds to the phoB tandem promoter exclusively within the phosphate-starvation-inducible promoter .
6473,6474,1029.txt,1,0,,,,"DNA damage has been shown to be sufficient to stimulate umuC transcription and the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes .2,3 -LRB- In Escherichia ."
6474,6475,1997.txt,1,0,,,,"STM3138 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .
"
6475,6476,1997.txt,2,0,,,,"STM3138 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop ."
6476,6477,2246.txt,1,0,,,,"The two-component regulatory OmpR/EnvZ function through HilD , thus inducing hilA ."
6477,6478,1072.txt,1,0,,,,"The OmpR/EnvZ two-component regulatory system regulates the porin genes ompF to changes in osmolarity .
"
6478,6479,1072.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhi , the OmpR/EnvZ system is involved in the regulation of ompF porin genes , where both OmpF are expressed as abundant outer-mem-brane proteins as in E. coli .
"
6479,6480,1072.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,S. Typhi;Typhi;E. coli,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhi , the OmpR/EnvZ system is involved in the regulation of ompF porin genes , where both OmpC are expressed as abundant outer-mem-brane proteins as in E. coli ."
6480,6481,1714.txt,1,0,,,,"The values of PhoP binding were obtained from normalization of ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein of the target promoter to that of the endogenous control rpoD promoter .
"
6481,6482,1714.txt,2,0,,,,The values of PhoP binding were obtained from normalization of ratio of DNA bound by the PhoP protein to DNA not bound by the PhoP protein of the target promoter to that of the endogenous control rpoD promoter .
6482,6483,280.txt,1,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have N all bases , respectively .
"
6483,6484,280.txt,2,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have D not C , respectively .
"
6484,6485,280.txt,3,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have short Lrp-binding motifs , 5-HNDWTTATTHND-3 -LSB- , respectively .
"
6485,6486,280.txt,4,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have T , respectively .
"
6486,6487,280.txt,5,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have W A , respectively .
"
6487,6488,280.txt,6,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have 5-GNN TTTT-3 , respectively .
"
6488,6489,280.txt,7,2,Salmonella;unidentified,Salmonella;none,unidentified;Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have none -RSB- , respectively .
"
6489,6490,280.txt,8,1,Salmonella,Salmonella,Salmonella,"Although the ilvIH , fimZ , pefB , and spvA genes are known to be regulated by Lrp in Salmonella , the upstream regions of these genes have all bases , respectively ."
6490,6491,294.txt,1,1,Escherichia coli,E. coli,Escherichia coli,In E. coli flagellar motility is negatively regulated by RcsA binding to the RcsAB box of the promoter of the flagellar master regulator flhDC .
6491,6492,1700.txt,1,0,,,,SirA-dependent regulation of flgA chromosomal lacZY fusions during chemotaxing through 0.3 % TS agar .
6492,6493,2209.txt,1,0,,,,T s of fliC expression is inverted in the absence of YdiV su en e c h T le layers of heterogeneity shape the fliC expression census ltip u M We hypothesized that modulating production of YdiV would reveal the extent to which fliC expression can be controlled by these two regulators .
6493,6494,1066.txt,1,1,Strawberry lethal yellows phytoplasma,Sly,Strawberry lethal yellows phytoplasma,"It is likely the effects of σE on SPI-2 transcription is mediated by SsrB because Sly , can complement the decrease of SPI-2 expression as a result of rpoE deletion .
"
6494,6495,1066.txt,2,0,,,,"It is likely the effects of σE on SPI-2 transcription is mediated by SsrB because overexpression of Ssr , can complement the decrease of SPI-2 expression as a result of rpoE deletion ."
6495,6496,1728.txt,1,0,,,,"We used qRT-PCR to demonstrate that SsrB has a modest effect in activating transcription in an hns background .
"
6496,6497,1728.txt,2,0,,,,We used quantitative reverse transcription polymerase chain reaction to demonstrate that SsrB has a modest effect in activating transcription in an hns background .
6497,6498,2221.txt,1,0,,,,narK -LRB- are positively regulated by SlyA
6498,6499,2235.txt,1,0,,,,Most of these genes were induced at a higher level in the RpoS-mutant background with sscB .
6499,6500,525.txt,1,0,,,,The following studies show that PhoPQ regulate hilE expression via the fimZ gene .
6500,6501,243.txt,1,0,,,,"In the soxRS system , SoxR protein is activated by nitrosylation to trigger transcription of the soxS gene .
"
6501,6502,243.txt,2,0,,,,"In the soxRS system , SoxR protein is activated by oxidation to trigger transcription of the soxS gene .
"
6502,6503,243.txt,3,0,,,,"When it is converted to an active form , SoxR , enhances transcription of soxS .
"
6503,6504,243.txt,4,0,,,,"Expression of soxS is activated by superoxide-generating agents via the conversion of its local transcriptional activator SoxR into SoxR * .
"
6504,6505,243.txt,5,0,,,,"Expression of soxS is activated by superoxide-generating agents via the conversion of its local transcriptional activator SoxR into an active form .
"
6505,6506,243.txt,6,0,,,,SoxR is an activator of soxS .
6506,6507,257.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"According with a LeuO-dual role regulator , it was found to be a positive regulator of yjjQ-bglJ operons in E. coli ."
6507,6508,531.txt,1,0,,,,"In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fig. 1F .
"
6508,6509,531.txt,2,0,,,,"In agreement with this notion , transcription of the Esche-richia coli yrbL gene was induced in low Mg2 in a PhoP-dependent fashion and repressed by PmrA in response to Fe3 ."
6509,6510,519.txt,1,0,,,,The same behavior has been described for other ArcA-controlled promoters in 6 Time : 14:6 # lpxO Expression Is Regulated by Fnr in Response to Oxygen Availability FIGURE 2 Main lipid-A species .
6510,6511,1933.txt,1,0,,,,"D. Alignment of the regulatory sequences of the PhoP-activated ugd , phoP , mgtA and mgrB genes .
"
6511,6512,1933.txt,2,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A gene homologous to mgrB in S. enterica has been shown to be activated by PhoP , suggesting that MgrB is part of a negative feedback loop in the PhoQ/PhoP signaling circuit ."
6512,6513,1927.txt,1,0,,,,"PhoP binds to the promoter region of phoN .
"
6513,6514,1927.txt,2,0,,,,"in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .
"
6514,6515,1927.txt,3,0,,,,"in contrast to what we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .
"
6515,6516,1927.txt,4,0,,,,"Interestingly we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-PQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .
"
6516,6517,1927.txt,5,0,,,,"Interestingly we had observed in the regulation of phoN , activation of pagN was similar in 4550 L1-SDQ24 , suggesting that different threshold levels of the activated PhoP are necessary to turn on the expression of different pag genes .
"
6517,6518,1927.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"A S. typhimurium strain expressing a reporter fusion to the PhoP-controlled gene encoding acid phosphatase ( phoN ) was used as a wild type ST-PhoQ reporter strain background .
"
6518,6519,1927.txt,7,1,unidentified,not shown,unidentified,"The results for 10 mM and 10 μM Mg2 + were also confirmed by RT-PCR for phoN and four additional PhoP-controlled genes ( data not shown ) , so this phenotype does not appear to be specific to the reporter system used .
"
6519,6520,1927.txt,8,0,,,,"phoN are known to be regulated by PhoP ,56
"
6520,6521,1927.txt,9,0,,,,"Considering that some PhoP-regulated genes such as pag loci and phoN , which encodes a nonspecific acid phosphatase , are maximally induced under starvation conditions ( Behlau and Miller , 1995 ; Kier et al. , 1997 ) , it is reasonable to conclude that induced synthesis of the tdc genes inside macrophages affects the expression of a subset of PhoP-dependent genes such as SPI2 .
"
6521,6522,1927.txt,10,0,,,,"As seen in Fig. 7B , PhoP was able to bind to the phoN promoter .
"
6522,6523,1927.txt,11,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
6523,6524,1099.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To determine if CpxR affects the autoregulation of hilD , the expression of the hilDcat fusion was determined in the WT S. Typhimurium strain and its derivatives 1cpxA , 1hilD , and 1hilD 1cpxA mutants .
"
6524,6525,1099.txt,2,0,,,,FIGURE 4 CpxR represses the autoregulation of hilD .
6525,6526,1516.txt,1,0,,,,that avrA translation is regulated positively in a post-transcriptional manner by CsrA/CsrB of the Csr regulatory system
6526,6527,1270.txt,1,0,,,,"Notably , CRP activates cobB ."
6527,6528,928.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
6528,6529,1264.txt,1,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels were approximately fourfold higher in wild-type S. Typh-imurium than in a fur mutant in Fe-rich-medium .
"
6529,6530,1264.txt,2,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( d .
"
6530,6531,1264.txt,3,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( ( Fig. .
"
6531,6532,1264.txt,4,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( d .
"
6532,6533,1264.txt,5,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( ( Fig. .
"
6533,6534,1264.txt,6,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( d .
"
6534,6535,1264.txt,7,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - ( d ( ( Fig. .
"
6535,6536,1264.txt,8,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( d .
"
6536,6537,1264.txt,9,0,,,,"Consistent with positive regulation by Fur , bfr mRNA levels reduced in the presence of the Fe chelator , 2,2 ′ - - dipyrid ( ( Fig. .
"
6537,6538,1264.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimu,Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , the S. Typhimu-rium bfr are positively regulated by Fe in a Fur-dependent manner , accounting for reduced total Fe in the fur mutant .
"
6538,6539,1264.txt,11,0,,,,"In the absence of Fe and/or Fur , repression of ryhB is relieved , leading to negative regulation of bfr ."
6539,6540,1502.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6540,6541,2023.txt,1,0,,,,"Indirect regulation of biofilm formation by STM1697 The EAL domain protein STM3611 , a c-di-GMP phosphodiesterase , is one of the negative regulators of CsgD expression ."
6541,6542,900.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , micF .
"
6542,6543,900.txt,2,0,,,,"SoxS protein , activates sodA , micF ."
6543,6544,914.txt,1,1,Salmonella,Salmonella,Salmonella,"hilA expression is regulated by Salmonella invasion regulator ; however , it is not known how SirA is it known how sirA expression is itself regulated .
"
6544,6545,914.txt,2,1,Salmonella,Salmonella,Salmonella,"hilA expression is regulated by Salmonella invasion regulator ; however , it is not known how SirA modulates hilA expression .
"
6545,6546,914.txt,3,0,,,,"hilA expression is regulated by SirA ; however , it is not known how SirA is it known how sirA expression is itself regulated .
"
6546,6547,914.txt,4,0,,,,"hilA expression is regulated by SirA ; however , it is not known how SirA modulates hilA expression .
"
6547,6548,914.txt,5,0,,,,"hilA expression is regulated by a protein ; however , it is not known how SirA is it known how sirA expression is itself regulated .
"
6548,6549,914.txt,6,0,,,,"hilA expression is regulated by a protein ; however , it is not known how SirA modulates hilA expression .
"
6549,6550,914.txt,7,0,,,,"Genes in SPI-5 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .
"
6550,6551,914.txt,8,0,,,,"Genes in SPI-5 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .
"
6551,6552,914.txt,9,0,,,,"Genes in SPI-4 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .
"
6552,6553,914.txt,10,0,,,,"Genes in SPI-4 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .
"
6553,6554,914.txt,11,0,,,,"SirA regulates hilA .
"
6554,6555,914.txt,12,0,,,,"Although it has been proposed that SirA directly controls expression of both hilA , it was also determined that HilC was not required for SirA to control hilA expression .
"
6555,6556,914.txt,13,0,,,,"Thus SirA controls expression of hilA .
"
6556,6557,914.txt,14,0,,,,"Thus SirA controls expression of the three hilA regulators .
"
6557,6558,914.txt,15,0,,,,"Previous attempts have been made to determine how SirA controls expression of hilA .
"
6558,6559,914.txt,16,0,,,,"This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both hilA .
"
6559,6560,914.txt,17,0,,,,"Once phosphorylated , SirA directly binds the hilA promoters .
"
6560,6561,914.txt,18,0,,,,"SirA controls these genes by directly binding the hilA .
"
6561,6562,914.txt,19,0,,,,"Conversely , previously published gel-shift data suggested that SirA is able to bind to the promoters of hilA .
"
6562,6563,914.txt,20,0,,,,"Whereas SirA might bind to the hilA promoters during in-vitro gel-shift experiments , genetic data shows that SirA is incapable of directly activating these promoters ; SirA binding to DNA in-vitro does not represent activation .
"
6563,6564,914.txt,21,0,,,,"SirA , directly regulates the hilA genes at the top of the invasion cascade ."
6564,6565,1258.txt,1,0,,,,"These redundant systems of propionyl-CoA synthesis are needed because the prpE gene is part of the prpBCDE operon under the control of the PrpR regulatory protein .
"
6565,6566,1258.txt,2,0,,,,"the PrpR regulatory protein controls the expression of the prpBCDE operon
"
6566,6567,1258.txt,3,0,,,,"the PrpR regulatory protein controls the expression of the prpBCDE operon
"
6567,6568,1258.txt,4,0,,,,PrpR protein bound to the DNA region between the prpBCDE operon and prpR .
6568,6569,2037.txt,1,1,Pasteurella multocida,Pasteurella multocida,Pasteurella multocida,Expression of the Pasteurella multocida ompH gene is negatively regulated by the Fur protein .
6569,6570,727.txt,1,0,,,,"In the present work , we demonstrate that OmpR-P functions as an activator at the spiC .
"
6570,6571,727.txt,2,0,,,,"OmpR-P also activates spiC , although it has not been established whether this is a indirect effect -LRB- denoted by a dashed arrow -RRB- .
"
6571,6572,727.txt,3,0,,,,"OmpR-P also activates spiC , although it has not been established whether this is a direct effect -LRB- denoted by a dashed arrow -RRB- .
"
6572,6573,727.txt,4,0,,,,"OmpR-P also activates spiC , although it has not been established whether this is a indirect effect -LRB- denoted by a dashed arrow -RRB- .
"
6573,6574,727.txt,5,0,,,,"OmpR-P also activates spiC , although it has not been established whether this is a direct effect -LRB- denoted by a dashed arrow -RRB- ."
6574,6575,733.txt,1,0,,,,"SprB , regulates the expression of avrA ."
6575,6576,1462.txt,1,0,,,,"Our results show that CpxR , induces the transcription of lon encoding the ClpXP protease ."
6576,6577,690.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Johnson , R.C. Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .
"
6577,6578,690.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"J. , R.C. Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .
"
6578,6579,690.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Xu , R.C. Fis activates the RpoSdependent stationary-phase expression of proP in Escherichia coli .
"
6579,6580,690.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,Fis activates the RpoS-dependent station-ary-phase expression of proP in Escherichia coli .
6580,6581,1304.txt,1,0,,,,A DNA bend is induced by OxyR in agn43 .
6581,6582,848.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
6582,6583,1310.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
6583,6584,1310.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6584,6585,684.txt,1,0,,,,"FlhD4C2 affects invasion by positive regulation of fliZ .
"
6585,6586,684.txt,2,0,,,,FliA-dependent activation of FlgM ensures an effectiv `` off 
6586,6587,1476.txt,1,0,,,,"Besides the mgtA gene , only 2 of phoPQ were directly regulated by the PhoPQ two-component system organisms .
"
6587,6588,1476.txt,2,0,,,,"Besides the mgtA gene , only 2 of phoPQ were directly regulated by the PhoPQ two-component system in .
"
6588,6589,1476.txt,3,0,,,,All of the genes belong to the phoPQ regulon although the pmrHFIJKL genes are regulated by PhoPQ indirectly through the PmrAB signal transduction system .
6589,6590,2157.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"that YncC are both able to induce expression of katN locus in E. coli K-12
"
6590,6591,2157.txt,2,1,Salmonella,Salmonella,Salmonella,that YncC are both able to induce expression of katN locus in Salmonella
6591,6592,34.txt,1,0,,,,"Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .
"
6592,6593,34.txt,2,0,,,,"Consistent with OmpR have recently shown that OmpR regulates the acid induction of the ssrAB two-component signal transduction system located within the Spi2 pathogenicity island .
"
6593,6594,34.txt,3,0,,,,"OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrB proteins .
"
6594,6595,34.txt,4,0,,,,"OmpR activates SPI-2 genes by binding to the promoter of the ssrAB operon to induce expression of SsrA proteins .
"
6595,6596,34.txt,5,0,,,,"Further , as mentioned previously , OmpR is a direct transcriptional activator of ssrAB ."
6596,6597,1338.txt,1,0,,,,We have previously shown that hilE is regulated by the transcriptional activator FimZ .
6597,6598,874.txt,1,0,,,,"In support of this , transcription from the P5flhDC promoter was slightly reduced upon rflM overexpression , although we detected no binding of the RcsB-RflM complex to a promoter fragment ."
6598,6599,20.txt,1,0,,,,"In addition , hmpA expression is upregulated under iron-limiting conditions through NsrR , but independently of Fur ."
6599,6600,860.txt,1,0,,,,"Interestingly , the regulation of the stiB locus ( unlike that of stiA ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .
"
6600,6601,860.txt,2,0,,,,"Interestingly , the regulation of the stiB locus ( unlike that of stiA ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts alone ."
6601,6602,2143.txt,1,1,Salmonella,Salmonellae,Salmonella,"pduD , were induced much more than two-fold in the RpoS-mutant than in the wild type Salmonellae ."
6602,6603,135.txt,1,0,,,,"Metered induction of YdiV reduced fliC expression , partitioning cells into the fliC-OFF subpopulation ."
6603,6604,653.txt,1,0,,,,"Thus , we concluded that H-NS all contribute towards the regulation of hlyE expression .
"
6604,6605,653.txt,2,0,,,,"H-NS binds at two regions of the hlyE promoter with high affinity .
"
6605,6606,653.txt,3,0,,,,"To investigate how much of this extensive H-NS protection is required for the observed regulation of hlyE expression , we used two approaches as follows .
"
6606,6607,653.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both csiD genes in E. coli is stimulated by H-NS .
"
6607,6608,653.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene ; for example , expression of both the malT in E. coli is stimulated by H-NS .
"
6608,6609,653.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"Lithgow JK , Haider F , Roberts IS , Green J H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .
"
6609,6610,653.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .
"
6610,6611,653.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12 .
6611,6612,647.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhimurium;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi;Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,3 4 5 12 Salmonella serovar Typhi gi 16761966 6.59 65.66 351.3 / 0 6 848.4 / 0 Salmonella serovar Typhi Salmonella serovar Typhimurium Salmonella serovar Typhi Salmonella serovar Typhi 32 44 gi 16759110 gi 16764195 7.20 5.17 47.51 19.80 7 57.7 / 261.2 54 8 123.8 / 287.5 38/222 .4 gi 16502500 gi 16503032 5.17 5.15 21.50 23.2 7.21 e 20 13 20 35 49.6 / 0 103.1 / 0 123.2 / 0-66/0 Salmonella serovar Typhi Salmonella serovar Typhi Salmonella serovar Typhi Salmonella serovar Typhi gi 16760937 gi 16760937 gi 16760937 gi 16504014 5.09 5.06 5.03 6.12 51.89 52.45 52.47 51.89 SS-III -RRB- / OD of Salmonella serovar Typhi leuO FIG. 2 166 FIG. 2 -- Continued 166 The proteomic data revealed that LeuO represses the expression of ompX .
6612,6613,121.txt,1,0,,,,"When DnaA IV-affinity gel was mixed with the DNAs , DnaA IV was found to bind with the dnaA box in the oriC fragment ."
6613,6614,109.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Calva E OmpR positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Calva E Negative osmoregulation of the Salmonella ompS1 porin independently of OmpR in an hns background .
"
6614,6615,109.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Puente JL OmpR positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Puente JL Negative osmoregulation of the Salmonella ompS1 porin independently of OmpR in an hns background ."
6615,6616,2194.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , the global regulator ss .
"
6616,6617,2194.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , phosphate regulation .
"
6617,6618,2194.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , PhoB .
"
6618,6619,2194.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , osmoregulation .
"
6619,6620,2194.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , OmpR .
"
6620,6621,2194.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , s32 of heat-shock response .
"
6621,6622,2194.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"UspA is induced during stationary-phase In E. coli , induction of uspA in response to diverse stresses is independent of RpoS , RpoH ."
6622,6623,2180.txt,1,0,,,,"Although it has been proposed that SirA directly controls expression of both hilC , it was also determined that HilC was not required for SirA to control hilA expression .
"
6623,6624,2180.txt,2,0,,,,"Our model suggests that SirA could control expression of hilC by regulating the expression of a single regulator .
"
6624,6625,2180.txt,3,0,,,,"Our model suggests that SirA could control expression of hilC by either independently activating each gene .
"
6625,6626,2180.txt,4,0,,,,"This suggests that SirA regulates expression of hilC via HilD .
"
6626,6627,2180.txt,5,0,,,,"This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds both the hilC .
"
6627,6628,2180.txt,6,0,,,,"Once phosphorylated , SirA directly binds the hilC promoters .
"
6628,6629,2180.txt,7,0,,,,"SirA controls these genes by directly binding hilC regulatory genes .
"
6629,6630,2180.txt,8,0,,,,"Conversely , previously published gel-shift data suggested that SirA is able to bind to the promoters of hilC .
"
6630,6631,2180.txt,9,0,,,,"Whereas SirA might bind to the hilC promoters during in-vitro gel-shift experiments , genetic data shows that SirA is incapable of directly activating these promoters ; SirA binding to DNA in-vitro does not represent activation .
"
6631,6632,2180.txt,10,0,,,,"To check if both regulators are important , the regulation of hilC gene expression by SirA is considered to check the possibility of one of the regulators being important , this dependency is taken as an OR gate .
"
6632,6633,2180.txt,11,0,,,,"To check if both regulators are important , the regulation of hilC gene expression by SirA is considered to function as gate , this dependency is taken as an OR gate .
"
6633,6634,2180.txt,12,0,,,,"To check if both regulators are important , the regulation of hilC gene expression by SirA is considered to function as an , this dependency is taken as an OR gate .
"
6634,6635,2180.txt,13,0,,,,"SirA , directly regulates the hilC genes at the top of the invasion cascade ."
6635,6636,1489.txt,1,0,,,,"PhoP-PhoQ also activates pagP , ."
6636,6637,1106.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) ."
6637,6638,492.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"Expression of the flagellar operons in the FliA-overproducing conditiona baflllehlDeCb pTrc99C pKKOPA99C Activity with plasmid : Class 1 flhD-lac 1 0.99 : : lac Class 2 fliA-lac + : : TnlO 1 3.58 0.18 3.34 0.18 13.3 0.09 17.6 0.13 6.00 0.16 19.1 0.12 14.3 0.12 0.19 1 0.17 1 0.11 1 0.15 1 0.18 1 0.13 1 0.15 + : : TnlO + : : TnlO + : : TnlO + : : TnlO + : : TnlO + : : TnlO flgA-lac flgB-lac flhB-lac fliE-lac fliF-lac fliL-lac Class 3 + 1 9.77 : : TnlO 0.18 5.70 fliC-lac flgK-lac fliD-lac + 1 10.0 : : TnlO 0.19 7.03 + 1 12.2 : : TnlO 0.12 4.17 + 1 10.4 : : TnlO 0.10 9.18 + 1 8.74 : : TnlO 0.22 6.53 a KK1004 ( flhDC + ) or KK2040 ( flhD : : TnJO ) carrying the lac fusions with the flagellar operons were transformed with the respective plasmids , and the activity of 0-galactosidase was assayed with each transformant after induction for 2 h with IPTG ."
6638,6639,1660.txt,1,0,,,,"While normally repressed by MarR , a mutation within the marO genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance .
"
6639,6640,1660.txt,2,0,,,,"While normally repressed by MarR , a mutation within the marR genes leads to constitutive transcriptional activation of marRAB , resulting in increased drug resistance .
"
6640,6641,1660.txt,3,0,,,,"The repressor MarR , binds to the marO operator region to negatively regulate expression of marRAB .
"
6641,6642,1660.txt,4,0,,,,"MarR inhibits binding of MarR to the marRAB promoter
"
6642,6643,1660.txt,5,0,,,,"MarR negatively regulates expression of marRAB by binding to the marO operator region .
"
6643,6644,1660.txt,6,0,,,,"MarR negatively regulates the expression of marRAB by binding to the marO operator region .
"
6644,6645,1660.txt,7,0,,,,Thus induction of marRAB by DEC without inhibition of the repression activity of MarR is expected to be less effective than induction with SAL .
6645,6646,1674.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Transcriptional regulation of flhD by sigma ( FliA ) in enterohaemorrhagic Escherichia coli .
6646,6647,486.txt,1,0,,,,"Apparently , HilA activates the expression of sicA ."
6647,6648,1112.txt,1,0,,,,"Thus , OmpR represses cadC/BA by directly binding to upstream DNA at cadB .
"
6648,6649,1112.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in SCV of macrophages .
"
6649,6650,1112.txt,3,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Importantly , a recent study suggests that Salmo-nella OmpR represses the cadC/BA operon by directly binding to both cadB promoters in the Salmonellacontaining vacuole of macrophages .
"
6650,6651,1112.txt,4,0,,,,"Activated OmpR then represses the cadC/BA operon by directly binding to both cadB promo-ters , leading to cytoplasmic acidification ."
6651,6652,1884.txt,1,0,,,,"We establish that the PmrA protein represses transcription of ssrB .
"
6652,6653,1884.txt,2,0,,,,"the ssrB promoter abolished repression by the PmrA protein
"
6653,6654,1884.txt,3,0,,,,"We establish that the PmrA protein down-regulates expression of spi/ssa genes by repressing transcription from the ssrB promoter .
"
6654,6655,1884.txt,4,0,,,,"The hypervirulence of the pmrA null mutant can be recapitulated by rendering the ssrB promoter resistant to repression by PmrA .
"
6655,6656,1884.txt,5,0,,,,"The PmrA protein appears to repress ssrB directly because : First , the purified PmrA protein protected the − 45 to − 16 region from ATG of of the ssrB gene in-vitro -LRB- Fig .
"
6656,6657,1884.txt,6,0,,,,"Finally , PmrA 
"
6657,6658,1884.txt,7,0,,,,"Finally , PmrA 
"
6658,6659,1884.txt,8,0,,,,"Finally , PmrA 
"
6659,6660,1884.txt,9,0,,,,"Finally , PmrA 
"
6660,6661,1884.txt,10,0,,,,"Finally , PmrA 
"
6661,6662,1884.txt,11,0,,,,"Finally , PmrA 
"
6662,6663,1884.txt,12,0,,,,"Finally , PmrA 
"
6663,6664,1884.txt,13,0,,,,"Finally , PmrA 
"
6664,6665,1884.txt,14,0,,,,"Taken together , the results indicate that PmrA 
"
6665,6666,1884.txt,15,0,,,,"To examine the physiological consequences of PmrA repression of ssrB transcription , we examined the kinetics of SPI-2 -- promoted macro-phage death .
"
6666,6667,1884.txt,16,0,,,,"The results presented above suggested that the hypervirulence phenotype of the pmrA null mutant might be due to PmrA repression of ssrB transcription .
"
6667,6668,1884.txt,17,0,,,,"the ssrB promoter mutant is refractory to repression by the PmrA protein
"
6668,6669,1884.txt,18,0,,,,"The antivirulence function of PmrA can be ascribed to its role as transcriptional repressor of the regulatory gene ssrB .
"
6669,6670,1884.txt,19,1,Salmonella,Salmonella,Salmonella,"These results suggest that PmrA repression of ssrB might enable Salmonella to favor dissemination to neighboring cells .
"
6670,6671,1884.txt,20,1,Salmonella,Salmonella,Salmonella,"These results suggest that PmrA repression of ssrB might enable Salmonella to control bacterial proliferation within a cell .
"
6671,6672,1884.txt,21,0,,,,"Moreover , it suggests that one of the roles of PhoP in promoting ssrB transcription might be to overcome PmrA-dependent repression of ssrB .
"
6672,6673,1884.txt,22,0,,,,"Interestingly , the PmrA protein repressed SPI-2 expression in a manner similar to the Fur regulator ; PmrA was shown to repress ssrB transcription ."
6673,6674,1648.txt,1,0,,,,"Our model suggests that SirA could control expression of hilD by regulating the expression of a single regulator .
"
6674,6675,1648.txt,2,0,,,,"Our model suggests that SirA could control expression of hilD by either independently activating each gene .
"
6675,6676,1648.txt,3,0,,,,"SirA apparently controls hilD at the level of the mRNA ; overproduction of SirA increased hilD expression in a HilD-independent fashion .
"
6676,6677,1648.txt,4,0,,,,"This genetic analysis is apparently inconsistent with previous gel shift data suggesting that SirA binds the hilD .
"
6677,6678,1648.txt,5,0,,,,"Conversely , previously published gel-shift data suggested that SirA is able to bind to that of hilD ."
6678,6679,1890.txt,1,0,,,,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of uhpT , in H7 .
"
6679,6680,1890.txt,2,0,,,,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of uhpT , in O157 .
"
6680,6681,1890.txt,3,0,,,,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of uhpT , in the enterohemorrhagic EHEC strain .
"
6681,6682,1890.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"CpxR-P also confers resistance to fosfomycin by directly repressing the expression of uhpT , in the enterohemorrhagic E. coli strain ."
6682,6683,451.txt,1,0,,,,"In this respect , in the footprinting experiments , OmpR-P bound to the ompS2 regulatory region at 0.8 M , similar to what was observed for the footprinting of OmpR-P on ssrA box A1 boxes .
"
6683,6684,451.txt,2,0,,,,"Thus , OmpR-P would then be allowed to bind at and around the consensus OmpR-binding box , permitting ompS2 expression mostly at high-osmolarity ."
6684,6685,337.txt,1,0,,,,"These findings suggest that STM1697 inhibits motility by interacting at the post-transcriptional level with the FlhD C functionality as demonstrated previously for STM1344 .
"
6685,6686,337.txt,2,0,,,,"These findings suggest that STM1697 inhibits motility by interacting at the post-transcriptional level with the FlhD C 4 2 expression .
"
6686,6687,337.txt,3,0,,,,The expression of the FlhD-free mutants of STM1697 showed similar motility phenotypes as the stm1697 strain suggesting that the motility inhibition of STM1697 is directly mediated by interaction with FlhD .
6687,6688,323.txt,1,0,,,,"While csgD is positively regulated by RpoS via MlrA , it itself stimulates the production of curli fimbriae through the transcriptional activation of the csgBAC operon .
"
6688,6689,323.txt,2,0,,,,"To further distinguish between the contribution of RpoS to csgD morphotype expression , we compared the phenotype of an arcZ mutant with an rpoS mutant in the MAE52 strain background .
"
6689,6690,323.txt,3,0,,,,"Consequently , we conclude that besides upregulation of RpoS , other Hfq-dependent factor are required to restore csgD morphotype expression in the hfq mutant of UMR1 .
"
6690,6691,323.txt,4,0,,,,"This finding also suggests that bistable expression of csgD is regulated via RpoS and/or upregulation of promoter activity .
"
6691,6692,323.txt,5,0,,,,"Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by RtsA .
"
6692,6693,323.txt,6,0,,,,"Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator .
"
6693,6694,323.txt,7,0,,,,"Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator .
"
6694,6695,323.txt,8,0,,,,"Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by another csgD transcriptional regulator ."
6695,6696,445.txt,1,2,Mus sp.;Salmonella,mice;Salmonella,Mus sp.;Salmonella,"Conversely , the iscR mutant was shown to be less virulent in mice compared to the wild‐type , consistent with a possible regulation of other genes involved in Salmonella pathogenesis by IscR .
"
6696,6697,445.txt,2,2,Mus sp.;Salmonella,mice;Salmonella,Mus sp.;Salmonella,"Conversely , the iscR mutant was shown to be more invasive in HeLa cells virulent in mice compared to the wild‐type , consistent with a possible regulation of other genes involved in Salmonella pathogenesis by IscR ."
6697,6698,1847.txt,1,0,,,,"an flhBAE operon _ activated by FlhD2C2 s n tra is The flhBA operon
"
6698,6699,1847.txt,2,0,,,,an flhBAE operon _ activated by FlhD2C2 s n tra is The flhBA operon
6699,6700,1853.txt,1,1,unidentified,not shown,unidentified,"In soft-rot bacteria , binding of KdgR to KDG releases the protein from its operator sites ; however , in our experiments the addition of KDG to lacZ reporter fusions in kdgR-regulated genes did not relieve data not shown .
"
6700,6701,1853.txt,2,0,,,,"In soft-rot bacteria , binding of KdgR to KDG releases the protein from its operator sites ; however , in our experiments the addition of KDG to lacZ reporter fusions in kdgR-regulated genes did not relieve the repression ."
6701,6702,479.txt,1,0,,,,"Furthermore , preliminary results indicate that HilD can bind directly to the invF promoter , supporting the hypothesis that there is an alternative HilA-independent mechanism for C. P. Lostroh , unpublished results .
"
6702,6703,479.txt,2,0,,,,"Furthermore , preliminary results indicate that HilD can bind directly to the invF promoter , supporting the hypothesis that there is an alternative HilA-independent mechanism for activating invF .
"
6703,6704,479.txt,3,0,,,,"We show that HilD can directly bind invF .
"
6704,6705,479.txt,4,0,,,,"Overproduction of HilD activate the expression of a chromosomal invF-lacZ fusion in the absence of hilA In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilA , respectively , under the control of the arabinose-inducible PBAD promoter .
"
6705,6706,479.txt,5,0,,,,"Overproduction of HilD activate the expression of a chromosomal invF-lacZ fusion in the absence of hilA In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilC , respectively , under the control of the arabinose-inducible PBAD promoter .
"
6706,6707,479.txt,6,0,,,,"Overproduction of HilD activate the expression of a chromosomal invF-lacZ fusion in the absence of hilA In order to study the activation of invF by HilD , we examined the expression of a chromosomal invF-lacZ fusion in a hilA hilD mutant strain , which express HilD , respectively , under the control of the arabinose-inducible PBAD promoter .
"
6707,6708,479.txt,7,0,,,,"These results suggest that HilD might directly activate invF expression by binding to sequences upstream of invF .
"
6708,6709,479.txt,8,0,,,,"HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
6709,6710,479.txt,9,0,,,,"HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
6710,6711,479.txt,10,0,,,,"In addition to binding upstream of invF , HilD also bind to sites upstream of hilC .
"
6711,6712,479.txt,11,0,,,,"In addition to binding upstream of invF , HilD also bind within S. Akbar , unpublished results .
"
6712,6713,479.txt,12,0,,,,"In addition to binding upstream of invF , HilD also bind within the prgH-hilD intergenic region .
"
6713,6714,479.txt,13,0,,,,"These gel shift assays indicate that HilD bind sequences downstream of the HilD-and HilC-dependent invF promoter .
"
6714,6715,479.txt,14,0,,,,"These gel shift assays indicate that HilD bind sequences upstream of the HilD-and HilC-dependent invF promoter .
"
6715,6716,479.txt,15,1,Salmonella,Salmonella,Salmonella,"given the cross regulation of SPI-2 by the SPI-1-encoded HilD regulator , it is possible that in-vivo invF is needed to control other genes in Salmonella
"
6716,6717,479.txt,16,1,Salmonella,Salmonella,Salmonella,"given the cross regulation of SPI-1 by the SPI-1-encoded HilD regulator , it is possible that in-vivo invF is needed to control other genes in Salmonella
"
6717,6718,479.txt,17,0,,,,"HilD also directly controls the expression of invF .
"
6718,6719,479.txt,18,0,,,,"However , HilD regulates invF by binding to downstream of the HilC/Ddependent invF promoter .
"
6719,6720,479.txt,19,0,,,,"However , HilD regulates invF by binding to downstream of the HilC/Ddependent invF promoter .
"
6720,6721,479.txt,20,0,,,,"However , HilD regulates invF by binding to downstream of the HilC/Ddependent invF promoter .
"
6721,6722,479.txt,21,0,,,,"However , HilD regulates invF by binding to regions upstream .
"
6722,6723,479.txt,22,0,,,,"However , HilD regulates invF by binding to regions located .
"
6723,6724,479.txt,23,0,,,,invF is positively regulated by HilD through HilA
6724,6725,1852.txt,1,0,,,,"the only chromosomal gene _ regulated by SdiA , srgE , except that it appears to be a single gene the predicted product contains a putative coiled-coil domain
"
6725,6726,1852.txt,2,0,,,,"the only chromosomal gene _ regulated by SdiA , srgE , except that it appears to be a single gene horizontal acquisition contains a putative coiled-coil domain
"
6726,6727,1852.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"srgE ( SdiA-regulated gene E ) is a chromosomal gene regulated by SdiA that also appears to be found on the virulence plasmid pSLT [ 13 ] .
"
6727,6728,1852.txt,4,0,,,,"Habyarimana , F. , Sabag-Daigle , A. , and Ahmer , B.M.M. ( 2014 ) The SdiA-regulated gene srgE encodes a type III secreted effector .
"
6728,6729,1852.txt,5,0,,,,"Besides the putative ` rck operon 
"
6729,6730,1852.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The other gene _ regulated by SdiA in S. Typhimurium , srgE ,
"
6730,6731,1852.txt,7,0,,,,"Another gene potentially regulated by SdiA is srgE .
"
6731,6732,1852.txt,8,0,,,,"The SdiA-regulated gene srgE encodes a type III secreted effector .
"
6732,6733,1852.txt,9,1,Salmonella,Salmonella,Salmonella,"Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 1 , 61 ) .
"
6733,6734,1852.txt,10,0,,,,"The second SdiA-regulated locus is encoded in the chromosome and consists of the gene srgE that is predicted to encode a protein containing a coiled-coil domain ( 2 , 61 ) .
"
6734,6735,1852.txt,11,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"AI-1 Signaling in Salmonella Upon detecting AHLs produced by other species of bacteria , SdiA in Salmonella activates expression of two srg ( SdiA-regulated gene ) loci , the rck operon that encodes seven genes and the srgE gene ( 19 , 35 ) .
"
6735,6736,1852.txt,12,0,,,,"The second SdiA-regulated locus is encoded in the chromosome and consists of the gene srgE that is predicted to encode a protein containing a coiled-coil domain ( 35 , 46 ) .
"
6736,6737,1852.txt,13,0,,,,The SdiA-regulated gene srgE encodes a type III secreted effector .
6737,6738,478.txt,1,0,,,,"Cumulatively , our data demonstrate that the iron-inducible PmrA/PmrB two-component regulatory system properly tunes the level of SPI-2 induction in phagocytes by repressing ssrB transcription ."
6738,6739,1846.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Felis catus,SL1344;SL1344;cat,Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,"Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .
"
6739,6740,1846.txt,2,0,,,,the fis promoter is repressed by the Fis protein
6740,6741,322.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .
"
6741,6742,322.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"By contrast , Zn2 + has been shown to promote transcription of the pmrA and pmrB genes as well as that of several PmrA-activated genes in E. coli ( Lee et al. , 2005 ) .
"
6742,6743,322.txt,3,0,,,,"ctivated Inner Membrane Peptide - A rA m P A We identified a PmrA-activated promoter immediately downstream of and transcribed towards the pmrB coding region that had not been reported in previous experimental and computational searches of PmrA-activated targets ( Aguirre et al. , 2000 ; Marchal et al. , 2004 ; Wosten and Groisman , 1999 ) ( Figure 2A ) .
"
6743,6744,322.txt,4,0,,,,"ctivated Inner Membrane Peptide - A rA m P A We identified a PmrA-activated promoter immediately downstream of and transcribed towards the pmrB coding region that had not been reported in previous experimental and computational searches of PmrA-activated targets ( Aguirre et al. , 2000 ; Marchal et al. , 2004 ; Wosten and Groisman , 1999 ) ( Figure 2A ) ."
6744,6745,444.txt,1,0,,,,"Studies of bacteria have , to date , revealed that hilA expression is regulated by a complex array of hilC/sirC/sprA , hilD , sirA/barA , fis , csrAB , envZ/ompR , phoB , fadD , fliZ , hha , H-NS , .
"
6745,6746,444.txt,2,0,,,,"Electrophoretic mobility-shift assays of he binding of H-NS of the hilA promoter .
"
6746,6747,444.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;Salmonella enterica;enterica;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 157 , 2504 -- 2514 Integration host factor alleviates H-NS silencing the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA of d Antonio Juárez1 Correspondence Antonio Juárez 1 Departament de Microbiologia , Facultat de Biologia , Universitat de Barcelona , Avda Diagonal , 645 , 08028 Barcelona , Spain ajuarez@ub.edu 2 Institut de a ( , Parc Cientıfic de Barcelona , Baldiri Reixach , 15-21 , 08028 Barcelona , Spain Coordination of the expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 ( SPI1 ) depends on a complex circuit involving ving several regul .
"
6747,6748,444.txt,4,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;Salmonella enterica;enterica;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 157 , 2504 -- 2514 Integration host factor alleviates H-NS silencing the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA of d Antonio Juárez1 Correspondence Antonio Juárez 1 Departament de Microbiologia , Facultat de Biologia , Universitat de Barcelona , Avda Diagonal , 645 , 08028 Barcelona , Spain ajuarez@ub.edu 2 Institut de de Bioenginyeria de Catal , Parc Cientıfic de Barcelona , Baldiri Reixach , 15-21 , 08028 Barcelona , Spain Coordination of the expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 ( SPI1 ) depends on a complex circuit involving ving several regul .
"
6748,6749,444.txt,5,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;Salmonella enterica;enterica;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 157 , 2504 -- 2514 Integration host factor alleviates H-NS silencing the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA of Mário H. Queiroz ,1 Cristina Madrid ,1 Sònia Paytubi ,1 Carlos Balsalobr Correspondence Antonio Juárez 1 Departament de Microbiologia , Facultat de Biologia , Universitat de Barcelona , Avda Diagonal , 645 , 08028 Barcelona , Spain ajuarez@ub.edu 2 Institut de a ( , Parc Cientıfic de Barcelona , Baldiri Reixach , 15-21 , 08028 Barcelona , Spain Coordination of the expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 ( SPI1 ) depends on a complex circuit involving ving several regul .
"
6749,6750,444.txt,6,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella;Salmonella enterica;Salmonella;Salmonella,Salmonella;Salmonella enterica;enterica;Typhimurium;Salmonella;Salmonella enterica;enterica;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Microbiology , 157 , 2504 -- 2514 Integration host factor alleviates H-NS silencing the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA of Mário H. Queiroz ,1 Cristina Madrid ,1 Sònia Paytubi ,1 Carlos Balsalobr Correspondence Antonio Juárez 1 Departament de Microbiologia , Facultat de Biologia , Universitat de Barcelona , Avda Diagonal , 645 , 08028 Barcelona , Spain ajuarez@ub.edu 2 Institut de de Bioenginyeria de Catal , Parc Cientıfic de Barcelona , Baldiri Reixach , 15-21 , 08028 Barcelona , Spain Coordination of the expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 ( SPI1 ) depends on a complex circuit involving ving several regul .
