RIs-GCs data sets

+SmtB	smtA	repressor	metal
+AraC	ygeA	UKNOWN: positively	arabinose
+GntR	gntT	UKNOWN: inducer	gluconate
+CRP	gntT	repressor	gluconate
+GntR	gntK	repressor	absence of gluconate
+OmpR	ompF	activator	osmolarity
+MarA	purA	UKNOWN: decline	IPTG
+Rob	zwf	activator	in vitro
+micF	OmpF	repressor	oxidative stress or weak acids
+MetJ	metE	repressor	AdoMet
+NagC	nagE	UKNOWN: binding	in vivo
+Mlc	nagE	UKNOWN: bind	in vivo
+NarL	nuo	regulator	O2 and nitrate
+IHF	nuo	regulator	O2 and nitrate
+NarP	pfl	repressor	nitrate
+NarP	nrf	activator	nitrite
+NarL	nrf	repressor	nitrate
+FNR	nirB	activator	anaerobic
+ArcA	hyb	UKNOWN: suppresses	anaerobic
+NarL	nrf	activator	low levels of nitrate
+NarL	nrf	repressor	high nitrate
+NarL	nrfA	repressor	nitrate
+NarL	nirB	activator	nitrate
+NarL	nrfA	activator	nitrite
+NarP	nrfA	activator	nitrate
+Fnr	nirB	activator	anaerobiosis
+NarL	fdnG	activator	nitrate
+NarL	fdhF	repressor	nitrate
+ModE	napF	activator	molybdate
+FNR	nrf	activator	anaerobically
+Fnr	aeg	activator	anaerobic
+NarP	aeg	activator	nitrate
+NarP	aeg	activator	nitrite rather than
+OxyR	dps	activator	during growth
+NarL	dcuB	repressor	nitrate
+ArcA	fumB	activator	anaerobic
+NarL	aspA	repressor	nitrate
+NarL	dcuSR	repressor	nitrate
+NarL	dcuS	repressor	nitrate
+NarP	hcp	activator	nitrate
+NarP	hcp	activator	nitrite
+Fis	yeaR	repressor	rich medium
+NarL	ogt	activator	nitrate
+Rob	fumC	activator	overexpression of Rob
+Rob	micF	activator	overexpression of Rob
+Rob	fumC	activator	in vitro
+Rob	nfo	activator	in vitro
+AraC	catabolic operons	activator	arabinose
+SoxS	zwf	activator	superoxide
+AraC	araBAD	activator	arabinose
+AraC	araE	activator	arabinose
+AraC	ydeNM	repressor	arabinose
+AraC	araBAD	repressor	absence of arabinose
+AraC	xylose promoter	repressor	arabinose
+AraC	araC	repressor	arabinose
+AraC	araJ	activator	arabinose
+Lrp	artPIQM	UKNOWN: regulated reciprocally	leucine
+Lrp	cycA	UKNOWN: regulated reciprocally	leucine
+Lrp	leuE	UKNOWN: regulated reciprocally	leucine
+Lrp	ilvKHMGF	UKNOWN: downregulated	leucine
+ArgP	argO	activator	arg
+ArgP	dapB	repressor	lysine
+ArgP	yggA	activator	Arg
+ArgP	dapB	repressor	lys
+ArgP	argO	UKNOWN: negative regulation	Lys
+ArgP	lysC	UKNOWN: negative regulation	Lys
+ArgP	dapB	UKNOWN: negative regulation	Lys
+ArgP	lysA	UKNOWN: negative regulation	Lys
+ArgP	argO	repressor	Lys
+ArgP	lysC	repressor	Lys
+ArgP	dapD	repressor	Lys
+ArgP	gdhA	repressor	Lys
+ArgP	dapB	regulator	lysine
+NagC	nagB	activator	chitin
+ChbR	chb	activator	chitobiose
+GntR	eda	activator	gluconate
+KdgR	eda	activator	galacturonate
+GntH	gntKU	repressor	even in the presence of gluconate
+GntR	GntI	activator	gluconate
+GntR	GntII	UKNOWN: initiates expression	gluconate
+GntH	idnD	activator	idonate
+MelR	melAB	activator	melibiose
+MelR	melAB	regulator	melibiose
+MelR	melR	UKNOWN: derepression	melibiose
+MelR	melR	repressor	absence and presence of melibiose
+CRP	melAB	activator	presence of MelR
+Fnr	oxidase gene	repressor	anaerobic
+CAP	manX	UKNOWN: expression	glucose and glycerol
+CAP	nanC	repressor	site
+CAP	nagB	activator	cAMP
+CRP	chb	activator	chitobiose
+NagC	chiP	repressor	absence of chitosugars
+ChiX	chbC	UKNOWN: downregulates	uninduced
+FNR	narGHJI	UKNOWN: expression	anaerobic growth
+NarL	narK	activator	nitrate
+NarL	frdABCD	repressor	nitrate
+narL	fdnCHI	activator	anaerobically by nitrate
+Fnr	dmsABC	regulator	oxygen and nitrate
+Fnr	frd	activator	anaerobic
+Fnr	dmsA	activator	anaerobic
+Fnr	napF	activator	anaerobiosis
+NarP	aeg	activator	nitrite
+Fnr	aeg	activator	nitrate
+Fnr	napF	activator	weakly
+NarL	napF	UKNOWN: antagonizes	in vitro
+NarL	napF	regulator	nitrate
+NarL	napF	regulator	nitrite
+NsrR	ytfE	activator	nitrite
+FNR	ydhY	activator	anaerobic
+CitB	citCDEFXGT	activator	citrate in the absence of oxygen and nitrate
+FNR	fdnGHI	UKNOWN: expression	anaerobic growth
+NarL	narGHJI	activator	nitrate
+NarL	dmsABC	repressor	nitrate
+fnr	fdnCHI	activator	anaerobically by nitrate
+RhaR	rhaSR	activator	rhamnose
+CTD	rhaSR	activator	presence of RhaR
+RhaS	rhamnose regulon	activator	rhamnose
+NarP	ydhY	regulator	nitrate
+ChbR	chb operon	activator	chitobiose
+CitA	dcuB	activator	citrate
+NarL	hcp	activator	nitrite
+CRP	fucPIK	activator	presence of fucose
+mar system	waaY	activator	antibiotics
+ArgP	argO	UKNOWN: abolish	lysine
+NorR	NorVW	activator	NO
+FNR	pnrf	activator	anaerobic
+GntH	idnO	activator	idonate