"
6750,6751,444.txt,7,0,,,,"In vitro binding of H-NS to the hilA regulatory region To further test the hypothesis that IHF interferes with H-NS-mediated silencing of hilA , we performed competitive EMSAs between H-NS on the hilA promoter region .
"
6751,6752,444.txt,8,0,,,,"In spite of the fact that several reports have shown that H-NS influences hilA expression , information is not yet available .
"
6752,6753,444.txt,9,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"M.H. Queiroz , C. Madrid , S. Paytubi , C. Balsalobre , A. Juárez , Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA , Microbiology 157 2504 .
"
6753,6754,444.txt,10,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Queiroz MH , Madrid C , Paytubi S , Balsalobre C , Juárez A : Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .
"
6754,6755,444.txt,11,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .
"
6755,6756,444.txt,12,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .
"
6756,6757,444.txt,13,0,,,,"four H-NS _ regulated hilA
"
6757,6758,444.txt,14,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .
"
6758,6759,444.txt,15,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Juarez , A. Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA .
"
6759,6760,444.txt,16,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Queiroz , M.H. , Madrid , C. , Paytubi , S. , Balsalobre , C. , alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1 , hilA ."
6760,6761,450.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Intriguingly , association of AraC with the site in dcp , as measured by ChIP/qPCR , is the highest of all AraC-bound regions in the E. coli genome ( Fig. 1A ) .
"
6761,6762,450.txt,2,0,,,,"Specifically , we identified three novel binding targets of AraC ( upstream of ytfQ and ydeN and within dcp ) and five novel AraC-regulated genes ( ytfQ , ydeN , ydeM , ygeA , and polB ) .
"
6762,6763,450.txt,3,0,,,,"AraC binding within dcp is not associated with detectable regulation of transcription .
"
6763,6764,450.txt,4,0,,,,We detected binding of AraC within dcp .
6764,6765,336.txt,1,0,,,,"The two-component regulatory SirA/BarA function through HilD , thus inducing hilC ."
6765,6766,1891.txt,1,0,,,,The two-component PhoP/Q system functions as a negative regulator of hilA gene expression ( reviewed in Ref .
6766,6767,1649.txt,1,0,,,,"Taken together , these results identified a regulatory role for unphosphorylated SsrB by orchestrating anti-silencing at the H-NS-repressed csgD locus ."
6767,6768,1885.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
6768,6769,1675.txt,1,0,,,,mlrA expression itself is positively regulated by RpoS .
6769,6770,1113.txt,1,0,,,,"Our RNA-seq data showed a significant down-regulation of sipB in the yqhC mutant , suggesting that YqhC therefore modulates induction of cytotoxicity in host cells ."
6770,6771,487.txt,1,0,,,,"plasmids _ expressing HhaWT under control of the native hha promoter
"
6771,6772,487.txt,2,0,,,,"plasmids _ expressing HhaWT under control of the native hha promoter
"
6772,6773,487.txt,3,0,,,,plasmids _ expressing HhaWT under control of the native hha promoter
6773,6774,493.txt,1,1,synthetic construct,Primer,synthetic construct,"Primer extension and DNase I footprinting identified multiple SsrB-regulated promoters within SPI-2 located upstream of ssaB , sseA , ssaG and ssaM ."
6774,6775,1107.txt,1,0,,,,"In addition , mntH is controlled by the hydrogen-peroxide sensor OxyR ."
6775,6776,1661.txt,1,0,,,,"The transcription of acnB , icdA , sdhC was most repressed by YdcI ."
6776,6777,1488.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,Putative regulation by ArgR was evaluated by generating three isogenic S. Typhi deletion mutants of fur .
6777,6778,2181.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In addition to its RNA splicing role , StpA induces OmpF expression in E. coli by destabilizing the micF antisense RNA ."
6778,6779,2195.txt,1,0,,,,"RT-PCR analysis independently showed an NO-dependent downregulation in the transcription of PhoP-activated genes phoP , phoQ , mig-14 and phoN , while RNS treatment did not affect ( e.g. , rpoD ) or even increased ( e.g. , hmpA ) the expression of other loci ( fig. 5B ) ."
6779,6780,108.txt,1,1,Cell fusing agent virus,CFA,Cell fusing agent virus,"They suggested that the difference in the CFA synthase level may be the result of different rpoS alleles , since the expression of another RpoS-regulated gene , poxB , was lower in FT1 than ZK126 ( Wang & Cronan , 1994 ) ."
6780,6781,646.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .
"
6781,6782,646.txt,2,0,,,,"The fact that mgtA was PhoP controlled led us to understand its physiological role .
"
6782,6783,646.txt,3,0,,,,"The fact that mgtA was PhoP controlled led us to define the inducing signal of the regulon .
"
6783,6784,646.txt,4,0,,,,"However , there is uncertainty about what consti - tutes a PhoP binding site because many PhoP-regulated pro- moters do not conform to the mgtA promoter model ( 14 , 15 ) .
"
6784,6785,646.txt,5,0,,,,"For example , one of the profiles encompassed promoters that belong to the same expression ( E1 ) , PhoP box submotif ( M2 ) , and promoter class ( P1 ) ( Fig. 1H ) and harbored not only the prototypical PhoP-regulated phoP and mgtA promoters ( 13 , 14 ) but also the yhiW promoter , which was not known to be under PhoP control .
"
6785,6786,646.txt,6,1,Salmonella,Salmonella,Salmonella,"The PhoP-acti-vated mig-14 , mgtC , virK , and pagC promoters of Salmonella do not harbor a typical PhoP box in place of the 35 region , as found in archetypal PhoP-regulated promoters such as the mgtA promoter ( 13 ) .
"
6786,6787,646.txt,7,1,Salmonella,Salmonella,Salmonella,"We established that when Salmonella experiences the PhoP protein binds to both the archetypal mgtA promoter as well as the mig-14 , mgtC , and pagC promoters .
"
6787,6788,646.txt,8,0,,,,"Although some genes regulated by PhoP do not display a consensus DNA recognition sequence for PhoP , other PhoP-regulated genes , such as the mgtA gene , contain a single conserved PhoP box in their promoter region ( Lejona et al. , 2003 ) .
"
6788,6789,646.txt,9,0,,,,"$ , PhoP ; # , PhoP ~ P by SPR A BIAcore biosensor was used to examine , in the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .
"
6789,6790,646.txt,10,0,,,,"$ , , % , PhoPHis ~ P. Response ( RU DNA binding of PhoP proteins by SPR A BIAcore biosensor was used to examine , in the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .
"
6790,6791,646.txt,11,0,,,,"$ , , % , PhoPHis ~ P. Response ( RU DNA binding of PhoP proteins by SPR A BIAcore biosensor was used to examine , in the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .
"
6791,6792,646.txt,12,0,,,,"$ , , PhoPHis , PhoPHis ~ P. Response ( RU DNA binding of PhoP proteins by SPR A BIAcore biosensor was used to examine , in the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .
"
6792,6793,646.txt,13,0,,,,"$ , , PhoPHis , PhoPHis ~ P. Response ( RU DNA binding of PhoP proteins by SPR A BIAcore biosensor was used to examine , in the binding of the various PhoP proteins to the promoter of mgtA ( a PhoP-activated gene that contains a PhoP box in its promoter ) .
"
6793,6794,646.txt,14,0,,,,"The graph shows the binding of PhoP to biotinylated oligonucleotide duplexes containing the PhoP box of the mgtA promoter .
"
6794,6795,646.txt,15,0,,,,"Our SPR experiments clearly showed that both PhoP ~ P bind to the PhoP box of the mgtA promoter .
"
6795,6796,646.txt,16,0,,,,"Our SPR experiments clearly showed that both PhoP bind to the PhoP box of the mgtA promoter .
"
6796,6797,646.txt,17,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"Overall , this study clearly showed that the S. enterica PhoP protein binds to the mgtA promoter regardless of its phosphorylation state .
"
6797,6798,646.txt,18,0,,,,"Specific binding of the various PhoP proteins to the PhoP box of the mgtA promoter .
"
6798,6799,646.txt,19,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , Fig. 4D , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
6799,6800,646.txt,20,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , one , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
6800,6801,646.txt,21,1,Escherichia coli,E. coli,Escherichia coli,"The existence of a pair of divergently transcribed genes , the other , is reminiscent of the mode of transcription regulation of the divergently transcribed mgtA genes of E. coli : while mgtA is activated , treR is repressed by PhoP .
"
6801,6802,646.txt,22,0,,,,"When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the mgtA promoters increased during the first 10 min .
"
6802,6803,646.txt,23,0,,,,"When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the mgtA promoters increased during the first 10 min .
"
6803,6804,646.txt,24,0,,,,"When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the mgtA promoters then asymptotically reached the steady-state levels .
"
6804,6805,646.txt,25,0,,,,"When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the mgtA promoters then asymptotically reached the steady-state levels .
"
6805,6806,646.txt,26,0,,,,"This motif in such promoters depends functionally on its orientation , probably because the reverse sequence in this box would change the interaction of PhoP and RNA polymerase , thereby nullifying PhoP-regulated mgtA transcription ( unpublished data ) .
"
6806,6807,646.txt,27,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .
"
6807,6808,646.txt,28,0,,,,"In both strains , transcription initiation from the mgtA promoter is controlled by the transcription factor PhoP in response to extracytoplasmic Mg2 .
"
6808,6809,646.txt,29,2,Salmonella;Mus sp.,Salmonella;mice,Mus sp.;Salmonella,"By contrast , the MgtA-mediated feedback takes place relatively late as it requires cytosolic Mg2 + levels to drop below a certain threshold ( Fig. 2A ) , and does not appear to be related to virulence because neither mgtA nor the PhoP-regulated genes whose expression is most affected upon mgtA deletion are necessary for Salmonella to cause a lethal infection in mice ( Gunn et al. , 1998 ; Gunn et al. , 1995 ; Blanc-Potard and Groisman , 1997 ) .
"
6809,6810,646.txt,30,2,Salmonella;Mus sp.,Salmonella;mice,Mus sp.;Salmonella,"By contrast , the MgtA-mediated feedback takes place relatively late as it requires cytosolic Mg2 + levels to drop below a certain threshold ( Fig. 2A ) , and does not appear to be related to virulence because neither mgtA nor the PhoP-regulated genes whose expression is most affected upon mgtA deletion are necessary for Salmonella to cause a lethal infection in mice ( Gunn et al. , 1998 ; Gunn et al. , 1995 ; Blanc-Potard and Groisman , 1997 ) .
"
6810,6811,646.txt,31,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .
"
6811,6812,646.txt,32,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .
"
6812,6813,646.txt,33,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , mgtA were selected to evaluate the role of Pat in the regulation of PhoP activity ."
6813,6814,120.txt,1,0,,,,"However , mutations in galS did not affect repression by NagC ."
6814,6815,134.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , rcnA , was found to be regulated by Fur .
"
6815,6816,134.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , rcnA expression has also been suggested to be under the control of iron-sensing Fur , implying some interplay of iron homeostasis .
"
6816,6817,134.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , rcnA expression has also been suggested to be under the control of iron-sensing Fur , implying some interplay of cobalt .
"
6817,6818,134.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , rcnA expression has also been suggested to be under the control of iron-sensing Fur , implying some interplay of nickel ."
6818,6819,652.txt,1,0,,,,"the SOS response .4,5 The initial response to DNA damage is induction of LexA repressed genes include umuDC"
6819,6820,861.txt,1,0,,,,"However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig .
"
6820,6821,861.txt,2,0,,,,"The increase in mutation rates in the lexA ( def ) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho .
"
6821,6822,861.txt,3,0,,,,"To examine whether lack of all four translesion DNA polymerases affects expression of other LexA-controlled functions , we used real-time PCR to measure uvrB expression in a lexA ( def ) mutant and a lexA ( def ) mutant lacking all four tranlesion DNA polymerases .
"
6822,6823,861.txt,4,0,,,,"This increase in DNA breaks in the lexA ( def ) strain is mediated by two endonucleases , UvrC and Cho , and the LexAcontrolled UvrB protein ( Koskiniemi and Andersson 2009 ) ."
6823,6824,21.txt,1,0,,,,"RamA was required for indole induction of acrAB .
"
6824,6825,21.txt,2,1,Salmonella,Salmonella,Salmonella,"Here we report on induction of acrAB in Salmonella via the specific regulator RamA in response to indole .
"
6825,6826,21.txt,3,1,Salmonella,Salmonella,Salmonella,"The results indicate that the RamA regulator is required for indole induction of acrAB in Salmonella .
"
6826,6827,21.txt,4,0,,,,"Requirement of RamA for induction of acrAB by bile .
"
6827,6828,21.txt,5,0,,,,"RamA Binds to the Upstream Regions of tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals .
"
6828,6829,21.txt,6,0,,,,"RamA Binds to the Upstream Regions of acrA -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to environmental signals .
"
6829,6830,21.txt,7,0,,,,"RamA Binds to the Upstream Regions of tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to bile .
"
6830,6831,21.txt,8,0,,,,"RamA Binds to the Upstream Regions of tolC -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to indole .
"
6831,6832,21.txt,9,0,,,,"RamA Binds to the Upstream Regions of acrA -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to bile .
"
6832,6833,21.txt,10,0,,,,"RamA Binds to the Upstream Regions of acrA -- The aforementioned results indicate that RamA plays a major role in inducing acrAB in response to indole .
"
6833,6834,21.txt,11,1,Escherichia coli,E. coli,Escherichia coli,"RamA induction of acrAB by conditioned-medium of E. coli .
"
6834,6835,21.txt,12,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"We found that acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .
"
6835,6836,21.txt,13,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"We found that acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .
"
6836,6837,21.txt,14,1,Salmonella,Salmonella,Salmonella,"However , our data indicate that bile induction of acrAB in Salmonella is completely dependent on RamA , not Rob .
"
6837,6838,21.txt,15,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .
"
6838,6839,21.txt,16,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The acrAB induction by these three signal sources is completely dependent on the Salmonella-specific regulator RamA , indicating that RamA plays a major role in inducing acrAB .
"
6839,6840,21.txt,17,1,Salmonella,Salmonella,Salmonella,"However , our data indicate that bile induction of acrAB in Salmonella is completely dependent on RamA , not Rob .
"
6840,6841,21.txt,18,0,,,,"Our results suggest that RamAmediated acrAB expression is induced either via overexpression of activation of poorly-expressed RamA .
"
6841,6842,21.txt,19,0,,,,"Our results suggest that RamAmediated acrAB expression is induced either via overexpression of a weakly active RamA protein .
"
6842,6843,21.txt,20,1,Salmonella,Salmonella,Salmonella,"In Salmonella , RamA is involved in inducing acrAB in addition to the abovementioned regulators .
"
6843,6844,21.txt,21,0,,,,"via the RamA regulator The induction of acrAB in response to paraquat suggested that this induction mechanism might be mediated by the RamA regulator
"
6844,6845,21.txt,22,0,,,,"acrAB induction by paraquat was observed in the DramA strain , indicating that RamA was not required for this induction response .
"
6845,6846,21.txt,23,0,,,,"RamA directly induces acrAB .
"
6846,6847,21.txt,24,0,,,,"In SI3 , RamA played predominant role in ciprofloxacin resistance via increasing the expression level of acrAB .
"
6847,6848,21.txt,25,0,,,,"Activation of the acrAB operon is achieved through the direct binding of RamA , to the operator regions of these genes .
"
6848,6849,21.txt,26,0,,,,"that acrAB induction by indole is dependent on RamA
"
6849,6850,21.txt,27,0,,,,"that acrAB induction by indole is dependent on RamA
"
6850,6851,21.txt,28,0,,,,"that acrAB induction by indole is dependent on RamA
"
6851,6852,21.txt,29,0,,,,"The acrAB genes are transcriptionally activated by RamA .
"
6852,6853,21.txt,30,0,,,,"As expected , since RamA is PramA , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB ,18 bile DNA fragment + -- + -- Figu .
"
6853,6854,21.txt,31,0,,,,"As expected , since RamA is PramA , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB ,18 bile DNA fragment + -- + - + .
"
6854,6855,21.txt,32,0,,,,"As expected , since RamA is the main the ramA promoter , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB ,18 bile DNA fragment + -- + -- Figu .
"
6855,6856,21.txt,33,0,,,,"As expected , since RamA is the main the ramA promoter , we first conducted EMSAs with a 97 bp transcriptional activator of the acrAB ,18 bile DNA fragment + -- + - + .
"
6856,6857,21.txt,34,0,,,,RamA plays a key role in increasing the expression level of the efflux pump by binding to the upstream promoter region of acrAB and to .
6857,6858,2142.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
6858,6859,2142.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6859,6860,2156.txt,1,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the occurrence of autogenous activation of hilD transcription .
"
6860,6861,2156.txt,2,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the presence , in the occurrence of autogenous activation of hilD transcription .
"
6861,6862,2156.txt,3,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .
"
6862,6863,2156.txt,4,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in the inhibition of HilD activity by HilE .
"
6863,6864,2156.txt,5,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the absence of LeuO , in accordance with two well known facts .
"
6864,6865,2156.txt,6,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE .
"
6865,6866,2156.txt,7,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the presence , in the inhibition of HilD activity by HilE .
"
6866,6867,2156.txt,8,0,,,,"We also observed that a hilE null mutation increased the HilD levels in the presence , in accordance with two well known facts .
"
6867,6868,2156.txt,9,0,,,,"However , our data show that PhoPQ can repress the system independently of HilD ; thus , this transcriptional induction of hilE is apparently superfluous ."
6868,6869,875.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"This raised the possibility that StpA could directly induce the expression of crp at LEP , as had been observed in E. coli ."
6869,6870,1339.txt,1,0,,,,"Thus , RtsA are also apparently indirectly regulating hilD , contributing to the feedforward loop .
"
6870,6871,1339.txt,2,0,,,,This work demonstrates the regulation of hilD by RtsA .
6871,6872,35.txt,1,0,,,,"The proV promoter were used as positive control regions , respectively , as H-NS binds to the proV promoter ."
6872,6873,685.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
6873,6874,1311.txt,1,0,,,,"A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR-P -LRB- as indicated -RRB- for 2 h at room temperature .
"
6874,6875,1311.txt,2,0,,,,A radiolabelled ompR promoter DNA fragment were incubated with increasing quantities of OmpR-P -LRB- as indicated -RRB- for 2 h at room temperature .
6875,6876,1477.txt,1,0,,,,the fact that induction of pgtP expression responds to exogenous inducer suggests that a mechanism involving protein-protein interactions between PgtA proteins occurs within the membrane .
6876,6877,1463.txt,1,3,Salmonella;Salmonella enterica;Salmonella;unidentified,Salmonella;Salmonella enterica;enterica;unknown,Salmonella enterica;unidentified;Salmonella,"In Salmonella enterica , overexpression of the RstA protein lowered the levels of the alternative sigma factor RpoS by an unknown mechanism , which consequently downregulated transcription of three RpoS-controlled genes , narZ , spvA , and bapA , in stationary-phase ( 4 ) ."
6877,6878,849.txt,1,0,,,,HilC-Myc appears to bind the same regions upstream of invF as HilD-Myc does .
6878,6879,1305.txt,1,0,,,,"Although we demonstrated that this phenotype results from strong repression of invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes ."
6879,6880,691.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6880,6881,732.txt,1,0,,,,"Interestingly , Hha played no role in the regulation of the hilD promoter ."
6881,6882,726.txt,1,0,,,,"These results revealed a reciprocal regulatory relationship between IHF at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA .
"
6882,6883,726.txt,2,0,,,,These results revealed a reciprocal regulatory relationship between HU at the level of transcription in which IHF represses hup gene transcription and HU upregulates the transcription of ihfA .
6883,6884,1259.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
6884,6885,1259.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
6885,6886,915.txt,1,0,,,,"Using site directed mutagenesis , Marchal et al. demonstrated that the fifth positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1253 promoters .
"
6886,6887,915.txt,2,0,,,,"Using site directed mutagenesis , Marchal et al. demonstrated that the third positions of the first hexameric repeat are essential for binding by PmrA ; these are conserved in the STM1253 promoters ."
6887,6888,2036.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To ascertain whether slyA expression is regulated by RpoS , an isogenic rpoS S. typhimurium mutant was transformed with the slyA : : the level of b-galactosidase expression was determined .
"
6888,6889,2036.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,S. typhimurium;typhimurium;plasmid,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"To ascertain whether slyA expression is regulated by RpoS , an isogenic rpoS S. typhimurium mutant was transformed with the slyA : : lacZ plasmid was determined ."
6889,6890,2022.txt,1,0,,,,Complex transcriptional control of the osmotically regulated osmY gene suggests novel roles for Lrp .
6890,6891,901.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcription of micF is controlled by Rob ."
6891,6892,1265.txt,1,0,,,,"If regulation by csr was mediated exclusively by modulating the level of HilA , null mutations in csrB would be without effect in these two settings because , in the ® rst case , HilA is absent and , in the second case , it is maintained at a constant level .
"
6892,6893,1265.txt,2,0,,,,"Together , these results suggest that the principal effects of chromosomal csrB are mediated by control of HilA levels"
6893,6894,929.txt,1,0,,,,"Repression by CytR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .
"
6894,6895,929.txt,2,0,,,,Repression by CytR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .
6895,6896,1503.txt,1,0,,,,"It is known that RcsB also interacts with TviA protein , to activate viaB transcription from the tviA promoter ."
6896,6897,1517.txt,1,0,,,,a two-gene operon -LRB- with dinF -RRB- is repressed by LexA protein
6897,6898,1271.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Interplay between global regulators of Escherichia coli : effect of Lrp on the transcription of the gene osmC .
"
6898,6899,1271.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Gutierrez , C. Interplay between global regulators of Escherichia coli : effect of Lrp on transcription of the gene osmC ."
6899,6900,1926.txt,1,0,,,,"Defining the cis-acting sequences required for ugd transcription We analysed the 281 bp region upstream of the ugd start codon and identified a motif that could correspond to a potential RcsB binding site ( Fig. 4B ) because it resembled the upstream regulatory region of other RcsB-regulated genes ( Fig. 4C ) .
"
6900,6901,1926.txt,2,0,,,,"The rcsA dependence of the tolB-promoted activation of ugd ( Fig. 2B ) places this RcsB-regulated gene in the first group .
"
6901,6902,1926.txt,3,0,,,,"Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6902,6903,1926.txt,4,0,,,,"Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6903,6904,1926.txt,5,0,,,,"47 , 335 -- 344 62 Mouslim , C. et al. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6904,6905,1926.txt,6,0,,,,"Mouslim C , Latifi T & Groisman EA ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6905,6906,1926.txt,7,0,,,,"Mouslim , C. , Latifi , T. , Groisman , E. Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6906,6907,1926.txt,8,0,,,,"Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6907,6908,1926.txt,9,0,,,,"Mouslim , C. , Latifi , T. , and Groisman , E. A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6908,6909,1926.txt,10,0,,,,"Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6909,6910,1926.txt,11,0,,,,"Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene .
"
6910,6911,1926.txt,12,0,,,,"Mouslim , C. , Latifi , T. , and Groisman , E.A. ( 2003 ) Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene ."
6911,6912,1098.txt,1,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; sdiA , a regulator of quorum-sensing and virulence ( Ahmer et al. 1998 ; Volf et al. 2002 ) ; permeases of oligopeptides , such as oppF and oppB ( Goodell and Higgins 1987 ; Orchard and Goodrich-Blair 2004 ) ; and several genes involved in drug resistance , such as emrE and nudF ."
6912,6913,518.txt,1,2,Escherichia coli;Salmonella;Escherichia coli,E. coli;Salmonella;E. coli,Escherichia coli;Salmonella,"This behavior is due to the highly divergent PmrD protein ( Figs. 6 and 7 ) , because replacement of the E. coli pmrD gene by the Salmonella pmrD gene endowed E. coli with the ability to transcribe the PmrA-activated pbgP gene and to exhibit resistance to polymyxin B in response to the low Mg2 signal ( Fig. 3 ) .
"
6913,6914,518.txt,2,6,Escherichia coli;Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,E. coli;Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris;Escherichia coli,"This phenotype was reflected also at the level of transcription ; the PmrA-activated pbgP gene was expressed by E. coli cells experiencing Fe3 but not in response to the low Mg2 signal ( Fig. 2C ) , whereas a pbgP transcript was made by Salmo-nella in both conditions ( Fig. 2D ) .
"
6914,6915,518.txt,3,1,Salmonella,Salmonella,Salmonella,"Although a non-cytotoxic form of polymyxin B -- termed polymyxin B nonapeptide ( Vaara and Vaara , 1983 ) -- could partially protect a Salmonella pmrA mutant from Fe ( III ) - mediated killing ( Chamnongpol et al. , 2002 ) inactivation of the PmrA-activated loci responsible for the lipid-A modification with 4-aminoarabinose ( i.e. pbgP ) or phosphoethanolamine ( i.e. pmrC ) did not render the organism susceptible to Fe ( III ) ( Lee et al. , 2004 ) .
"
6915,6916,518.txt,4,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
6916,6917,518.txt,5,0,,,,"DpbgE2 DpbgE3 pbgP Ugd DpbgE2/vector DpbgE2/ppbgE2 DpbgE3/vector DpbgE3/ppbgE3 pbgPDpbgE2 pbgPDpbgE3 ugdDpbgE2 ugdDpbgE3 DpmrAB/vector DpmrAB/ppmrAB DpmrAB/vector DpmrAB/ppbgE2 DpmrAB/ppbgE3 DpmrAB/ppbgE2E3 DpmrG DpmrC DpbgPE Dugd DyibD DpbgPE pmrC ugd pmrG yibD DpmrC ugd pmrG yibD DpmrC ugd DpmrC pmrG DpmrC yibD DyibD ugd DyibD pmrG Dugd pmrG DpmrC ugd yibD DpmrC pmrG yibD Dugd pmrG yibD DpmrC ugd pmrG pmrA505DpmrC ugd pmrG DpmrC ugd pmrG/vector DpmrC ugd pmrG/ppmrC DpmrC ugd pmrG/pugd DpmrC ugd pmrG/ppmrG DpmrG pbgPE DpmrC pbgPE DpmrC pbgPE pmrG The PmrA-activated ugd , pbgP , pmrC and pmrG genes are required for Fe ( III ) resistance To examine whether the pmrG and pmrC genes are necessary for Fe ( III ) resistance , we constructed strains deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
6917,6918,518.txt,6,1,Salmonella,Salmonella,Salmonella,"For example , activation of the PmrA/PmrB system ( 26 , 27 ) by growing Salmonella in media containing a high ( 10 mM ) Mg2 + concentration and then shifting it to media containing a low 2 + 3 + ( 50 mM ) Mg concentration and 100 mM Fe resulted in an increase in the mRNA levels corresponding to the PmrA-activated pbgP and pmrC genes , which peaked and then reached new steady-state levels ( fig .
"
6918,6919,518.txt,7,1,Salmonella,Salmonella,Salmonella,"Synthesis of Ara4N and addition to the lipid-A is mediated by the Salmonella PmrA-activated genes pmrE ( also known as ugd ) and pmrHFIJKLM ( the pmrH operon , also known as the pbgP or arn operon ) ( Gunn et al. , 2000 ) .
"
6919,6920,518.txt,8,0,,,,"To test this hypothesis , we determined the β2 galactosidase activity produced by strains harboring chromosomal lac transcriptional-fusions to the PmrA-activated pbgP operon and ugd gene ."
6920,6921,1932.txt,1,0,,,,"The sitABCD operon is Fur led us to examine the regulation of this fusion in-vitro under ironstarvation conditions .
"
6921,6922,1932.txt,2,0,,,,"Fur _ regulated Both the identification of sitABCD in an IVET selection for genes
"
6922,6923,1932.txt,3,0,,,,"Thus , sitABCD is primarily regulated by Fur in response to iron levels .
"
6923,6924,1932.txt,4,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Slauch , J.M. Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
"
6924,6925,1932.txt,5,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Ikeda , J.S. , Janakiraman , A. , Kehres , D.G. , Maguire , M.E. , Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
"
6925,6926,1932.txt,6,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
"
6926,6927,1932.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar effects of manganese on Fur-mediated regulation of the S. Typhimurium sitABCD operon have been observed .
"
6927,6928,1932.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar effects of cobalt on Fur-mediated regulation of the S. Typhimurium sitABCD operon have been observed .
"
6928,6929,1932.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Similar effects of iron on Fur-mediated regulation of the S. Typhimurium sitABCD operon have been observed .
"
6929,6930,1932.txt,10,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
"
6930,6931,1932.txt,11,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
"
6931,6932,1932.txt,12,0,,,,"Both mntH and sitABCD are under the control of Fur
"
6932,6933,1932.txt,13,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
"
6933,6934,1932.txt,14,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Slauch , J. M. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6934,6935,1932.txt,15,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"M. E. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6935,6936,1932.txt,16,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Maguire Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6936,6937,1932.txt,17,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"D. G. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6937,6938,1932.txt,18,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Kehres Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6938,6939,1932.txt,19,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"A. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6939,6940,1932.txt,20,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Janakiraman Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6940,6941,1932.txt,21,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"J. S. Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6941,6942,1932.txt,22,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Ikeda Transcriptional regulation of sitABCD of Salmonella enterica serovar typhimurium by Fur .
"
6942,6943,1932.txt,23,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by Fur .
6943,6944,256.txt,1,0,,,,"This suggests that the detrimental effect of an hns mutation is due to derepression of one or more sS-and PhoP-activated loci and might explain why hns mutations are not lethal in some laboratory strains , given that rpoS mutant alleles are commonly acquired after laboratory passage ( 5 ) ."
6944,6945,530.txt,1,0,,,,"spiC is regulated by both SsrB A two-component regulatory system regulates a two-component regulatory system We are aware of two previous reports of regulation of one two-component system by another .
"
6945,6946,530.txt,2,0,,,,spiC is regulated by both SsrB A two-component regulatory system regulates a two-component regulatory system We are aware of two previous reports of regulation of one two-component system by another .
6946,6947,524.txt,1,0,,,,then Crp polymerase activate the transcription of the araBAD genes
6947,6948,242.txt,1,0,,,,"Moreover , ftnB are repressed by the Fe-responsive regulator Fur and induced under conditions of Fe limitation , whereas ftnA are maximally expressed when Fe is abundant .
"
6948,6949,242.txt,2,0,,,,"Moreover , ftnB are repressed by the Fe-responsive regulator Fur and induced under conditions of Fe limitation , whereas bfr are maximally expressed when Fe is abundant .
"
6949,6950,242.txt,3,0,,,,"These data suggest that ftnB are negatively regulated by Fur in Fe-rich-medium .
"
6950,6951,242.txt,4,0,,,,"Whether Fur represses ftnB by indirect mechanisms remains to be determined .
"
6951,6952,242.txt,5,0,,,,"Whether Fur represses ftnB by direct mechanisms remains to be determined .
"
6952,6953,242.txt,6,0,,,,"hence are expressed under iron-replete conditions consistent with iron storage/detoxification roles , while both ftnB are negatively regulated by Fur"
6953,6954,2234.txt,1,0,,,,"Like marRAB , acrAB are positively regulated by MarA .
"
6954,6955,2234.txt,2,1,Salmonella,Salmonella,Salmonella,"Other regulators of MarA did not contrib-ute to acrAB induction by indole in Salmonella .
"
6955,6956,2234.txt,3,0,,,,"8 -- 13 _ shown that MarA , play a role in antimicrobial resistance by activating acrAB
"
6956,6957,2234.txt,4,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"However , acrAB are also induced by stress signals in additional ways , it was suggested that S. enterica to salicylate activates MarA through binding to its repressor , MarR .
"
6957,6958,2234.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"However , acrAB are also induced by stress signals in additional ways , it was suggested that exposure of E. coli activates MarA through binding to its repressor , MarR .
"
6958,6959,2234.txt,6,0,,,,"These results , together with the results of the induction of acrAB by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6959,6960,2234.txt,7,0,,,,"These results , together with the results of the induction of acrAB by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6960,6961,2234.txt,8,0,,,,"These results , together with the results of the induction of acrAB by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6961,6962,2234.txt,9,0,,,,"These results , together with the results of the induction of acrAB by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6962,6963,2234.txt,10,0,,,,"These results , together with the results of the induction of acrAB by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6963,6964,2234.txt,11,0,,,,"These results , together with the results of the induction of micF by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6964,6965,2234.txt,12,0,,,,"These results , together with the results of the induction of micF by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6965,6966,2234.txt,13,0,,,,"These results , together with the results of the induction of marA by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6966,6967,2234.txt,14,0,,,,"These results , together with the results of the induction of marA by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
6967,6968,2234.txt,15,0,,,,"The MarA proteins can activate acrAB expression .
"
6968,6969,2234.txt,16,0,,,,"MarA is induced following acrAB
"
6969,6970,2234.txt,17,0,,,,The MarA protein positively regulates transcription of acrAB
6970,6971,2220.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,S. typhimurium;typhimurium;Salmonella,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of pCMPG5643 , resulted in restoration of Salmonella bio-film formation in the luxS mutant .
"
6971,6972,2220.txt,2,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,S. typhimurium;typhimurium;Salmonella,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of pCMPG5643 , resulted in restoration of Salmonella bio-film formation in the luxS mutant .
"
6972,6973,2220.txt,3,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,S. typhimurium;typhimurium;Salmonella,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter , resulted in restoration of Salmonella bio-film formation in the luxS mutant .
"
6973,6974,2220.txt,4,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,S. typhimurium;typhimurium;Salmonella,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"To explore the hypothesis that controlled synthesis of AI-2 at tight control of LuxS activity , is required for S. typhimurium biofilm formation as suggested from the previous experiments , we tested whether introducing luxS under the control of the strong constitutive nptII promoter , resulted in restoration of Salmonella bio-film formation in the luxS mutant ."
6974,6975,1729.txt,1,0,,,,"ArcA binds to the regulatory region of the ompD gene ompD transcription assessments suggest the existence of a regulatory mechanism .
"
6975,6976,1729.txt,2,0,,,,"Although unphosphorylated ArcA was also able to bind the ompD promoter , the electro-phoretic mobility pattern was different from that .
"
6976,6977,1729.txt,3,0,,,,"ompD downregulation is lost in arcA mutants To investigate ArcA-mediated regulation of ompD expression upon 3 xFLAG genetic background .
"
6977,6978,1729.txt,4,0,,,,"ompD downregulation is lost in arcA mutants To investigate ArcA-mediated regulation of ompD expression upon hydrogen-peroxide exposure , ΔarcA strains were constructed in wild type and OmpD .
"
6978,6979,1729.txt,5,0,,,,"negative regulation of ompD expression as previously observed in wild type cell _ supporting the idea that ArcA is directly involved in downregulating ompD expressio
"
6979,6980,1729.txt,6,0,,,,"Although results from gel shift assays suggest that ArcA-mediated control of ompD expression under oxidative-stress is dependent on ArcA phosphorylation , additional evidence is required to elucidate the signaling pathway .
"
6980,6981,1729.txt,7,0,,,,"Although results from gel shift assays suggest that ArcA-mediated control of ompD expression under oxidative-stress is dependent on ArcA phosphorylation , additional evidence is required to elucidate molecular mechanisms ."
6981,6982,2208.txt,1,0,,,,"Stimulation of CysB protein binding to a cysJIH promoter fragment by N-acetyl-L-serine .
"
6982,6983,2208.txt,2,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .
"
6983,6984,2208.txt,3,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .
"
6984,6985,2208.txt,4,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .
"
6985,6986,2208.txt,5,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .
"
6986,6987,2208.txt,6,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .
"
6987,6988,2208.txt,7,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .
"
6988,6989,2208.txt,8,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .
"
6989,6990,2208.txt,9,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .
"
6990,6991,2208.txt,10,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .
"
6991,6992,2208.txt,11,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .
"
6992,6993,2208.txt,12,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .
"
6993,6994,2208.txt,13,0,,,,"cysJIH expression is upregulated by CysB in response to menadione In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .
"
6994,6995,2208.txt,14,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .
"
6995,6996,2208.txt,15,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in DcysB strains in sulfate medium .
"
6996,6997,2208.txt,16,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .
"
6997,6998,2208.txt,17,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysH genes in wild type in sulfate medium .
"
6998,6999,2208.txt,18,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .
"
6999,7000,2208.txt,19,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in DcysB strains in sulfate medium .
"
7000,7001,2208.txt,20,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .
"
7001,7002,2208.txt,21,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysI genes in wild type in sulfate medium .
"
7002,7003,2208.txt,22,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .
"
7003,7004,2208.txt,23,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in DcysB strains in sulfate medium .
"
7004,7005,2208.txt,24,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .
"
7005,7006,2208.txt,25,0,,,,"cysJIH expression is upregulated by CysB in response to ceftriaxone In order to correlate a possible regulation of cysJIH by CysB in ROS treatment , we evaluated the transcript levels of cysJ genes in wild type in sulfate medium .
"
7006,7007,2208.txt,26,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,CysB-dependent upregulation of the Salmonella Typhimurium cysJIH operon in response to antimicrobial compounds .
7007,7008,1701.txt,1,0,,,,"It contained a part of the pef operon and the srg ( SdiA-regulated gene ) region , including srgA , a homolog of dsbA ( disulfide bond isomerase ) ; srgB ; rck ( resistance to complement killing ) ; and srgC , a homolog of the AraC family of transcriptional regulators .
"
7008,7009,1701.txt,2,0,,,,"The genes , including the pef operon , PSLT026 , PSLT025 , PSLT024 , rsk , repA2 , srg ( srgA and srgB , SdiA-regulated gene ) , rck and srgC , are located in a region of about 11-kb in pSTLT2 ( McClelland et al. , 2001 ) ; however , in pOU1113 , the genes as well as the nucleotide sequences in this region ( 12 255 -- 23 104 bp ) were very different , occupied instead by a unique segment ."
7009,7010,295.txt,1,0,,,,"HilA , regulates the expression of phoH ."
7010,7011,1067.txt,1,0,,,,"One HilD-activated gene product , acts to repress flhDC transcription , providing a feedback loop for the entire fla-gellar-Spi1 regulon .
"
7011,7012,1067.txt,2,0,,,,Posttranscriptional activation of flhDC occurs at the level of the flagellar regulator FliZ via regulation of HilD activity and repression of the antiFlhD4C2 factor YdiV .
7012,7013,1073.txt,1,0,,,,"As the Ipro values of spvR regulatory mutants were lower than those of phoP mutants , we investigated whether the function of these proteins as negative regulators of bacterial intracellular growth was dependent on the PhoP-PhoQ system .
"
7013,7014,1073.txt,2,0,,,,"As the Ipro values of rpoS regulatory mutants were lower than those of phoP mutants , we investigated whether the function of these proteins as negative regulators of bacterial intracellular growth was dependent on the PhoP-PhoQ system .
"
7014,7015,1073.txt,3,0,,,,"As the Ipro values of slyA regulatory mutants were lower than those of phoP mutants , we investigated whether the function of these proteins as negative regulators of bacterial intracellular growth was dependent on the PhoP-PhoQ system ."
7015,7016,281.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"STM2123 _ upregulated expression of CsgD-like AdrA overexpression from a plasmid
"
7016,7017,281.txt,2,0,,,,"On the other hand , STM2123 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a post-transcriptional level .
"
7017,7018,281.txt,3,0,,,,"On the other hand , STM2123 activated rdar morphotype expression by activation of expression of the transcriptional regulator CsgD on a transcriptional level .
"
7018,7019,281.txt,4,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"For curli production in S. enterica , STM2123 activate CsgD , while four Citation Cowles KN , Willis DK , Engel TN , Jones JB , Barak JD .
"
7019,7020,281.txt,5,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"For cellulose production in S. enterica , STM2123 activate CsgD , while four Citation Cowles KN , Willis DK , Engel TN , Jones JB , Barak JD .
"
7020,7021,281.txt,6,0,,,,"For example , although both STM2123 and STM3388 are important for CsgD expression , STM2123 contributes early in in-vitro biofilm formation , while STM3388 is involved later ."
7021,7022,1715.txt,1,0,,,,"The following studies show that PhoPQ regulate hilE expression via the fimZ gene .
"
7022,7023,1715.txt,2,0,,,,"Since the PhoPQ signal processes through fimZ to regulate hilA , we wanted to determine whether PhoPQ regulates fimZ transcription ."
7023,7024,1065.txt,1,0,,,,"Recent studies indicate that HilA binds to specific sequences in the prgH promoters .
"
7024,7025,1065.txt,2,0,,,,"It is known that prgH is under the regulation of HilA .
"
7025,7026,1065.txt,3,0,,,,"Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) ."
7026,7027,297.txt,1,0,,,,RhaS activates the rhaT genes via binding to another inverted repeat of two sites .
7027,7028,1703.txt,1,0,,,,CueR directly stimulates the transcription of cueO .
7028,7029,1717.txt,1,0,,,,"Therefore , entry into stationary-phase does appear to regulate MviA activity , whereas upregulation of rpoS translation alone is responsible for acid shock accumulation .
"
7029,7030,1717.txt,2,0,,,,"MviA Activity Is Not Affected by Acid Shock Induction of ÛS in Nonstressed Cells Is Sufficient to Increase Half-Life The results presented thus far suggest that increases in rpoS expression can lead to increased ÛS half-li without affecting the activity of MviA .
"
7030,7031,1717.txt,3,0,,,,"MviA Activity Is Not Affected by Acid Shock Induction of ÛS in Nonstressed Cells Is Sufficient to Increase Half-Life The results presented thus far suggest that increases in rpoS expression can overwhelm the degradation comple without affecting the activity of MviA .
"
7031,7032,1717.txt,4,0,,,,"Instead , increased rpoS translation produces an imbalance between the limited amount of MviA recognition protein in the cel , thus decreasing ÛS turnover ."
7032,7033,283.txt,1,0,,,,"Interestingly , the genes encoding these proteins , STM4315 ( rtsA ) and STM4314 ( rtsB ) were among the most strongly Fis-activated genes detected in our microarray study ( supplementary data Tables S1 and S2 at http://mic ."
7033,7034,1071.txt,1,0,,,,H-NS-deficient mutants strongly increased RpoS due to enhanced rpoS translation .
7034,7035,1059.txt,1,0,,,,"While the functions of STM2180 are uncharacterized , MetR is known to be involved in the regulation of methionine biosynthesis ."
7035,7036,2236.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site .
7036,7037,2222.txt,1,0,,,,"The ydcI gene encodes a putative transcriptional regulator of the LysR family , while the STM2372 gene is predicted to encode a putative membrane transporter ."
7037,7038,532.txt,1,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , pBT-RcsB pTRG-Gal11P , pBT-LGF2 pTRG-RflM ( EM580 , open triangles ) .
"
7038,7039,532.txt,2,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , pBT-LGF2 pTRG-RflM ( EM580 , open triangles ) .
"
7039,7040,532.txt,3,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , pBT-LGF2 pTRG-RflM ( EM580 , open triangles ) .
"
7040,7041,532.txt,4,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , EM577 , pBT-LGF2 pTRG-RflM ( EM580 , open triangles ) .
"
7041,7042,532.txt,5,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , EM577 , pBT-LGF2 pTRG-RflM ( EM580 , open triangles ) .
"
7042,7043,532.txt,6,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , EM577 , pBT-LGF2 pTRG-RflM ( EM580 , open triangles ) .
"
7043,7044,532.txt,7,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , pBT-RcsB pTRG-Gal11P , EM578 , open circles ( EM580 , open triangles ) .
"
7044,7045,532.txt,8,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , pBT-RcsB pTRG-Gal11P , pBT-RflM pTRG-Gal11P ( EM580 , open triangles ) .
"
7045,7046,532.txt,9,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , EM578 , open circles ( EM580 , open triangles ) .
"
7046,7047,532.txt,10,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , pBT-RflM pTRG-Gal11P ( EM580 , open triangles ) .
"
7047,7048,532.txt,11,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , EM578 , open circles ( EM580 , open triangles ) .
"
7048,7049,532.txt,12,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , pBT-RflM pTRG-Gal11P ( EM580 , open triangles ) .
"
7049,7050,532.txt,13,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , EM577 , EM578 , open circles ( EM580 , open triangles ) .
"
7050,7051,532.txt,14,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , EM577 , pBT-RflM pTRG-Gal11P ( EM580 , open triangles ) .
"
7051,7052,532.txt,15,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , EM577 , EM578 , open circles ( EM580 , open triangles ) .
"
7052,7053,532.txt,16,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , EM577 , pBT-RflM pTRG-Gal11P ( EM580 , open triangles ) .
"
7053,7054,532.txt,17,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , EM577 , EM578 , open circles ( EM580 , open triangles ) .
"
7054,7055,532.txt,18,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , EM577 , pBT-RflM pTRG-Gal11P ( EM580 , open triangles ) .
"
7055,7056,532.txt,19,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , pBT-RcsB pTRG-Gal11P , pBT-LGF2 pTRG-RcsB ( EM580 , open triangles ) .
"
7056,7057,532.txt,20,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , pBT-LGF2 pTRG-RcsB ( EM580 , open triangles ) .
"
7057,7058,532.txt,21,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , pBT-LGF2 pTRG-RcsB ( EM580 , open triangles ) .
"
7058,7059,532.txt,22,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , EM577 , pBT-LGF2 pTRG-RcsB ( EM580 , open triangles ) .
"
7059,7060,532.txt,23,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , EM577 , pBT-LGF2 pTRG-RcsB ( EM580 , open triangles ) .
"
7060,7061,532.txt,24,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , EM577 , pBT-LGF2 pTRG-RcsB ( EM580 , open triangles ) .
"
7061,7062,532.txt,25,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , pBT-RcsB pTRG-Gal11P , EM579 ( EM580 , open triangles ) .
"
7062,7063,532.txt,26,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , EM579 ( EM580 , open triangles ) .
"
7063,7064,532.txt,27,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , pBT-RcsB pTRG-Gal11P , EM579 ( EM580 , open triangles ) .
"
7064,7065,532.txt,28,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM572 , open squares , EM577 , EM579 ( EM580 , open triangles ) .
"
7065,7066,532.txt,29,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for pBT-RcsB pTRG-RflM , pBT-RflM pTRG-RcsB , EM577 , EM579 ( EM580 , open triangles ) .
"
7066,7067,532.txt,30,0,,,,"A. Induction of lacZ transcription by interaction of RcsB-RflM was assessed at different IPTG inducer concentrations for EM575 , pBT-RflM pTRG-RcsB , EM577 , EM579 ( EM580 , open triangles ) ."
7067,7068,254.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , recA null mutants are unable to stimulate the LexA cleavage reaction ."
7068,7069,1918.txt,1,0,,,,"These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C ."
7069,7070,240.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , fumC .
"
7070,7071,240.txt,2,0,,,,"SoxS protein , activates sodA , fumC ."
7071,7072,526.txt,1,0,,,,The SpvR protein is a positive transcriptional regulator of the LysR family and binds to inverted repeat recognition sequences upstream of the spvA promoter .
7072,7073,268.txt,1,0,,,,"Data in Fig. 6 show that entB transcription increased proportionally with the cobalt in the medium , consistent with cobalt competing for the iron-binding site of Fur .
"
7073,7074,268.txt,2,0,,,,"Data in Fig. 6 show that entB transcription increased proportionally with the cobalt in the medium , consistent with iron competing for the iron-binding site of Fur ."
7074,7075,1924.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
7075,7076,1924.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
7076,7077,1930.txt,1,0,,,,"A particularly intriguing antisense RNA is positively regulated by RtsA from a binding site within slrP .
"
7077,7078,1930.txt,2,0,,,,"slrP is bound by RtsA
"
7078,7079,1930.txt,3,0,,,,"that an additional level of regulation by RtsA occurs via the antisense RNA within the slrP gene
"
7079,7080,1930.txt,4,0,,,,"that the previously observed regulation of slrP by RtsA occurs indirectly , via SprB"
7080,7081,2008.txt,1,1,Escherichia coli;Escherichia coli,E. coli;E. coli,Escherichia coli,"In E. coli , it was questioned whether csrC was directly regulated by UvrY because the amount of LacZ was only two-fold higher whe using S-30 extracts of wild-type E. coli compared to extracts from a uvrY mutant ."
7081,7082,1501.txt,1,0,,,,"FlhD4C2 , via the flagella regulon members FliA and FliZ positively regulates expression of the type III secretion system through hilA ."
7082,7083,1267.txt,1,0,,,,"Interestingly , the results indicate that H-NS is a positive regulator of tpx ; one possibility is that in an hns mutant the levels of LeuO increase since leuO is repressed by H-NS ."
7083,7084,1273.txt,1,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
7084,7085,1515.txt,1,0,,,,"Based on the rpoS transcription in the nuoG mutant the authors propose that the decrease in the NADH serves as a signal for increased rpoS transcription , while active respiration controlled by ArcA downregulates rpoS transcription .
"
7085,7086,1515.txt,2,0,,,,"Based on the rpoS transcription in the nuoG mutant the authors propose that the decrease in NAD ratio serves as a signal for increased rpoS transcription , while active respiration controlled by ArcA downregulates rpoS transcription .
"
7086,7087,1515.txt,3,0,,,,"This means that controlled by ArcA is possible , rpoS transcription is decreased ."
7087,7088,2034.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"E. coli strains were shown to express higher levels of flagellum genes and increased motility , possibly due to the inhibition of flhDC promoters by DksA .
"
7088,7089,2034.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"E. coli strains were shown to express higher levels of che-motaxis genes and increased motility , possibly due to the inhibition of flhDC promoters by DksA ."
7089,7090,917.txt,1,2,Salmonella;Escherichia coli;Salmonella,Salmonella;E. coli;Salmonella,Escherichia coli;Salmonella,"Like the D-Ala , the phosphatases of Salmonella are regulated differently : the E. coli phoA gene is transcriptionally induced under phosphate-starvation conditions by the PhoB-PhoR regulatory system , whereas the Salmonella phoN is transcriptionally regulated by the PhoP-PhoQ system .
"
7090,7091,917.txt,2,2,Escherichia coli;Escherichia coli;Salmonella,E. coli;E. coli;Salmonella,Escherichia coli;Salmonella,"Like the D-Ala , the phosphatases of E. coli are regulated differently : the E. coli phoA gene is transcriptionally induced under phosphate-starvation conditions by the PhoB-PhoR regulatory system , whereas the Salmonella phoN is transcriptionally regulated by the PhoP-PhoQ system .
"
7091,7092,917.txt,3,2,Salmonella;Escherichia coli;Salmonella,Salmonella;E. coli;Salmonella,Escherichia coli;Salmonella,"Like D-Ala dipeptidases , the phosphatases of Salmonella are regulated differently : the E. coli phoA gene is transcriptionally induced under phosphate-starvation conditions by the PhoB-PhoR regulatory system , whereas the Salmonella phoN is transcriptionally regulated by the PhoP-PhoQ system .
"
7092,7093,917.txt,4,2,Escherichia coli;Escherichia coli;Salmonella,E. coli;E. coli;Salmonella,Escherichia coli;Salmonella,"Like D-Ala dipeptidases , the phosphatases of E. coli are regulated differently : the E. coli phoA gene is transcriptionally induced under phosphate-starvation conditions by the PhoB-PhoR regulatory system , whereas the Salmonella phoN is transcriptionally regulated by the PhoP-PhoQ system ."
7093,7094,903.txt,1,0,,,,the deletion of fliZ _ encoding a strong positive regulator of HilD
7094,7095,2020.txt,1,0,,,,Deletion of either hilC in this experiment did not block regulation by either Fur .
7095,7096,1529.txt,1,1,Escherichia coli,E. coli,Escherichia coli,The aldB gene was repressed by Fis in agreement with previous data from E. coli .
7096,7097,730.txt,1,0,,,,"These data suggest that ftnB are negatively regulated by Fur in Fe-rich-medium .
"
7097,7098,730.txt,2,0,,,,"hence are expressed under iron-replete conditions consistent with iron storage/detoxification roles , while both ftnB are negatively regulated by Fur"
7098,7099,724.txt,1,0,,,,"As the Ipro values of spvR regulatory mutants were lower than those of phoQ mutants , we investigated whether the function of these proteins as negative regulators of bacterial intracellular growth was dependent on the PhoP-PhoQ system .
"
7099,7100,724.txt,2,0,,,,"As the Ipro values of rpoS regulatory mutants were lower than those of phoQ mutants , we investigated whether the function of these proteins as negative regulators of bacterial intracellular growth was dependent on the PhoP-PhoQ system .
"
7100,7101,724.txt,3,0,,,,"As the Ipro values of slyA regulatory mutants were lower than those of phoQ mutants , we investigated whether the function of these proteins as negative regulators of bacterial intracellular growth was dependent on the PhoP-PhoQ system ."
7101,7102,1298.txt,1,0,,,,"It has been assumed that there is a direct correlation between hilA transcription , production of the HilA protein and HilA-activated gene expression .
"
7102,7103,1298.txt,2,0,,,,"These results suggest that repression of hilA transcription by oxygen leads to a decrease in HilA protein production , which in turn reduces the expression of HilA-activated genes , such as prgH .
"
7103,7104,1298.txt,3,0,,,,"These data demonstrated that the expression of the SPI-1 activator , hilA , as well as of the HilA-activated genes invF and sipC , was transcriptionally repressed by growth at 42 °C ."
7104,7105,718.txt,1,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Falkow , S. OmpR regulates the two-component system ssrA ± ssrB in Salmo-nella pathogenicity island 2 .
"
7105,7106,718.txt,2,5,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella,Salmo;Salmo;Salmo;Salmo;Salmo-nella,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris,"Lee , A.K. , Detweiler , C.S. , , S. OmpR regulates the two-component system ssrA ± ssrB in Salmo-nella pathogenicity island 2 .
"
7106,7107,718.txt,3,0,,,,"OmpR binds directly to the promoter of ssrA .
"
7107,7108,718.txt,4,0,,,,"Phosphorylation of OmpR has a large effect on DNA binding at ssrA
"
7108,7109,718.txt,5,0,,,,"Phosphorylation of OmpR stimulates DNA binding to ssrA We next measured equilibrium binding of OmpR-P to the ssrA-1 binding site .
"
7109,7110,718.txt,6,0,,,,"Phosphorylation of OmpR stimulates DNA binding to ssrA We next measured equilibrium binding of OmpR to the ssrA-1 binding site .
"
7110,7111,718.txt,7,0,,,,"OmpR did not examine the effect of OmpR phosphorylation on DNA binding at ssrA
"
7111,7112,718.txt,8,0,,,,"that OmpR binds directly to the ssrA to affect their expression
"
7112,7113,718.txt,9,0,,,,"Previous results from gene fusions suggest that regulation of ssrA by OmpR is distinct .
"
7113,7114,718.txt,10,0,,,,"Previous results from gene fusions suggest that regulation of ssrA by OmpR is uncoupled .
"
7114,7115,718.txt,11,1,synthetic construct,primer,synthetic construct,"Previous results from primer-extension analysis suggest that regulation of ssrA by OmpR is distinct .
"
7115,7116,718.txt,12,1,synthetic construct,primer,synthetic construct,"Previous results from primer-extension analysis suggest that regulation of ssrA by OmpR is uncoupled .
"
7116,7117,718.txt,13,0,,,,"Other examples of genes include ssrA known regulators of SPI-2 previously reported to be influenced by OmpR Figure 7 .
"
7117,7118,718.txt,14,0,,,,"Other examples of genes include ssrA known regulators of SPI-2 previously reported to be influenced by OmpR Figure 7 .
"
7118,7119,718.txt,15,1,Salmonella,Salmonella,Salmonella,"previous work in Salmonella has shown that phosphorylated OmpR can bind to either sensor kinase gene ssrA within SPI-2
"
7119,7120,718.txt,16,0,,,,"In low-osmolarity conditions , OmpR and/or OmpR-P -LRB- phosphorylayted OmpR present in low levels -RRB- can bind to the upstream regions of ssrA genes .
"
7120,7121,718.txt,17,0,,,,"Under low osmolality , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .
"
7121,7122,718.txt,18,0,,,,"Under acidic pH , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .
"
7122,7123,718.txt,19,0,,,,"The global regulator OmpR regulates positively SsrAB directly by binding to the ssrA promoter .
"
7123,7124,718.txt,20,0,,,,"The global regulator OmpR regulates positively SsrAB directly by binding to the ssrA promoter .
"
7124,7125,718.txt,21,0,,,,"For example , OmpR promotes SPI-2 expression by directly binding to both the ssrA ."
7125,7126,1475.txt,1,0,,,,"Furthermore , STM1330 are regulated by the master regulators of the SsrB regulon .
"
7126,7127,1475.txt,2,0,,,,"Furthermore , STM1330 are regulated by the master regulators of the SsrB regulon ."
7127,7128,1313.txt,1,0,,,,"Because inactivation of the lsrR gene results in high-level expression of the lsr operon in a luxS null background , these results strongly suggest that the wild-type function of LsrR is to repress the expression of the lsr operon in the absence of AI-2 ."
7128,7129,687.txt,1,0,,,,The biofilm master regulatory gene csgD is repressed upon RcsB phosphorylation .
7129,7130,693.txt,1,0,,,,"Of these genes , a master regulator of the flagellar operon , tsr are known to bind CRP .
"
7130,7131,693.txt,2,0,,,,"Of these genes , flhD , tsr are known to bind CRP .
"
7131,7132,693.txt,3,0,,,,"Of these genes , a master regulator of the flagellar operon , tsr are predicted to have CRP ."
7132,7133,1307.txt,1,1,Escherichia coli,E. coli,Escherichia coli,In E. coli uspA has been shown to be regulated by FadR .
7133,7134,1461.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7134,7135,1461.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7135,7136,1461.txt,3,0,,,,"Regulation of flagellar synthesis and chemotaxis by CsrA In E. chemotaxis/aerotaxis are co-ordinately regulated by flhDC Table 1 .
"
7136,7137,1461.txt,4,0,,,,"Regulation of flagellar synthesis and chemotaxis by CsrA In E. chemotaxis/aerotaxis are co-ordinately regulated by flhDC Table 1 .
"
7137,7138,1461.txt,5,0,,,,"Regulation of flagellar synthesis and chemotaxis by CsrA In E. flagellar biosynthesis are co-ordinately regulated by flhDC Table 1 .
"
7138,7139,1461.txt,6,0,,,,"Regulation of flagellar synthesis and chemotaxis by CsrA In E. flagellar biosynthesis are co-ordinately regulated by flhDC Table 1 .
"
7139,7140,1461.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"Regulation of flagellar synthesis and chemotaxis by CsrA In E. coli are co-ordinately regulated by flhDC Table 1 .
"
7140,7141,1461.txt,8,1,Escherichia coli,E. coli,Escherichia coli,"Regulation of flagellar synthesis and chemotaxis by CsrA In E. coli are co-ordinately regulated by flhDC Table 1 .
"
7141,7142,1461.txt,9,1,Salmonella,Salmonella,Salmonella,"Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella chemotaxis/aerotaxis are co-ordinately regulated by flhDC Table 1 .
"
7142,7143,1461.txt,10,1,Salmonella,Salmonella,Salmonella,"Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella chemotaxis/aerotaxis are co-ordinately regulated by flhDC Table 1 .
"
7143,7144,1461.txt,11,1,Salmonella,Salmonella,Salmonella,"Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella flagellar biosynthesis are co-ordinately regulated by flhDC Table 1 .
"
7144,7145,1461.txt,12,1,Salmonella,Salmonella,Salmonella,"Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella flagellar biosynthesis are co-ordinately regulated by flhDC Table 1 .
"
7145,7146,1461.txt,13,1,Salmonella,Salmonella,Salmonella,"Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella coli are co-ordinately regulated by flhDC Table 1 .
"
7146,7147,1461.txt,14,1,Salmonella,Salmonella,Salmonella,"Regulation of flagellar synthesis and chemotaxis by CsrA In Salmonella coli are co-ordinately regulated by flhDC Table 1 .
"
7147,7148,1461.txt,15,1,Escherichia coli,E. coli,Escherichia coli,"flhDC _ known in E. coli to be controlled by CsrA
"
7148,7149,1461.txt,16,1,Escherichia coli,Escherichia coli,Escherichia coli,"Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7149,7150,1461.txt,17,1,Escherichia coli,Escherichia coli,Escherichia coli,"Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7150,7151,1461.txt,18,1,Escherichia coli,Escherichia coli,Escherichia coli,"Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7151,7152,1461.txt,19,1,Escherichia coli,Escherichia coli,Escherichia coli,"Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7152,7153,1461.txt,20,1,Escherichia coli,Escherichia coli,Escherichia coli,"Wei , B.L. , Brun-Zinkernagel , A.M. , Simecka , J.W. , Pruss , B.M. , Babitzke , P. , Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7153,7154,1461.txt,21,1,Escherichia coli,Escherichia coli,Escherichia coli,"Wei , B.L. ; Brun-Zinkernagel , A.M. ; Simecka , J.W. ; Pruss , B.M. ; Babitzke , P. ; Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7154,7155,1461.txt,22,1,Escherichia coli,Escherichia coli,Escherichia coli,"Nat Rev Microbiol 7 : 765 -- 774 Wei BL , Brun-Zinkernagel AM , Simecka JW , Pruss BM , Babitzke P , Romeo T Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7155,7156,1461.txt,23,0,,,,"CsrA is a positive regulator of flhDC mRNA stability
"
7156,7157,1461.txt,24,1,Escherichia coli,Escherichia coli,Escherichia coli,"Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7157,7158,1461.txt,25,1,Escherichia coli,Escherichia coli,Escherichia coli,"Wei BL , Brun-Zinkernagel AM , Simecka JW , Prüss BM , Babitzke P , Romeo T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7158,7159,1461.txt,26,1,Escherichia coli,Escherichia coli,Escherichia coli,"J Mol Biol 355:798 -- 808 Epub 2005 Nov 2022 Wei BL , Brun-Zinkernagel AM , Simecka JW , Pruss BM , Babitzke P , Romeo T Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7159,7160,1461.txt,27,1,Escherichia coli,Escherichia coli,Escherichia coli,"Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7160,7161,1461.txt,28,1,Escherichia coli,Escherichia coli,Escherichia coli,"Romeo , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7161,7162,1461.txt,29,1,Escherichia coli,Escherichia coli,Escherichia coli,"P. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7162,7163,1461.txt,30,1,Escherichia coli,Escherichia coli,Escherichia coli,"Babitzke , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7163,7164,1461.txt,31,1,Escherichia coli,Escherichia coli,Escherichia coli,"B.M. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7164,7165,1461.txt,32,1,Escherichia coli,Escherichia coli,Escherichia coli,"Pruss , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7165,7166,1461.txt,33,1,Escherichia coli,Escherichia coli,Escherichia coli,"J.W. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7166,7167,1461.txt,34,1,Escherichia coli,Escherichia coli,Escherichia coli,"Simecka , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7167,7168,1461.txt,35,1,Escherichia coli,Escherichia coli,Escherichia coli,"A.M. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7168,7169,1461.txt,36,1,Escherichia coli,Escherichia coli,Escherichia coli,"Brun-Zinkernagel , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7169,7170,1461.txt,37,1,Escherichia coli,Escherichia coli,Escherichia coli,"B.L. , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7170,7171,1461.txt,38,1,Escherichia coli,Escherichia coli,Escherichia coli,"Wei , T. Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
"
7171,7172,1461.txt,39,0,,,,"This is in line with the fact that the flhDC operon is controlled by CsrA in soft rot .
"
7172,7173,1461.txt,40,1,Escherichia coli,Escherichia coli,Escherichia coli,Positive regulation of flhDC expression by the RNA-binding protein CsrA of Escherichia coli .
7173,7174,2168.txt,1,0,,,,"On the other hand , the FimY-FimZ complex might also bind the fimY promoters to regulate these genes ."
7174,7175,1449.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"While H-NS usually acts as a negative regulator of gene expression , hlyE is not the only example of a CRP-regulated gene whose expression is positively regulated by H-NS ; for example , expression of both the malT and csiD genes in E. coli is stimulated by H-NS ( 8 , 14 ) ."
7175,7176,2140.txt,1,0,,,,"The methylation at the Cys-69 residue converts the Ada protein into an efficient transcriptional activator of its own gene and other ( alkB , alkA , genes and aidB ) ( 15 , 30 , 32 , 52 , 55 , 60 , 61 ) ."
7176,7177,23.txt,1,0,,,,"MarR inhibits binding of MarR to the marRAB promoter
"
7177,7178,23.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Alekshun M.N. , Levy S.B. Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in-vitro .
"
7178,7179,23.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Alteration of the repressor activity of MarR , the negative regulator of the Escherichia coli marRAB locus , by multiple chemicals in-vitro .
"
7179,7180,863.txt,1,0,,,,"a LysR-like transcription activator positively regulates both its own gene and the spvABCD operon of structural genes
"
7180,7181,863.txt,2,0,,,,a LysR-like transcription activator positively regulates both its own gene and the spvABCD operon of structural genes
7181,7182,37.txt,1,0,,,,DksA appears to positively regulate the expression of rpoS at the level of translation .
7182,7183,877.txt,1,0,,,,The same behavior has been described for other ArcA-controlled promoters in 6 Time : 14:6 # lpxO Expression Is Regulated by ArcA in Response to Oxygen Availability FIGURE 2 Main lipid-A species .
7183,7184,2154.txt,1,0,,,,"Global transcriptomic analysis of an yfeR mutant To further search for additional YfeR-regulated genes we performed a transcriptomic analysis in LB at low-osmolarity , which are the conditions rendering higher yfeR expression levels .
"
7184,7185,2154.txt,2,0,,,,"Global transcriptomic analysis of an yfeR mutant To further search for additional YfeR-regulated genes we performed a transcriptomic analysis in LB at low-osmolarity , which are the conditions rendering higher yfeR expression levels .
"
7185,7186,2154.txt,3,0,,,,"0 M NaCl 0.5 M NaCl 15 10 Determination of binding of YfeR protein to the yfeR-yfeH intergenic region 5 0 A common property of members of the LysR family is that they regulate the adjacent gene , located in inverted orientation ."
7186,7187,122.txt,1,2,Salmonella;Salmonella;Escherichia coli,S. enterica;enterica;E. coli,Escherichia coli;Salmonella,"B rpoS clpP/pBAD24Ap-UTR-rpoS JF4911 JF4919 JF4920 JF4921 JF4922 UTR +1 -- 566 UTR +1 -- 51 UTR +1 -- 324 UTR +1 -- 433 UTR +1 -- 464 pH 7.7 4.5 7.7 4.5 7.7 4.5 7.7 4.5 7.7 4.5 RpoS 52 -- 324 325 -- 432 433 -- 463 464 -- 566 ABCT BCT CT T clpP : : Tn10 JF4471 dksA : : Mud JF4914 hfq : Does Not Actively Stabilize Û In S. enterica and E. coli , ÛS proteolysis is regulated by ( RssB/Sp .
"
7187,7188,122.txt,2,2,Salmonella;Salmonella;Escherichia coli,S. enterica;enterica;E. coli,Escherichia coli;Salmonella,"B rpoS clpP/pBAD24Ap-UTR-rpoS JF4911 JF4919 JF4920 JF4921 JF4922 UTR +1 -- 566 UTR +1 -- 51 UTR +1 -- 324 UTR +1 -- 433 UTR +1 -- 464 pH 7.7 4.5 7.7 4.5 7.7 4.5 7.7 4.5 7.7 4.5 RpoS 52 -- 324 325 -- 432 433 -- 463 464 -- 566 ABCT BCT CT T clpP : : Tn10 JF4471 dksA : : Mud JF4914 hfq : Does Not Actively Stabilize Û In S. enterica and E. coli , ÛS proteolysis is regulated by y the two-component response regulator Mv .
"
7188,7189,122.txt,3,0,,,,"Expression of ArcZ in the hfq mutant restored RpoS : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : + 45 ; cmr curli fimbriae is also downregulated in -LRB- data not sh .
"
7189,7190,122.txt,4,0,,,,"Expression of ArcZ in the hfq mutant restored RpoS : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : + 45 ; cmr curli fimbriae is also downregulated in in the arcZ mut .
"
7190,7191,122.txt,5,0,,,,"Expression of ArcZ in the hfq mutant restored RpoS : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : : Lsc ; cmr curli fimbriae is also downregulated in -LRB- data not sh .
"
7191,7192,122.txt,6,0,,,,"Expression of ArcZ in the hfq mutant restored RpoS : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : : Lsc ; cmr curli fimbriae is also downregulated in in the arcZ mut ."
7192,7193,644.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Fis is required for full induction of chromosomal S. typhimurium hilA : : Tn5lacZY expression .
"
7193,7194,644.txt,2,0,,,,"Using a genetic approach , Fis was shown to be necessary for the induction of hilA expression , genes .
"
7194,7195,644.txt,3,0,,,,"Fis is involved in SPI expression Positive regulation of SPI-1 genes by Fis was expected considering the fact that hilA , is upregulated by Fis .
"
7195,7196,644.txt,4,0,,,,"Expression of hilA is increased by the Factor for Inversion Stimulation , Fis ."
7196,7197,888.txt,1,0,,,,conditions under which either ssrA was repressed by OmpR
7197,7198,650.txt,1,1,unidentified,not shown,unidentified,"The katE promoter , was hardly repressed by H-NS and was insensitive to YncC , in agreement with in-vivo data -LRB- not shown -RRB- ."
7198,7199,136.txt,1,0,,,,"Almiron et al. reported that expression of the dps gene is induced by the cessation of bacterial growth under S control of RpoS .
"
7199,7200,136.txt,2,0,,,,"Then , in the transition to stationary-phase growth , RpoS , contribute to increase dps transcription to up to 200 000 molecules per cell ."
7200,7201,2183.txt,1,0,,,,"To demonstrate the interaction of CRP with gat promoters by EMSA , CRP-His6 was added in increasing concentrations to the 300-bp fragments located upstream of gatR ."
7201,7202,678.txt,1,0,,,,"OmpR , in response to a drop in pH , induces the expression of ssrA ± ssr .
"
7202,7203,678.txt,2,0,,,,"The OmpR-dependent stimulation of ssrA -- lacZ requires the sensor kinase EnvZ , as the activity of an envZ deletion strain is similar to that of the ompR deletion strain .
"
7203,7204,678.txt,3,0,,,,"OmpR appears to function as an activator of ssrA , as reported previously
"
7204,7205,678.txt,4,0,,,,"L. J. Kenney Fig. 2 suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .
"
7205,7206,678.txt,5,0,,,,"R. Oropeza suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .
"
7206,7207,678.txt,6,0,,,,"1134 X. Feng suggest that OmpR activates ssrA and , to a lesser extent , SsrB also activates ssrA , whereas both OmpR and SsrB have a significant effect on ssrB .
"
7207,7208,678.txt,7,0,,,,"How does OmpR activate expression of ssrA ?
"
7208,7209,678.txt,8,0,,,,"Under low osmolality , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn .
"
7209,7210,678.txt,9,0,,,,"Under acidic pH , the ssrA genes are transcriptionally activated by the binding of OmpR ~ P to their promoters whose levels are in turn ."
7210,7211,2197.txt,1,0,,,,"The regulator of aromatic amino-acid metabolism , TyrR , controls the tyrosine requirement for aniC expression ."
7211,7212,485.txt,1,0,,,,"Taken together , these results show that CpxR represses the autoregulation of sseB located in SPI-2 ."
7212,7213,1111.txt,1,0,,,,"Results Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by ¯ iA * mutan .
"
7213,7214,1111.txt,2,0,,,,"Results Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by ¯ iA * mutan .
"
7214,7215,1111.txt,3,0,,,,"Results Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by Flg .
"
7215,7216,1111.txt,4,0,,,,"Results Isolation of fliA * mutants resistant to inhibition by FlgM Models for negative regulation of s28 by FlgM predict a direct , potentially multipartite , interaction between the two proteins .39,40 To identify amino-acid-residues of s28 , we carried out a selection for ¯ iA mutants defective for negative regulation by Flg .
"
7216,7217,1111.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,Isolation of fliA * mutants Spontaneous mutants defective for negative regulation by FlgM were isolated by selecting for expression of s28-dependent promoters in various S. typhimurium mutant strains defective for FlgM export .
7217,7218,1677.txt,1,0,,,,"FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgH by introduction of a null mutation in J. Bacteriol .
"
7218,7219,1677.txt,2,0,,,,"FlgM inhibition of s28-dependent class 3 flagellar gene transcription was relieved in flgH by introduction of a null mutation in the flk gene ( J. E. Karlinsey et al. .
"
7219,7220,1677.txt,3,0,,,,"Like all genes , mutations in any of flgH result in FlgM-dependent inhibition of s28 activity ."
7220,7221,1663.txt,1,1,Salmonella,Salmonellae,Salmonella,"siiE , were induced much more than two-fold in the RpoS-mutant than in the wild type Salmonellae ."
7221,7222,1105.txt,1,0,,,,"Initially , it was proposed as a putative effector because the gene srfJ is positively regulated by SsrB ."
7222,7223,491.txt,1,0,,,,"Altogether , these results indicated that lack of AsmA does not increase acrAB transcription and suggested that bile resistance mediated by asmA mutations may involve MarRAB-regulated genes other than acrAB ."
7223,7224,1893.txt,1,0,,,,"those bacteria in which SdiA becomes activated stay in the Peyer 
"
7224,7225,1893.txt,2,0,,,,those bacteria in which SdiA becomes activated stay in the sdiA bacteria
7225,7226,1887.txt,1,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
7226,7227,1139.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium;S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"wild-type strains of S. typhimurium were indistinguishable , as were inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype"
7227,7228,446.txt,1,0,,,,narK -LRB- are positively regulated by SlyA
7228,7229,320.txt,1,0,,,,Antagonistic involvement of FIS proteins in the transcriptional control of hns expression .
7229,7230,1878.txt,1,0,,,,"These data suggest that FadD act independently to control hilA expression .
"
7230,7231,1878.txt,2,0,,,,"In line with these observations , Lucas et al. 66 have shown that FadD is a positive regulator of the hilA expression ."
7231,7232,334.txt,1,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of prgK remains unaffected .
"
7232,7233,334.txt,2,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of prgK remains unaffected .
"
7233,7234,334.txt,3,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgK remains unaffected ."
7234,7235,452.txt,1,0,,,,"Although full resist-ance to polymyxin B requires pmrA , these genes appear to be differentially regulated by PhoP in that transcription of Fig. 1A
"
7235,7236,452.txt,2,0,,,,"Although full resist-ance to polymyxin B requires pmrA , these genes appear to be differentially regulated by PhoP in that transcription of the former
"
7236,7237,452.txt,3,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance .
"
7237,7238,452.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .
"
7238,7239,452.txt,5,1,Salmonella,Salmonella,Salmonella,"A phoP mutant is > 20 times more polymyxin B sensitive than a pmrA mutant when bacteria are grown in low Mg2 + and > 20 times more sensitive than wild-type Salmonella when bacteria are grown in the presence of Fe3 + ( Wosten et al. , 2000 ) , indicating that a PhoP-regulated PmrA-independent gene ( s ) participate ( s ) in polymyxin B resistance .
"
7239,7240,452.txt,6,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , several known PhoP-regulated genes including mgtA , mgtC , pmrA and pagC were selected to evaluate the role of Pat in the regulation of PhoP activity .
"
7240,7241,452.txt,7,0,,,,"To determine whether acetylation affects the activity of PhoP as a transcription factor , pmrA were selected to evaluate the role of Pat in the regulation of PhoP activity ."
7241,7242,1850.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .
"
7242,7243,1850.txt,2,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .
"
7243,7244,1850.txt,3,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .
"
7244,7245,1850.txt,4,1,Salmonella,Salmonella,Salmonella,"a global gene regulator controls genes in Salmonella , among which fimZ was shown to be activated by Lrp
"
7245,7246,1850.txt,5,1,Salmonella,Salmonella,Salmonella,"a global gene regulator controls a variety in Salmonella , among which fimZ was shown to be activated by Lrp
"
7246,7247,1850.txt,6,1,Salmonella,Salmonella,Salmonella,"a global gene regulator controls genes in Salmonella , among which fimZ was shown to be activated by Lrp
"
7247,7248,1850.txt,7,1,Salmonella,Salmonella,Salmonella,"a global gene regulator controls a variety in Salmonella , among which fimZ was shown to be activated by Lrp
"
7248,7249,1850.txt,8,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lrp , activates transcription of the fim operon in Salmonella enterica serovar Typhimurium via the fimZ regulatory gene .
"
7249,7250,1850.txt,9,0,,,,"Among them , fimZ are shown to be activated by Lrp .
"
7250,7251,1850.txt,10,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Lrp , activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene ."
7251,7252,1688.txt,1,0,,,,"LeuO positively regulated the ompS1 expression by derepressing both promoters and antagonizing the negative effect of StpA , displacing them from the 5 ′ regulatory region .
"
7252,7253,1688.txt,2,0,,,,"LeuO positively regulated the ompS1 expression by derepressing both promoters and antagonizing the negative effect of H-NS , displacing them from the 5 ′ regulatory region .
"
7253,7254,1688.txt,3,0,,,,"Interestingly , the pRO310 ompS1 was also positively regulated by LeuO .
"
7254,7255,1688.txt,4,0,,,,"The highest level of ompS1 expression was obtained when LeuO was induced at 100 mM IPTG .
"
7255,7256,1688.txt,5,0,,,,"LeuO acted as a derepressor , displacing H-NS from the ompS1 regulatory region The highest level of ompS1 expression was attained either upon induction of LeuO in the wild type or else in an hns stpA background .
"
7256,7257,1688.txt,6,0,,,,"Thus , whereas the induction of ompS2 expression by LeuO is from a sole OmpR-dependent promoter , the induction of ompS1 can occur independent of OmpR .
"
7257,7258,1688.txt,7,0,,,,"the transcriptional results showed that LeuO positively induced ompS1 at different points of the growth curve
"
7258,7259,1688.txt,8,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Calva E LeuO positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Calva E Negative osmoregulation of the Salmonella ompS1 porin independently of OmpR in an hns background .
"
7259,7260,1688.txt,9,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella,Salmonella;Salmonella enterica;enterica;Typhi;Salmonella,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Fernandez-Mora M , Puente JL LeuO positively regulate the Salmonella enterica serovar Typhi Flores-Valdez MA , Puente JL Negative osmoregulation of the Salmonella ompS1 porin independently of OmpR in an hns background .
"
7260,7261,1688.txt,10,0,,,,"LeuO positively regulates the ompS1 expression by derepressing both the promoters .
"
7261,7262,1688.txt,11,0,,,,"LeuO positively regulates the ompS1 expression by antagonizing the negative effect of StpA .
"
7262,7263,1688.txt,12,0,,,,"LeuO positively regulates the ompS1 expression by antagonizing the negative effect of H-NS .
"
7263,7264,1688.txt,13,0,,,,"Previously , we demonstrated that a TATgTcATAT region located at positions 125 to 134 with respect to the transcriptional start site was necessary for the LeuO induction of the ompS1 gene .
"
7264,7265,1688.txt,14,0,,,,"LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 , consistent with LeuO .
"
7265,7266,1688.txt,15,0,,,,"LeuO is known to induce ompS2 expression at a lower concentration than required for the induction of ompS1 , consistent with LeuO .
"
7266,7267,1688.txt,16,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhi,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In Salmonella enterica serovar Typhi , LeuO activates the expression of ompS1 ."
7267,7268,1844.txt,1,0,,,,"It is interesting to note that several regulators of HilA , were found in significantly lower levels in the dam mutant ."
7268,7269,308.txt,1,0,,,,"The PhoP Proteins Bind to the ugtL Promoter -- We conducted gel shift assays .
"
7269,7270,308.txt,2,0,,,,The PhoP Proteins Bind to the ugtL Promoter -- We conducted a 536-bp DNA fragment .
7270,7271,309.txt,1,0,,,,"glpF , are activated by CRP-cAMP in Table S1 .
"
7271,7272,309.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"glpF , are activated by CRP-cAMP in E. coli ."
7272,7273,1845.txt,1,1,Salmonella,Salmonella,Salmonella,"ZupT determines changes in intracellular zinc concentration of Lack Previous studies have shown that zinT are coregulated by Zur and that ZinT accumulation is strongly induced by EDTA and repressed by zinc .23 The addition of 0.5 μM ZnSO4 to the culture medium causes the complete abrogation of ZinT accumulation in a wild type Salmonella strai
"
7273,7274,1845.txt,2,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"As zinT expression is under the direct control of Zur , the main transcriptional regulator strongly support the hypothesis that the absence of zupT further reduces the ability of Salmonella enterica to import zinc from the environment ."
7274,7275,1689.txt,1,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , acnA .
"
7275,7276,1689.txt,2,0,,,,"SoxS protein , activates sodA , acnA ."
7276,7277,1851.txt,1,2,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,Genetic evidence has implicated HU in the control of SPI-1 virulence gene expression while IHF has been shown to bind to the promoter region of the spvR regulatory virulence gene on the 96-kb plasmid of S. Typhimurium where it has a positive effect in stationary-phase .
7277,7278,335.txt,1,0,,,,"These results , together with the results of the induction of marA by salicylate in the lack of the induction of acrAB by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
7278,7279,335.txt,2,0,,,,"These results , together with the results of the induction of marA by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate .
"
7279,7280,335.txt,3,0,,,,"These results , together with the results of the induction of marA by salicylate in broth at 378C by salicylate in the DmarA mutant strongly support the hypothesis that the salicylate-dependent increase in tolerance to ciprofloxacin in broth at 378C is mediated by the induction of MarA by salicylate ."
7280,7281,1879.txt,1,1,unidentified,unknown,unidentified,"Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .
"
7281,7282,1879.txt,2,1,unidentified,unknown,unidentified,"Two of these loci , STM4118 , hereafter called cptA , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .
"
7282,7283,1879.txt,3,1,unidentified,unknown,unidentified,"Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .
"
7283,7284,1879.txt,4,1,unidentified,unknown,unidentified,"Two of these loci , yijP , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .
"
7284,7285,1879.txt,5,1,unidentified,unknown,unidentified,"Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .
"
7285,7286,1879.txt,6,1,unidentified,unknown,unidentified,"Two of these loci , pmrC , have been previously shown to be regulated by PmrA , while the role of PmrA-PmrB in the regulation of STM3635 was unknown .
"
7286,7287,1879.txt,7,0,,,,This analysis demonstrated that neither STM3635 was regulated by PmrA .
7287,7288,453.txt,1,0,,,,"Expression of assT was induced in an hns mutant , consistent with the notion that H-NS represses these genes ; transcriptional activity was lower for STY1978 in an hns background , suggesting that this global regulatory protein has a positive effect .
"
7288,7289,453.txt,2,0,,,,"The transcriptional profile was consistent with the hypothesis that H-NS represses the expression of assT , .
"
7289,7290,453.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhi,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"The results of our experiments concur with the concept that H-NS represses the expression of assT in Salmonella serovar Typhi .
"
7290,7291,453.txt,4,6,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmo;Salmo;Salmo;Salmo;Salmo-nella;Typhimurium,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris;Salmonella enterica subsp. enterica serovar Typhimurium,"Previous studies also showed that assT are repressed by H-NS in Salmo-nella serovar Typhimurium .
"
7291,7292,453.txt,5,0,,,,"The H-NS nucleoid protein repressed the expression of the assT transcriptional units .
"
7292,7293,453.txt,6,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Since previous reports have shown that H-NS negatively regulates assT transcription in S. Typhi IMSS-1 , the assT transcriptional-fusions were analyzed in an hns background , in N-minimal-medium .
"
7293,7294,453.txt,7,0,,,,"In contrast , low levels of assT expression were detected in the absence of P2 , in a STYhns99 strain , suggesting that the upstream PLeuO promoter activity is also repressed by the H-NS global regulator in N-minimal-medium .
"
7294,7295,453.txt,8,0,,,,"In contrast , low levels of assT expression were detected in the absence of P1 , in a STYhns99 strain , suggesting that the upstream PLeuO promoter activity is also repressed by the H-NS global regulator in N-minimal-medium ."
7295,7296,447.txt,1,0,,,,ygeA are positively regulated by AraC due to partial read-through of Rho-independent terminators .
7296,7297,321.txt,1,0,,,,"Regulation of yfeH expression The location of yfeH divergently transcribed makes yfeH a likely candidate to be regulated by YfeR .
"
7297,7298,321.txt,2,0,,,,"Regulation of yfeH expression The location of yfeH divergently transcribed makes yfeH a likely candidate to be regulated by YfeR .
"
7298,7299,321.txt,3,0,,,,"Regulation of yfeH expression The location of yfeH adjacent to yfeR makes yfeH a likely candidate to be regulated by YfeR .
"
7299,7300,321.txt,4,0,,,,Regulation of yfeH expression The location of yfeH adjacent to yfeR makes yfeH a likely candidate to be regulated by YfeR .
7300,7301,1886.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , expression of ygbA is repressed by the oxygen sensitive regulator Fnr ."
7301,7302,1138.txt,1,0,,,,"As AraC activates araE transcription , suppression in an AraCˉ background might be caused by a decrease of intracellular L-arabinose due to lack of AraE permease ."
7302,7303,1892.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
7303,7304,1662.txt,1,0,,,,"However , our data show that PhoPQ can repress the system independently of HilE ; thus , this transcriptional induction of hilE is apparently superfluous ."
7304,7305,490.txt,1,0,,,,HilC/D in the invasion pathway independently activate the expression of invF .
7305,7306,1104.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"RamA induction of tolC by conditioned-medium of E. coli .
"
7306,7307,1104.txt,2,0,,,,"Activation of tolC gene transcription is achieved through the direct binding of RamA , to the operator regions of these genes .
"
7307,7308,1104.txt,3,0,,,,"The tolC genes are transcriptionally activated by RamA .
"
7308,7309,1104.txt,4,0,,,,"As expected , since RamA is PramA , we first conducted EMSAs with a 97 bp transcriptional activator of tolC efflux genes ,18 bile DNA fragment + -- + -- Figu .
"
7309,7310,1104.txt,5,0,,,,"As expected , since RamA is PramA , we first conducted EMSAs with a 97 bp transcriptional activator of tolC efflux genes ,18 bile DNA fragment + -- + - + .
"
7310,7311,1104.txt,6,0,,,,"As expected , since RamA is the main the ramA promoter , we first conducted EMSAs with a 97 bp transcriptional activator of tolC efflux genes ,18 bile DNA fragment + -- + -- Figu .
"
7311,7312,1104.txt,7,0,,,,"As expected , since RamA is the main the ramA promoter , we first conducted EMSAs with a 97 bp transcriptional activator of tolC efflux genes ,18 bile DNA fragment + -- + - + ."
7312,7313,1110.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In support of this explanation , inactivation of the histone-like protein H-NS , has been shown to abrogate the requirement of the rpoS gene for expression of curli by E. coli K-12 ."
7313,7314,484.txt,1,0,,,,This resembles the situation observed for the H-NS-regulated proU operon where H-NS binds to the DRE ( downstream-regul-atory element ) within the proV structural gene [ 50 ] .
7314,7315,1676.txt,1,1,unidentified,not shown,unidentified,"On the other hand , ArcZ contributes indirectly to csgD expression as the direct ArcZ target tpx contributes to downregulation of CsgD levels -LRB- data not shown -RRB- ."
7315,7316,2196.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"To investigate the contribution of the ClpXP protease to the virulence of serovar Typhimurium we initially cloned the clpX operon from the pathogenic strain serovar Typhimurium x3306
"
7316,7317,2196.txt,2,0,,,,"Levels of FlhC , in the ClpXP protease-depleted mutant Our previous study showed that the level of bgalactosidase activity in cells was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpX .
"
7317,7318,2196.txt,3,0,,,,"Levels of FlhD , in the ClpXP protease-depleted mutant Our previous study showed that the level of bgalactosidase activity in cells was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpX .
"
7318,7319,2196.txt,4,0,,,,"Levels of master regulators , in the ClpXP protease-depleted mutant Our previous study showed that the level of bgalactosidase activity in cells was not changed , in contrast to the marked increase of bgalactosidase levels , by mutations in either clpX ."
7319,7320,2182.txt,1,1,Salmonella,Salmonella,Salmonella,"csrA encodes the CsrA regulator of Salmonella pathogeni-city
"
7320,7321,2182.txt,2,1,Salmonella,Salmonella,Salmonella,csrA encodes the CsrA regulator of Salmonella pathogeni-city
7321,7322,679.txt,1,0,,,,"Expression of the fis gene was more easily induced under low-aeration conditions , confirming that other factors play a role in this low-aeration induction of the Fis protein ."
7322,7323,651.txt,1,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; sdiA , a regulator of quorum-sensing and virulence ( Ahmer et al. 1998 ; Volf et al. 2002 ) ; permeases of oligopeptides , such as oppF and oppB ( Goodell and Higgins 1987 ; Orchard and Goodrich-Blair 2004 ) ; and several genes involved in drug resistance , such as emrE and nudF ."
7323,7324,889.txt,1,0,,,,"The StpA were incorporated into pHSG576 in the opposite orientation of such that stpA expression levels were controlled by the native stpA promoter .
"
7324,7325,889.txt,2,0,,,,The StpA were incorporated into pHSG576 in the opposite orientation of the lac promoter that stpA expression levels were controlled by the native stpA promoter .
7325,7326,137.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
7326,7327,123.txt,1,0,,,,SPR profiles of the influence of FliD on the ability of FliT to inhibit the FlhD4C2 :P flgB DNA interaction .
7327,7328,645.txt,1,0,,,,"( B ) - Galactosidase activity from GolS-or CueR-regulated transcriptional-fusions golB : : lacZ ( PgolB ) or copA-lacZ ( PcopA ) , respectively , on cells carrying either wild-type golS and cueR , or golSL , golSsL , or golSC111S , replacing the wild-type copy of golS , or cueRL , replacing cueR ."
7328,7329,876.txt,1,0,,,,"As H-NS binding regions largely overlap , RcdA might activate the csgD promoter via an antisilencing mechanism by displacing the silencer H-NS .
"
7329,7330,876.txt,2,0,,,,"As RcdA binding regions largely overlap , RcdA might activate the csgD promoter via an antisilencing mechanism by displacing the silencer H-NS ."
7330,7331,36.txt,1,0,,,,"Strong matches to this sequence were detected in the promoter regions of STM4118 , STM1253 and STM1269 , but not in the other PmrA-activated genes .
"
7331,7332,36.txt,2,0,,,,"Those that supported the original findings of the array consist of the following PmrA-activated genes ( including the predicted protein products ) : STM1253 , putative inner membrane protein ; STM1269 , putative chorismate mutase ; STM4118 , putative integral membrane protein ; STM3968 , uridine phosphorylase ; STM4568 , thymidine phosphorylase ; STM0459 , AsnC family transcriptiona independent assays ."
7332,7333,2155.txt,1,0,,,,"For genes , we found two genes , ydhJ are negatively regulated by SlyA ."
7333,7334,2141.txt,1,0,,,,"To better characterize the contribution of RcsA to persistence within tomatoes , rcsA genes were deleted"
7334,7335,1448.txt,1,0,,,,Downregulation of outer membrane proteins by noncoding RNAs : Unraveling the cAMP CRP-and σE -- ompX regulatory cas .
7335,7336,862.txt,1,0,,,,"It has also been demonstrated that FimZ can induce hilE .
"
7336,7337,862.txt,2,0,,,,"In our studies , we showed that FimZ upregulates hilE expression , thereby playing a significant role in whether hilA is expressed or not .
"
7337,7338,862.txt,3,0,,,,FimZ should lead to increased expression of hilE -LRB- not tested -RRB-
7338,7339,22.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"Research A Proteomic Analysis Reveals Differential S - Regulation of the Dependent yciGFE Locus by H-NS in Salmonella r , and Françoise Norel § Norel § ¶ ‡ The stationary-phase s controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Esch .
"
7339,7340,22.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"Our results indicate that differences between E. coli K-12 , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by H-NS in these two enterobacteria .
"
7340,7341,22.txt,3,1,Salmonella,Salmonella,Salmonella,"Our results indicate that differences between Salmonella , in the architecture of cis-acting regulatory sequences upstream of pyciG , contribute to the differential regulation of the yciGFE -LRB- katN -RRB- genes by H-NS in these two enterobacteria .
"
7341,7342,22.txt,4,0,,,,"The results reveal differential regulation of the yciGFE locus by H-NS in these two closely related bacteria .
"
7342,7343,22.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"H-NS are also able to bind to the promoter region of the E. coli K-12 yciGFE genes .
"
7343,7344,22.txt,6,1,Salmonella,Salmonella,Salmonella,"However , the sequence , the length , , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by H-NS .
"
7344,7345,22.txt,7,1,Salmonella,Salmonella,Salmonella,"However , the position of H-NS binding regions , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by H-NS .
"
7345,7346,22.txt,8,1,Salmonella,Salmonella,Salmonella,"However , the position of the McbR/YncC , relative to the yciGFE promoter , are different in Salmonella , resulting in differential mechanisms of regulation of these genes by H-NS .
"
7346,7347,22.txt,9,2,Escherichia coli;Salmonella,E. coli;Salmonella,Escherichia coli;Salmonella,"It is remarkable that in E. coli K-12 , regulation of yciGFE by H-NS are intimately linked , whereas in Salmonella , YncC directly activates transcription
"
7347,7348,22.txt,10,1,Escherichia coli,Escherichia coli,Escherichia coli,"A proteomic analysis reveals differential regulation of the S-dependent yciGFE locus by H-NS in Escherichia coli K-12 .
"
7348,7349,22.txt,11,1,Salmonella,Salmonella,Salmonella,A proteomic analysis reveals differential regulation of the S-dependent yciGFE locus by H-NS in Salmonella .
7349,7350,1306.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The trehalose synthesis gene otsA is regulated by RpoS in S. typhimurium
"
7350,7351,1306.txt,2,0,,,,"Previous workers have shown that the otsA gene is regulated by RpoS to the stationary-phase of growth .
"
7351,7352,1306.txt,3,0,,,,"Previous workers have shown that the otsA gene is regulated by RpoS to nutrient deprivation .
"
7352,7353,1306.txt,4,0,,,,"Previous workers have shown that the otsA gene is regulated by RpoS to stresses .
"
7353,7354,1306.txt,5,0,,,,"the RpoS _ regulated genes katE and otsA , indicating that the overexpressed RpoS protein is functional as a positive regulator"
7354,7355,692.txt,1,0,,,,"The repression of YgaE to ompF means less pathways for antibiotics .
"
7355,7356,692.txt,2,0,,,,"The repression of YgaE to ompF means less pathways for nutrition .
"
7356,7357,692.txt,3,0,,,,"One explanation for these phenomena is the repression of YgaE to ompF occurs only in the very early stage of hyperosmotic-stress as an emergency approach to protect the bacteria .
"
7357,7358,692.txt,4,0,,,,"As time goes by , other mechanisms are involved in the process of handling the hyperosmotic-stress , the repression of YgaE to ompF relieves .
"
7358,7359,692.txt,5,0,,,,the expressions of ompF were obviously repressed by YgaE at the early stage
7359,7360,2169.txt,1,0,,,,"Under conditions of low-osmolarity , the transcription of invF is negatively controlled by the RcsB regulator , acting in concert with the TviA protein .
"
7360,7361,2169.txt,2,0,,,,"Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system ."
7361,7362,1460.txt,1,0,,,,"To determine whether either ydeN or ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ and measured-galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN or ydeM ."
7362,7363,1474.txt,1,0,,,,"Titration of FeCl3 into the medium with 80 M CoCl2 resulted in increasing repression of entB transcription , showing that the Fur protein had not been damaged by the presence of cobalt .
"
7363,7364,1474.txt,2,0,,,,Increased entB expression reflects decreased Fur activity .
7364,7365,686.txt,1,0,,,,"PmrAB-regulated genes include pmrHFIJKL , whose product results in the addition of aminoarabinose to the 1 and 4 = phosphates of lipid-A ( D ) ; pmrC , whose product results in the addition of phosphoethanolamine to the 1 and 4 = phosphates of lipid-A ( E ) ; cptA , whose product results in the addition of phosphoethanolamine to the LPS core ( F ) ; pmrG , whose product results in the addition of phosphate to heptose present in the LPS core ( G ) ; and cld , whose product results in an O-antigen chain length determinant ( H ) ."
7365,7366,1312.txt,1,0,,,,"FliZ was required for WT levels of fliC expression , however , bistable populations continued to form in a ΔfliZ strain , indicating that reciprocal repression by Fli is not crucial for fliC bistability .
"
7366,7367,1312.txt,2,0,,,,"FliZ was required for WT levels of fliC expression , however , bistable populations continued to form in a ΔfliZ strain , indicating that reciprocal repression by Ydi is not crucial for fliC bistability ."
7367,7368,719.txt,1,0,,,,"In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator or by furthering expression of an ssaG repressor .
"
7368,7369,719.txt,2,0,,,,"In principle , PmrA could repress ssaG transcription directly , by binding to the ssaG promoter , or , indirectly , by hindering transcription of an ssaG activator or by furthering expression of an ssaG repressor ."
7369,7370,1299.txt,1,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
7370,7371,1299.txt,2,0,,,,"Together with a bioinformatic analysis of other Enterobacteriaceae species , these data identify a conserved AraC regulon that includes 7 previously described AraC-regulated genes ( araB , araA , araD , araE , araF , araG , and araH ) as well as three novel targets identified in this work ( ytfQ , araT , and araU ) ."
7371,7372,725.txt,1,0,,,,"hilA invF-2 hilA _ known to be directly activated , although only slightly upregulating , by HilC/HilD"
7372,7373,731.txt,1,2,Salmonella;unidentified,Salmonella;unknown,unidentified;Salmonella,"Network Analyses of Functional Associations and/or Interactions Among ArcA-Regulated Proteins -- To further under ¬ Classification of differentially expressed Salmonella proteins in the arcA mutant according to Clusters of Orthologous Groups ( COGs ) Number of Proteins ArcA-ArcA-repressed activated 34 10 20 12 2 8 10 6 0 4 8 4 74 44 0 14 4 5 0 2 8 3 6 1 4 0 Nucleotide metabolism and transport Carbohydrate metabolism and transport Coenzyme metabolism Lipid metabolism a Metabolism Translation Transcription Replication and repair Cell wall/membrane/envelop biogenesis Cell motility Post-translational modification , protein turnover , chaperone functions Inorganic ion transport and metabolism 7 6 Secondary structure 4 1 Signal transduction 11 3 Intracellular trafficking and secretion 3 1 General functional prediction only 8 7 Function unknown 41 28 a The bolded functional category contains a summary of the unbolded COG functional groups above associated with metabolism .
"
7373,7374,731.txt,2,0,,,,"Several proteins of the ethanolamine utilization operon , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7374,7375,731.txt,3,0,,,,"Several proteins of the ethanolamine utilization operon , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) .
"
7375,7376,731.txt,4,0,,,,"Repression of the Ethanolamine Utilization Operon by ArcA , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7376,7377,731.txt,5,0,,,,"Repression of the Ethanolamine Utilization Operon by ArcA , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7377,7378,731.txt,6,0,,,,"Repression of the Ethanolamine Utilization Operon by ArcA , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) .
"
7378,7379,731.txt,7,0,,,,"Repression of the Ethanolamine Utilization Operon by ArcA , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) .
"
7379,7380,731.txt,8,0,,,,"EutQ , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7380,7381,731.txt,9,0,,,,"EutQ , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) .
"
7381,7382,731.txt,10,0,,,,"EutE , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7382,7383,731.txt,11,0,,,,"EutE , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) .
"
7383,7384,731.txt,12,0,,,,"EutC , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7384,7385,731.txt,13,0,,,,"EutC , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) .
"
7385,7386,731.txt,14,0,,,,"EutB , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( 2B ) .
"
7386,7387,731.txt,15,0,,,,"EutB , are of significantly higher levels in arcA cells , suggesting their repression by ArcA ( Fig. 2A ) ."
7387,7388,902.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhi where StpA represses only in an hns background
"
7388,7389,902.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhi where StpA represses only in an hns background
"
7389,7390,902.txt,3,0,,,,"Because StpA potentially represses hns , we downregulated in a DstpA strain .
"
7390,7391,902.txt,4,0,,,,"Because StpA potentially represses hns , we expected such genes to be upregulated in an hns mutant .
"
7391,7392,902.txt,5,0,,,,"Point mutations M4T enhance StpA repression of select hns .
"
7392,7393,902.txt,6,0,,,,"Point mutations A77D enhance StpA repression of select hns .
"
7393,7394,902.txt,7,0,,,,One possibility worth investigating is that the partial repression of the proU operon in media of low osmolality in hns mutants is mediated by the StpA protein .
7394,7395,1528.txt,1,0,,,,"the lpxO gene is partly regulated by PhoP-PhoQ
"
7395,7396,1528.txt,2,0,,,,"The regulation of lpxO , is also mediated , at least in part , by PhoP-PhoQ ."
7396,7397,2021.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Multiple regulators of hmp gene of Salmonella enterica serovar Typhimurium include RamA .
7397,7398,2035.txt,1,0,,,,"In vitro characterization of transcriptional-fusions to virulence genes As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) ."
7398,7399,916.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Felis catus,SL1344;SL1344;cat,Felis catus;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,Filled bars indicate the percentage of genes more highly expressed in SL1344 than in the fis mutant ( i.e. considered as Fis-activated ) ; hatched bars represent the percentage of genes more highly expressed in the SL1344fis : : cat mutant than in the wild-type ( considered as Fis-repressed ) .
7399,7400,1272.txt,1,0,,,,"29 pagC survival pagD pagK PhoPQ-regulated 0 ?
"
7400,7401,1272.txt,2,0,,,,"Although not significantly enriched within the set of directly PhoPQ-regulated genes , the functional class related to pathogenicity and virulence also contained potential PhoPQ-dependent targets ( pagC , mgtC , virK , and STM0306 ) ."
7401,7402,1514.txt,1,0,,,,"This conclusion is confirmed We also assessed the effect of the phoP mutation on SseK1 by the positive effect of the activating mutation phoQ24 on at the protein level Next , we reasoned that since PhoP regulates sseK1 in an SsrB-independent manner , it could be a direct regulator of this gene ."
7402,7403,1500.txt,1,0,,,,"MlrA represents a newly defined transcriptional regulator of csgD
"
7403,7404,1500.txt,2,0,,,,"These results suggest that , as with RpoS , control of curli regulation by MlrA acts at the level of transcription of csgD .
"
7404,7405,1500.txt,3,0,,,,"These results suggest that , as with RpoS , control of curli regulation by MlrA acts at the level of transcription of csgD .
"
7405,7406,1500.txt,4,0,,,,"In addition , MlrA , controls csgD expression .
"
7406,7407,1500.txt,5,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,strain SL;SL1344;S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium,"MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene in S. typhimurium .
"
7407,7408,1500.txt,6,3,Sediminispirochaeta sinaica;Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli,strain SL;SL1344;E. coli,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Escherichia coli;Sediminispirochaeta sinaica,"MlrA transcription is defective in strain SL1344 The mlrA gene has been identified as a positive regulator of the csgD gene in E. coli .
"
7408,7409,1500.txt,7,1,Escherichia coli,Escherichia coli,Escherichia coli,"Ogasawara , H. ; Yamamoto , K. ; Ishihama , A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .
"
7409,7410,1500.txt,8,1,unidentified,unknown,unidentified,"Under the influence of unknown environmental signals , MlrA induces the csgD expression .
"
7410,7411,1500.txt,9,0,,,,"The MerR-like regulator MlrA is another positive regulator of csgD expression .
"
7411,7412,1500.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The direct regulation of csgD expression by MlrA in S. Typhimurium needs to be experimentally confirmed .
"
7412,7413,1500.txt,11,1,Escherichia coli,Escherichia coli,Escherichia coli,"Ogasawara H , Yamamoto K , Ishihama A. Regulatory role of MlrA in transcription activation of csgD , the master regulator of biofilm formation in Escherichia coli .
"
7413,7414,1500.txt,12,0,,,,"that _ described in wt , indicating that MlrA is not required for the regulation of csgD by the composition of the culture media
"
7414,7415,1500.txt,13,0,,,,"that _ described in wt , indicating that MlrA is not required for the regulation of csgD by the composition of the culture media"
7415,7416,2009.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella specific,Salmonella,"Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .
"
7416,7417,2009.txt,2,1,Salmonella;Salmonella,Salmonella;Salmonella specific,Salmonella,"Salmonella specific STM1697 binds to FlhD , a component of FlhDC , the master transcription regulator of flagella biosynthesis .
"
7417,7418,2009.txt,3,0,,,,"Besides positive regulation of FlhDC , CsrA indirectly inhibits the expression of several GGDEF and/or EAL domain proteins STM1697 .
"
7418,7419,2009.txt,4,0,,,,"Besides positive regulation of FlhDC , CsrA directly inhibits the expression of several GGDEF and/or EAL domain proteins STM1697 .
"
7419,7420,2009.txt,5,0,,,,These data support our hypothesis that the binding of STM1697 to the periphery of the FlhDC complex prevents RNA polymerase from binding to the promoter .
7420,7421,1266.txt,1,0,,,,"STM3216 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop .
"
7421,7422,1266.txt,2,0,,,,"STM3216 , are not regulated by HilA suggesting they are controlled by the HilD feed-forward loop ."
7422,7423,1931.txt,1,0,,,,"In contrast , the presence of both dam mutations in the donor strain restored the repression of pSLT transfer to a level similar to that of an Lrp-mutant ."
7423,7424,1925.txt,1,0,,,,"In conclusion , our findings highlight the function of the PmrA/PmrB system in the regulation of the O-Ag VL region by the direct control of the wzz gene .
"
7424,7425,1925.txt,2,0,,,,"In conclusion , our findings highlight the function of the PmrA/PmrB system in the regulation of the O-Ag VL region by the direct control of the wzz gene ."
7425,7426,269.txt,1,0,,,,"Deoxycholate specifically interacts with MarR an inducer of marRAB activity , has been shown to bind the repressor MarR , leading to an increase in transcriptional activity of the operon .
"
7426,7427,269.txt,2,0,,,,Thus induction of marRAB by DEC without inhibition of the repression activity of MarR is expected to be less effective than induction with SAL .
7427,7428,241.txt,1,0,,,,"The stimulation of Rho-dependent termination by high Mg2 + is specific to the mgtA leader because high Mg2 .
"
7428,7429,241.txt,2,0,,,,"If the nucleotides in the R2 regions of the mgtA leader are essential for stimulation of Rho activity , mutations in R2 should overcome the silencing effect of the C145G substitution .
"
7429,7430,241.txt,3,0,,,,"If the nucleotides in the R2 regions of the mgtA leader are essential for stimulation of Rho activity , mutations in R1 should overcome the silencing effect of the C145G substitution .
"
7430,7431,241.txt,4,0,,,,"If the nucleotides in the R1 regions of the mgtA leader are essential for stimulation of Rho activity , mutations in R2 should overcome the silencing effect of the C145G substitution .
"
7431,7432,241.txt,5,0,,,,"If the nucleotides in the R1 regions of the mgtA leader are essential for stimulation of Rho activity , mutations in R1 should overcome the silencing effect of the C145G substitution ."
7432,7433,527.txt,1,1,Salmonella,Salmonella,Salmonella,"We report here that the silencing proteins H-NS are the main negative regulators of ompS1 expression in Salmonella .
"
7433,7434,527.txt,2,1,Salmonella,Salmonella,Salmonella,"We report here that the silencing proteins H-NS are the main positive regulators of ompS1 expression in Salmonella .
"
7434,7435,527.txt,3,0,,,,"DNase footprinting was performed to determine the binding of H-NS to the ompS1 regulatory region in the vicinity of -70 to -200 bp upstream E of the P1 transcriptional start .
"
7435,7436,527.txt,4,0,,,,"DNase footprinting was performed to determine the binding of H-NS to the ompS1 regulatory region in the vicinity of OmpR-binding box IV .
"
7436,7437,527.txt,5,0,,,,"Moreover , previous genetic data show that the removal of upstream regions from -310 to -88 gradually caused the derepression of ompS1 expression which , together with Fig. 4D , suggest that H-NS binds at the two nucleation sites .
"
7437,7438,527.txt,6,0,,,,"Moreover , previous genetic data show that the removal of upstream regions from -310 to -88 gradually caused the derepression of ompS1 expression which , together with the H-NS DNase footprinting data , suggest that H-NS binds at the two nucleation sites .
"
7438,7439,527.txt,7,0,,,,"In addition , our model contemplates that LeuO physically LeuO antagonizes StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at its polymerization .
"
7439,7440,527.txt,8,0,,,,"In addition , our model contemplates that LeuO physically LeuO antagonizes StpA in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites .
"
7440,7441,527.txt,9,0,,,,"In addition , our model contemplates that LeuO physically LeuO antagonizes H-NS in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at its polymerization .
"
7441,7442,527.txt,10,0,,,,"In addition , our model contemplates that LeuO physically LeuO antagonizes H-NS in ompS1 739 does not block the progress of H-NS but rather causes a displacement of H-NS , hence preventing its binding at the nucleation sites .
"
7442,7443,527.txt,11,0,,,,"H-NS are involved in regulation of ompS1 .
"
7443,7444,527.txt,12,1,Salmonella,Salmonella,Salmonella,"Moreover it has been reported that the silencing proteins H-NS are the main negative regulators of ompS1 expression in Salmonella .
"
7444,7445,527.txt,13,1,Salmonella,Salmonella,Salmonella,Moreover it has been reported that the silencing proteins H-NS are the main positive regulators of ompS1 expression in Salmonella .
7445,7446,533.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS ."
7446,7447,1919.txt,1,0,,,,"pmrCAB itself , are activated by PhoPQ ."
7447,7448,255.txt,1,0,,,,"CsgD transcription remained unchanged in buffered medium whereas in unbuffered rich-medium csgD activity was repressed by our unpublished data .
"
7448,7449,255.txt,2,0,,,,"CsgD transcription remained unchanged in buffered medium whereas in unbuffered rich-medium csgD activity was repressed by glucose .
"
7449,7450,255.txt,3,0,,,,"a positive feedback-loop includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of slightly reduced CsgD levels
"
7450,7451,255.txt,4,0,,,,"a positive feedback-loop includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of Fig. 3B
"
7451,7452,255.txt,5,0,,,,"a positive feedback-loop includes the transcriptional activation of the RpoS-stabilizing factor IraP by CsgD .35 In addition , we investigated the phenotype of an hfq mutant in strain MAE52 shows RpoS independent transcription of csgD due to a promoter mutation .2 An hfq mutant in the MAE52 background showed a clear downregulation of the rdar morphotype"
7452,7453,2223.txt,1,0,,,,"the hemX gene were used as positive control regions , respectively , as H-NS binds to the proV promoter ."
7453,7454,1058.txt,1,0,,,,"inactivation of narL did not reduce growth in the intes-tinal lumen , although NarL regulates metabolic genes
"
7454,7455,1058.txt,2,0,,,,"inactivation of narL did not reduce growth in the intes-tinal lumen , although NarL regulates a variety"
7455,7456,2237.txt,1,0,,,,The MetR protein acts as an activator for the transcription of metE .
7456,7457,282.txt,1,0,,,,narJ are positively regulated by SlyA
7457,7458,1716.txt,1,0,,,,H-NS specifically repressed transcription of sifA
7458,7459,1070.txt,1,0,,,,"the control of the DnaA binding to oriC can be related with the partial reestablishment of the replication asynchrony _ observed at every seqA mutant
"
7459,7460,1070.txt,2,0,,,,the control of the DnaA binding to oriC in-vitro _ observed at every seqA mutant
7460,7461,1064.txt,1,0,,,,"Thus , SsrB regulates transcription of sseJ by both relief of H-NS repression .
"
7461,7462,1064.txt,2,0,,,,"Thus , SsrB regulates transcription of sseJ by both direct activation of H-NS repression ."
7462,7463,1702.txt,1,2,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,plasmid;S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,"Genetic evidence has implicated HU in the control of SPI-1 virulence gene expression while IHF has been shown to bind to the promoter region of the spvR regulatory virulence gene on the 96-kb plasmid of S. Typhimurium where it has a positive effect in stationary-phase .
"
7463,7464,1702.txt,2,0,,,,IHF binds to DNA sequences upstream of the spvR regulatory region
7464,7465,296.txt,1,0,,,,"PhoP also binds to the promoter region of the amgR with lower affinity and transcribes the AmgR antisense RNA , resulting in an RNase E-dependent degradation of the mgtC portion of the mgtCBR messages .
"
7465,7466,296.txt,2,0,,,,"At the same time , PhoP also binds to the amgR promoter located in the intergenic region between the mgtB genes .
"
7466,7467,296.txt,3,0,,,,"At the same time , PhoP also binds to the amgR promoter located in the intergenic region between the mgtC genes .
"
7467,7468,296.txt,4,0,,,,"PhoP binds to the amgR with different affinities , the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition .
"
7468,7469,296.txt,5,0,,,,"PhoP binds to the amgR with different affinities , the former higher , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in a PhoP-inducing condition .
"
7469,7470,296.txt,6,0,,,,"PhoP binds to the amgR with different affinities , the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in media .
"
7470,7471,296.txt,7,0,,,,"PhoP binds to the amgR with different affinities , the latter lower , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in low Mg2 .
"
7471,7472,296.txt,8,0,,,,"PhoP binds to the amgR with different affinities , the former higher , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in media .
"
7472,7473,296.txt,9,0,,,,"PhoP binds to the amgR with different affinities , the former higher , resulting in an initial increase but a subsequent decrease in MgtC protein levels relative to MgtB protein levels in low Mg2 ."
7473,7474,2233.txt,1,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;typhimu,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Conversely , two glyoxyate shunt genes under the positive control of CsrA in E. coli , aceB , were induced twofold in the S. typhimu-rium csrA mutant ."
7474,7475,1048.txt,1,0,,,,"Other genes of interest include pagP , a PhoPQ-regulated palmitoyl transferase for lipid-A ; sdiA , a regulator of quorum-sensing and virulence ( Ahmer et al. 1998 ; Volf et al. 2002 ) ; permeases of oligopeptides , such as oppF and oppB ( Goodell and Higgins 1987 ; Orchard and Goodrich-Blair 2004 ) ; and several genes involved in drug resistance , such as emrE and nudF ."
7475,7476,2227.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .
"
7476,7477,2227.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;S. Typhimurium;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Interestingly , Salmonella tehB is not transcriptionally regulated by NsrR ; this study -RRB- , suggesting that both the regulation and function of this protein may have diverged in S. Typhimurium ."
7477,7478,292.txt,1,1,Felis catus,cat,Felis catus,"As shown in Fig. 2 , induction of the dominant negative H-NSQ92am domain , but not of WT H-NS , restored the expression of the ssrB-cat 302/478 fusion in the hilD mutant .
"
7478,7479,292.txt,2,1,Felis catus,cat,Felis catus,"Induction of H-NSQ92am derepressed ssrAB-cat 55 fusions in the hilD mutant to levels similar to those .
"
7479,7480,292.txt,3,1,Felis catus,cat,Felis catus,"Induction of H-NSQ92am derepressed ssrAB-cat 106 in the hilD mutant to levels similar to those .
"
7480,7481,292.txt,4,1,Felis catus,cat,Felis catus,Induction of H-NSQ92am derepressed ssrAB-cat 208 in the hilD mutant to levels similar to those .
7481,7482,1706.txt,1,0,,,,"Enhanced HilC/RtsA levels , in turn , activate hilA transcription ."
7482,7483,1060.txt,1,0,,,,"Another ` Fur-activated 
"
7483,7484,1060.txt,2,0,,,,"These data suggest that Fur activates SPI1 in a manner different from that of Fur activation of sodB .
"
7484,7485,1060.txt,3,0,,,,"One such `` Fur-activated 
"
7485,7486,1060.txt,4,0,,,,"Known `` Fur-activated 
"
7486,7487,1060.txt,5,0,,,,"Fur activates sodB by repressing the expression of ryhB under high-iron conditions .
"
7487,7488,1060.txt,6,0,,,,"Thus , Fur positively controls sodB at the posttranscriptional level .
"
7488,7489,1060.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , expression of sodB is activated by Fur via repression of the small RNA RyhB ."
7489,7490,1074.txt,1,1,Salmonella,Salmonella,Salmonella,"HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .
"
7490,7491,1074.txt,2,1,Salmonella,Salmonella,Salmonella,"HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .
"
7491,7492,1074.txt,3,1,Salmonella,Salmonella,Salmonella,"HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .
"
7492,7493,1074.txt,4,1,Salmonella,Salmonella,Salmonella,"HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .
"
7493,7494,1074.txt,5,1,Salmonella,Salmonella,Salmonella,"HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .
"
7494,7495,1074.txt,6,1,Salmonella,Salmonella,Salmonella,HilD induces expression of Salmonella pathogenicity island 2 genes by displacing the global negative regulator H-NS from ssrAB .
7495,7496,1712.txt,1,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) ."
7496,7497,286.txt,1,1,Salmonella,Salmonella,Salmonella,"PtsJ from Salmonella typhimur-ium controls the expression of the pdxK gene
"
7497,7498,286.txt,2,0,,,,"In the present study , we showed that PtsJ is actually involved in the regulation of pdxK and therefore in the transcriptional control of B6 vitamers salvage pathway .
"
7498,7499,286.txt,3,0,,,,"In the present study , we showed that PtsJ is actually involved in the regulation of pdxK and therefore in the transcriptional control of B6 vitamers salvage pathway ."
7499,7500,1921.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"S. Typhimurium virK is positively regulated by PhoP/PhoQ .
"
7500,7501,1921.txt,2,0,,,,"Since the PhoP/PhoQ system represses hilA expression , it can be speculated that either virK are regulated by PhoP/PhoQ in an opposite way or VirK negatively influences hilA expression ."
7501,7502,279.txt,1,0,,,,"To test whether the loss of ydgT could overcome the requirement for positive regulation of SPI-2 , we introduced the ydgT deletion into an ssrB mutant lacking the response regulator of the SsrA SsrB two-component regulatory system .
"
7502,7503,279.txt,2,0,,,,"To test whether the loss of ydgT could overcome the requirement for positive regulation of SPI-2 , we introduced the ydgT deletion into an ssrB mutant lacking the response regulator of the SsrA SsrB two-component regulatory system ."
7503,7504,1935.txt,1,0,,,,"Several PmrA-regulated loci involved in modification of LPS have been identified , including pmrE ( pagA , ugd ) , which encodes a putative UDP-glucose dehydrogenase , and the pmrHFIJKLM operon ( 17 ) ."
7504,7505,251.txt,1,0,,,,"The results of this analysis suggest that LeuO activates transcription of envR , perhaps by antagonizing H-NS ."
7505,7506,537.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Notably , our observation that deletion of all of the IS200 copies in S. Typhimurium impacted on the expression of prgH not under the control of InvF is consistent with tnpA producing either a multi-functional regulatory RNA or , as in the case of IS1341 , multiple regulatory sRNAs .
"
7506,7507,537.txt,2,0,,,,It is known that prgH is under the regulation of InvF .
7507,7508,523.txt,1,0,,,,"The AdaST protein increased expression of the ada 
"
7508,7509,523.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"AdaST , was found to be a weak activator of expression from the ada promoter of E. coli .
"
7509,7510,523.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"that AdaST can activate ada transcription in E. coli to some extent
"
7510,7511,523.txt,4,0,,,,The AdaST protein increased expression of the ada 
7511,7512,245.txt,1,1,Homo sapiens,human,Homo sapiens,"It has been shown recently that the TviA regulatory protein controls transcription of the flagellin gene fliC , thereby reducing TLR5-mediated IL-8 production in human intestinal epithelial cells by reducing flagellin secretion ."
7512,7513,1909.txt,1,0,,,,The hilA gene _ activated by The SPI-1-encoded HilC/D
7513,7514,912.txt,1,0,,,,"An increase in OmpR-P levels would enable OmpR-P to bind to lower affinity sites , repressing ssrB ."
7514,7515,1538.txt,1,0,,,,"PhoPc derivatives of the pagA : : pagB : : Mu dJ strains produced 980 U , respectively , of P-galactosidase in an increase of 9-to 10-fold over values for the fusion strains with a wild-type phoP locus .
"
7515,7516,1538.txt,2,0,,,,"PhoPc derivatives of the pagA : : pagB : : Mu dJ strains produced 480 U , respectively , of P-galactosidase in an increase of 9-to 10-fold over values for the fusion strains with a wild-type phoP locus .
"
7516,7517,1538.txt,3,0,,,,"PhoPc derivatives of the pagA : : Mu dJ : : Mu dJ strains produced 980 U , respectively , of P-galactosidase in an increase of 9-to 10-fold over values for the fusion strains with a wild-type phoP locus .
"
7517,7518,1538.txt,4,0,,,,"PhoPc derivatives of the pagA : : Mu dJ : : Mu dJ strains produced 480 U , respectively , of P-galactosidase in an increase of 9-to 10-fold over values for the fusion strains with a wild-type phoP locus ."
7518,7519,2031.txt,1,0,,,,"An rpoS mutant displayed elevated levels of Fis .
"
7519,7520,2031.txt,2,0,,,,"an rpoS mutant _ displaying elevated levels of Fis expression under these conditions
"
7520,7521,2031.txt,3,2,Salmonella;Salmonella enterica;Salmonella,Salmonella;Salmonella enterica;enterica,Salmonella enterica;Salmonella,"Hirsch M , Elliot T. Fis regulates transcriptional induction of rpoS in Salmonella enterica .
"
7521,7522,2031.txt,4,0,,,,"The exponential phase expression of PtopAEc was slightly elevated in the absence of rpoS , perhaps due to stimulation by elevated FIS levels ."
7522,7523,2025.txt,1,0,,,,"Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in nagEBACD , glmUS , chbBCARFG , fimB , although the galP gene is controlled via a single operator with high affinity .
"
7523,7524,2025.txt,2,0,,,,"Co-operative binding of NagC to two sites is required for regulation of most NagC controlled operons in nagEBACD , glmUS , chbBCARFG , fimB , although the galP gene is controlled via a single operator with high affinity ."
7524,7525,906.txt,1,0,,,,"Repression by DeoR is relieved by cytidine ; these nucleosides are inducers of the tsx gene .
"
7525,7526,906.txt,2,0,,,,Repression by DeoR is relieved by adenosine ; these nucleosides are inducers of the tsx gene .
7526,7527,1262.txt,1,0,,,,EmrR is reported to be a repressor for the emrAB efflux genes .
7527,7528,1504.txt,1,0,,,,"HilA is a master regulator of SPI1 genes like sipB , sipC , sopD , sopB etc. .
"
7528,7529,1504.txt,2,0,,,,"Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) ."
7529,7530,1510.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"that McbR are both able to induce expression of katN locus in E. coli K-12
"
7530,7531,1510.txt,2,1,Salmonella,Salmonella,Salmonella,that McbR are both able to induce expression of katN locus in Salmonella
7531,7532,2019.txt,1,0,,,,"Hence , combined repression of stpA mRNAs by SdsR endorses down-regulation of the CRP regulon ."
7532,7533,1276.txt,1,0,,,,"RNA-seq data for InvF confirm direct regulation of sopE2 ( Fig. 2 ; see also Fig .
"
7533,7534,1276.txt,2,0,,,,Our ChIP-seq for InvF confirm direct regulation of sopE2 ( Fig. 2 ; see also Fig .
7534,7535,709.txt,1,0,,,,"Selected proteins with differential expression in LoT compared with L696 Expression ratio a Description Protein Function enoyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , arcA glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in LoT relative to L696 .
"
7535,7536,709.txt,2,0,,,,"Selected proteins with differential expression in LoT compared with L696 Expression ratio a Description Protein Function enoyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , putative regulator putative arginine deiminase glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in LoT relative to L696 .
"
7536,7537,709.txt,3,0,,,,"Selected proteins with differential expression in L700 compared with L696 Expression ratio a Description Protein Function enoyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , arcA glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in L700 relative to L696 .
"
7537,7538,709.txt,4,0,,,,"Selected proteins with differential expression in L700 compared with L696 Expression ratio a Description Protein Function enoyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , putative regulator putative arginine deiminase glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in L700 relative to L696 .
"
7538,7539,709.txt,5,0,,,,"Selected proteins with differential expression in LoT compared with L696 Expression ratio NADH 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , arcA glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in LoT relative to L696 .
"
7539,7540,709.txt,6,0,,,,"Selected proteins with differential expression in LoT compared with L696 Expression ratio NADH 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , putative regulator putative arginine deiminase glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in LoT relative to L696 .
"
7540,7541,709.txt,7,0,,,,"Selected proteins with differential expression in LoT compared with L696 Expression ratio [ acyl-carrier-protein ] reductase 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , arcA glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in LoT relative to L696 .
"
7541,7542,709.txt,8,0,,,,"Selected proteins with differential expression in LoT compared with L696 Expression ratio [ acyl-carrier-protein ] reductase 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , putative regulator putative arginine deiminase glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in LoT relative to L696 .
"
7542,7543,709.txt,9,0,,,,"Selected proteins with differential expression in L700 compared with L696 Expression ratio NADH 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , arcA glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in L700 relative to L696 .
"
7543,7544,709.txt,10,0,,,,"Selected proteins with differential expression in L700 compared with L696 Expression ratio NADH 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , putative regulator putative arginine deiminase glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in L700 relative to L696 .
"
7544,7545,709.txt,11,0,,,,"Selected proteins with differential expression in L700 compared with L696 Expression ratio [ acyl-carrier-protein ] reductase 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , arcA glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in L700 relative to L696 .
"
7545,7546,709.txt,12,0,,,,"Selected proteins with differential expression in L700 compared with L696 Expression ratio [ acyl-carrier-protein ] reductase 3-oxoacyl - [ acyl-carrier-protein ] synthase I FabI FabB Fatty acid biosynthesis/metabolism 3.8 2.2 3.0 2.4 2.1 1.6 7.0 2.2 0.3 0.3 0.2 0.2 0.3 0.2 3-hydroxyacyl-coA dehydrogenase DNA-binding protein ; pleiotropic regulator RNA chaperone , negative regulator of cspA transcription cold-shock protein , putative regulator putative arginine deiminase glycine cleavage complex protein P , glycine decarboxylase flagellar biosynthesis ; flagellin , filament structural protein putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein I , serine sensor receptor sensory histidine protein kinase putative methyl-accepting chemotaxis protein methyl-accepting chemotaxis protein II FadB HNS CspE CspC STM4467 GcvP FliC STM3216 Tsr CheA STM3152 CheM Global regulation Cold shock Amino acid metabolism Motility/chemotaxis a Ratio indicates expression in L700 relative to L696 ."
7546,7547,1289.txt,1,2,Salmonella;Salmonella;unidentified plasmid,Salmonella;Salmonella;plasmid,Salmonella;unidentified plasmid,"Gene targets included : 16S rDNA ( Lin and Tsen 1996 ) , a Salmonella pathogenicity island I virulence gene ( hilA ) ( Guo et al. 2000 ) , Salmonella enterotoxin gene ( stn ) ( Makino et al. 1999 ) , invA gene ( Ferretti et al. 2001 ) , Fur-regulated gene ( iroB ) ( Bäumler et al. 1997 ) , histidine transport operon ( Cohen et al. 1993 ) , the junction between sipB and sipC virulence genes ( sipB-sipC ) ( Carlson et al. 1999 ) , a Salmon-ella-specific repetitive DNA fragment ( Jitrapakdee et al. 1995 ) , and a multiplex targeting invA gene and spvC gene of the virulence plasmid ( invA/spvC ) ( Chiu and Ou 1996 ) .
"
7547,7548,1289.txt,2,0,,,,"In this work , we demonstrated that Fur regulates expression of hilA via control of HilD .
"
7548,7549,1289.txt,3,0,,,,"that Fur plays a major role in this metal regulation of hilA and therefore SPI1 expression
"
7549,7550,1289.txt,4,0,,,,"Taken together , these data indicate that Fur acts as a positive regulator of hilA expression .
"
7550,7551,1289.txt,5,0,,,,"Fur regulates expression of hilA by working through HilD .
"
7551,7552,1289.txt,6,0,,,,"Having established that Fur controls hilA expression , we wanted to see how Fur fits into the feed forward loop model of SPI1 regulation that we previously defined .
"
7552,7553,1289.txt,7,0,,,,"Figure 3 shows that Fur regulation of hilA was abrogated in any background ; in all hilD strains there was no significant difference in hilA expression between the fur strains .
"
7553,7554,1289.txt,8,0,,,,"Figure 3 shows that Fur regulation of hilA was abrogated in any background ; in all hilD strains there was no significant difference in hilA expression between the fur strains .
"
7554,7555,1289.txt,9,0,,,,"As expected , based on our model , deletion of rtsA affected the overall expression of hilA but di not prevent Fur regulation of hilA .
"
7555,7556,1289.txt,10,0,,,,"As expected , based on our model , deletion of hilC affected the overall expression of hilA but di not prevent Fur regulation of hilA .
"
7556,7557,1289.txt,11,0,,,,"To further test the requirement for HilD for Fur-mediated regulation of hilA , we examined the effects of Fur overexpression in strains .
"
7557,7558,1289.txt,12,0,,,,"This provides clear genetic evidence that HilD is absolutely required for Fur regulation of hilA .
"
7558,7559,1289.txt,13,0,,,,"Given that HilD is required for Fur regulation of hilA , it seemed possible that Fur regulates hilD expression in some manner .
"
7559,7560,1289.txt,14,0,,,,"Fur regulates expression of hilA via HilD .
"
7560,7561,1289.txt,15,0,,,,"However , the data suggest that Hfq plays no role in the Fur regulation of hilA , again differentiating sodB regulation .
"
7561,7562,1289.txt,16,0,,,,"However , the data suggest that Hfq plays no role in the Fur regulation of hilA , again differentiating SPI1 regulation .
"
7562,7563,1289.txt,17,0,,,,"However , the data suggest that Hfq plays little role in the Fur regulation of hilA , again differentiating sodB regulation .
"
7563,7564,1289.txt,18,0,,,,"However , the data suggest that Hfq plays little role in the Fur regulation of hilA , again differentiating SPI1 regulation .
"
7564,7565,1289.txt,19,0,,,,"Fur does not regulate hilA expression by controlling HilE .
"
7565,7566,1289.txt,20,0,,,,"Fur regulation of hilA are mechanistically different .
"
7566,7567,1289.txt,21,0,,,,"Either way , Fur regulates hilA by posttranslationally affecting the HilD protein .
"
7567,7568,1289.txt,22,0,,,,"Also , while deletion of rtsA affected the fold effect of fur , it did not prevent Fur regulation of hilA .
"
7568,7569,1289.txt,23,0,,,,"Also , while deletion of rtsA decreased the expression of hilA , it did not prevent Fur regulation of hilA .
"
7569,7570,1289.txt,24,0,,,,"Also , while deletion of hilC affected the fold effect of fur , it did not prevent Fur regulation of hilA .
"
7570,7571,1289.txt,25,0,,,,"Also , while deletion of hilC decreased the expression of hilA , it did not prevent Fur regulation of hilA ."
7571,7572,735.txt,1,0,,,,"In turn , fliA is positively controlled by the gene products FlhD ."
7572,7573,721.txt,1,0,,,,"Moreover , Fur significantly regulates translational hilD
"
7573,7574,721.txt,2,0,,,,"Given that HilD is required for Fur regulation of hilA , it seemed possible that Fur regulates hilD expression in some manner .
"
7574,7575,721.txt,3,0,,,,"To further examine potential Fur-mediated regulation of hilD , w was dependent on both transcription and translation of hilD .
"
7575,7576,721.txt,4,0,,,,"Again , when hilD was deleted in these strains , Fur regulation of hilD was abrogated , while overproduction of HilC still induced hilD expression .
"
7576,7577,721.txt,5,0,,,,"When the hilD translational fusion was placed under control of the lacUV5 promoter , overproduction of Fur had no effect .
"
7577,7578,721.txt,6,0,,,,"Taken together , these data rule out the possibility that there is Fur control of SPI1 by simple activation of hilD transcription or translation .
"
7578,7579,721.txt,7,0,,,,"Fur regulation of hilD requires the HilD protein .
"
7579,7580,721.txt,8,0,,,,"Fur does not directly regulate hilD transcription .
"
7580,7581,721.txt,9,0,,,,"Although data suggest that hilD is not controlled at the translational level , we wanted to determine if RyhB was involved in Fur-mediated regulation of SPI1 .
"
7581,7582,721.txt,10,0,,,,"Although data suggest that hilD is not controlled at the translational level , we wanted to determine if RyhB was involved in Fur-mediated regulation of SPI1 .
"
7582,7583,721.txt,11,0,,,,"If small RNAs are involved in the Fur regulation of hilD , deletion of hfq could increase expression of hilA in the fur background .
"
7583,7584,721.txt,12,0,,,,"Fur directly binds to the hilD promoter .
"
7584,7585,721.txt,13,0,,,,Metal-bound Fur has also been shown to bind to an AT-rich region of the hilD promoter to stimulate hilD transcription .
7585,7586,26.txt,1,0,,,,"These features of the ugtL promoter are atypical for PhoP-regulated promoters and could be the reason that ugtL transcription also requires the SlyA protein ( Fig. 1A ) .
"
7586,7587,26.txt,2,0,,,,"These features of the ugtL promoter are atypical for PhoP-regulated promoters and could be the reason that ugtL transcription also requires the SlyA protein ( Fig. 1A ) .
"
7587,7588,26.txt,3,0,,,,"The PhoP and SlyA protein appear to be part of a feed-forward loop that controls transcription of the ugtL gene and possibly additional PhoP-regulated genes .
"
7588,7589,26.txt,4,0,,,,"We propose that the PhoP proteins control ugtL transcription .
"
7589,7590,26.txt,5,0,,,,"Then , we found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region overlapping the potential 10 of the ugtL promoter .
"
7590,7591,26.txt,6,0,,,,"Then , we found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring a 1-proximal region with no resemblance to the PhoP box .
"
7591,7592,26.txt,7,0,,,,"Then , we found that the PhoP protein binds to two regions of the ugtL promoter : an upstream region harboring an imperfect hexanucleotide repeat .
"
7592,7593,26.txt,8,0,,,,"These results demonstrate that the PhoP proteins bind to the ugtL promoter .
"
7593,7594,26.txt,9,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either downstream PhoP binding sites in the ugtL promoter .
"
7594,7595,26.txt,10,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either the upstream in the ugtL promoter .
"
7595,7596,26.txt,11,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either downstream PhoP binding sites in the ugtL promoter .
"
7596,7597,26.txt,12,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein for Transcription of the ugtL Gene in Vivo -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either the upstream in the ugtL promoter .
"
7597,7598,26.txt,13,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either downstream PhoP binding sites in the ugtL promoter .
"
7598,7599,26.txt,14,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring nucleotide substitutions at either the upstream in the ugtL promoter .
"
7599,7600,26.txt,15,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either downstream PhoP binding sites in the ugtL promoter .
"
7600,7601,26.txt,16,0,,,,"The PhoP Binding Sites in the ugtL Promoter Are Required for Binding of the PhoP Protein to the ugtL Promoter in Vitro -- To examine the role of the PhoP binding sites in the ugtL promoter , we generated a set of isogenic strains harboring wild-type sequences at either the upstream in the ugtL promoter .
"
7601,7602,26.txt,17,0,,,,"These results demonstrate that binding of the PhoP protein to both PhoP binding sites in the ugtL promoter is required for ugtL transcription .
"
7602,7603,26.txt,18,0,,,,"The PhoP proteins bind to the ugtL promoter .
"
7603,7604,26.txt,19,0,,,,"We have established that transcription of polymyxin B resistance gene ugtL is controlled by the PhoP proteins in what appears to be a feedforward loop design .
"
7604,7605,26.txt,20,0,,,,"Mutation of the PhoP2 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .
"
7605,7606,26.txt,21,0,,,,"Mutation of the PhoP2 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .
"
7606,7607,26.txt,22,0,,,,"Mutation of the PhoP2 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .
"
7607,7608,26.txt,23,0,,,,"Mutation of the PhoP2 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .
"
7608,7609,26.txt,24,0,,,,"Mutation of the PhoP1 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .
"
7609,7610,26.txt,25,0,,,,"Mutation of the PhoP1 sites abolished Fig. 3A , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .
"
7610,7611,26.txt,26,0,,,,"Mutation of the PhoP1 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase Fig. 3B .
"
7611,7612,26.txt,27,0,,,,"Mutation of the PhoP1 sites abolished ugtL transcription , possibly because it prevented binding of the PhoP protein to the ugtL promoter as suggested by the DNase I footprinting results .
"
7612,7613,26.txt,28,0,,,,"Taken together with the identification of binding sites for both PhoP proteins in Fig. 2C , these results support the notion of a feedforward design in the regulation of ugtL transcription .
"
7613,7614,26.txt,29,0,,,,"Taken together with the identification of binding sites for both PhoP proteins in the ugtL promoter , these results support the notion of a feedforward design in the regulation of ugtL transcription .
"
7614,7615,26.txt,30,0,,,,"Although full resist-ance to polymyxin B requires ugtL , these genes appear to be differentially regulated by PhoP in that transcription of Fig. 1A
"
7615,7616,26.txt,31,0,,,,"Although full resist-ance to polymyxin B requires ugtL , these genes appear to be differentially regulated by PhoP in that transcription of the former
"
7616,7617,26.txt,32,0,,,,"Model _ illustrating the feed-forward regulation of the ugtL gene by the PhoP proteins
"
7617,7618,26.txt,33,0,,,,"PhoP along with SlyA bind to the ugtL promoter
"
7618,7619,26.txt,34,0,,,,"The PhoP-regulated ugtL gene is required for resistance to magainin 2 and other alpha-helical antimicrobial peptides To examine whether the ugtL and STM1600 genes were required for resistance to magainin 2 , we constructed strains completely deleted for the chromosomal copies of these genes ( see Experimental procedures ) .
"
7619,7620,26.txt,35,0,,,,"Having demonstrated previously that ugtL is a PhoP-activated gene ( Hilbert et al. , 1999 ) , these results validated our strategy for the recovery of the PhoP-regulated peptide resistance determinants .
"
7620,7621,26.txt,36,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance .
"
7621,7622,26.txt,37,0,,,,"These results demonstrate that PhoP-regulated polymyxin B resistance is mediated by the ugtL gene and by some of the targets of PmrA -- PmrB regulation ( Groisman et al. , 1997 ; Gunn et al. , 1998 ) .
"
7622,7623,26.txt,38,0,,,,"w ild-type + y v q e jA cto + r y v q e jA cto + r pyqj PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .
"
7623,7624,26.txt,39,0,,,,"w ild-type + y v q e jA cto + r y v q e jA cto + r pyqj PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .
"
7624,7625,26.txt,40,0,,,,"A ugtL pagP double mutant was more sensitive than either the ugtL or pagP single mutants but still more resistant than the phoP mutant ( Fig. 2C ) , indicating that the ugtL and pagP genes participate in different pathways of magainin 2 resistance and that additional PhoP-regulated genes contribute to magainin 2 resistance .
"
7625,7626,26.txt,41,1,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .
"
7626,7627,26.txt,42,1,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .
"
7627,7628,26.txt,43,0,,,,"In addition to ugtL , PhoP-regulated magainin 2 resistance requires the pagP and yqjA genes ( Fig. 2C ) .
"
7628,7629,26.txt,44,0,,,,"The PhoP-regulated ugtL gene mediates the formation of a monophosphorylated lipid-A .
"
7629,7630,26.txt,45,0,,,,"two genes -- ugtL -- are both transcriptionally regulated by the PhoP
"
7630,7631,26.txt,46,1,Salmonella,Salmonella,Salmonella,"Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .
"
7631,7632,26.txt,47,1,Salmonella,Salmonella,Salmonella,"Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .
"
7632,7633,26.txt,48,1,Salmonella,Salmonella,Salmonella,"Shi Y , Groisman E-A Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .
"
7633,7634,26.txt,49,1,Salmonella,Salmonella,Salmonella,"Shi Y , Groisman EA Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .
"
7634,7635,26.txt,50,1,Salmonella,Salmonella,Salmonella,"Shi Y , Groisman EA Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .
"
7635,7636,26.txt,51,0,,,,"Two StpA-repressed PhoP-dependent genes _ bound by ugtL
"
7636,7637,26.txt,52,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The S. Typhimurium ugtL are regulated by a similar mechanism , involving the response regulator of the PhoP/PhoQ two-component system .
"
7637,7638,26.txt,53,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The S. Typhimurium ugtL are regulated by a similar mechanism , involving the response regulator of the PhoP/PhoQ two-component system .
"
7638,7639,26.txt,54,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The S. Typhimurium ugtL are regulated by a similar mechanism , involving PhoP .
"
7639,7640,26.txt,55,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .
"
7640,7641,26.txt,56,1,Salmonella,Salmonella,Salmonella,Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP .
7641,7642,866.txt,1,1,unidentified,unknown,unidentified,"In addition , the PTS permease STM4538 is positively involved in regulation of CadC proteolysis through an unknown mechanism ."
7642,7643,2145.txt,1,0,,,,"Under low osmolality , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
7643,7644,2145.txt,2,0,,,,"Under acidic pH , the ssrB genes are transcriptionally activated by the binding of PhoP ~ P to their promoters whose levels are in turn .
"
7644,7645,2145.txt,3,1,Salmonella,Salmonella,Salmonella,"PhoP upregulates the expression of SPI-2 by directly activating transcription of ssrB , therefore PhoP is indispensible for Salmonella within phagosomes ."
7645,7646,2151.txt,1,0,,,,"If a condition exists in which hilA is repressed while invF expression is induced through HilC , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?
"
7646,7647,2151.txt,2,0,,,,"Transcriptional activation by HilC relieves repression of the hilA promoter by the nucleoid proteins H-NS and Hha .
"
7647,7648,2151.txt,3,0,,,,"In addition , a role of HilC mediated repression of hilA was not investigated .
"
7648,7649,2151.txt,4,0,,,,"HilC relieve repression of the hilA promoter by the nucleoid proteins H-NS and Hha .
"
7649,7650,2151.txt,5,0,,,,H-NS repression of hilA counteracts transcriptional activation by HilC
7650,7651,1458.txt,1,0,,,,"For SPI3 , the PhoP-activated mgtCBR operon [ 40 ] was up-regulated > 15 fold within mac-rophages , while other SPI3 genes ( slsA , marT and rhuM ) were moderately up-regulated ."
7651,7652,32.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,Transcription of the hilE gene is activated by FimZY in serovar Typhimurium .
7652,7653,872.txt,1,0,,,,"pBAD24-CadC-HA expressed CadC-HA under the control of araBAD promoter
"
7653,7654,872.txt,2,0,,,,a pBAD24 derivative expressed CadC-HA under the control of araBAD promoter
7654,7655,1316.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) ."
7655,7656,682.txt,1,0,,,,"potassium permanganate reactivity experiments with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the adrA promoters .
"
7656,7657,682.txt,2,0,,,,"In vitro transcription assays with purified His6-Crl showed that Crl directly activated S-dependent transcription initiation at the adrA promoters .
"
7657,7658,682.txt,3,1,Salmonella,Salmonella,Salmonella,"In vitro transcription experiments with purified Crl protein of Salmonella showed that Crl stimulates S-dependent transcription at the adrA promoters .
"
7658,7659,682.txt,4,0,,,,"Crl protein activates in-vitro-transcription by E S from the adrA promoters .
"
7659,7660,682.txt,5,0,,,,"Together , these results showed that Crl enhanced both the rate of formation of open complexes by E S from the adrA promoters .
"
7660,7661,682.txt,6,0,,,,"Together , these results showed that Crl enhanced both the quantity of open complexes by E S from the adrA promoters .
"
7661,7662,682.txt,7,0,,,,"In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA genes ; these genes are involved in the biosynthesis of cellulose .
"
7662,7663,682.txt,8,0,,,,In vitro transcription experiments with the Crl protein showed that Crl stimulates S-dependent transcription at promoters of the adrA genes ; these genes are involved in the biosynthesis of curli .
7663,7664,2179.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"ompR In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress _ mediating the reciprocal osmotic control of ompC
"
7664,7665,2179.txt,2,0,,,,"Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompC is not clearly understood .
"
7665,7666,2179.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"ompR In E. coli , OmpR is clearly involved in the cellular response to osmotic-stress _ mediating the reciprocal osmotic control of ompC
"
7666,7667,2179.txt,4,0,,,,"Phosphorylation of OmpR induces a conformational change how this change influ-ences OmpR control of ompC is not clearly understood .
"
7667,7668,2179.txt,5,0,,,,"Expression of the ompC is under the control of OmpR .
"
7668,7669,2179.txt,6,1,Salmonella,Salmonella,Salmonella,"The two-component regulatory system OmpR = EnvZ regulates ompC in response to osmolarity changes in Salmonella .
"
7669,7670,2179.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Genes previously characterised as OmpR-regulated with decreased levels of expression in S. Typhi Ty2 ompR mutants were tviABCDE , vexABCDE , ompC and ompS .
"
7670,7671,2179.txt,8,0,,,,"Transcription regulation of ompC by OmpR .
"
7671,7672,2179.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"These results support the model where the LtrR protein directly induces ompR expression , upon which OmpR binds to the regulatory region of ompC to induce their synthesis in S. Typhi IMSS-1 .
"
7672,7673,2179.txt,10,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"ompC are required for resistance to the bile salt sodium deoxycholate in S. Typhi We have shown that LtrR has a role in the synthesis of the major outer membrane proteins OmpF and OmpC through its direct regulation of OmpR .
"
7673,7674,2179.txt,11,0,,,,"Cytoplasmic acidification was completely dependent on the OmpR response regulator , but did not require known OmpR-regulated genes such as ompC , ompF , or ssaC ( SPI-2 ) .
"
7674,7675,2179.txt,12,0,,,,Transcription regulation of ompC by OmpR .
7675,7676,1470.txt,1,0,,,,"LacI expression in 14028 was also under the control of its native promoter by inserting both lacI gene sequence to pACYC184 .
"
7676,7677,1470.txt,2,0,,,,LacI expression in 14028 was also under the control of its native promoter by inserting both lacI promoter to pACYC184 .
7677,7678,1464.txt,1,0,,,,"Collectively , these results strongly suggest that the pmrC , ugd and pmrG genes and the pbgPE operon are the only PmrA-regulated determinants required for Fe ( III ) resistance .
"
7678,7679,1464.txt,2,0,,,,"PmrA-regulated genes described and the modifications their products mediate are : pmrHFIJKL/pmrE , 4-aminoarabinose ; cptA , heptose I phosphoethanolamine phosphotransferase ; pmrC , lipid-A phosphoethanolamine phosphotransferase ; cld , O-antigen chain length determinant ; pmrG , heptose II phosphatase ."
7679,7680,696.txt,1,0,,,,"These results suggest that the induction of tdcA expression by anaerobic conditions is observable when tdcA expression is low owing to the absence of TdcR .
"
7680,7681,696.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , TdcR overexpression increased tdcA expression under both conditions ."
7681,7682,1302.txt,1,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance ."
7682,7683,2186.txt,1,0,,,,"Both the phoN mutant induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : a phoN fliC fljB mutant , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
7683,7684,2186.txt,2,0,,,,"Both the phoN mutant induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : tviA mutant fliC fljB mutant , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
7684,7685,2186.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Both the S. Typhimurium wild type induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : a phoN fliC fljB mutant , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
7685,7686,2186.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Both the S. Typhimurium wild type induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : tviA mutant fliC fljB mutant , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion ."
7686,7687,2192.txt,1,0,,,,"The spv locus is composed of a regulatory gene , spvR , coding for a LysR-like transcription activator that positively regulates both its own gene and the spvABCD operon of structural genes ( Fang et al. 1991 , 1992 ; Krause et al. 1992 ; Guiney et al. 1995 ; Pullinger et al. 1989 ; Sheehan & Dorman 1998 ) ."
7687,7688,669.txt,1,0,,,,pmrC are both transcriptionally activated by PmrAB .
7688,7689,899.txt,1,0,,,,Fur also positively regulates sipC .
7689,7690,641.txt,1,0,,,,"Indeed , a StpA-dependent decrease of crp expression was observed in 1.6-fold .
"
7690,7691,641.txt,2,0,,,,"Indeed , a StpA-dependent decrease of crp expression was observed in our experiment ."
7691,7692,127.txt,1,0,,,,"Teixido et al. showed evidence that transcription of narP , was regulated by the Fur protein regardless of oxygen conditions ."
7692,7693,133.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
7693,7694,655.txt,1,0,,,,"In the rpoS mutant , the amount of KatE is also significantly decreased ; this confirms that katE expression is also controlled by RpoS .
"
7694,7695,655.txt,2,0,,,,"Moreover , the comparison of katE expression patterns during the bacterial growth suggests that rfaH may not be regulated by RpoS .
"
7695,7696,655.txt,3,0,,,,"the RpoS _ regulated genes katE and otsA , indicating that the overexpressed RpoS protein is functional as a positive regulator
"
7696,7697,655.txt,4,0,,,,"katE _ regulated by RpoS
"
7697,7698,655.txt,5,0,,,,"The katE gene ( encoding catalase hydroperoxidase II [ HPII ] ) , is under the control of RpoS .
"
7698,7699,655.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"It is well known that in E. coli , RpoS controls the expression of katE to oxygen under nutrient-limiting conditions .
"
7699,7700,655.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"It is well known that in E. coli , RpoS controls the expression of katE to water under nutrient-limiting conditions .
"
7700,7701,655.txt,8,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"It is well known that in S. Typhimurium , RpoS controls the expression of katE to oxygen under nutrient-limiting conditions .
"
7701,7702,655.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"It is well known that in S. Typhimurium , RpoS controls the expression of katE to water under nutrient-limiting conditions ."
7702,7703,1896.txt,1,0,,,,The transcription of fumA genes was most repressed by YdcI .
7703,7704,1128.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium;S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Results Changes in S. Typhimurium gene expression after chromosomal insertion of tviA In S. Typhi , TviA-regulated genes have been identified and encompass the flagella regulon and genes encoding T3SS-1 [ 8 ] .
"
7704,7705,1128.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,typhoidal;S. Typhimurium;Typhimurium;S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"To determine how TviA affects gene expression in a non-typhoidal serotype , the tviA gene was introduced into the S. Typhimurium chromosome and the gene expression profile compared to a published gene expression profile of TviA-regulated genes in S. Typhi [ 8 ] ."
7705,7706,1882.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"that YncC are both able to induce expression of the yciGFE locus in E. coli K-12
"
7706,7707,1882.txt,2,1,Salmonella,Salmonella,Salmonella,that YncC are both able to induce expression of the yciGFE locus in Salmonella
7707,7708,1672.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
7708,7709,480.txt,1,0,,,,"The constitutive phoP gene was placed under the control of an arabinose-inducible promoter to examine the kinetics of PhoP-activated gene induction .
"
7709,7710,480.txt,2,0,,,,"A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence .
"
7710,7711,480.txt,3,0,,,,"A differential regulation of a PhoP-dependent gene during the infection period might be related to the fact that tight regulation of the phoP regulon is required for virulence .
"
7711,7712,480.txt,4,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : phoP .
"
7712,7713,480.txt,5,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : phoP .
"
7713,7714,480.txt,6,0,,,,"PhoP-regulated genes were further identified by transcriptional profiling using microarrays of strain CS022 containing a phoQ mutation that results in increased expression of PhoP-activated genes and a phoP null mutant ( W.N. , unpubl .
"
7714,7715,480.txt,7,1,unidentified plasmid,plasmid,unidentified plasmid,"To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .
"
7715,7716,480.txt,8,0,,,,"PhoP binds to the promoter regions of the phoP , mgtA , slyB , pcgL .
"
7716,7717,480.txt,9,0,,,,"The PhoP/PhoQ system is required for transcription from one of the promoters of the slyA gene ( 20 ) , suggesting that some of the phenotypes displayed phoP and phoQ mutants could be caused by their inability to express the SlyA protein and implying that SlyA participates in transcription of a subset of PhoP-regulated genes .
"
7717,7718,480.txt,10,3,Salmonella;Salmonella enterica;Salmonella;unidentified plasmid,Salmonella;Salmonella enterica;enterica;plasmid,Salmonella enterica;Salmonella;unidentified plasmid,"Summary In Salmonella enterica , the PhoP -- PhoQ two-component system governs resistance to structurally different antimicrobial peptides including the alphahelical magainin 2 , the b-sheet defensins and the cyclic lipopeptide polymyxin B. To identify the PhoP-regulated determinants mediating peptide resistance , we prepared a plasmid library from a phoP mutant , introduced it into a phoP mutant and selected for magainin-resistant clones .
"
7718,7719,480.txt,11,1,Salmonella,Salmonella,Salmonella,"The ugtL gene mediates polymyxin B resistance independently of the PmrA-PmrB system phoP Salmonella are > 20 times more polymyxin sensitive than a pmrA mutant when bacteria are grown in low ygjU 3394555 3392617 rfaB rfaI 3914096 3915562 slsA STM3760 cigR 3959077 3960805 rhaT rhaR 4260472 4262386 STM0725 STM0726 STM0724 792487 790384 Mg2 + ( Wosten et al. , 2000 ) , indicating that a PmrA-inde-pendent PhoP-regulated gene ( s ) is necessary for poly-myxin resistance .
"
7719,7720,480.txt,12,0,,,,"w ild-type + y v q e jA cto + r y v q e jA cto + r pyqj PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .
"
7720,7721,480.txt,13,0,,,,"w ild-type + y v q e jA cto + r y v q e jA cto + r pyqj PhoP-regulated magainin 2 resistance is mediated by the ugtL , pagP and yqjA genes Because the ugtL mutant was not as susceptible to magai-nin 2 as the phoP mutant ( Fig. 2A ) , we reasoned that another PhoP-regulated gene ( s ) must be involved in magainin 2 resistance .
"
7721,7722,480.txt,14,1,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,14028s,Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"The ugtL and pmrA genes mediate PhoP-controlled resistance to polymyxin B. A. Percentage survival of wild-type ( 14028s ) , phoP ( MS7953s ) and ugtL ( EG13682 ) strains after incubation with polymyxin B ( 1.0 mg ml-1 ) .
"
7722,7723,480.txt,15,3,Iris germanica;Salmonella enterica subsp. enterica serovar Typhimurium 14028S;Iris germanica;Iris germanica;unidentified,FLAG;14028s;flag;flag;unknown,Salmonella enterica subsp. enterica serovar Typhimurium 14028S;unidentified;Iris germanica,"% surviva A B C 100 10 1 r r to to gtL c c u ve ve p e L tL + + + typ gt ug u-ild w pe P y o-t h ld p w i L e oP rA gtL h m u p p A r m p gt u yp-t ld w i A Mg2 + L L L H b-galactosidase activity YqjA-FLAG w ild-type 14028s p h o yqjA-flag P B yqjA w 10µM Mg2 + 2 + - flag ; phoP 10mM Mg ild-type 5 0 40 p Discussion The PhoP -- PhoQ regulatory system controls resistance to a variety of structurally different antimicrobial peptides ( Groisman et al. , 1992 ) , but the identity of the PhoP-regulated determinants mediating peptide resistance has remained largely unknown .
"
7723,7724,480.txt,16,1,Salmonella,Salmonella,Salmonella,"A phoP mutant is > 20 times more polymyxin B sensitive than a pmrA mutant when bacteria are grown in low Mg2 + and > 20 times more sensitive than wild-type Salmonella when bacteria are grown in the presence of Fe3 + ( Wosten et al. , 2000 ) , indicating that a PhoP-regulated PmrA-independent gene ( s ) participate ( s ) in polymyxin B resistance .
"
7724,7725,480.txt,17,0,,,,"Moreover , we are able to recapitulate the susceptibility of the phoP mutant to magainin 2 and polymyxin B by constructing strains defective in different combinations of PhoP-regulated genes .
"
7725,7726,480.txt,18,3,Methanosarcina barkeri;unidentified plasmid;Cloning vector pUC19,strain MS;plasmid;plasmid pUC19,Cloning vector pUC19;Methanosarcina barkeri;unidentified plasmid,"To identify PhoP-regulated genes mediating magainin 2 resistance , we prepared a genomic library from the phoP mutant strain MS7953s in the multicopy number plasmid pUC19 ( Norrander et al. , 1983 ) , introduced the library into the same phoP mutant and exposed the transformants to magainin 2 ( see Experimental procedures ) .
"
7726,7727,480.txt,19,0,,,,"This strategy was based on the premise that PhoP-regulated genes might be expressed from the lac promoter in pUC19 and confer magainin 2 resistance upon the phoP mutant .
"
7727,7728,480.txt,20,1,Escherichia coli;Escherichia coli,Escherichia coli;Escherichia coli,Escherichia coli,"These results were unexpected because acid resistance genes were not identified as PhoP-regulated genes in two previous microarray experiments that compared expression of wild-type and phoP Escherichia coli strains ( 14 , 35 ) nor had mutations in phoP been uncovered in screenings for acid regulatory genes in Escherichia coli .
"
7728,7729,480.txt,21,0,,,,"For example , one of the profiles encompassed promoters that belong to the same expression ( E1 ) , PhoP box submotif ( M2 ) , and promoter class ( P1 ) ( Fig. 1H ) and harbored not only the prototypical PhoP-regulated phoP and mgtA promoters ( 13 , 14 ) but also the yhiW promoter , which was not known to be under PhoP control .
"
7729,7730,480.txt,22,0,,,,"pagC was downregulated almost 100-fold in the phoP mutant , validating this method for investigating gene regulation by PhoP inside macrophages .
"
7730,7731,480.txt,23,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) .
"
7731,7732,480.txt,24,0,,,,"The PhoP homodimer functions as a transcription factor by recognizing and binding to phoP boxes in promoters of PhoP-regulated genes .
"
7732,7733,480.txt,25,0,,,,"The PhoP homodimer functions as a transcription factor by binding to phoP boxes in promoters of PhoP-regulated genes .
"
7733,7734,480.txt,26,0,,,,"The PhoP homodimer binds to phoP boxes in promoters of PhoP-regu-lated genes to modulate virulence gene expression .
"
7734,7735,480.txt,27,0,,,,"Expression of the fusions in phoP backgrounds indicated that the cloned region contained the signals necessary for PhoP-mediated regulation of sseK1 .
"
7735,7736,480.txt,28,0,,,,"In contrast , intracellular induction was not observed in a phoP null mutant , giving additional support to the conclusion that PhoP is a positive regulator of the expression of sseK1 .
"
7736,7737,480.txt,29,0,,,,"Subsequently , the phosphoryl of PhoQ is transferred to the conserved aspartyl of PhoP , and then the phosphorylated PhoP activates the transcription of phoP itself and PhoP-regulated genes .
"
7737,7738,480.txt,30,0,,,,"It has been shown that the transcription of phoP and PhoP-regulated genes were completely inhibited by 10 mM magnesium [ 41 ] , which caused about one third of PhoP K201 was acetylated , suggesting low acetylation proportion of PhoP K201 is required for PhoP activity .
"
7738,7739,480.txt,31,0,,,,"The underlying reason is that PhoP K201R kept the ability to activate phoP transcription initiated from P1 promoter and PhoP-regulated gene transcription during infection , while PhoP K201Q inhibited these genes transcription due to its low DNA-binding affinity .
"
7739,7740,480.txt,32,0,,,,"Acetylation of lysine residue located in the DNA-binding motif inhibits DNA-binding ability of PhoP , and further alters the transcription of phoP and PhoP-regulated genes .
"
7740,7741,480.txt,33,0,,,,"Acetylation inhibits the transcription of phoP and PhoP-regulated genes As a major transcription factor , PhoP regulates the expression of ~ 5 % of genes in S. Typhimur-ium genome , including itself , and the positive feedback boosts the level of PhoP to extend the response range of the PhoP-PhoQ circuit under conditions that strongly activate PhoQ [ 30 ] .
"
7741,7742,480.txt,34,0,,,,"The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .
"
7742,7743,480.txt,35,0,,,,"The quantitative real-time PCR ( qPCR ) result showed that phoP and PhoP-regulated genes were all up-regulated in the pat deletion mutant compared with those in the wild type strain ( Fig 2A ) , while the transcriptional level of phoP did not change in the cobB deletion mutant ( S2 Fig ) .
"
7743,7744,480.txt,36,0,,,,"We next ask whether deletion of pat increases the transcription of phoP and PhoP-regulated genes in-vivo .
"
7744,7745,480.txt,37,0,,,,"mRNA levels of phoP and PhoP-regulated genes in the pat deletion mutant were also elevated significantly compared with the wild type strain in macrophage cells ( Fig 2C ) .
"
7745,7746,480.txt,38,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The qPCR assay demonstrated that both K201Q and K201A mutations led to significant transcriptional reduction of phoP and PhoP-regulated genes compared with the wild type strain , while K201R mimicking non-acetylated lysine residue activated the transcription of these genes dramatically ( Fig 3C ) , suggesting acetylation of K201 is involved in regulating the binding of PhoP to its DNA site and thus its ability to regulate its regulon in S. Typhimurium in-vivo ."
7746,7747,1114.txt,1,0,,,,"We have recently established that the PhoP-activated ugtL gene is required for resistance to the antimicrobial peptides magainin 2 and polymyxin B .
"
7747,7748,1114.txt,2,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The ugtL gene is part of a Salmonella-specific gene cluster that includes the PhoP-activated pcgL gene ( 22 ) and the sifB gene , which is expressed in response to the low Mg2 conditions that normally activate the PhoP/PhoQ system ( 23 ) .
"
7748,7749,1114.txt,3,0,,,,"Transcriptional Activation of the ugtL Promoter -- The majority of PhoP-activated promoters described to date harbor a conserved hexanucleotide repeat separated by 5 nucleotides , termed the PhoP box , located 12 bp upstream of the 10 region ( 14 ) .
"
7749,7750,1114.txt,4,0,,,,"We have demonstrated recently that the PhoP-activated ugtL gene is required for a modification of the lipid-A mediating resistance to the antimicrobial peptides magainin 2 and poly-myxin B ( 21 ) .
"
7750,7751,1114.txt,5,0,,,,"the ugtL promoter _ performed with increasing amounts of PhoP proteins
"
7751,7752,1114.txt,6,0,,,,"the ugtL promoter _ performed with increasing amounts of the PhoP protein
"
7752,7753,1114.txt,7,1,Salmonella,Salmonella,Salmonella,"One of the clones harboured the PhoP-activated ugtL gene , deletion of which rendered Salmonella susceptible to magainin 2 and polymyxin B , but not defensin HNP-1 .
"
7753,7754,1114.txt,8,2,Salmonella;Salmonella;unidentified,Salmonella;Salmonella-specific;unknown,unidentified;Salmonella,"Three of the plasmids harboured two complete Salmonella-specific open reading frames ( ORFs ) : ugtL , a PhoP-activated gene of unknown function ( Hilbert et al. , 1999 ) ; and STM1600 , an uncharacterized ORF .
"
7754,7755,1114.txt,9,0,,,,"The PhoP-activated ugtL , pagP and yqjA genes are required for resistance to the alpha-helical peptides magainin 2 and cecropin A but not to the b-sheet defensin HNP-1 .
"
7755,7756,1114.txt,10,0,,,,"Cumulatively , these results demonstrate that yqjA is a PhoP-activated gene required for magainin 2 resistance and that yqjA confers magainin resistance by a pathway that is different from those mediated by the ugtL and pagP genes .
"
7756,7757,1114.txt,11,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"The ugtL gene was first identified as part of a Salmonella-specific DNA region harbouring the PhoP-activated pcgL gene , which encodes a D-Ala-D-Ala dipeptidase ( Hilbert et al. , 1999 ) .
"
7757,7758,1114.txt,12,2,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,SL1344;14028s,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella enterica subsp. enterica serovar Typhimurium 14028S,"We determined that a ugtL pmrA double mutant was as susceptible to polymyxin B as a phoP mutant ( Fig. 3C ) , which suggests that both types of lipid-A modifications may operate at the same time and argues against the participation of other PhoP-regulated genes in resistance to polymxyin B. Thus , the increased polymyxin B susceptibility reported for mutants defective in the PhoP-activated mig-14 , virK and somA genes may be characteristic of the SL1344 genetic background used in those studies ( Brodsky et al. , 2002 ; Detweiler et al. , 2003 ) because derivatives of the 14028s strain deleted for the mig-14 gene or harbouring a MudJ transposon insertion in the virK gene retained wild-type resistance to both polymxyin B and magainin 2 ( our unpublished results ) .
"
7758,7759,1114.txt,13,0,,,,"We establish that the PhoP-activated ugtL gene is required for resistance to magainin 2 and poly-myxin B , and determine that it encodes an inner membrane protein needed for the modification of the lipid-A .
"
7759,7760,1114.txt,14,0,,,,"both ugtL is post-tran-scriptionally activated by the PhoP
"
7760,7761,1114.txt,15,0,,,,"To activate transcription of ugtL , both PhoP must bind to its promoter simultaneously .
"
7761,7762,1114.txt,16,0,,,,"otes time-dependent resistance to polymyxin B MgtA prom The PhoP-activated pmrD and ugtL genes encode products mediating the chemical modification of negatively charged residues in the lipopolysaccharide ( LPS ) , thereby conferring resistance to the cationic peptide antibiotic polymyxin B ( Kox et al. , 2000 ; Shi et al. , 2004 ) ."
7762,7763,1100.txt,1,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Escherichia coli,Salmonella;S. Typhimurium;Typhimurium;E. coli,Escherichia coli;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Together these results indicate that the csrA expression level in Salmonella is controlled by RpoS , consistent with previous observations in S. Typhimurium , E. coli and Er .
"
7763,7764,1100.txt,2,0,,,,"the stationary sigma factor RpoS controls the expression of csrA
"
7764,7765,1100.txt,3,0,,,,the stationary sigma factor RpoS controls the expression of csrA
7765,7766,494.txt,1,0,,,,"Under these conditions , however , the growth of phoP mutants was severely limited compared to the growth of wild-type bacteria ; thus , it was not clear if the decreased SsrAB-dependent gene expression in phoP mutants was due to direct regulation by PhoPQ effects on bacterial physiology .
"
7766,7767,494.txt,2,0,,,,"the locus _ encoding the response regulator for the PhoPQ TCRS ( phoP ) gene
"
7767,7768,494.txt,3,1,unidentified,not shown,unidentified,"The unique pattern of expression of phoP was also found not to be attributable to coordinate regulation by PhoPQ ( not shown ) .
"
7768,7769,494.txt,4,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( examples include genes ) .
"
7769,7770,494.txt,5,0,,,,"Expression of the phoP gene was not increased in intracellular bacteria , although we did observe the expected PhoPQ-regulated control of PhoP-activated genes ( pag include genes ) .
"
7770,7771,494.txt,6,0,,,,"The isogenic phoP tolC strain showed intermediate permeability , as expected from the fact that some of the PhoPQ-regulated modification reactions , especially the palmitoylation of lipid-A , occur in the wild-type strain to a considerable extent ( 21 ) .
"
7771,7772,494.txt,7,0,,,,"The failure of the phoP mutant to survive in A. polyphaga cells further supports the theory that survival within survival within macrophages are largely analogous , as the PhoPQ two-component regulatory system , although associated with regulation of many genes , is key to activation of the SPI-2-encoded T3SS within phagocytes .
"
7772,7773,494.txt,8,0,,,,"The failure of the phoP mutant to survive in A. polyphaga cells further supports the theory that survival within amoebae within macrophages are largely analogous , as the PhoPQ two-component regulatory system , although associated with regulation of many genes , is key to activation of the SPI-2-encoded T3SS within phagocytes .
"
7773,7774,494.txt,9,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"Both S. Typhi PhoPQ directly control expression of phoP itself , .
"
7774,7775,494.txt,10,0,,,,phoP genes _ controlled by the PhoPQ TCS
7775,7776,1666.txt,1,0,,,,"In vitro characterization of transcriptional-fusions to virulence genes As a first application of the two-colour flow cytometric technique , the in-vivo activities of three promoters that drive the expression of genes with differential roles in virulence were studied : PsicA , which drives the expression of the operon sicA sipBCDA iacP within SPI1 ( Darwin and Miller , 2000 ) , P ( Valdivia and Falkow , 1997 ; called ssaH PssaG by Hensel et al. , 1998 ) , which drives the expression of the operon ssaHIJKLMV within SPI2 ( Cirillo et al. , 1998 ) , and PpagC , which drives the PhoP-activated expression of pagC ( Gunn et al. , 1995 ) .
"
7776,7777,1666.txt,2,0,,,,"In order to obtain direct evidence for this novel mode of PhoP regulation , we performed real time PCR analysis of pagC , a previously identified PhoP-activated gene .
"
7777,7778,1666.txt,3,0,,,,"We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ , mgtA , slyB , pmrD , pcgL , phoN , pagC , and mgtCB .
"
7778,7779,1666.txt,4,0,,,,"The mgtC and pagC genes are both PhoP-activated genes required for intramacrophage growth [ 2,5 -- 7 ] .
"
7779,7780,1666.txt,5,1,Salmonella,Salmonella,Salmonella,"The pagD and pagC genes are PhoP-activated genes ( 9 ) located next to each other in the Salmonella chromosome but transcribed in opposite directions from a shared intergenic region .
"
7780,7781,1666.txt,6,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"The PhoP-activated gene C ( pagC ) promoter of Salmonella is an inducible promoter , which is inhibited by Mg2 + in-vitro and activated after Salmonella phagocytosis by macrophages and dendritic cells in-vivo [ 52,53 ] .
"
7781,7782,1666.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,"The PhoP-activated gene pagC regulated by the PhoP/PhoQ system was identified as an IVI virulence protein in S. Typhi , and the PagC antibody was detected in sera from 11 of 14 patients , which shows that it has the potential to be developed as a diagnostic antigen ( 12 ) .
"
7782,7783,1666.txt,8,1,Salmonella,Salmonella,Salmonella,"Distinct temporal expression of PhoP-activated genes in response to mildly acidic pH and low Mg2 + We examined the mRNA levels of the PhoP-activated genes pagC and pagK at 2 h and 4 h after Salmonella was shifted from non-inducing conditions for the PhoQ protein to media containing either mildly acidic pH or low ( i.e. , 10 μM ) Mg2 + .
"
7783,7784,1666.txt,9,0,,,,"Distinct temporal expression of PhoP-activated genes in response to mildly acidic pH and low Mg2 + he MgtA protein is necessary for full transcription of a subset of PhoP-activated genes hen the PhoQ inducing signal is low Mg2 + T w Wild-type and mgtA strains had similar pagC and pagK mRNA levels at 2 h post induction ( Fig. 2A ) ( i.e. , ratio of wild-type/mgtA of 1 ) .
"
7784,7785,1666.txt,10,0,,,,PhoP dephosphorylation subsequently inhibits the PhoPQ to activate the pagC in S. Choleraesuis
7785,7786,1855.txt,1,0,,,,"Like marRAB , acrAB are positively regulated by Rob .
"
7786,7787,1855.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"While Rob appears to be an important positive regulator of acrAB in E. coli , we present data .
"
7787,7788,1855.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"Rob has been demonstrated to directly regulate transcription of acrAB in E. coli .
"
7788,7789,1855.txt,4,1,Salmonella,Salmonella,Salmonella,"Other regulators of Rob did not contrib-ute to acrAB induction by indole in Salmonella .
"
7789,7790,1855.txt,5,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , the transcription of acrAB is controlled by Rob .
"
7790,7791,1855.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"the Rob protein _ involved in regulation of acrAB in E. coli
"
7791,7792,1855.txt,7,0,,,,"In particular , the expression of acrAB is regulated by Rob .
"
7792,7793,1855.txt,8,0,,,,"a high activity state _ allowing the activation of acrAB .18 Such a mechanism would be reminiscent of the binding of bile to the Rob protein 34
"
7793,7794,1855.txt,9,1,Escherichia coli,E. coli,Escherichia coli,"the Rob protein 34 _ involved in the regulation of acrAB in E. coli
"
7794,7795,1855.txt,10,1,Salmonella,Salmonella,Salmonella,"For example , acrAB transcription in Salmonella is controlled by Rob ."
7795,7796,319.txt,1,0,,,,"A LexA-repressed gene , sulA , is not constitutively expressed , allowing detection of SOS response activation ."
7796,7797,1841.txt,1,0,,,,"HilD positively regulate sprB , most likely cotrans-criptionally with hilC itself , since sprB are cotranscribed -LRB- see Fig .
"
7797,7798,1841.txt,2,0,,,,"HilD positively regulate sprB , most likely cotrans-criptionally with hilC itself , since hilC are cotranscribed -LRB- see Fig ."
7798,7799,1699.txt,1,0,,,,"For this purpose , we analyzed the effect of L-arabinose on the expression of three HilD-activated genes ( hilC , rtsA , and invH ) ."
7799,7800,1869.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"This positive control must be mediated by binding of the S. typhimurium Fur protein to the flhD promoter as indicated by the fact that this promoter tests positive in a Fur titration assay .
"
7800,7801,1869.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"This result demonstrates that the Fur protein must bind to the S. typhimurium flhD promoter .
"
7801,7802,1869.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Moreover , the S. typhimurium flhD master operon , is positively regulated by Fur through an iron-independent mechanism ."
7802,7803,325.txt,1,0,,,,dgoA was previously shown to be regulated by PmrAB
7803,7804,443.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , five transcription factors have been implicated : hmp transcription is activated by MetR .
"
7804,7805,443.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , five transcription factors have been implicated : hmp transcription is activated by MetR .
"
7805,7806,443.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA -- hmp intergenic region .
"
7806,7807,443.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA -- hmp intergenic region .
"
7807,7808,443.txt,5,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser 
"
7808,7809,443.txt,6,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser 
"
7809,7810,443.txt,7,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA-hmp intergenic region .
"
7810,7811,443.txt,8,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA-hmp intergenic region .
"
7811,7812,443.txt,9,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser 
"
7812,7813,443.txt,10,0,,,,"A novel mechanism for upregulation of the flavohaemoglobin gene by the ` NO releaser 
"
7813,7814,443.txt,11,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of modulation of MetR binding to the glyA-hmp intergenic region .
"
7814,7815,443.txt,12,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by S-nitrosoglutathione : nitrosation of homocysteine of MetR binding to the glyA-hmp intergenic region .
"
7815,7816,443.txt,13,1,Escherichia coli,Escherichia coli,Escherichia coli,"A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser 
"
7816,7817,443.txt,14,1,Escherichia coli,Escherichia coli,Escherichia coli,A novel mechanism for upregulation of the Escherichia coli K-12 hmp gene by the ` NO releaser 
7817,7818,457.txt,1,0,,,,"Other genes varied in prevalence , including trhH ( encoding pilus assembly protein ) , sirA ( two-component system with barA ) , pagK ( PhoPQ-activated protein ) , and sseK1 ( encoding putative-secreted effector protein ) ."
7818,7819,331.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,CRP-cAMP regulates csgD formation by uropathogenic Escherichia coli .
7819,7820,456.txt,1,0,,,,"These results showed that , whereas OmpR-mediated regulation of hilA expression was dampened in a DhilC DrtsA background , regulation was blocked only in strains missing HilD , suggesting that OmpR controls SPI1 expression by regulating hilD expression ."
7820,7821,330.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
7821,7822,324.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"Negative regulation of mutH RpoS global regulators of Escherichia coli K-12 .
"
7822,7823,324.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Negative regulation of mutH RpoS global regulators of Escherichia coli K-12 .
"
7823,7824,324.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Negative regulation of mutH RpoS global regulators of Escherichia coli K-12 .
"
7824,7825,324.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,Negative regulation of mutH RpoS global regulators of Escherichia coli K-12 .
7825,7826,1868.txt,1,0,,,,"pH coordinately affect the transcription of hilA in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .
"
7826,7827,1868.txt,2,0,,,,"oxygen coordinately affect the transcription of hilA in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .
"
7827,7828,1868.txt,3,0,,,,"Osmolarity coordinately affect the transcription of hilA in the level of HilA mediate the regulation of TTSS-1 by the same environmental conditions .
"
7828,7829,1868.txt,4,0,,,,"Although a great deal is known about the complex regulation of hilA gene expression , very little is known about the HilA protein .
"
7829,7830,1868.txt,5,0,,,,"Genes in SPI-5 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .
"
7830,7831,1868.txt,6,0,,,,"Genes in SPI-4 are controlled by HilA , a transcriptional regulator by SirA , a regulator of hilA .
"
7831,7832,1868.txt,7,1,Salmonella,Salmonella,Salmonella,"HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in internal organs in poultry , animals were infected with 10 CFU of its parent strain at day of hatch .
"
7832,7833,1868.txt,8,1,Salmonella;Salmonella,Salmonella;Enteritidis,Salmonella,"HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in internal organs in poultry , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis .
"
7833,7834,1868.txt,9,1,Salmonella,Salmonella,Salmonella,"HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut , animals were infected with 10 CFU of its parent strain at day of hatch .
"
7834,7835,1868.txt,10,1,Salmonella;Salmonella,Salmonella;Enteritidis,Salmonella,"HilA is the key regulator of the Salmonella Pathogenicity Island I. To assess the role of hilA in colonization of gut , animals were infected with 10 CFU of a DhilA mutant of S. 8 Enteritidis .
"
7835,7836,1868.txt,11,0,,,,"3 s 4 Model 2 : Two feedforward loops with OR gate logic for regulation of P by monomer hilA activation ðModel 4Þ s 5 1/2 6 a3 HilA : ðModel 2Þ e activators are set to 2 , the the activation of PhilA by If Hill coefficients of all th model generated represents homodimers .
"
7836,7837,1868.txt,12,0,,,,"The X-axis shows the time in arbitrary units while the Y-axis shows the level of HilA in arbitrary units Comparison of P regulation by AND and OR hilA architectures .
"
7837,7838,1868.txt,13,1,Salmonella,Salmonella,Salmonella,"As HilA is an important transcriptional regulator of SPI-1 , Bohez et al. discovered that Salmonella with hilA mutant is the promising vaccines due to its remarkable role in reducing colonization .
"
7838,7839,1868.txt,14,1,Salmonella,Salmonella,Salmonella,"As HilA is an important transcriptional regulator of SPI-1 , Bohez et al. discovered that Salmonella with hilA mutant is the promising vaccines due to its remarkable role in reducing invasion .
"
7839,7840,1868.txt,15,0,,,,"Differential expression of the hilA gene The HilA protein is the master regulator of SPI-1 typically decrease on invasion .
"
7840,7841,1868.txt,16,0,,,,"Differential expression of the hilA gene The HilA protein is the master regulator of SPI-1 typically have a corresponding increase .
"
7841,7842,1868.txt,17,0,,,,"However , RNA-seq data from a hilA strain with/without transient overexpression of HilA were consistent with regulation of transcripts within SPI-1 .
"
7842,7843,1868.txt,18,0,,,,"Our data show that Gre factors are involved in the transcriptional expression of both hilA and HilA-regulated genes .
"
7843,7844,1868.txt,19,0,,,,"Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) .
"
7844,7845,1868.txt,20,0,,,,"We can infer that this negative regulation is a consequence of SlyA binding to the hilA promoter region ( Fig. 4C ) , which affects the expression of all HilA-regulated genes in a downstream cascade ."
7845,7846,442.txt,1,0,,,,"( C ) Alignment of the promoter regions of steA and six PhoP-activated genes with a similar architecture ( 49 ) .
"
7846,7847,442.txt,2,0,,,,"Here , we show that steA possesses a PhoP-activated promoter with a PhoP box located 12 nucleotides upstream of the 10 hexamer , resembling promoters with architecture I .
"
7847,7848,442.txt,3,0,,,,"These results establish that regulation of steA by PhoQ/PhoP suggest that PhoP could be a direct activator of steA .
"
7848,7849,442.txt,4,0,,,,"Results suggest that PhoP could be a direct activator of steA transcription .
"
7849,7850,442.txt,5,0,,,,"that PhoP directly activates steA
"
7850,7851,442.txt,6,0,,,,"A similar motif is found in the promoters of a subset of PhoP-activated genes , including steA , phoP , mgtA , pmrD , slyB , and orgB ( Fig. 6B ) ."
7851,7852,1698.txt,1,0,,,,"We also determined that the Fur protein was acting as a transcriptional repressor of the feoAB operon because deletion of the fur gene resulted in a twofold increase of Fig. 2A .
"
7852,7853,1698.txt,2,0,,,,"We also determined that the Fur protein was acting as a transcriptional repressor of the feoAB operon because deletion of the fur gene resulted in a twofold increase of the wild-type feoAB transcripts .
"
7853,7854,1698.txt,3,0,,,,"Fur directly binds to the hilD promoter and enhances its own expression ( 15 ) , and HilD functions as an activator of SPI-1 expression ( 17 ) ."
7854,7855,1840.txt,1,1,Salmonella,Salmonella,Salmonella,"somA require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rpoS .
"
7855,7856,1840.txt,2,1,Salmonella,Salmonella,Salmonella,"VirK require the response regulator PhoP for expression To determine whether the expression of somA is regulated by transcription factors , the GFP report-ers were transduced into Salmonella strains with mutations in one of the following genes : rpoS .
"
7856,7857,1840.txt,3,0,,,,"These results indicate that phoP may control the expression of the rpoS gene , as substantiated by previous reports that PhoP controls the expression of rpoS gene ."
7857,7858,318.txt,1,0,,,,"We chose to start with examination of the rpoS gene since , among gram-negative bacteria , many genes are regulated by RpoS .
"
7858,7859,318.txt,2,1,Salmonella,Salmonella,Salmonella,"Consistent with a role for RpoS in the regulation of the KatN protein was not produced in the Salmonella rpoS Fig. 2A .
"
7859,7860,318.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium SL1344,Salmonella;SL1344,Salmonella enterica subsp. enterica serovar Typhimurium SL1344;Salmonella,"Consistent with a role for RpoS in the regulation of the KatN protein was not produced in the Salmonella rpoS mutant SL1344K .
"
7860,7861,318.txt,4,0,,,,"The increased sensitivity of the rpoS minus mutant suggests a role for RpoS-controlled gene expression for the higher resistance of stationary-phase cells to UV-C .
"
7861,7862,318.txt,5,0,,,,"Investigation of the KatE level in sequence analysis of rpoS genes Spv-genes are expressed during stationary-phase under control of RpoS .
"
7862,7863,318.txt,6,0,,,,"Investigation of the KatE level in strains of rpoS genes Spv-genes are expressed during stationary-phase under control of RpoS .
"
7863,7864,318.txt,7,1,Cell fusing agent virus,CFA,Cell fusing agent virus,"They suggested that the difference in the CFA synthase level may be the result of different rpoS alleles , since the expression of another RpoS-regulated gene , poxB , was lower in FT1 than ZK126 ( Wang & Cronan , 1994 ) .
"
7864,7865,318.txt,8,0,,,,"Nickerson and Curtiss found that RpoS-regulated genes are essential for colonisation of gut-associated lymphoid tissue despite the fact that the rpoS mutant colonised the gut as eficiently as did the wild-type strain [ 38 ] .
"
7865,7866,318.txt,9,0,,,,"Total rpoS expression is controlled at all levels starting from regulation of RpoS proteolysis .
"
7866,7867,318.txt,10,0,,,,"Total rpoS expression is controlled at all levels starting from regulation of RpoS proteolysis .
"
7867,7868,318.txt,11,0,,,,"An isogenic rpoS mutant strain of rpoS and a pACYC/rpoS-complemented strain ( rpoS ) were included as controls for RpoS activity .
"
7868,7869,318.txt,12,0,,,,"An isogenic rpoS mutant strain of ATCC 14028 and a pACYC/rpoS-complemented strain ( rpoS ) were included as controls for RpoS activity .
"
7869,7870,318.txt,13,0,,,,"Negative control by RpoS appears to result in the selection of rpoS mutants in bacterial populations .
"
7870,7871,318.txt,14,0,,,,"Negative control by RpoS appears to result in a growth advantage of rpoS mutants in bacterial populations .
"
7871,7872,318.txt,15,0,,,,"These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .
"
7872,7873,318.txt,16,0,,,,"These results indicate that phoP may control the expression of the rpoS gene ( Table 2 and Fig. 2 ) , as substantiated by previous reports that PhoP controls the expression of the RpoS-regulated spv virulence genes and rpoS gene ( Heithoff et al. , 1997 ; Tu et al. , 2006 ) .
"
7873,7874,318.txt,17,0,,,,"Presumably , the posttranscriptional mechanisms responsible for regulation of RpoS protein expression were sufficiently robust to withstand our attempts at overwhelming them through ectopic transcriptional upregulation of the rpoS gene .
"
7874,7875,318.txt,18,0,,,,"To verify the role of RpoS in the regulation of entry of KLX2 into the VBNC state , the rpoS gene was deleted in KLX2 DrpoS , KLX6 strain .
"
7875,7876,318.txt,19,0,,,,"To verify the role of RpoS in the regulation of entry of KLX2 into the VBNC state , the rpoS gene was deleted in KLX2 .
"
7876,7877,318.txt,20,0,,,,"Since rpoS is regulated at multiple levels , we determined whether the changes in the rpoS transcription also lead to changes in RpoS accumulation .
"
7877,7878,318.txt,21,0,,,,"A study showed the expression of rpoS by RhlR ,61 while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .
"
7878,7879,318.txt,22,0,,,,"A study showed the expression of rpoS by RhlR ,61 while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .
"
7879,7880,318.txt,23,0,,,,"A study showed the expression of rpoS by LasR while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .
"
7880,7881,318.txt,24,0,,,,"A study showed the expression of rpoS by LasR while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .
"
7881,7882,318.txt,25,0,,,,"A study showed the expression of rpoS by QS regulators while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .
"
7882,7883,318.txt,26,0,,,,"A study showed the expression of rpoS by QS regulators while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in P. aeruginosa .
"
7883,7884,318.txt,27,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A study showed the expression of rpoS by RhlR ,61 while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .
"
7884,7885,318.txt,28,1,Escherichia coli,E. coli,Escherichia coli,"A study showed the expression of rpoS by RhlR ,61 while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .
"
7885,7886,318.txt,29,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A study showed the expression of rpoS by RhlR ,61 while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .
"
7886,7887,318.txt,30,1,Escherichia coli,E. coli,Escherichia coli,"A study showed the expression of rpoS by RhlR ,61 while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .
"
7887,7888,318.txt,31,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A study showed the expression of rpoS by LasR while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .
"
7888,7889,318.txt,32,1,Escherichia coli,E. coli,Escherichia coli,"A study showed the expression of rpoS by LasR while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .
"
7889,7890,318.txt,33,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A study showed the expression of rpoS by LasR while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .
"
7890,7891,318.txt,34,1,Escherichia coli,E. coli,Escherichia coli,"A study showed the expression of rpoS by LasR while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .
"
7891,7892,318.txt,35,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A study showed the expression of rpoS by QS regulators while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .
"
7892,7893,318.txt,36,1,Escherichia coli,E. coli,Escherichia coli,"A study showed the expression of rpoS by QS regulators while coworkers reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .
"
7893,7894,318.txt,37,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"A study showed the expression of rpoS by QS regulators while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in S. enterica .
"
7894,7895,318.txt,38,1,Escherichia coli,E. coli,Escherichia coli,"A study showed the expression of rpoS by QS regulators while Whiteley reported little impact of QS on the transcription of rpoS .62 Our study suggested no QS-based regulation of RpoS in E. coli .
"
7895,7896,318.txt,39,0,,,,"Since stiC loci are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .
"
7896,7897,318.txt,40,0,,,,"Since stiB are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival .
"
7897,7898,318.txt,41,0,,,,"Since the stiA are regulated by RpoS , we wanted to examine the combined effects of rpoS mutations on starvation survival ."
7898,7899,1854.txt,1,0,,,,"The class I flhDC operon is the master regulator , with FlhC ."
7899,7900,495.txt,1,0,,,,These included the cold-shock-responsive hns gene previously shown to be activated by Fis and -LRB- like H-NS -RRB- regulates several virulence genes in response to temperature .
7900,7901,1101.txt,1,0,,,,"To further investigate the association between tdcA with phoP , we constructed chromosomal lacZ fusion strains of PhoP-regulated ( mgtA and pagD ) and SPI2 genes ( ssaG and sseA ) ( Navarre et al. , 2005 ) ."
7901,7902,1667.txt,1,1,Salmonella,Salmonellae,Salmonella,"cbiD , were induced much more than two-fold in the RpoS-mutant than in the wild type Salmonellae ."
7902,7903,1673.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"NagC _ participating with GalS in the repression of galP in E. coli
"
7903,7904,1673.txt,2,1,Escherichia coli,E. coli,Escherichia coli,NagC _ participating with GalS in the repression of galP in E. coli
7904,7905,1115.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In addition to the autoregulation , the S. Typhimurium rpoE regulon is also likely to be regulated by negative regulation by possibly the cAMP-CRP complex .
"
7905,7906,1115.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In addition to the autoregulation , the S. Typhimurium rpoE regulon is also likely to be regulated by negative regulation by possibly the cAMP-CRP complex ."
7906,7907,481.txt,1,2,unidentified plasmid;Escherichia coli,plasmid;E. coli,Escherichia coli;unidentified plasmid,"RESULTS AND DISCUSSIONS Screen for Fur-regulated Promoters and Sequence Analyses of DNA Regions Identified by FURTA Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .
"
7907,7908,481.txt,2,2,unidentified plasmid;Escherichia coli,plasmid;E. coli,Escherichia coli;unidentified plasmid,"RESULTS AND DISCUSSIONS Screen for Fur-regulated Promoters and Sequence Analyses of DNA Regions Identified by FURTA Fur-regulated promoters and iron binding proteins carried on a plasmid can be identified by transference into E. coli H1717 ( Stojiljkovic et al. , 1994 ) , which carries fhuF < lacZ ; a Fur-regulated gene fusion sensitive to changes in repressor ( Fur-Fe ) þ2 concentration .
"
7908,7909,481.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Members of the Fur protein family regulate iron and zinc transport in Escherichia coli and characteristics of the Fur-regulated fhuF protein .
"
7909,7910,481.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein .
"
7910,7911,481.txt,5,0,,,,"Regardless of the explanation , these results appear at odds with previous studies , which established that cells exposed to Co contain less iron and reported up-regulation of Fur-controlled entB and fhuF also directly destabilize particularly labile Fe -- S clusters such as those present on Fe -- S scaffolds ."
7911,7912,1883.txt,1,0,,,,"Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of RyhB .
"
7912,7913,1883.txt,2,0,,,,"Similar to ftnA genes are activated by Fe in a Fur-dependent manner , most likely via Fur-mediated repression of the small RNA ."
7913,7914,1897.txt,1,0,,,,polB are positively regulated by AraC due to partial read-through of Rho-independent terminators .
7914,7915,1129.txt,1,0,,,,The promoters of gatZ are negatively regulated by GatR .
7915,7916,132.txt,1,0,,,,"Five of the HilD/HilC/RtsA-bound regions associated with direct transcription activation of protein-coding genes outside SPI-1 overlap regions that are likely bound by H-NS ( HilD/HilC/RtsA binding sites associated with regulation of lpxR , , siiA , mcpC , and ssaG ) .
"
7916,7917,132.txt,2,0,,,,"Five of the HilD/HilC/RtsA-bound regions overlap regions bound by HilD/HilC/RtsA binding sites , siiA , mcpC , and ssaG ."
7917,7918,654.txt,1,0,,,,"As suggested by our previous study , establishing the Mg2-responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the phoP mutants in low-Mg2 conditions .
"
7918,7919,654.txt,2,0,,,,"As suggested by our previous study , establishing the Mg2-responsive regulation of these loci requires the transcriptional repressor H-NS ; thus the mRNA level is reduced greatly in the phoP mutants in PhoP-activating conditions ."
7919,7920,640.txt,1,0,,,,"the double hns/lrp mutant showed 5,002 activity units , hence demonstrating the role of both H-NS in the repression of casA
"
7920,7921,640.txt,2,1,Terfezia albida,to 15,Terfezia albida,"In the wild type and the hns , lrp , and the activity values for the pKK-51 / 49 fusion ( which contains the promoter region without cis-acting negative elements ) were around 14,000 to 15,000 , supporting the conclusion that H-NS are the main repressors of casA expression .
"
7921,7922,640.txt,3,1,Terfezia albida,to 15,Terfezia albida,"In the wild type and the hns , lrp , and double hns/lrp mutants / 49 fusion ( which contains the promoter region without cis-acting negative elements ) were around 14,000 to 15,000 , supporting the conclusion that H-NS are the main repressors of casA expression ."
7922,7923,898.txt,1,0,,,,"The interconnection between the PhoP-PhoQ system and the SlyA , RpoS , and SpvR regulators is at present undefined , although it has been proposed previously that the PhoP-PhoQ system may control in a positive manner the expression of the spvABCD operon ."
7923,7924,126.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"In this regard , it has been reported that expression of cysK in E. coli is under the control of a LysR-family transcription factor ."
7924,7925,2193.txt,1,0,,,,"In accordance with apparent phosphod-iesterase activity in-vivo , the absence of STM4264 significantly activated CsgD expression whereby 361 STM1703 particularly was also required for temperature regulation of the rdar morphotype .
"
7925,7926,2193.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Overcoming the temperature regulation of Salmonella serovar Typhimurium UMR1 by mutations in STM4264 demonstrated that both gene products act as suppressors of the rdar morphotype expression upstream of CsgD at 37 °C .
"
7926,7927,2193.txt,3,0,,,,"Consequently , STM1344 acts upstream of STM3611 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 .
"
7927,7928,2193.txt,4,0,,,,"Consequently , STM1344 acts upstream of STM1703 in the regulation of CsgD , whereas STM1344 is either located downstream of STM4264 ."
7928,7929,668.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Regulation of these genes likely happens through StpA-dependent activation of crp expression , as observed in E. coli ."
7929,7930,2187.txt,1,0,,,,"For example , the apparent activation of flagellar genes by H-NS most likely occurs by mediated repression of hdfR .
"
7930,7931,2187.txt,2,0,,,,"H-NS indirectly stimulates flagellar gene expression by repressing hdfR , a known repressor of the flhDC regulatory locus and , in addition , H-NS directly binds to the flagellar protein FliG and helps organize rotor subunit assembly ."
7931,7932,1465.txt,1,0,,,,"From the data , it is apparent that both SsrB activate the transcriptional-fusions to spiC .
"
7932,7933,1465.txt,2,0,,,,"The response regulator SsrB , in turn , is autoregulated , activating outside of spiC ssrA ssrB srfH , etc Asp-P SsrB Fig. 1 .
"
7933,7934,1465.txt,3,0,,,,"SsrB , in turn , activates spiC .
"
7934,7935,1465.txt,4,0,,,,"SsrB , in turn , activates spiC ."
7935,7936,1303.txt,1,0,,,,"SoxS _ regulated , including lpxC"
7936,7937,697.txt,1,0,,,,"Interestingly , EnvZ was not absolutely necessary for OmpR-dependent acid induction of ompF suggesting that unlike osmolarity , the EnvZ sensor is not required for full expression of the pH-dependent OmpR regulon .
"
7937,7938,697.txt,2,1,Escherichia coli,Escherichia coli,Escherichia coli,"Forst S , Delgado J , Rampersaud A et al In vivo phosphorylation of OmpR , the transcription activator of the ompF genes in Escherichia coli .
"
7938,7939,697.txt,3,0,,,,These data indicate that an OmpR-independent ompF induction contribute towards the genetic expression of ompF .
7939,7940,683.txt,1,0,,,,"plasmids _ expressing HhaR26A under control of the native hha promoter
"
7940,7941,683.txt,2,0,,,,"plasmids _ expressing HhaR26A under control of the native hha promoter
"
7941,7942,683.txt,3,0,,,,plasmids _ expressing HhaR26A under control of the native hha promoter
7942,7943,1317.txt,1,0,,,,"Fur represses ryhB transcription .
"
7943,7944,1317.txt,2,0,,,,"In the absence of Fe and/or Fur , repression of ryhB is relieved , leading to negative regulation of ftnA .
"
7944,7945,1317.txt,3,0,,,,"In the absence of Fe and/or Fur , repression of ryhB is relieved , leading to negative regulation of bfr .
"
7945,7946,1317.txt,4,0,,,,"Fur activates sodB by repressing the expression of ryhB under high-iron conditions .
"
7946,7947,1317.txt,5,0,,,,"The expression of ryhB , in turn , is repressed by Fur under high-iron conditions .
"
7947,7948,1317.txt,6,0,,,,"Consequently , if Fur acts as a simple repressor of the factor , as it does with ryhB controlling sodB , then the Fur binding site must be far from consensus , leading to weak binding of Fur under normal laboratory conditions ; overproduction of Fur leads to further repression .
"
7948,7949,1317.txt,7,1,Escherichia coli,E. coli,Escherichia coli,"However , E. coli Fur is also known to activate the expression of many genes indirect mechanisms , the latter involving repression of a small regulatory RNA , ryhB .
"
7949,7950,1317.txt,8,1,Escherichia coli,E. coli,Escherichia coli,"However , E. coli Fur is also known to activate the expression of many genes direct mechanisms , the latter involving repression of a small regulatory RNA , ryhB .
"
7950,7951,1317.txt,9,0,,,,"Under iron-rich conditions , it has been shown that expression of ryhB gene is repressed by Fe2 + - Fur , whereas transcription of genes is elevated .
"
7951,7952,1317.txt,10,0,,,,Fur repression of ryhB transcription is abated
7952,7953,1471.txt,1,0,,,,"PreA activated the transcription of pmrCAB indirectly in PmrA RR-independent fashion .
"
7953,7954,1471.txt,2,0,,,,PreA activated the transcription of pmrCAB indirectly in a PhoP .
7954,7955,2178.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"NagC _ participating with GalR in the repression of galP in E. coli
"
7955,7956,2178.txt,2,1,Escherichia coli,E. coli,Escherichia coli,NagC _ participating with GalR in the repression of galP in E. coli
7956,7957,1459.txt,1,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipC , whereas expression of orgA remains unaffected .
"
7957,7958,1459.txt,2,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of sipA , whereas expression of orgA remains unaffected .
"
7958,7959,1459.txt,3,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of orgA remains unaffected ."
7959,7960,2150.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
7960,7961,873.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,typhimu,Salmonella enterica subsp. enterica serovar Typhimurium,"Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9-minimal-medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative-stress ."
7961,7962,33.txt,1,0,,,,"These results suggest that the lysine signal represses lysP expression , thereby eliminating the negative regulation of CadC activation by LysP ."
7962,7963,867.txt,1,0,,,,"In addition , at low-osmolarity , RcsB , negatively controls the transcription of flhDC .
"
7963,7964,867.txt,2,0,,,,"In addition , RcsB inhibits flhDC expression .
"
7964,7965,867.txt,3,0,,,,"ecnR in turn results in repression of flhDC transcription in concert with the RcsB protein
"
7965,7966,867.txt,4,0,,,,"RcsB , is a known repressor of flhDC transcription .
"
7966,7967,867.txt,5,0,,,,"To test a putative link between RcsB in repression of flhDC , we performed an unbiased genetic screen using random transposon mutagenesis .
"
7967,7968,867.txt,6,0,,,,"The transposon mutagenesis thus provided further evidence for a functional link between RcsB in repression of flhDC .
"
7968,7969,867.txt,7,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to the RcsCDB regulon were regulated by RcsB independently of the presence of RflM .
"
7969,7970,867.txt,8,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to csgD were regulated by RcsB independently of the presence of RflM .
"
7970,7971,867.txt,9,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to dps were regulated by RcsB independently of the presence of RflM .
"
7971,7972,867.txt,10,0,,,,"To test for the specificity of RflM in promoting RcsB-dependent repression of flhDC , we analyzed the transcript levels of various RcsB targets in the absence or presence of rflM ing to wzzB were regulated by RcsB independently of the presence of RflM .
"
7972,7973,867.txt,11,0,,,,"This demonstrated that RcsB is indispensable for the rflM-dependent repression of flhDC was analyzed using several rcsB mutants .
"
7973,7974,867.txt,12,0,,,,"flhDC is consistent with previous The role of RcsB in repression of flhDC expression
"
7974,7975,867.txt,13,0,,,,"Coordinated repression of flhDC transcription by RcsB .
"
7975,7976,867.txt,14,0,,,,"A. Schematic regulatory model of repression of the flagellar master regulator flhDC by coordinated action of RcsB .
"
7976,7977,867.txt,15,0,,,,"Moreover , the results above indicated that rcsB overexpression bypassed the need for RcsB phosphorylation in repression of flhDC transcription .
"
7977,7978,867.txt,16,0,,,,"expression of flhC-lac _ providing further evidence for a cooperative action of RcsB in repression of flhDC
"
7978,7979,867.txt,17,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC Discussion Regulation of flagellar synthesis is controlled by the RcsCDB phosphorelay system in both S. enterica serovar Typhimurium .
"
7979,7980,867.txt,18,1,Escherichia coli,E. coli,Escherichia coli,"In summary , our results demonstrate that RflM protein promotes RcsB target specificity for repression of flhDC Discussion Regulation of flagellar synthesis is controlled by the RcsCDB phosphorelay system in both E. coli .
"
7980,7981,867.txt,19,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , it has been shown that RcsA , enhan-ces RcsB-dependent repression of flhDC .
"
7981,7982,867.txt,20,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , it has been shown that an auxiliary regulatory protein , enhan-ces RcsB-dependent repression of flhDC .
"
7982,7983,867.txt,21,0,,,,"We dem-onstrate that RflM mediates target specificity of unphosphoryl-ated RcsB for repression of flhDC .
"
7983,7984,867.txt,22,0,,,,"RcsB-mediated repression of flhDC increased significantly in the presence of RflM
"
7984,7985,867.txt,23,0,,,,"Overexpressed RcsB were able to repress flhDC
"
7985,7986,867.txt,24,0,,,,"As mentioned , we found that phosphorylation of RcsB was not essential for repression of flhDC in the presence of RflM , but for RcsB-mediated repression of flhDC in the absence of RflM .
"
7986,7987,867.txt,25,0,,,,"As mentioned , we found that phosphorylation of RcsB was not essential for repression of flhDC in the presence of RflM , but for RcsB-mediated repression of flhDC in the absence of RflM .
"
7987,7988,867.txt,26,0,,,,"These results indicated that RflM directs RcsB to specifically repress flhDC gene transcription independently of external stimuli .
"
7988,7989,867.txt,27,0,,,,"Phosphorylated RcsB would be able to repress flhDC with low affinity by binding to the RcsB box in the flhDC promoter region as a homodimer .
"
7989,7990,867.txt,28,0,,,,"Phosphorylated RcsB would be able to repress flhDC with low affinity by binding to the RcsB box in the flhDC promoter region as a homodimer .
"
7990,7991,867.txt,29,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"RcsB is known to repress transcription of flhDC in both S. enterica .
"
7991,7992,867.txt,30,1,Escherichia coli,E. coli,Escherichia coli,RcsB is known to repress transcription of flhDC in both E. coli .
7992,7993,27.txt,1,0,,,,"It is probable that CsrA binds to the hilD mRNA to .
"
7993,7994,27.txt,2,0,,,,"However , with the potential exception of CsrA , post-transcriptional regulators of hilD seem to affect either HilD protein activity .
"
7994,7995,27.txt,3,0,,,,"However , with the potential exception of CsrA , post-transcriptional regulators of hilD seem to affect either the HilD protein level .
"
7995,7996,27.txt,4,0,,,,"This CsrA-mediated repression of hilD is caused by binding of CsrA to Dalgarno sequence of hilD mRNA .
"
7996,7997,27.txt,5,0,,,,"This CsrA-mediated repression of hilD is caused by binding of CsrA to the Shine .
"
7997,7998,27.txt,6,0,,,,"Regulation of hilD expression at the mRNA level has also been proposed : overproduction of the RNA binding protein CsrA represses Long 3 untranslated regions are common in eukaryotic mRNAs .
"
7998,7999,27.txt,7,0,,,,"CsrA has been shown to bind a hilD mRNA region
"
7999,8000,27.txt,8,0,,,,CsrA post-transcriptionally regulates hilD .
8000,8001,2144.txt,1,0,,,,"However , increased amounts of breaks seem to be associated with increased deletion rates , as shown by previous studies ( 18 , 31 ) , and our demonstration that in a lexA ( def ) mutant overexpressing the translesion polymerases , removal of 3 LexA-controlled endo-nucleases ( uvrB , uvrC , and cho ) causes both a reduction in deletion formation ( Fig. 3 ) and DNA breaks ( Fig ."
8001,8002,720.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The marRAB operon , controls multiple antibiotic resistance in E. coli by production of MarA , a 127-amino-acid protein of the XylS/AraC family of transcriptional activator proteins .
"
8002,8003,720.txt,2,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8003,8004,720.txt,3,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8004,8005,720.txt,4,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8005,8006,720.txt,5,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to antibiotics and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8006,8007,720.txt,6,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8007,8008,720.txt,7,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8008,8009,720.txt,8,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8009,8010,720.txt,9,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8010,8011,720.txt,10,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8011,8012,720.txt,11,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8012,8013,720.txt,12,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8013,8014,720.txt,13,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8014,8015,720.txt,14,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8015,8016,720.txt,15,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to fluoroquinolones ,11,12 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8016,8017,720.txt,16,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to chloramphenicol and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8017,8018,720.txt,17,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to tetracycline and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8018,8019,720.txt,18,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8019,8020,720.txt,19,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also the expression of many genes A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8020,8021,720.txt,20,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8021,8022,720.txt,21,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also antimicrobials .10 A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8022,8023,720.txt,22,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8023,8024,720.txt,23,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also heavy metals A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8024,8025,720.txt,24,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to triclosan13 and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16
"
8025,8026,720.txt,25,0,,,,"further _ activated when MarA binds marbox in the operator of marRAB .7 MarA not only regulates its own expression , but also oxidative-stress A well-known example of an adaptive phenotype is increased tolerance to other anti-microbial compounds and pine oil .14 This is achieved mainly due to control of efflux by up-regulation of 15 the AcrAB-TolC efflux pump and control of influx by the induction of micF ,13,16"
8026,8027,734.txt,1,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family CAP , CRP family STM3466 crp 10.1371 / journal.ppat .1000306 .
"
8027,8028,734.txt,2,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family CAP , CRP family STM3466 crp doi .
"
8028,8029,734.txt,3,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family CAP , cyclic-AMP-receptor-protein STM3466 crp 10.1371 / journal.ppat .1000306 .
"
8029,8030,734.txt,4,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family CAP , cyclic-AMP-receptor-protein STM3466 crp doi .
"
8030,8031,734.txt,5,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family catabolite activator protein , CRP family STM3466 crp 10.1371 / journal.ppat .1000306 .
"
8031,8032,734.txt,6,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family catabolite activator protein , CRP family STM3466 crp doi .
"
8032,8033,734.txt,7,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family catabolite activator protein , cyclic-AMP-receptor-protein STM3466 crp 10.1371 / journal.ppat .1000306 .
"
8033,8034,734.txt,8,0,,,,"g001 STM1444 slyA transcriptional regulator for MarR family catabolite activator protein , cyclic-AMP-receptor-protein STM3466 crp doi ."
8034,8035,1288.txt,1,0,,,,"For example , aeration represses the TTSS-1 cascade , yet mutations in regulators commonly associated with oxygen-sensing do not ablate regulation of hilA by e.g. , OxrA/Fnr , ArcA ."
8035,8036,708.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"In S. Typhimurium , previous studies have determined that NsrR negatively regulates the expression of the ygbA genes ."
8036,8037,2018.txt,1,0,,,,"As both ArcA and Fnr contribute to regulation of respiration , the same explanation may be relevant for the GNS phenotype of the arcA mutants ."
8037,8038,1511.txt,1,0,,,,"These data showed that cAMP-CRP binds to the promoters of gatY , ."
8038,8039,1277.txt,1,0,,,,"pagK are known to be regulated by PhoP ,56
"
8039,8040,1277.txt,2,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
8040,8041,1263.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;unidentified plasmid,S. Typhimurium;Typhimurium;plasmid,unidentified plasmid;Salmonella enterica subsp. enterica serovar Typhimurium,"Chromosomally encoded adrA is not required for curli fimbriae in S. Typhimurium UMR1 Overexpression of AdrA from plasmid pWJB30 enhanced the expression of CsgD .
"
8041,8042,1263.txt,2,1,unidentified plasmid,plasmid,unidentified plasmid,"Chromosomally encoded adrA is not required for the expression of CsgD from plasmid pWJB30 enhanced the expression of CsgD .
"
8042,8043,1263.txt,3,0,,,,"the regulatory network where CsgD activates transcription of adrA
"
8043,8044,1263.txt,4,0,,,,"CsgD also stimulates cellulose production via activation of transcription of adrA .
"
8044,8045,1263.txt,5,0,,,,"Experiments with purified CsgD are needed to determine whether CsgD can activate transcription by E S and/or E 70 at the adrA promoters .
"
8045,8046,1263.txt,6,0,,,,"In agreement with in-vivo findings ( Romling et al. , 2000 ) , CsgD-activated transcription at the adrA promoter occurred with RNA polymerase loaded with RpoS and RpoD .
"
8046,8047,1263.txt,7,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"However , we discovered that c-di-GMP , an integral part of the regulatory network promoting CsgD expression in S. Typhimurium , is not required for binding of CsgD to the csgBA and adrA promoters or for CsgD-activated transcription .
"
8047,8048,1263.txt,8,0,,,,"In addition , CsgD contributes indirectly to cellulose production by activating the transcription of adrA .
"
8048,8049,1263.txt,9,0,,,,"In this study , we dem-onstrated for the first time that CsgD activates transcription of the promoter regions of adrA .
"
8049,8050,1263.txt,10,0,,,,"CsgD is also indirectly involved in cellulose production by activating transcription of adrA .
"
8050,8051,1263.txt,11,0,,,,"CsgD positively regulates the expression of adrA
"
8051,8052,1263.txt,12,0,,,,"CsgD is essential for , among other things , biofilm matrix production by inducing curli cellulose production , via adrA .
"
8052,8053,1263.txt,13,0,,,,"CsgD is essential for , among other things , biofilm matrix production by inducing curli production -LRB- via csgBAC regulation -RRB- , via adrA .
"
8053,8054,1263.txt,14,0,,,,"CsgD also positively controls expression of the diguanylate cyclase AdrA by direct binding to the promoter region upstream of adrA .
"
8054,8055,1263.txt,15,0,,,,"In contrast , CsgD activated adrA transcription only with RNA polymerase .
"
8055,8056,1263.txt,16,0,,,,"Cellulose production is initiated through CsgD-activated transcription of adrA ( 11 ) .
"
8056,8057,1263.txt,17,0,,,,"CsgD also activates expression of adrA , activating the cellulose biosynthetic operon bcsABZC .
"
8057,8058,1263.txt,18,0,,,,"CsgD also activates expression of adrA , increasing intracellular c-di-GMP levels .
"
8058,8059,1263.txt,19,0,,,,"Expression of the two biofilm-promoting factors is co-regulated , since the response regulator CsgD stimulates expression of both adrA ."
8059,8060,1505.txt,1,2,Salmonella;unidentified plasmid;unidentified plasmid,Salmonella;plasmid;plasmid,Salmonella;unidentified plasmid,"Lrp-regulated genes in Salmonella include fimZ , for type 1 fimbria expression ( 67 ) ; ilvIH , for branched amino-acid biosynthesis ( 93 ) ; hisJ , for D-histidine utilization ( 44 ) ; traJ , for conjugal transfer of virulence plasmid pSLT ( 13 ) ; and pef , for pSLT plasmid-encoded fimbriae ( 74 ) ."
8060,8061,2024.txt,1,0,,,,"Fur activates hilA transcription in a HilD-dependent manner .
"
8061,8062,2024.txt,2,0,,,,"RESULTS Fur induces expression of hilA .
"
8062,8063,2024.txt,3,0,,,,"As expected from the results , deletion of rtsA did not abrogate Fur-dependent induction of hilA .
"
8063,8064,2024.txt,4,0,,,,"As expected from the results , deletion of hilC did not abrogate Fur-dependent induction of hilA .
"
8064,8065,2024.txt,5,0,,,,"Fur activates expression of hilA .
"
8065,8066,2024.txt,6,0,,,,"Taken together , these data show that Fur activates hilA expression in a manner .
"
8066,8067,2024.txt,7,0,,,,"Our study shows that Fur plays a significant role in the expression of the SPI1 T3SS by genetically activating hilA transcription .
"
8067,8068,2024.txt,8,1,unidentified,not shown,unidentified,"wort _ noting that while overproduction of Fur caused an eightfold increase in hilA expression in low-oxygen conditions , Fur overproduction induced hilA expression only threefold in data not shown
"
8068,8069,2024.txt,9,0,,,,"wort _ noting that while overproduction of Fur caused an eightfold increase in hilA expression in low-oxygen conditions , Fur overproduction induced hilA expression only threefold in highoxygen conditions
"
8069,8070,2024.txt,10,0,,,,"Fur has been recently shown to induce the expression of hilA , throug post-translational mechanisms ."
8070,8071,907.txt,1,0,,,,"Like marRAB , acrAB are positively regulated by SoxS .
"
8071,8072,907.txt,2,0,,,,"SoxS protein , activates Mn-containing superoxid dismutase , acrAB .
"
8072,8073,907.txt,3,0,,,,"SoxS protein , activates sodA , acrAB .
"
8073,8074,907.txt,4,0,,,,"both MarA and SoxS can activate acrAB expression
"
8074,8075,907.txt,5,1,Salmonella,Salmonella,Salmonella,"Other regulators of SoxS did not contrib-ute to acrAB induction by indole in Salmonella .
"
8075,8076,907.txt,6,0,,,,"8 -- 13 _ shown that SoxS , play a role in antimicrobial resistance by activating acrAB
"
8076,8077,907.txt,7,0,,,,"Therefore , SoxS is proposed to directly induce acrAB .
"
8077,8078,907.txt,8,0,,,,The SoxS proteins can activate acrAB expression .
8078,8079,913.txt,1,0,,,,"RpoS-dependent expression was induced around 50-fold in the hns mutan
"
8079,8080,913.txt,2,0,,,,"RpoS-dependent expression was induced around 50-fold in the hns mutan
"
8080,8081,913.txt,3,0,,,,"RpoS-dependent expression was induced around 50-fold in the hns mutan
"
8081,8082,913.txt,4,0,,,,"RpoS-dependent expression was induced around 50-fold in the hns mutan
"
8082,8083,913.txt,5,0,,,,RpoS-dependent expression of osmY-lac in LBON medium was increased around 6-fold by hns and around 25-fold by growth at 10 ° .
8083,8084,2030.txt,1,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 .
"
8084,8085,2030.txt,2,2,Salmonella;Apple stem pitting virus,salmonellae;aspV,Apple stem pitting virus;Salmonella,"in kb ) of salmonellae aspV ( 304.7 ) GEI 0266/0307 ( SPI-6 ) 46.7 42 52.3 STM0272 , STM0291 , safC , sinR STM0274A ( invasol ) , STM0284 ( putative shiga-like toxin A subunit ) , STM0306 ( SlyA-activated ; homologue to sapA involved in resistance to antimicrobial peptides and homologue to putative invasin pagN ) , STM307 ( homologue to Shigella VirG protein ) 51.1 STM1031 , STM1033 , STM1041 , STM1042 pncB ( 1098.2 ) 45.5 52 GEI 1005/1056 ( Gifsy-2 ) STM1044 ( sodC ) , STM1055 ( gtgE , SlyA-activated ) , STM1056 ( msgA homologue ) 47.2 1672 , 1677 orf ( 1757.9 ) 14.0 14 orf ( 2099.7 ) 36.3 40 GEI 1664/1678 GEI 2016/2058 STM1669 ( invC homologue ) 54.8 cobS , pocR , pduK orf ( 2729.0 ) 47.8 53 GEI 2584/2636 ( Gifsy-1 ) 51.6 STM2585A , STM2589 , STM2585 ( pagJ , SlyA-activated gene ; STM2595 , gipA , STM2603 , Navarre et al. , 2005 ) STM2605 , STM2633 52.1 STM2781 ( virK ) fljA ( 2912.6 ) 34.3 19 GEI 2770/2788 STM2780 ( pipB2 ; Navarre et al. , 2005 ) , mig-14 Fig. 3 ."
8085,8086,1539.txt,1,0,,,,"To evaluate the role of the activators HilD and HilC in the regulation of rtsA transcription , the single-copy rtsA-lac transcriptional-fusion was tested in the hilD hilC background in the presence and absence of hns mutations ."
8086,8087,522.txt,1,0,,,,"The role of HilD in the regulation of slrP were further studied at the protein level .
"
8087,8088,522.txt,2,0,,,,"Similarly , the expression of slrP , also encoding an effector protein , is controlled by HilD in SPI-1-inducing conditions ."
8088,8089,1908.txt,1,0,,,,this effect was reflected by induction of cspD and proteins ( CspE ) in response to preadaptation to cold-stress
8089,8090,244.txt,1,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. typhimurium;typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Consistent with the situation for E. coli hya , anaerobic control of S. typhimurium hyaB did not require Fnr upstream of the aniC homolog .
"
8090,8091,244.txt,2,2,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,E. coli;S. typhimurium;typhimurium,Escherichia coli;Salmonella enterica subsp. enterica serovar Typhimurium,"Consistent with the situation for E. coli hya , anaerobic control of S. typhimurium hyaB did not require Fnr upstream of orf326a ."
8091,8092,250.txt,1,0,,,,"STM1344 positively regulated the expression of its major regulator CsgD .
"
8092,8093,250.txt,2,0,,,,"The effect of STM1344 on c-di-GMP concentrations as determined in this study is , however , in agreement with the effect of STM1344 on the motility phenotypes , e.g. , the expression of STM1344 leads to the upregulation of CsgD .
"
8093,8094,250.txt,3,0,,,,"The effect of STM1344 on c-di-GMP concentrations as determined in this study is , however , in agreement with the effect of STM1344 on the multicellular phenotypes , e.g. , the expression of STM1344 leads to the upregulation of CsgD ."
8094,8095,536.txt,1,0,,,,"The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A .
"
8095,8096,536.txt,2,0,,,,"yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .
"
8096,8097,536.txt,3,0,,,,"While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) ."
8097,8098,1934.txt,1,1,Escherichia coli,E. coli,Escherichia coli,the OxyR repressor for hemi-methylated GATC sites has been shown to regulate phase variation in the E. coli agn43 gene .
8098,8099,278.txt,1,0,,,,FlhDC controls expression of fliC .
8099,8100,1920.txt,1,0,,,,"prgI are known to be repressed , respectively , by the active form of PhoP .
"
8100,8101,1920.txt,2,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
8101,8102,1075.txt,1,0,,,,"These results suggest that SlyA controls expression of magainin 2 resistance determinants in addition to the ugtL gene , which appears to be the sole SlyA-regulated gene mediating polymyxin B resistance .
"
8102,8103,1075.txt,2,1,unidentified plasmid,plasmid,unidentified plasmid,"The polymyxin B susceptibility of the slyA mutant was the same as that exhibited by the ugtL mutant ( Fig. 5A ) and could be complemented to wild-type levels by a plasmid that expressed the ugtL gene from a heterologous promoter ( Fig. 5B ) , suggesting that ugtL is the only SlyA-regulated gene mediating polymyxin B resistance .
"
8103,8104,1075.txt,3,0,,,,"We propose that the SlyA proteins control ugtL transcription .
"
8104,8105,1075.txt,4,0,,,,"that both SlyA proteins bind to the ugtL promoter , suggesting that these two proteins use a feed-forward loop to control ugtL expression
"
8105,8106,1075.txt,5,0,,,,"These results demonstrate that the SlyA proteins bind to the ugtL promoter .
"
8106,8107,1075.txt,6,0,,,,"The SlyA proteins bind to the ugtL promoter .
"
8107,8108,1075.txt,7,0,,,,"These results suggest that SlyA controls expression of magainin 2 resistance determinants in addition to the ugtL gene .
"
8108,8109,1075.txt,8,0,,,,"We have established that transcription of polymyxin B resistance gene ugtL is controlled by the SlyA proteins in what appears to be a feedforward loop design .
"
8109,8110,1075.txt,9,0,,,,"The SlyA protein bound to a region located downstream from the ugtL transcription start site for a regulatory protein -LRB- Fig. 1A -RRB- .
"
8110,8111,1075.txt,10,0,,,,"Taken together with the identification of binding sites for both the SlyA in Fig. 2C , these results support the notion of a feedforward design in the regulation of ugtL transcription .
"
8111,8112,1075.txt,11,0,,,,"Taken together with the identification of binding sites for both the SlyA in the ugtL promoter , these results support the notion of a feedforward design in the regulation of ugtL transcription .
"
8112,8113,1075.txt,12,0,,,,"Model _ illustrating the feed-forward regulation of the ugtL gene by the SlyA proteins
"
8113,8114,1075.txt,13,0,,,,"Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .
"
8114,8115,1075.txt,14,0,,,,"Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .
"
8115,8116,1075.txt,15,1,Salmonella,Salmonella,Salmonella,"Consistently , results from different laboratories showed that SlyA regulates a subset of PhoP-dependent genes , including ugtL , in Salmonella .
"
8116,8117,1075.txt,16,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"The S. Typhimurium ugtL are regulated by a similar mechanism , involving the coordinated actions of SlyA .
"
8117,8118,1075.txt,17,0,,,,Transcriptional control of the antimicrobial peptide resistance ugtL gene by SlyA regulatory proteins .
8118,8119,287.txt,1,0,,,,"If regulation by barA was mediated exclusively by modulating the level of HilA , null mutations in barAB would be without effect in these two settings because , in the ® rst case , HilA is absent and , in the second case , it is maintained at a constant level ."
8119,8120,1713.txt,1,0,,,,"Thus , SsrBC directly regulates transcription of sifA by binding upstream of the respective promoters ."
8120,8121,1707.txt,1,0,,,,"An ssaH reporter , was regulated by OmpR similarly to previously described results .
"
8121,8122,1707.txt,2,0,,,,"The ssaH promoter was previously shown to be regulated by OmpR through SsrA -- both protein pairs being two-component regulators -- and not by PhoQ .
"
8122,8123,1707.txt,3,0,,,,"The ssaH promoter was previously shown to be regulated by OmpR through SsrA -- both protein pairs being two-component regulators -- and not by PhoP .
"
8123,8124,1707.txt,4,0,,,,"The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoQ .
"
8124,8125,1707.txt,5,0,,,,The ssaH promoter was previously shown to be regulated by OmpR through SsrB -- both protein pairs being two-component regulators -- and not by PhoP .
8125,8126,293.txt,1,0,,,,"Activated OxyR induces katN , dps ahpCF .
"
8126,8127,293.txt,2,0,,,,"Activated OxyR induces katN , dps lipids .
"
8127,8128,293.txt,3,0,,,,"Activated OxyR induces katN , DNA-protection ahpCF .
"
8128,8129,293.txt,4,0,,,,"Activated OxyR induces katN , DNA-protection lipids ."
8129,8130,1061.txt,1,0,,,,"These results show that HilD positively controls the expression of the sinR genes , independently of InvF .
"
8130,8131,1061.txt,2,0,,,,"These results show that HilD positively controls the expression of the sinR genes , independently of HilA .
"
8131,8132,1061.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella-specific,Salmonella,"HilD induces the expression of sinR , in the absence of other Salmonella-specific regulators .
"
8132,8133,1061.txt,4,0,,,,"Thus , HilD positively regulates the expression of the sinR genes , and positively .
"
8133,8134,1061.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"HilD positively regulates sinR in S. Typhimurium .
"
8134,8135,1061.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"HilD induces the expression of sinR , in E. coli MC4100 ."
8135,8136,1049.txt,1,0,,,,"Inactivation of Crl , results in reduced expression of csgD biofilm-related genes ."
8136,8137,2226.txt,1,1,Mrakia cryoconiti,A ( 15,Mrakia cryoconiti,"Both the pmrF operon and pmrE are necessary for the PmrA-PmrB-regulated attachment of aminoarabinose to lipid-A ( 15 , 45 ) .
"
8137,8138,2226.txt,2,1,unidentified,not shown,unidentified,"The absence of transcriptional linkage between the RpoN and the PmrA regulons was corroborated because no significant differences were observed when the expression of PmrAcontrolled genes ( pmrI , pmrC , pmrF , and ugd ) was compared either in a RpoN or in a 1 DrpoN strain grown in LB ( exponential or stationary-phase ) or in a low-Mg N-21 minimal-medium , which are PhoP-and PmrA-inducing conditions ( Soncini & Groisman , 1996 ) ( Fig. 3a and data not shown ) .
"
8138,8139,2226.txt,3,0,,,,"( a ) b-Galactosidase activities were determined for pmrI : : MudJ , pmrC : : MudJ , pmrF : : MudJ and ugd : : MudJ ( all PmrA-regulated genes ) in an rpoN ( W-1 t ) or in a DrpoN strain ."
8139,8140,2232.txt,1,0,,,,"RtsA are each capable of partially activating invF
"
8140,8141,2232.txt,2,0,,,,RtsA all positively regulate invF .
8141,8142,2224.txt,1,0,,,,"Regulation at the level of transcription initiation Transcription initiation of the mgtCBR operon is controlled by the PhoP/PhoQ two component regulatory system .
"
8142,8143,2224.txt,2,0,,,,Regulation at the level of transcription initiation Transcription initiation of the mgtCBR operon is controlled by the PhoP/PhoQ two component regulatory system .
8143,8144,2230.txt,1,0,,,,"Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by RtsA .
"
8144,8145,2230.txt,2,0,,,,"Adding to complexity , the alternative sigma factor RpoS not only activates and is activated by small RNAs , but also activates the csgD transcriptional regulator MlrA , while RpoS degradation is indirectly stimulated by RtsA ."
8145,8146,1739.txt,1,0,,,,FliZ regulates expression of class 2 genes through a non-flagellar gene ydiV
8146,8147,2218.txt,1,0,,,,"STEPHEN C. DARNELL , AND ALISON D. O
"
8147,8148,2218.txt,2,0,,,,"STEPHEN C. DARNELL , AND ALISON D. O"
8148,8149,1711.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,Growth phase-regulated expression of bolA of stationary-phase Escherichia coli cells is controlled by the novel sigma factor RpoS .
8149,8150,285.txt,1,0,,,,"The StpAA77D variant provided even greater repression of ssrA by reducing their transcript levels by 20-fold relative to StpAWT .
"
8150,8151,285.txt,2,0,,,,The StpAA77D variant provided even greater repression of ssrA by reducing their transcript levels by 4-fold relative to StpAWT .
8151,8152,1077.txt,1,2,Escherichia coli;Salmonella;Salmonella,E. coli;Salmonella;Salmonella specific,Escherichia coli;Salmonella,"A set of PhoP-regulated loci , including the phoPQ operon , can be found in other enterobacteria such as E. coli , while other pag genes are Salmonella specific ( 31 ) .
"
8152,8153,1077.txt,2,0,,,,multiple genomes found that the only targets directly regulated by PhoP in all species were the phoPQ operon itself
8153,8154,1063.txt,1,0,,,,"PmrA-regulated loci identified included dgoA and yibD and demonstrated 500-and 2,500-fold activation by PmrA , respectively .
"
8154,8155,1063.txt,2,0,,,,"The remaining PMs mutants ( surA and tolB ) , as well as the two PmrA-regulated gene ( yibD and dgoA ) mutants , retained aminoarabinose on lipid-A .
"
8155,8156,1063.txt,3,0,,,,"The PmrA-regulated gene mutants JSG897 ( yibD ) and JSG899 ( dgoA ) were also analyzed for sensitivity to PM by MIC assay .
"
8156,8157,1063.txt,4,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
8157,8158,1063.txt,5,0,,,,"Mutants identified in the MudJ transposon mutagenesis screen Tn insertion site Description Strain PM sensitive imp/surA tolB gnd gnd yibD dgoA pmrC pmrC pmrC pmrC pmrI pmrI 851 895 JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG JSG 1272-1290-897-899 901-918-973-1036 923 925 PmrA regulated PmrA regulated , PM sensitive PmrA-regulated genes identified in the screen in iron resistance , JSG897 ( yibD ) and JSG899 ( dgoA ) were grown on solid N-minimal-medium supplemented with 100 M FeSO4 .
"
8158,8159,1063.txt,6,0,,,,"For further characterization of the PmrA-regulated gene mutants , the promoter regions of yibD and dgoA were analyzed for the presence of a putative PmrA-binding site , which was defined by the occurrence of the consensus binding sequence for PmrA , YTTAAK-N5-YTTAAK ( 1 ) .
"
8159,8160,1063.txt,7,0,,,,"yibD , dgoA , and gnd ( likely affecting pmrE ) played no role in PmrA-regulated resistance to high iron concentrations , while surA and tolB mutations grew poorly on high iron media .
"
8160,8161,1063.txt,8,0,,,,"JSG897 and JSG899 , with mutations in PmrA-regulated genes yibD and dgoA , respectively , also still possessed Ara4N modification of lipid-A in similar amounts to the parental PmrAc strain .
"
8161,8162,1063.txt,9,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"PmrA-regulated gene mutants JSG1525 ( yibD ) and JSG1526 ( dgoA ) were as virulent as wild-type Salmonella serovar Typhimurium , so the genes interrupted have no essential role in the infection process ( Table 4 ) .
"
8162,8163,1063.txt,10,3,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Mus sp.;Mus sp.,Salmonella;Typhimurium;mice;mice,Mus sp.;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"All PMs mutants identified in this study demonstrated a defect in virulence compared to wild-type Salmonella serovar Typhimurium when administered orally to mice , while the PmrA-regulated gene ( yibD and dgoA ) mutants showed normal virulence in mice .
"
8163,8164,1063.txt,11,0,,,,"Sequencing of the MudJ insertion site of JSG899 identified dgoA as a PmrA-regulated gene .
"
8164,8165,1063.txt,12,0,,,,"While it is possible that these PmrA-regulated genes ( as well as the genes involved in PM resistance ) could affect the other known PmrA-induced LPS modification , pEtN , we feel that this is unlikely based on what is known about the identified genes ( surA , tolB , and pmrE ) and because yibD and dgoA do not affect virulence or PM resistance , which are predicted phenotypes of the loss of pEtN modification from the core ( 59 ) ."
8165,8166,291.txt,1,0,,,,"Thus , SsrB regulates transcription of sifA by both relief of H-NS repression .
"
8166,8167,291.txt,2,0,,,,"Thus , SsrB regulates transcription of sifA by both direct activation of H-NS repression .
"
8167,8168,291.txt,3,0,,,,"Furthermore , DNase I footprinting suggests that SsrB directly competes for binding with H-NS at sifA ."
8168,8169,1705.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,QseB regulation of S. Typhi invasion of SPI-1 gene invF .
8169,8170,1936.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Moreover , while in E. coli the expression of dps in logarithmic phase is modulated by the exposition to sources of hydrogen-peroxide -LRB- mediated by OxyR -RRB- , in the stationary-phase its expression is regulated by σ ."
8170,8171,1088.txt,1,1,Salmonella,Salmonella,Salmonella,"Distinct temporal expression of PhoP-activated genes in response to mildly acidic pH and low Mg2 + We examined the mRNA levels of the PhoP-activated genes pagC and pagK at 2 h and 4 h after Salmonella was shifted from non-inducing conditions for the PhoQ protein to media containing either mildly acidic pH or low ( i.e. , 10 μM ) Mg2 + .
"
8171,8172,1088.txt,2,0,,,,"Distinct temporal expression of PhoP-activated genes in response to mildly acidic pH and low Mg2 + he MgtA protein is necessary for full transcription of a subset of PhoP-activated genes hen the PhoQ inducing signal is low Mg2 + T w Wild-type and mgtA strains had similar pagC and pagK mRNA levels at 2 h post induction ( Fig. 2A ) ( i.e. , ratio of wild-type/mgtA of 1 ) ."
8172,8173,508.txt,1,0,,,,"Specifically , RtsA binds to the hilA regulatory gene promoter in SPI-1 while RtsB binds to the flhDC regulatory operon promoter in the flagellar regulon .
"
8173,8174,508.txt,2,0,,,,"RtsB have also been shown to regulate SPI-1 genes and flhDC , respectively .
"
8174,8175,508.txt,3,0,,,,"However , unlike HilD , RtsB is a negative regulator of flhDC .
"
8175,8176,508.txt,4,0,,,,RtsB also regulate cell motility by interacting with the flhDC promoter .
8176,8177,1922.txt,1,0,,,,"We detected direct regulation of sprB by HilD from a binding site immediately upstream of sprB .
"
8177,8178,1922.txt,2,0,,,,"S1B ) , we conclude that HilD regulation of sprB occurs predominantly through regulation of the hilC-sprB transcript .
"
8178,8179,1922.txt,3,0,,,,"S1B ) , we conclude that HilD regulation of sprB occurs predominantly through regulation of the hilC-sprB transcript ."
8179,8180,246.txt,1,0,,,,"Besides the negative regulation , mntH transcription is activated through the H2O2-sensing regulator OxyR ."
8180,8181,520.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .
"
8181,8182,520.txt,2,0,,,,PhoP binds to the promoter regions of pmrC genes .
8182,8183,534.txt,1,0,,,,"Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates Fig. 3G .
"
8183,8184,534.txt,2,0,,,,"Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression ."
8184,8185,252.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) ."
8185,8186,905.txt,1,0,,,,"SprB , regulates the expression of sopB ."
8186,8187,1249.txt,1,3,Salmonella;Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella enterica;enterica;Typhimurium,Salmonella enterica;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Transcriptional regulation of sdiA by LeuO in Salmonella enterica serovar Typhimurium .
8187,8188,2026.txt,1,0,,,,"SirA also directly activates the evolutionarily conserved csrB gene .
"
8188,8189,2026.txt,2,0,,,,"SirA also directly activates the csrB regulatory RNA gene .
"
8189,8190,2026.txt,3,1,Salmonella,Salmonella,Salmonella,"SirA of Salmonella both control the csr system by directly activating the csrB gene .
"
8190,8191,2026.txt,4,0,,,,Data have shown that SirA acts by inducing expression of csrB .
8191,8192,2032.txt,1,0,,,,"We next examined the expression of FlhD at bacterial growth phase of OD600 of 0.7 in LB , because the spiC expression is induced at over an OD600 of 1.5 when the bacteria are grown in LB ."
8192,8193,911.txt,1,0,,,,RcnR binds directly to the rcnA promoter to repress transcription
8193,8194,939.txt,1,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , yibJ are regulated by the alternative sigma factor RpoS ."
8194,8195,1275.txt,1,0,,,,HilC do not seem to regulate expression of prgH .
8195,8196,1513.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Thus , the TviA-mediated repression of flagellin expression could be recapitulated by introducing the tviA regulatory gene into S. Typhimurium .
"
8196,8197,1513.txt,2,0,,,,"Both the phoN mutant induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : tviA mutant Fig. 4A , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
8197,8198,1513.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Both the S. Typhimurium wild type induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : tviA mutant Fig. 4A , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
8198,8199,1513.txt,4,0,,,,"Both the phoN mutant induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : tviA mutant SW681 , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion .
"
8199,8200,1513.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Both the S. Typhimurium wild type induced processing of caspase-1 , while no caspase-1 cleavage was detected in cells : : tviA mutant SW681 , thus providing direct support for the hypothesis that TviA-mediated repression of flagellin expression can mediate inflammasome evasion ."
8200,8201,1507.txt,1,0,,,,"Candidate genes for this activity include virK because inactivation of these PhoP-activated genes results in strains .
"
8201,8202,1507.txt,2,0,,,,"These regulated genes included induction of PhoP-activated genes ( pags ) pagCDPOK , virK , mgtBC , and pgtE , and repression of sopBD2 and the PhoP-repressed genes ( prgs ) prgHIJK ."
8202,8203,1261.txt,1,0,,,,"To test the hypothesis that Hmp overexpression , and not that of other NsrR-regulated gene products ( such as ytfE , hcp -- hcr , tehA , tehB and ygbA ) is responsible for hypersensitivity to peroxynitrite , we determined the effect of peroxynitrite on a double mutant ( hmp and nsrR ) .
"
8203,8204,1261.txt,2,0,,,,"A novel NsrR-regulated gene designated STM1808 has been identified , along with hmp , hcp-hcr , yeaR-yoaG , ygbA and ytfE .
"
8204,8205,1261.txt,3,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in hcp , ygbA , ytfE , STM1808 and yeaR ( Experimental Procedures ) .
"
8205,8206,1261.txt,4,0,,,,"These include the NsrR-regulated ygbA , yeaR-yoaG and STM1808 genes ( Bang , 2006 ; Gilberthorpe et al. , 2007 ; Karlinsey et al. , 2012 ; Rodionov et al. , 2005 ) ."
8206,8207,722.txt,1,0,,,,"Interestingly , the regulation of the stiB locus ( unlike that of stiC ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .
"
8207,8208,722.txt,2,0,,,,"Interestingly , the regulation of the stiB locus ( unlike that of stiA ) was unaffected by a cya mutation , suggesting that cAMP-receptor-protein acts with a different signal-molecule in the repression of stiB .
"
8208,8209,722.txt,3,0,,,,This putative repressor would not function during log phase ; the repression of stiB during log phase is mediated by cAMP-receptor-protein in a cAMP-independent manner .
8209,8210,736.txt,1,1,Solanum lycopersicum,tomato,Solanum lycopersicum,"The oxygen tension within tomato fruits under normal storage conditions , however , has been shown to be near that of ambient air , suggesting the presence of some additional environmental signal for the induction of the Fur regulon in our experiments ."
8210,8211,31.txt,1,0,,,,The FlhD levels were determined by immunoblotting analysis at various times after flhD transcription was induced by 50 µM IPTG .
8211,8212,871.txt,1,0,,,,"HilA , regulates the expression of lpxR ."
8212,8213,2152.txt,1,0,,,,"plasmids _ expressing HhaR14A under control of the native hha promoter
"
8213,8214,2152.txt,2,0,,,,"plasmids _ expressing HhaR14A under control of the native hha promoter
"
8214,8215,2152.txt,3,0,,,,plasmids _ expressing HhaR14A under control of the native hha promoter
8215,8216,2146.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
8216,8217,1329.txt,1,0,,,,"Among other genes with significantly reduced expression in LP strains , yeaG , yncC , rpsV , osmE , yiaG , otsA , fbaB , talA , poxB , yehY , dps , sodC , katE , bfr , yddX are regulated by the alternative sigma factor RpoS ."
8217,8218,25.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,"and Rosner , J.L. Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .
"
8218,8219,25.txt,2,0,,,,"MarA is a transcriptional activator for marRAB .
"
8219,8220,25.txt,3,1,Escherichia coli,Escherichia coli,Escherichia coli,"Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .
"
8220,8221,25.txt,4,1,Escherichia coli,Escherichia coli,Escherichia coli,"Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .
"
8221,8222,25.txt,5,0,,,,"MarA is a transcriptional activator for marRAB .
"
8222,8223,25.txt,6,0,,,,"By far the greatest impact induction of marRAB has is the overexpression and accumulation of MarA .
"
8223,8224,25.txt,7,0,,,,"The MarA homologs SoxS activate marRAB transcription .
"
8224,8225,25.txt,8,1,Escherichia coli,Escherichia coli,Escherichia coli,"Mol Microbiol 44:1611 -- 1624 Martin RG , Jair KW , Wolf RE Jr , Rosner JL Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .
"
8225,8226,25.txt,9,1,Escherichia coli,Escherichia coli,Escherichia coli,Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .
8226,8227,865.txt,1,0,,,,"The RNA-binding protein CsrA positively regulate class 2 expression through enhancing translation of flhDC mRNA .
"
8227,8228,865.txt,2,0,,,,"CsrA , regulates flagellar gene expression by enhancing translation of flhDC mRNA
"
8228,8229,865.txt,3,0,,,,"Babitzke , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8229,8230,865.txt,4,0,,,,"T. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8230,8231,865.txt,5,0,,,,"Romeo , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8231,8232,865.txt,6,0,,,,"I. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8232,8233,865.txt,7,0,,,,"Berezin , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8233,8234,865.txt,8,0,,,,"H. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8234,8235,865.txt,9,0,,,,"Yakhnin , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8235,8236,865.txt,10,0,,,,"C.A. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8236,8237,865.txt,11,0,,,,"Vakulskas , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8237,8238,865.txt,12,0,,,,"C.S. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8238,8239,865.txt,13,0,,,,"Baker , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8239,8240,865.txt,14,0,,,,"A.V. , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage .
"
8240,8241,865.txt,15,0,,,,"Yakhnin , P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage ."
8241,8242,695.txt,1,0,,,,"These screens identified the response regulator PhoP as positive regulators of steA .
"
8242,8243,695.txt,2,0,,,,"phoN promoter promphoNdir promphoNrev FIG 1 PhoP are regulators of steA expression .
"
8243,8244,695.txt,3,0,,,,"In summary , our T-POP-based screens detected PhoP as positive regulators and MgrB as a negative regulator of steA .
"
8244,8245,695.txt,4,0,,,,"These results establish that regulation of steA by PhoQ/PhoP suggest that PhoP could be a direct activator of steA .
"
8245,8246,695.txt,5,0,,,,"These results establish that regulation of steA by PhoQ/PhoP does not occur through activation of the SsrA/SsrB system .
"
8246,8247,695.txt,6,0,,,,"Direct binding of PhoP to the steA promoter .
"
8247,8248,695.txt,7,0,,,,"A slot blot method was used to analyze the binding of PhoP to the promoter of steA .
"
8248,8249,695.txt,8,0,,,,"As seen in Fig. 5 , phosphorylated PhoP was able to bind to the promoter of steA with similar kinetics , whereas no binding was detected to the promoter of phoN .
"
8249,8250,695.txt,9,0,,,,"Finally , slot blot analysis was carried out to test the effect of these mutations in the binding of PhoP to steA promoter .
"
8250,8251,695.txt,10,0,,,,"FIG 5 PhoP binds directly to the promoter of steA .
"
8251,8252,695.txt,11,0,,,,"A direct target of DsbA is SpiA ( also known as FIG 6 The integrity of a putative PhoP box is essential for binding of regulation of steA expression by PhoP .
"
8252,8253,695.txt,12,0,,,,"A direct target of DsbA is SpiA ( also known as FIG 6 The integrity of a putative PhoP box is essential for binding of regulation of steA expression by PhoP .
"
8253,8254,695.txt,13,0,,,,"A direct target of DsbA is SpiA ( also known as FIG 6 The integrity of a putative PhoP box is essential for binding of PhoP of steA expression by PhoP .
"
8254,8255,695.txt,14,0,,,,phosphorylated PhoP binds then to the steA promoter to directly activate transcription of this gene
8255,8256,1301.txt,1,1,Salmonella,Salmonella,Salmonella,"In Salmonella , five transcription factors have been implicated : hmp transcription is activated by RamA .
"
8256,8257,1301.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , five transcription factors have been implicated : hmp transcription is activated by RamA ."
8257,8258,1467.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Examination of the sequence revealed that SoxS binds with high affinity in a manner characteristic of class I promoters in the sodA promoters of E. coli .
"
8258,8259,1467.txt,2,0,,,,"SoxS _ regulated , including sodA"
8259,8260,1473.txt,1,0,,,,"Expression of ArcZ in the hfq mutant restored CsgD levels : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : + 45 ; cmr curli fimbriae is also downregulated in -LRB- data not sh .
"
8260,8261,1473.txt,2,0,,,,"Expression of ArcZ in the hfq mutant restored CsgD levels : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : + 45 ; cmr curli fimbriae is also downregulated in in the arcZ mut .
"
8261,8262,1473.txt,3,0,,,,"Expression of ArcZ in the hfq mutant restored CsgD levels : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : : Lsc ; cmr curli fimbriae is also downregulated in -LRB- data not sh .
"
8262,8263,1473.txt,4,0,,,,"Expression of ArcZ in the hfq mutant restored CsgD levels : : arcZ , Ampr pBAD30 : : sdsR , Ampr pArcZ pRyeB Jörg Vogel pXG-1 pXG-10 p-GFp ; GFp under control of p promoter LtetO-1 LtetO-1 p-Gfp , psc101 * replicon , cmr , translational LtetO-1 fusion vector 30 30 pcpM17 This study pXG-10 : : : Lsc ; cmr curli fimbriae is also downregulated in in the arcZ mut ."
8263,8264,1315.txt,1,0,,,,"This suggests that SlyA might downregulate sopE2 in all conditions .
"
8264,8265,1315.txt,2,0,,,,"Our results showed that at 3 h post-infection only , sopE2 were negatively regulated by SlyA , with DslyA expression increased two-and five-times , respectively ."
8265,8266,681.txt,1,1,Leiostomus xanthurus;Leiostomus xanthurus;Leiostomus xanthurus,spoT;spoT;spoT,Leiostomus xanthurus,"The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both relA spoT strain , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of Lrp was not due to repression by these of a hilA-lacZ fusion in relA spoT strains .
"
8266,8267,681.txt,2,1,Leiostomus xanthurus,spoT,Leiostomus xanthurus,"The introduction of mutations in either of rtsAB contributed to reduced invasion gene expression in the these genes reduced hilA expression in both the wild type , we examined the effects of both mutations relA spoT strains , indicating that the loss of hilA expression and overexpression of Lrp was not due to repression by these of a hilA-lacZ fusion in the wild types .
"
8267,8268,681.txt,3,0,,,,"Lrp tightly represses hilA expression .
"
8268,8269,681.txt,4,0,,,,It is possible that Lrp acts as a master repressor for the expression of hilA .
8269,8270,19.txt,1,1,Escherichia coli,Escherichia coli,Escherichia coli,GcvA interacts with both σ subuni of RNA polymerase to activate e the Escherichia coli gcvB ge .
8270,8271,859.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To circumvent this issue and facilitate the examination of YdcRregulated srfN transcription in-vitro , we further introduced a YdcR-expressing plasmid into the ydcR strain , whose expression is under the control of arabinose .
"
8271,8272,859.txt,2,1,Salmonella,Salmonella,Salmonella,"Herein we quantitatively studied the protein expression of a Salmonella mutant lacking ydcR ( ydcR ) within host cells in comparison to that of its parental strain , which provides a powerful means to uncover potential YdcR-regulated proteins under physiological conditions .
"
8272,8273,859.txt,3,0,,,,"Experimental Design and Statistical Rationale -- To uncover potential YdcR-regulated proteins , we performed proteomic analyses of the intracellular ydcR mutant at 18 hpi , whereas the wild-type strain was used as a control .
"
8273,8274,859.txt,4,1,Salmonella;Salmonella,Sal-monella;monella,Salmonella,"To uncover YdcR-regulated proteins , we exploited quantitative proteomics to compare intracellular Sal-monella protein expression between the wild-type and the isogenic ydcR strains .
"
8274,8275,859.txt,5,2,Salmonella;Iris germanica,Salmonella;FLAG,Iris germanica;Salmonella,"In contrast , the expression level of PipB did not differ significantly for Salmonella strains chromosomally expressing 3 FLAG-tagged PipB in ydcR deletion backgrounds , indicating the specific regulation of SrfN by YdcR ."
8275,8276,1498.txt,1,0,,,,"For example , sopB seem to be regulated directly indirectly by HilA through modulation of invF expression ."
8276,8277,2191.txt,1,0,,,,"In spite of the fact that several reports have shown that an H-NS/Hha complex influences hilA expression , information is not yet available ."
8277,8278,2185.txt,1,0,,,,"Moreover , the pagC gene is positively regulated by SlyA .
"
8278,8279,2185.txt,2,0,,,,"Finally , relative pagC gene expression showed a significant decrease of ~ 0.9-fold in DSlyA in this condition , suggesting that SlyA positively regulates pagC expression .
"
8279,8280,2185.txt,3,0,,,,"Within the virulence coincident genes , we determined that pagC is positively regulated by SlyA .
"
8280,8281,2185.txt,4,0,,,,"SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of Fig. 4G , suggesting that SlyA positively regulates pagC expression .
"
8281,8282,2185.txt,5,0,,,,"SlyA interaction with the promoter region of pagC occurred at a SlyA concentration of 9.09 nM , suggesting that SlyA positively regulates pagC expression ."
8282,8283,118.txt,1,0,,,,"However , whether the repression of hilA by Fnr was induced by low O2 was not clarified in those studies ."
8283,8284,656.txt,1,0,,,,"For genes , we found two genes , ydhI are negatively regulated by SlyA ."
8284,8285,130.txt,1,0,,,,"whether the regulation of YgaE to ompF is direct
"
8285,8286,130.txt,2,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhi;Typhi,Salmonella enterica subsp. enterica serovar Typhimurium,This result suggested that YgaE does not influence the growth of S. Typhi by the regulation of ompF .
8286,8287,124.txt,1,0,,,,"However , we provide evidence that LeuO mainly exerts SPI-1 repression by an indirect mechanism , hitherto unsuspected : LeuO activates transcription of the hilE gene .
"
8287,8288,124.txt,2,0,,,,"LeuO downregulates SPI-1 expression via hilE Because SPI-1 expression is responsive to multiple regulators , we devised a genetic screen to ascertain whether a single cell function might transmit LeuO-mediated regulation to SPI-1 .
"
8288,8289,124.txt,3,0,,,,"Furthermore , even though a hilD mutation was epistatic over hilE , moderate repression of SPI-1 by LeuO was still observed in a HilD − HilE − background .
"
8289,8290,124.txt,4,0,,,,"A genetic screen for loss-of-function mutations provided evidence that the hilE gene is necessary for LeuOmediated repression of an hypothesis confirmed upon directed construction of a HilE − muta .
"
8290,8291,124.txt,5,0,,,,A genetic screen for loss-of-function mutations provided evidence that the hilE gene is necessary for LeuOmediated repression of SPI-1 .
8291,8292,642.txt,1,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
8292,8293,642.txt,2,1,unidentified,not shown,unidentified,"The tolB effect appears to be specific to the ugd gene because transcription of the PhoP-activated PmrA-dependent pbgP gene and the PhoP-activated PmrA-independent mgtA gene was not affected by the tolB mutation regardless of the presence of functional phoP or pmrA genes ( Fig. 2A ; data not shown ) .
"
8293,8294,642.txt,3,0,,,,"b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) .
"
8294,8295,642.txt,4,0,,,,"b-Galactosidase activity ( Miller units ) expressed by strains grown in LB-medium was determined for strains harbouring lac transcriptional-fusions to the PhoP-activated PmrA-dependent ugd ( A -- C ) and pbgP ( A ) genes , and the PhoP-activated PmrA-independent mgtA gene ( A ) ."
8295,8296,1659.txt,1,0,,,,"These data showed that cAMP-CRP binds to the promoters of gatR , ."
8296,8297,1881.txt,1,0,,,,"While transcriptional regulation of sopB by HilA/InvF has been described in the literature , sopD regulation is less well understood ( indicated by a dashed black arrow ) ."
8297,8298,1895.txt,1,1,Salmonella,Salmonella,Salmonella,"ChbR only binds in Salmonella DNase I footprinting confirmed that NagC bound to a site upstream of chiP as well as in E.
"
8298,8299,1895.txt,2,0,,,,"The chiP gene is under the transcriptional control of the NagC repressor As the next step in our comparative study , we examined the effects of chbR mutations on regulation of chiP .
"
8299,8300,1895.txt,3,0,,,,"The chiP gene is under the transcriptional control of the NagC repressor As the next step in our comparative study , we examined the effects of chbR mutations on regulation of chiP .
"
8300,8301,1895.txt,4,0,,,,"The chiP gene is under the transcriptional control of the NagC repressor As the next step in our comparative study , we examined the effects of nagC mutations on regulation of chiP .
"
8301,8302,1895.txt,5,1,Salmonella,Salmonella,Salmonella,"Discussion We have shown that the chiP gene , is under the control of GlcNAc operon repressor , NagC , in Salmonella .
"
8302,8303,1895.txt,6,1,Escherichia coli,E. coli,Escherichia coli,"Discussion We have shown that the chiP gene , is under the control of GlcNAc operon repressor , NagC , in both E. coli .
"
8303,8304,1895.txt,7,1,Salmonella,Salmonella,Salmonella,"Discussion We have shown that the chiP gene , is under the control of the N-acetylglucosamine operon repressor , NagC , in Salmonella .
"
8304,8305,1895.txt,8,1,Escherichia coli,E. coli,Escherichia coli,"Discussion We have shown that the chiP gene , is under the control of the N-acetylglucosamine operon repressor , NagC , in both E. coli .
"
8305,8306,1895.txt,9,0,,,,"NagC binds to two sites upstream of the chiP gene , one .
"
8306,8307,1895.txt,10,0,,,,The strong conservation of the NagC1 site clearly implies that NagC regulation of chiP is important for these bacteria .
8307,8308,1665.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) .
"
8308,8309,1665.txt,2,1,Salmonella,Salmonella,Salmonella,"Although a non-cytotoxic form of polymyxin B -- termed polymyxin B nonapeptide ( Vaara and Vaara , 1983 ) -- could partially protect a Salmonella pmrA mutant from Fe ( III ) - mediated killing ( Chamnongpol et al. , 2002 ) inactivation of the PmrA-activated loci responsible for the lipid-A modification with 4-aminoarabinose ( i.e. pbgP ) or phosphoethanolamine ( i.e. pmrC ) did not render the organism susceptible to Fe ( III ) ( Lee et al. , 2004 ) .
"
8309,8310,1665.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"By contrast , Zn2 + has been shown to promote transcription of the pmrA and pmrB genes as well as that of several PmrA-activated genes in E. coli ( Lee et al. , 2005 ) ."
8310,8311,1103.txt,1,0,,,,ssaG are regulated by HilC
8311,8312,497.txt,1,6,Prochilodus marggravii;Salmo platycephalus;Salmo obtusirostris;Salmo ohridanus;Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Salmo;Salmo;Salmo;Salmo;Salmo-nella;enterica;Typhimurium,Salmo platycephalus;Prochilodus marggravii;Salmonella;Salmo ohridanus;Salmo obtusirostris;Salmonella enterica subsp. enterica serovar Typhimurium,"E. Morales , hydrogen-peroxide-induced negative regulation of Salmo-nella enterica serovar Typhimurium ompW by the response regulator ArcA , BMC Microbiol ."
8312,8313,483.txt,1,0,,,,dgoR encodes a GntR/FadR-related regulator likely acting as a D-galactonate-responsive transcriptional repressor of the dgo operon
8313,8314,1117.txt,1,0,,,,Fis binds directly to the promoter regions of spiR
8314,8315,1671.txt,1,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in Fig. 4A and Fig. 4B in macrophage cells , as measured by Northern hybridization
"
8315,8316,1671.txt,2,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in Fig. 4A and Mx in macrophage cells , as measured by Northern hybridization
"
8316,8317,1671.txt,3,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in activating iNOS and Fig. 4B in macrophage cells , as measured by Northern hybridization
"
8317,8318,1671.txt,4,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in activating iNOS and Mx in macrophage cells , as measured by Northern hybridization
"
8318,8319,1671.txt,5,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in Fig. 4A and Fig. 4B in macrophage cells , as measured by Northern hybridization
"
8319,8320,1671.txt,6,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in Fig. 4A and Mx in macrophage cells , as measured by Northern hybridization
"
8320,8321,1671.txt,7,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in activating iNOS and Fig. 4B in macrophage cells , as measured by Northern hybridization
"
8321,8322,1671.txt,8,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"the gene _ encoding the global regulator of flagellin production , flhC .19 The Salmonella mutant deficient in FlhC expression was as efficient as WT Salmonella in activating iNOS and Mx in macrophage cells , as measured by Northern hybridization"
8322,8323,1842.txt,1,0,,,,"However , unlike pagC , cdtB is not regulated by the PhoP/PhoQ two-component system ."
8323,8324,468.txt,1,2,Tacca leontopetaloides;Escherichia coli,Tia;E. coli,Escherichia coli;Tacca leontopetaloides,"The pagN gene is activated by PhoP with the Tia invasins/adhesins of pathogenic E. coli .
"
8324,8325,468.txt,2,1,Escherichia coli,E. coli,Escherichia coli,The pagN gene is activated by PhoP with the Hek invasins/adhesins of pathogenic E. coli .
8325,8326,1856.txt,1,0,,,,"This suggests that HilD induces the expression of ssrAB also by counteracting H-NS-me-diated repression of its promoter .
"
8326,8327,1856.txt,2,0,,,,"However , how HilD counteracts the H-NS-mediated repression of ssrAB , or even of other target genes , had not yet been determined .
"
8327,8328,1856.txt,3,0,,,,"all the cis elements _ required for the H-NS-mediated repression of ssrAB
"
8328,8329,1856.txt,4,0,,,,"Thus , these results indicate that the sequence upstream of position 55 is not required for the H-NS-mediated repression of ssrAB .
"
8329,8330,1856.txt,5,0,,,,"multiple cis elements _ required for the H-NS-mediated repression of ssrAB
"
8330,8331,1856.txt,6,0,,,,"further _ supporting the role of HilD as an antagonist of H-NS-mediated repression of ssrAB
"
8331,8332,1856.txt,7,0,,,,"further _ supporting the role of HilD as an antagonist of H-NS-mediated repression of ssrAB
"
8332,8333,1856.txt,8,0,,,,"FIG 4 Analysis of the cis-acting sequences required for the H-NS-mediated repression of ssrAB .
"
8333,8334,1856.txt,9,0,,,,"that the sequence upstream of position 55 is not required for the H-NS-mediated repression of ssrAB
"
8334,8335,1856.txt,10,0,,,,"that consecutive deletion of the 119/240 regions results in a gradual release of the H-NS-me-diated repression of ssrAB
"
8335,8336,1856.txt,11,0,,,,"that consecutive deletion of the 240/336 regions results in a gradual release of the H-NS-me-diated repression of ssrAB
"
8336,8337,1856.txt,12,0,,,,"another regulator may act along with HilD to counteract a double mechanism of H-NS-mediated repression of ssrAB
"
8337,8338,1856.txt,13,1,Salmonella,Salmonella,Salmonella,"Therefore , SlyA might replace HilD to counteract H-NS-mediated repression of ssrAB when Salmonella is grown in minimal media .
"
8338,8339,1856.txt,14,0,,,,"Mechanistically , HilD indirectly regulates SsrB-regulated genes by antagonizing the H-NS-mediated repression of ssrAB at stationary-phase under SPI-1 ."
8339,8340,332.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"E. coli AraC activates transcription of araJ transcripts in the presence of its inducer , L-arabinose ."
8340,8341,454.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"The absence of consensus sequences for the CytR protein within the udp regulatory region of V. cholerae suggests that reduced CytR regulation of udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters Fig. 3 .
"
8341,8342,454.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"The absence of consensus sequences for the CytR protein within the udp regulatory region of V. cholerae suggests that reduced CytR regulation of udpPYp c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters Fig. 3 .
"
8342,8343,454.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis suggests that reduced CytR regulation of udpPV c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters Fig. 3 .
"
8343,8344,454.txt,4,1,Escherichia coli,E. coli,Escherichia coli,"The absence of consensus sequences for the CytR protein within the udp regulatory region of Y. pseudotuberculosis suggests that reduced CytR regulation of udpPYp c was due to the reduced ability of the E. coli CytR protein to bind heterlogous promoters Fig. 3 .
"
8344,8345,454.txt,5,0,,,,"Both cdd and udp are members of the CytR regulon , i.e. , the expression of these genes is negatively regulated by the CytR repressor protein ."
8345,8346,440.txt,1,0,,,,"According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .
"
8346,8347,440.txt,2,0,,,,"Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling ."
8347,8348,326.txt,1,0,,,,"Under the same growth-conditions , the RstA protein was unable to repress transcription of fhuA ."
8348,8349,441.txt,1,0,,,,spvR encodes a transcriptional activator of the LysR/MetR family of bacterial regulatory proteins .
8349,8350,327.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
8350,8351,333.txt,1,0,,,,"To determine the contribution of other NsrR-regulated genes to nitrosative-stress resistance , we constructed insertion mutations in ytfE ."
8351,8352,455.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"E. coli showed that RpoS production is increased by a crl mutation
"
8352,8353,455.txt,2,0,,,,"When present in HB101 , crl may increase an otherwise low level of RpoS activity"
8353,8354,1857.txt,1,0,,,,"The locations of the SlyA sites within PslyA were consistent with the observed autoregulation of slyA expression .
"
8354,8355,1857.txt,2,0,,,,"The region protected by SlyA includes the imperfect palindrome TTTAG-N7-CTTAA , which is similar to the SlyA binding sequence TTAG-N4-CTAA described for the slyA promoter ( 32 ) , the only SlyA-regulated promoter investigated in molecular detail .
"
8355,8356,1857.txt,3,1,unidentified plasmid,plasmid,unidentified plasmid,"The polymyxin B susceptibility of the slyA mutant was the same as that exhibited by the ugtL mutant ( Fig. 5A ) and could be complemented to wild-type levels by a plasmid that expressed the ugtL gene from a heterologous promoter ( Fig. 5B ) , suggesting that ugtL is the only SlyA-regulated gene mediating polymyxin B resistance .
"
8356,8357,1857.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"Sensitivity to CAMPs is also regulated by SlyA , a transcriptional regulator ; mutation of slyA renders S. typhimurium highly sensitive to the CAMP polymyxin B .
"
8357,8358,1857.txt,5,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"2 to CAMPs is also regulated by SlyA , a transcriptional regulator ; mutation of slyA renders S. typhimurium highly sensitive to the CAMP polymyxin B .
"
8358,8359,1857.txt,6,1,Salmonella,Salmonella,Salmonella,"Although slyA mutants are able to invade deep tissues , they are unable to proliferate efficiently within the reticuloendothelial cells of murine hosts , suggesting that Salmonella strains are unable to withstand host cellular antimicrobial mechanisms in the absence of SlyA-regulated genes ."
8359,8360,1843.txt,1,0,,,,"However , if Fis regulates hilD , it might be expected that activation of the hilD promoter in pJB1 could not occur in the fis background ."
8360,8361,469.txt,1,1,unidentified plasmid,plasmid,unidentified plasmid,"To distinguish between these alternatives , we first analyzed the expression of mgtA , pcgL , mgtC , and pmrC as an indirectly PhoP-regulated gene ( 21 , 43 ) in a phoP : : Tn10 strain , expressing PhoP from the IPTG-regu-lated plasmid pEG9014 .
"
8361,8362,469.txt,2,0,,,,"To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) ."
8362,8363,1116.txt,1,0,,,,We predicted the PmrAB-dependent regulation of four additional targets : yibD .
8363,8364,482.txt,1,0,,,,FIG 7 Model for the HilD-and H-NS-mediated regulation of ssrAB .
8364,8365,1670.txt,1,0,,,,"Transient increased sensitivity of a norV mutant to NO suggests that the NorR-regulated NO reductase is part of a multiple enzyme response to NO stress during the infection process ( Mills et al. , 2005 ) ."
8365,8366,1664.txt,1,0,,,,"Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant .
"
8366,8367,1664.txt,2,0,,,,"Protein Domain class Enzymatic Phenotypes affected by a deletion mutation ‡ Comments † GGDEF EAL activity STM1344 -- III no PDE activity , Downregulation of motility , upregulation of rdar morphotype Complements a STM1697 no c-di-GMP Stimulation of CsgD expression mutant ."
8367,8368,496.txt,1,0,,,,"Like marRAB , tolC are positively regulated by Rob .
"
8368,8369,496.txt,2,0,,,,"8 -- 13 _ shown that Rob , play a role in antimicrobial resistance by activating tolC"
8369,8370,1102.txt,1,0,,,,hilD whose products are both AraC/XylS-type transcription activators for unpublished results
8370,8371,1894.txt,1,0,,,,"For instance , expression of hilC in the absence of HilA was not tested because hilC is not regulated by hilA ."
8371,8372,1880.txt,1,0,,,,aa of the 216 aa long CsgD were shown to upregulate expression of the glyA gene .
8372,8373,1658.txt,1,0,,,,"In this study , we elucidated the molecular mechanism of RflM-dependent repression of flhDC .
"
8373,8374,1658.txt,2,0,,,,"RflM functions by repression of flhDC transcription .
"
8374,8375,1658.txt,3,0,,,,"To test a putative link between RflM in repression of flhDC , we performed an unbiased genetic screen using random transposon mutagenesis .
"
8375,8376,1658.txt,4,0,,,,"The transposon mutagenesis thus provided further evidence for a functional link between RflM in repression of flhDC .
"
8376,8377,1658.txt,5,0,,,,"Coordinated repression of flhDC transcription by RflM .
"
8377,8378,1658.txt,6,0,,,,"A. Schematic regulatory model of repression of the flagellar master regulator flhDC by coordinated action of RflM .
"
8378,8379,1658.txt,7,0,,,,"expression of flhC-lac _ providing further evidence for a cooperative action of RflM in repression of flhDC
"
8379,8380,1658.txt,8,0,,,,"RflM , however , did not repress flhDC transcription in the absence of RcsB protein ."
8380,8381,125.txt,1,0,,,,"Expression of the SPI-1 master regulatory gene hilA and five HilA-regulated SPI-1 genes ( sipB , spaO , invH , prgH and invF ) was tested in the loiA mutant , in comparison with the wild-type strain , grown under SPI-1-inducing conditions ( low O2 , high salt ) ."
8381,8382,643.txt,1,0,,,,"At 10 °C , there was a 30-to100-fold induction of RpoS-dependent expression in the rho mutan ."
8382,8383,657.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
8383,8384,131.txt,1,0,,,,"Navarre et al. can selectively silence horizontally acquired their microarray data revealed 6.7-fold repression of srfN expression by H-NS .
"
8384,8385,131.txt,2,0,,,,"Navarre et al. can selectively silence horizontally acquired genes revealed 6.7-fold repression of srfN expression by H-NS .
"
8385,8386,131.txt,3,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB activate the expression of srfN .
"
8386,8387,131.txt,4,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB activate the expression of srfN .
"
8387,8388,131.txt,5,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells and SsrB may come into play .
"
8388,8389,131.txt,6,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR activate the expression of srfN .
"
8389,8390,131.txt,7,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR activate the expression of srfN .
"
8390,8391,131.txt,8,0,,,,"It is interesting to speculate that srfN is initially repressed by H-NS in-vitro , whereas during infection of host cells YdcR may come into play ."
8391,8392,119.txt,1,0,,,,The BaeR D61A protein showed lower aYnity for the mdtA promoter at the same concentrations
8392,8393,2184.txt,1,0,,,,"Thus , one explanation for the transcription we observe following overexpression of ssrB may be that both SlyA and SsrB counteract binding of both H-NS and YdgD/Hha in this A+T rich SPI-2 region ."
8393,8394,2190.txt,1,0,,,,that either SdiA regulates flhC
8394,8395,1499.txt,1,0,,,,"Significant reductions in expression levels were also observed for yqhC , an AraC/xylS family of transcriptional regulator ; a periplasmic repressor of Cpx regulon ."
8395,8396,1472.txt,1,1,Salmonella;Salmonella,S. enterica;enterica,Salmonella,"Finally , we show that Crp , regulates acs expression in S. enterica .
"
8396,8397,1472.txt,2,1,Escherichia coli,E. coli,Escherichia coli,"In E. coli , Crp controls the expression of acs ."
8397,8398,858.txt,1,0,,,,"InvF , regulates the expression of gtgE ."
8398,8399,18.txt,1,0,,,,"Although we demonstrated that this phenotype results from strong repression of hilA , invF , sipC and invG RcsB-regulated genes , we consider that the attenuation requires expression of other genes involved in the bacterial resistance to the host immune system ."
8399,8400,680.txt,1,0,,,,"In the absence of these negative cis elements , ssrAB was no longer repressed by the global regulator H-NS .
"
8400,8401,680.txt,2,0,,,,"that H-NS directly represses ssrAB
"
8401,8402,680.txt,3,0,,,,"In this work , by combining biochemical strategies , we determined that H-NS represses the expression of ssrAB by initially binding to sequences located downstream of the promoter of this operon .
"
8402,8403,680.txt,4,0,,,,"In this work , by combining genetic strategies , we determined that H-NS represses the expression of ssrAB by initially binding to sequences located downstream of the promoter of this operon .
"
8403,8404,680.txt,5,0,,,,"cis elements required for the repression of ssrAB by H-NS .
"
8404,8405,680.txt,6,1,Salmonella,Salmonella,Salmonella,"H-NS represses ssrAB as well as many other Salmonella genes .
"
8405,8406,680.txt,7,0,,,,"This indicates that the 302/478 region contains the cis elements necessary for the repression of ssrAB by H-NS .
"
8406,8407,680.txt,8,0,,,,"the regulatory sequences _ required for the repression of ssrAB by H-NS
"
8407,8408,680.txt,9,1,Felis catus,cat,Felis catus,"ssrAB-cat 69 indicates that when H-NS is inactivated , the 119/336 region is not able to mediate repression of ssrAB
"
8408,8409,680.txt,10,1,Felis catus,cat,Felis catus,"ssrAB-cat 119 indicates that when H-NS is inactivated , the 119/336 region is not able to mediate repression of ssrAB
"
8409,8410,680.txt,11,0,,,,"ssrABcat Fig. 4B indicates that when H-NS is inactivated , the 119/336 region is not able to mediate repression of ssrAB
"
8410,8411,680.txt,12,0,,,,"ssrABcat 10 fusions indicates that when H-NS is inactivated , the 119/336 region is not able to mediate repression of ssrAB
"
8411,8412,680.txt,13,1,Felis catus,cat,Felis catus,"a level of expression higher than that reached by the ssrAB-cat 302/478 fusion _ indicating that the 336/478 region mediates H-NS-indepen-dent repression of ssrAB
"
8412,8413,680.txt,14,0,,,,"a level of expression higher than that reached by B _ indicating that the 336/478 region mediates H-NS-indepen-dent repression of ssrAB
"
8413,8414,680.txt,15,0,,,,"a level of expression higher than that reached by Fig. 4A _ indicating that the 336/478 region mediates H-NS-indepen-dent repression of ssrAB
"
8414,8415,680.txt,16,0,,,,"In the absence of the 119/336 region , the expression of ssrAB was no longer repressed by H-NS , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of FIG 6 HilD displaces H-NS from ssrAB .
"
8415,8416,680.txt,17,0,,,,"In the absence of the 119/336 region , the expression of ssrAB was no longer repressed by H-NS , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of FIG 6 HilD displaces H-NS from ssrAB .
"
8416,8417,680.txt,18,0,,,,"In the absence of the 119/336 region , the expression of ssrAB was no longer repressed by H-NS , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of ssrAB -LRB- Fig. 3 .
"
8417,8418,680.txt,19,0,,,,"In the absence of the 119/336 region , the expression of ssrAB was no longer repressed by H-NS , whereas deletion of the sequence upstream of the position 55 did not affect the H-NS-mediated repression of ssrAB -LRB- Fig. 3 .
"
8418,8419,680.txt,20,0,,,,"Taken together , these results indicate that H-NS represses the expression of ssrAB by acting on the 55/287 region .
"
8419,8420,680.txt,21,0,,,,"the model in which H-NS represses the expression of ssrAB initially by binding by forming a nucleoprotein filament on the promoter
"
8420,8421,680.txt,22,0,,,,"the model in which H-NS represses the expression of ssrAB initially by binding to two nucleation sites
"
8421,8422,680.txt,23,0,,,,"Thus , these results indicate that the 336/478 region mediates H-NS-independent repression of ssrAB .
"
8422,8423,680.txt,24,0,,,,"some of these H-NS binding sites may be unproductive for the repression of ssrAB
"
8423,8424,680.txt,25,0,,,,H-NS represses ssrAB by binding to multiple sites located in a region .
8424,8425,1314.txt,1,1,Leiostomus xanthurus,Spot,Leiostomus xanthurus,"Table 1 Identi cents cation of possible Fis-induced proteins and Fis-repressed proteins by MALDI-TOF Fold changea Spot Protein Gene Group MW ( kDa ) pI Fis-induced proteins Flagella phase-2 # agellin phase-1 # agellin 306.0 2.2 2.1 2.3 2.2 3.0 3.5 2.1 2.9 168.9 2.5 4.75 4.76 6.20 6.32 9.37 5.30 5.87 6.40 5.82 5.37 5.66 52.54 51.34 74.18 53.31 26.60 43.25 50.60 54.03 34.99 31.10 28.56 1 # jB # iC 2 SipA , SPI-1 e ¡ ector protein SseC , SPI-2 translocon SopE2 , SPI-1 e ¡ ector protein EF-Tu lipoamide dehydrogenase mannose 1-phosphate guanylyl transferase mannose-speci cents c enzyme II AB putative sugar binding protein 2-deoxyribose-5-phosphate aldolase 3 SPI sipA sseC sopE2 tufB lpdA manC manX STY2817 deoC 4 5 Translation 6 Sugar metabolism 7 8 9 10 11 Fis-repressed proteins Chaperone Catabolism 0.5 4.83 5.71 5.45 5.43 5.53 6.9 4.50 69.23 32.83 33.35 24.10 23.53 26.17 19.17 DnaK putative aldose 1-epimerase 12 13 14 15 16 17 18 dnaK yeaD 0.43 0.47 0.36 0.48 0.34 0.47 STM4466 pudB adk aphA aacC4 putative carbamate kinase propanediol utilization : polyhedral bodies adenylate kinase class B acid phosphatase 6-N-aminoglycoside acetyltransferase ASCOT ."
8425,8426,1300.txt,1,2,Salmonella;Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,S. enterica;enterica;Typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"In S. enterica serovar Typhimurium , LeuO was reported to increase sdiA expression in low levels ."
8426,8427,694.txt,1,1,Salmonella,Salmonella,Salmonella,PhoP-P activates transcription from the phoP promoter soon after Salmonella experiences low Mg2 + .
8427,8428,1466.txt,1,1,Salmonella,Salmonella,Salmonella,"Additionally , transcription of many genes in SPI-1 declined in Δpat , including the prg ( PhoP-repressed products ) genes prgK , prgJ , prgI , and prgH ( to ) , encoding component of the needle complex ; the sip ( Salmonella invasion protein ) genes sipA , sipD , sipC , and sipB ( approximately ) , encoding translocation machinery component ; and the inv ( invasion ) genes invJ , invI , invC , invB , invA , invE , invG , invF , and invH ( approximately ) , which were essential for invasion of cells ( Supplementary Table 4 ) ."
8428,8429,2147.txt,1,0,,,,"In turn , fliA is positively controlled by FlhC ."
8429,8430,864.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Nou , X. , Braaten , B. , Kaltenbach , L. , regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for anaerobic induction of hyaB in Salmonella typhimurium .
"
8430,8431,864.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Nou , X. , Braaten , B. , Kaltenbach , L. , regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for acid-pH induction of hyaB in Salmonella typhimurium .
"
8431,8432,864.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for anaerobic induction of hyaB in Salmonella typhimurium .
"
8432,8433,864.txt,4,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Low , D.A. Differential binding of Lrp to two sets of pap DNA binding sites regulates Pap phase variation in Escherichia Park , K.R. , Giard , J.C. , Eom , J.H. , Bearson , S. , and Foster , J.W. Cyclic-AMP-receptor-protein and TyrR are required for acid-pH induction of hyaB in Salmonella typhimurium ."
8433,8434,24.txt,1,0,,,,"the hemX gene were used as negative control regions , respectively , as H-NS binds to the proV promoter ."
8434,8435,1328.txt,1,0,,,,"Like marRAB , tolC are positively regulated by MarA .
"
8435,8436,1328.txt,2,0,,,,"8 -- 13 _ shown that MarA , play a role in antimicrobial resistance by activating tolC"
8436,8437,870.txt,1,0,,,,"In this study , we demonstrate that SsrB directly stimulates transcription of sseJ by binding upstream of their respective promoters ."
8437,8438,30.txt,1,0,,,,"According to the idea that NO represses PhoPQ signaling , transcription of the PhoP-repressed genes ( prg ) fliA ( fig. 5B ) , fliC and hilA was upregulated in response to spermine NONOate treatment ( table S2 ) .
"
8438,8439,30.txt,2,0,,,,"Induction of several PhoP-repressed genes including the SPI-1 transcriptional activator hilA , and fliA and fliC components of the flagellar type III secretion systems [ 47,53,54 ] further support a model in which RNS target PhoPQ signaling ."
8439,8440,2153.txt,1,1,Felis catus;Felis catus,cat;cat,Felis catus,"Moreover , Q92am induction of H-NS derepressed the ssrAB-cat ssrAB-cat 240 fusions in the hilD mutant to levels similar to those .
"
8440,8441,2153.txt,2,1,Felis catus,cat,Felis catus,"Moreover , Q92am induction of H-NS derepressed the ssrAB-cat 336 240 fusions in the hilD mutant to levels similar to those .
"
8441,8442,2153.txt,3,1,Felis catus,cat,Felis catus,"Moreover , Q92am induction of H-NS did not affect the expression of ssrAB-cat 69 .
"
8442,8443,2153.txt,4,1,Felis catus,cat,Felis catus,"Moreover , Q92am induction of H-NS did not affect the expression of ssrAB-cat 119 ."
8443,8444,737.txt,1,0,,,,"We did not detect significant AraC-dependent or arabinose-dependent regulation of xylA , a previously described AraC-regulated gene ( 36 ) , nor did we detect binding of AraC upstream of xylA .
"
8444,8445,737.txt,2,0,,,,"We did not detect significant AraC-dependent or arabinose-dependent regulation of xylA , a previously described AraC-regulated gene ( 36 ) , nor did we detect binding of AraC upstream of xylA .
"
8445,8446,737.txt,3,0,,,,"With the exception of xylA , the last AraC-regulated gene to be identified was araJ , more than 30 years ago ( 27 ) .
"
8446,8447,737.txt,4,0,,,,did we detect binding of AraC upstream of xylA
8447,8448,723.txt,1,0,,,,"InvF , regulates the expression of lpxR ."
8448,8449,1506.txt,1,0,,,,The effects of SgrR variants on expression of lacZ from pDM1402 with and without induction by-MG were measured in nutrient medium .
8449,8450,1260.txt,1,1,Salmonella,Salmonella,Salmonella,"Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8450,8451,1260.txt,2,1,Salmonella,Salmonella,Salmonella,"Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8451,8452,1260.txt,3,1,Salmonella,Salmonella,Salmonella,"Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8452,8453,1260.txt,4,1,Salmonella,Salmonella,Salmonella,"Lim S , Yun J , Yoon H , Park C , Kim B , Jeon B , Kim D , Ryu S : Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8453,8454,1260.txt,5,1,Salmonella,Salmonella,Salmonella,"Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8454,8455,1260.txt,6,1,Salmonella,Salmonella,Salmonella,"Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8455,8456,1260.txt,7,1,Salmonella,Salmonella,Salmonella,"Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8456,8457,1260.txt,8,1,Salmonella,Salmonella,Salmonella,"Lim , S. , J. Yun , H. Yoon , C. Park , B. Kim et al. , 2007 Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
"
8457,8458,1260.txt,9,1,Salmonella,Salmonella,Salmonella,Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression .
8458,8459,1274.txt,1,0,,,,ygeA are positively regulated by arabinose due to partial read-through of Rho-independent terminators .
8459,8460,938.txt,1,0,,,,CsgDD59N-His6 bound with affinities comparable to wildtype CsgD to both adrA promoter fragments .
8460,8461,1512.txt,1,0,,,,"In addition , deletional inactivation of STM4538 in the wild-type background leads to the impaired proteolytic cleavage of CadC .
"
8461,8462,1512.txt,2,0,,,,"for CadC activity Inactivation of STM4538 prevents proteolytic cleavage of CadC To assess the potential role of STM4538 in the proteolytic activation of CadC , we performed an immunoblot analysis of total protein extracts from DSTM4538 strains .
"
8462,8463,1512.txt,3,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. Typhimurium;Typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"for CadC activity Inactivation of STM4538 prevents proteolytic cleavage of CadC To assess the potential role of STM4538 in the proteolytic activation of CadC , we performed an immunoblot analysis of total protein extracts from the S. Typhimurium wild-type .
"
8463,8464,1512.txt,4,0,,,,"In particular , we demonstrated that inactivation of STM4538 impaired the proteolytic processing of CadC ."
8464,8465,2033.txt,1,1,Salmonella,Salmonella,Salmonella,"the 9 bp deletion in the promoter region of mutant ramA in fluoroquinolone-resistant Salmonella _ suggesting that it might be the 51 binding site for a local repressor of RamA
"
8465,8466,2033.txt,2,1,Salmonella;Salmonella,Salmonella;Salmonella,Salmonella,"RamR is a local repressor of ramA , and RamA are involved in AcrABmediated multidrug resistance in Salmonella .28 In this study , we investigated the roles of Salmonella multidrug efflux pumps in resistance to tigecycline and other glycylcyclines ."
8466,8467,910.txt,1,0,,,,The MetR protein acts as an activator for the transcription of metH .
8467,8468,1248.txt,1,0,,,,"PhoPQ , seem to convert pH decreases into the regulation of different virulence-factors while the primary role of rpoS appears to be protection against acid stress itself ."
8468,8469,904.txt,1,0,,,,"As expected , expression of known AraC-regulated genes , i.e. , araB , araA , araD , araE , araF , araG , araH , and araJ , increased substantially upon addition of arabinose in wild-type cells and was substantially higher in wildtype cells than araC cells in the presence of arabinose ( Table 2 ) .
"
8469,8470,904.txt,2,0,,,,"Together with a bioinformatic analysis of other Enterobacteriaceae species , these data identify a conserved AraC regulon that includes 7 previously described AraC-regulated genes ( araB , araA , araD , araE , araF , araG , and araH ) as well as three novel targets identified in this work ( ytfQ , araT , and araU ) .
"
8470,8471,904.txt,3,0,,,,"To determine whether either ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to measured-galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeM .
"
8471,8472,904.txt,4,0,,,,"To determine whether either ydeM is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ activity in a wildtype strain and in isogenic strains containing deletions of either ydeM .
"
8472,8473,904.txt,5,0,,,,"To determine whether either ydeN is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to measured-galactosidase activity in a wildtype strain and in isogenic strains containing deletions of either ydeN .
"
8473,8474,904.txt,6,0,,,,"To determine whether either ydeN is required for normal regulation of AraC-activated genes , we constructed a translational fusion of the araE upstream region to lacZ activity in a wildtype strain and in isogenic strains containing deletions of either ydeN .
"
8474,8475,904.txt,7,0,,,,"If suppression of SPI-1 regulation by L-arabinose in AraCˉ background was due to lack of AraE permease , an araE mutation should be epistatic over an araC mutation ."
8475,8476,2027.txt,1,0,,,,"The PmrA training set consisted of the promoter regions of three known PmrAB-regulated genes ( ugd [ 7,15,17 ] , pmrH [ 7,14,17,19 ] and pmrC [ 2,14 ] ) for which the binding of the PmrA protein to the promoter regions was verified by DNA footprint analysis [ 14,15 ] .
"
8476,8477,2027.txt,2,0,,,,All of the genes belong to the phoPQ regulon although the ugd genes are regulated by PhoPQ indirectly through the PmrAB signal transduction system .
8477,8478,535.txt,1,0,,,,"phoN , is regulated by PhoPQ"
8478,8479,253.txt,1,0,,,,We also observed negative regulation of yddX by RtsB .
8479,8480,247.txt,1,0,,,,"Importantly , the enrichment in ssrB promoter DNA was comparable to that of other known PmrA-regulated genes , including pmrC ( Fig. 4C ) .
"
8480,8481,247.txt,2,0,,,,"This analysis suggested that PmrA might bind to the ssrB promoter .
"
8481,8482,247.txt,3,0,,,,"Second , chromatin immunoprecipitation experiments revealed that an HA-tagged PmrA bound to the ssrB promoter in-vivo .
"
8482,8483,247.txt,4,0,,,,"The PmrA protein directly binds to a specific sequence in the promoter of ssrB , repressing its expression .
"
8483,8484,247.txt,5,0,,,,"To identify the binding of PmrA to the promoter region of the ssrB gene were carried out as described .
"
8484,8485,247.txt,6,0,,,,"Interestingly , the PmrA protein repressed SPI-2 expression in a manner similar to the Fur regulator ; PmrA was shown to bind to a region overlapping with the SsrB-binding site on the ssrB promoter ."
8485,8486,521.txt,1,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"-- 10 , 2002 FimZ Binds the Salmonella typhimurium fimA Promoter Region and May"
8486,8487,509.txt,1,1,unidentified,unknown,unidentified,"In the presence of an unknown environmental condition , HilD may activate invF expression .
"
8487,8488,509.txt,2,0,,,,"If a condition exists in which hilA is repressed while invF expression is induced through HilD , it begs the question : Why produce InvF-dependent effectors in the absence of hilA expression when an intact type III secretion apparatus is not thought to be formed ?
"
8488,8489,509.txt,3,0,,,,"Under inducing conditions , HilD also activates a second promoter far upstream of the invF translation start site , termed PinvF-2 -LRB- dotted arrow -RRB- .
"
8489,8490,509.txt,4,1,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,S. typhimurium;typhimurium,Salmonella enterica subsp. enterica serovar Typhimurium,"We have evidence that HilD modestly activates invF expression independently of its effects on hilA , even in WT S. typhimurium .
"
8490,8491,509.txt,5,0,,,,"Our studies show that HilD activate transcription of invF from a promoter .
"
8491,8492,509.txt,6,0,,,,"We show that HilD can directly activate invF .
"
8492,8493,509.txt,7,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of orgA remains unaffected .
"
8493,8494,509.txt,8,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgK remains unaffected .
"
8494,8495,509.txt,9,0,,,,"Figure 2B shows that in the hilA hilD mutant , HilD overproduction induces expression of invF , whereas expression of prgH remains unaffected .
"
8495,8496,509.txt,10,0,,,,"We propose that HilD can independently activate invF expression .
"
8496,8497,509.txt,11,0,,,,"HilD do not activate invF expression from the HilA-dependent invF promoter Previously , we had shown that HilA activates invF expression by direct interaction with sequences upstream of invF called the HilA box .
"
8497,8498,509.txt,12,2,unidentified plasmid;Prairie vole hantavirus;Prairie vole hantavirus,plasmid;pVV;pVV,Prairie vole hantavirus;unidentified plasmid,"These results also explain why our invF-lacZ reporter plasmid , pVV448 , was not activated by HilD to the same extent as the chromosomal invF-lacZ fusion because pVV448 does not contain the HilD-and HilC-dependent +1 of invF .
"
8498,8499,509.txt,13,0,,,,"It is possible that HilD , activates invF expression from a second promoter .
"
8499,8500,509.txt,14,1,Escherichia coli,E. coli,Escherichia coli,"In order to address whether additional S. typhimuriumspecific genes are required for HilD to activate invF , we examined both pSA7 reporters in E. coli TOP-10 cells .
"
8500,8501,509.txt,15,2,Prairie vole hantavirus;Escherichia coli,pVV;E. coli,Escherichia coli;Prairie vole hantavirus,"In order to address whether additional S. typhimuriumspecific genes are required for HilD to activate invF , we examined both pVV448 reporters in E. coli TOP-10 cells .
"
8501,8502,509.txt,16,1,Escherichia coli,E. coli,Escherichia coli,"We found that HilD induce invF expression from pSA7 in E. coli , comparable to that .
"
8502,8503,509.txt,17,1,Prairie vole hantavirus,pVV,Prairie vole hantavirus,"We also found that HilD , activates invF expression from pVV448 , also comparable to that .
"
8503,8504,509.txt,18,0,,,,"These results suggest that HilD might directly activate invF expression by binding to sequences upstream of invF .
"
8504,8505,509.txt,19,0,,,,"These results suggest that HilD might directly activate invF expression by binding to sequences upstream of invF .
"
8505,8506,509.txt,20,0,,,,"HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
8506,8507,509.txt,21,0,,,,"HilD bind to the invF promoter fragment in-vitro To examine whether HilD might directly activate the invF promoter by binding to sequences upstream of invF , we performed gel shift analyses .
"
8507,8508,509.txt,22,0,,,,"HilC directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
8508,8509,509.txt,23,0,,,,"HilC directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
8509,8510,509.txt,24,0,,,,"Discussion HilD directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
8510,8511,509.txt,25,0,,,,"Discussion HilD directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
8511,8512,509.txt,26,0,,,,"Discussion HilD directly activate invF expression by binding downstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
8512,8513,509.txt,27,0,,,,"Discussion HilD directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilC can indirectly activate invF expression by derepressing hilA .
"
8513,8514,509.txt,28,0,,,,"Discussion HilD directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
8514,8515,509.txt,29,0,,,,"Discussion HilD directly activate invF expression by binding upstream of a HilD/C-dependent promoter Previous studies have shown that HilD can indirectly activate invF expression by derepressing hilA .
"
8515,8516,509.txt,30,0,,,,"HilD appear to activate transcription of invF from a HilD/C-dependent start site .
"
8516,8517,509.txt,31,0,,,,"Our studies also suggest that the downstream binding site is required for HilD to activate invF .
"
8517,8518,509.txt,32,0,,,,"In fact , there is evidence that SipC HilD directly activate invF expression 723 can be secreted independently of SPI1 .
"
8518,8519,509.txt,33,0,,,,"In fact , there is evidence that SipA HilD directly activate invF expression 723 can be secreted independently of SPI1 .
"
8519,8520,509.txt,34,0,,,,"HilD are each capable of partially activating invF
"
8520,8521,509.txt,35,0,,,,"HilD activate transcription from the p promoters in an apparently redundant invF sicA manner .
"
8521,8522,509.txt,36,0,,,,"HilD activate transcription from the p promoters in an apparently redundant invF sicA manner .
"
8522,8523,509.txt,37,0,,,,"In addition , HilD directly activate invF in non-HilA dependent manner .
"
8523,8524,509.txt,38,0,,,,"HilD can activate expression of the invF and sicA/sip transcriptional units independently of HilA .
"
8524,8525,509.txt,39,0,,,,"HilD , activate directly the expression of the invF operon , independently of HilA .
"
8525,8526,509.txt,40,0,,,,"HilD all positively regulate invF .
"
8526,8527,509.txt,41,0,,,,"invF is positively regulated by HilD through HilA
"
8527,8528,509.txt,42,0,,,,"Moreover , HilD can activate invF expression in a aY ."
8528,8529,1923.txt,1,1,Salmonella enterica subsp. enterica serovar Typhimurium,typhimu,Salmonella enterica subsp. enterica serovar Typhimurium,"Wild-type S. typhimu-rium containing CysB-regulated promoter reporters for sbp , cysP , and cysJ were grown in M9-minimal-medium with sulfate as the sole sulfur source with and without 50 mM methyl viologen to cause mild oxidative-stress .
"
8529,8530,1923.txt,2,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,"Stoichiometry of binding of CysB to cysP promoter regions of Salmonella typhimurium .
"
8530,8531,1923.txt,3,2,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium,Salmonella;Salmonella typhimurium;typhimurium,Salmonella;Salmonella enterica subsp. enterica serovar Typhimurium,Stoichiometry of binding of CysB to cysP promoter regions of Salmonella typhimurium .
8531,8532,1937.txt,1,0,,,,"AraC has previously been shown to repress its own transcription by binding to a region overlapping the araC promoter elements ( 32 ) .
"
8532,8533,1937.txt,2,0,,,,"In the absence-of-arabinose , AraC represses transcription of araC by forming a repression loop .
"
8533,8534,1937.txt,3,0,,,,"Unlike AraC-dependent repression of araC , repression of ydeN occurs only in the presence of arabinose .
"
8534,8535,1937.txt,4,0,,,,"Unlike AraC-dependent repression of araC , repression of ydeN occurs only in the presence of arabinose ."
8535,8536,1089.txt,1,0,,,,"Among the genes were several previously characterized PmrA-activated genes : pmrH ( STM2297 ) , pmrF , pmrC ( yjdB ) , pmrA ( basR ) , pmrB ( basS ) , yibD and pmrG ( ais ) ."
8536,8537,1062.txt,1,0,,,,"an hfq-ompR double mutant were used to determine whether the regulation of tviA expression by Hfq is associated with the OmpR-EnvZ system .
"
8537,8538,1062.txt,2,0,,,,An ompR mutant double mutant were used to determine whether the regulation of tviA expression by Hfq is associated with the OmpR-EnvZ system .
8538,8539,1704.txt,1,1,Hypostomus robinii,tetA,Hypostomus robinii,"The rtsA gene was under the control of a tetA promoter , hilD was deleted , and HilE was overexpressed as indicated .
"
8539,8540,1704.txt,2,1,Hypostomus robinii,tetA,Hypostomus robinii,"The rtsA gene was under the control of a tetA promoter , hilD was left unaltered , and HilE was overexpressed as indicated ."
8540,8541,290.txt,1,0,,,,"SirA , positively regulates another regulatory gene , hilA .
"
8541,8542,290.txt,2,0,,,,"A second formal possibility is that SirA activates expression of hilA .
"
8542,8543,290.txt,3,0,,,,"For example , the response regulator SirA has been shown to activate hilA transcription in the presence of suitable environmental signals , providing us with tools for both an on - -LRB- S i r M i l A -RRB- .
"
8543,8544,290.txt,4,0,,,,"For example , the response regulator SirA has been shown to activate hilA transcription in PhoPmediated prg response for invasion .
"
8544,8545,290.txt,5,0,,,,"For example , the response regulator SirA has been shown to activate hilA transcription in off-switch for invasion .
"
8545,8546,290.txt,6,1,Salmonella,Salmonella,Salmonella,"In Salmonella , SirA also directly activates the horizontally acquired regulatory genes hilA .
"
8546,8547,290.txt,7,0,,,,"-RRB- b-galactosidase Activity b-galactosidase Activit SirA induction of hilA requires HilD Previous evidence suggested that SirA required the HilC/HilD/RtsA binding sites in the hilA promoter to induce thus the entire SPI1 TTSS b-galactosidase Activity b-galactosidase Activit Fig. 5 .
"
8547,8548,290.txt,8,0,,,,"-RRB- b-galactosidase Activity b-galactosidase Activit SirA induction of hilA requires HilD Previous evidence suggested that SirA required the HilC/HilD/RtsA binding sites in the hilA promoter to induce expression of hilA .
"
8548,8549,290.txt,9,0,,,,"Therefore , our model predicts that SirA induces expression of hilA -LRB- and invF -RRB- via HilD .
"
8549,8550,290.txt,10,0,,,,"We determined if SirA was still capable of inducing expression of hilA -- and invF -- lac fusions .
"
8550,8551,290.txt,11,0,,,,"This suggests that SirA induction of hilA expression requires the presence of HilD .
"
8551,8552,290.txt,12,0,,,,"In support of our model , we demonstrate that SirA induction of hilA requires the presence of HilD .
"
8552,8553,290.txt,13,0,,,,"However , the data in Fig. 5 show that SirA , even overproduced , can activate neither hilA in the absence of HilD .
"
8553,8554,290.txt,14,0,,,,"SirA does this by directly activating the hilA .
"
8554,8555,290.txt,15,0,,,,"SirA controls these genes by directly activating the hilA .
"
8555,8556,290.txt,16,0,,,,"Deletions of rtsA do not affect the induction of hilA by SirA .
"
8556,8557,290.txt,17,0,,,,"Deletions of hilC do not affect the induction of hilA by SirA .
"
8557,8558,290.txt,18,0,,,,"On the basis of these data , the authors concluded that SirA activates the system by direct action on hilA .
"
8558,8559,290.txt,19,0,,,,"SirA , positively regulates the expression of hilA .
"
8559,8560,290.txt,20,0,,,,"SirA , positively regulates the transcription of hilA ."
8560,8561,284.txt,1,2,Salmonella enterica subsp. enterica serovar Typhimurium;Salmonella enterica subsp. enterica serovar Typhimurium;Chryseobacterium gallinarum,S. typhimurium;typhimurium;strain ( 100,Chryseobacterium gallinarum;Salmonella enterica subsp. enterica serovar Typhimurium,"The overlay was prepared in a Falcon tube in conditions of sterility by mixing sterile LB-medium ( 20 mL ) containing agar ( 0.12 g ) at ca. 42 °C , with 20 mg/mL solution of X-gal ( 333 μL ) , 50 μg/mL solution of kanamycin ( 20 μL ) and 1 × 10 CFU/mL 8 of the S. typhimurium strain ( 100 μL ) that harbours reporter transcriptional lacZ-fusions to either the archetypal PhoP-activated gene virK ( 14028 virK : : lacZ ) or to a gene activated by the OmpR -- EnvZ two-compo-nent system , tppB ( 14028 tppB : : MudI ) ."
8561,8562,1710.txt,1,0,,,,"To test whether environmental sulfur availability affected induction of the CysB regulon in swarm cells , cysJ expression was used to represent CysB regulon activity , as the cells swim media with sulfur sources added .
"
8562,8563,1710.txt,2,0,,,,"To test whether environmental sulfur availability affected induction of the CysB regulon in swarm cells , cysJ expression was used to represent CysB regulon activity , as the cells were grown in NBG swarm ."
8563,8564,2219.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"However , in the presence of H2O2 , transcription of fur is also activated by OxyR in E. coli , resulting in repression of target mRNAs for iron-uptake proteins ."
8564,8565,1076.txt,1,0,,,,"More recently it has been shown that the leuO gene is activated by the transcriptional regulators RcsB and BglJ .
"
8565,8566,1076.txt,2,0,,,,"the response regulator RcsB activates leuO transcription in conjunction with BglJ , counteracting H-NS repression of leuO transcription
"
8566,8567,1076.txt,3,1,Escherichia coli,E. coli,Escherichia coli,"More recently , it was shown that leuO expression in E. coli can be activated by the RcsB regulators .
"
8567,8568,1076.txt,4,0,,,,"Also , LeuO expression was detected in a phosphate-restricted media ; and recently it was shown that the expression of the leuO gene can be activated by the RcsB HAS SEVERAL FUNCTIONS IN VIVO Even though LeuO is expressed at very low level in standard laboratory conditions , it seems that in-vivo it has a role in bacterial survival ."
8568,8569,1738.txt,1,0,,,,"InvF positively regulates effector proteins within sptP and located outside -LRB- sopE -RRB- with the help of chaperone SicA .
"
8569,8570,1738.txt,2,0,,,,"InvF positively regulates effector proteins within sptP and located outside -LRB- sopD -RRB- with the help of chaperone SicA .
"
8570,8571,1738.txt,3,0,,,,InvF positively regulates effector proteins within sptP and located outside -LRB- sopB -RRB- with the help of chaperone SicA .
8571,8572,2231.txt,1,1,Escherichia coli,E. coli,Escherichia coli,"Cells were grown d also on LB ag at , a growth-condition used to study the regulation of crl expression by Fur in E. coli W3 ."
8572,8573,2225.txt,1,0,,,,"A DNAseI footprinting assay demonstrated that the TetR-type transcriptional regulator RcdA binds to four high-affinity sites between -308 upstream of the csgD transcription start site .
"
8573,8574,2225.txt,2,0,,,,A DNAseI footprinting assay demonstrated that the TetR-type transcriptional regulator RcdA binds to four high-affinity sites between -192 upstream of the csgD transcription start site .