+NarL	fumB	repressor	nitrate
+NarL	pfl	repressor	nitrate
+ArgP	asd	repressor	Lys
+ArgP	dapB	repressor	Lys
+MelR	melR	repressor	melibiose
+IHF	dps	activator	stationary phase
+CAP	gntK	repressor	glucose
+MetJ	MetR	repressor	AdoMet
+XylR	xyl	repressor	arabinose
+narP	hyb	repressor	nitrate
+NarL	dmsABC	UKNOWN: negatively	nitrate
+NarP	ydhY	regulator	nitrite
+NagC	chiP	repressor	absence of chitobiose
+NsrR	ytfE	activator	nitric oxide
+MarA	waaY	regulator	salicylate
+FNR	nuo	regulator	O2 and nitrate
+CRP	araBAD	activator	glucose starvation
+Fnr	dmsABC	UKNOWN: positively	anaerobic
+Lrp	argO	UKNOWN: binding	leucine
+AraC	araFGH	activator	arabinose
+NarL	hcp	activator	nitrate
+GntH	GntI	repressor	metabolites derived from gluconate
+AppY	appA	activator	carbon and phosphate starvation
+MetR	metE	activator	in vitro
+NarP	nirB	activator	nitrate
+NorR	norV	activator	reactive nitrogen species
+ArgP	lysP	UKNOWN: negative regulation	Lys
+Fnr	yeaR	activator	nitrite
+Fnr	dmsA	activator	activation
+NagC	nag	repressor	absence of chitosugars
+Fis	ogt	repressor	rich medium
+NarL	nirB	activator	nitrite
+NarP	nrfA	activator	nitrite
+NarP	fdnG	activator	nitrate
+NarL	dmsABC	regulator	oxygen and nitrate

+9409145	2306	SmtB is a metal - dependent repressor of the cyanobacterial metallothionein gene smtA : identification of a Zn inhibited DNA - protein complex .
+24272778	360	ygeA and polB are positively regulated by AraC and arabinose due to partial read - through of Rho - independent terminators ( Fig . 2 , 4 , and 5 ) .
+9537375	35	In this study , we show for the first time that the operator sequence is indeed the binding site for the negative regulator GntR and that gluconate is the true inducer of gntT , by inactivation of GntR binding to the operator .
+9537375	121	To investigate the role of the CRP and adenylate cyclase in catabolite repression of the gntT gene by glucose and gluconate , crp and cya null mutations were transduced into the strain carrying the chromosomal gntT : : lacZ fusion .
+12618441	114	COLI 1787 Downloaded from http : / / jb . asm . org / FIG . 2 — Continued . on January 11 , 2016 by Instituto de Biotecnologia , UNAM the gntK expression was repressed by GntR in the absence of gluconate .
+7836283	154	OmpR can activate or repress the ompF gene depending on osmolarity conditions and the strength of the promoter ( 30 ) .
+14701822	86	After a 1 - h induction of MarA by IPTG , a decline was seen in the levels of transcripts of purA ( Fig . 1A ) and hdeA ( Fig . 1B ) .
+12100559	143	For instance , Rob has been shown to bind and activate the zwf promoter in vitro but whole cell zwf regulation cannot be activated by Rob , although the gene responds to SoxS and MarA ( Ariza et al . , 1995 ; Jair et al . , 1995 1996a ; b ) .
+11601842	90	For example , both the AcrAB efflux pump and micF induced - decreases in OmpF porin are turned on in response to oxidative stress or weak acids .
+2543976	66	The addition of MetJ and AdoMet to incubations containing MetR also results in a 75 % inhibition of metE expression but no effect on MetH expression ( line 2 vs . line 4 ) .
+11139621	176	Binding of NagC and Mlc to nagE operators in vivo As Mlc showed a stronger affinity for the nagE operator than NagC , it seemed possible that Mlc might be able to regulate the nagE promoter in the absence of NagC in vivo . ThreenagE – lacZ fusions were tested : the standard ‘ loop - forming ’ nagBE – lacZ fusion , whose expression is repressed by NagC binding co - operatively to the nagE and nagB operators ; and two single operator nagE – lacZ fusions , missing the nagB promoter / operator , but carrying the same nagE – lacZ junction .
+11139621	188	To verify that Mlc does bind preferentially to the nagE operator in vivo , the effect of plasmids overproducing either Mlc or NagC was tested in a strain mutated for both mlc and nagC . Plasmids expressing either NagC or Mlc produce considerable repression of the nagBE – lacZ looped fusion , reducing expression 88 - and 56 - fold ( Table 2 ) .
+7565112	12	Therefore , expression of nuo is regulated by O2 and nitrate via ArcA , NarL , FNR and IHF at sites within the - 277 region , and by other factors including C4 dicarboxyiates at a site between - 277 and - 899 .
+7601827	117	RESULTS Maximal nitrate repression of pfl expression is dependent on functional NarL , NarP , NarX , and NarQ proteins .
+7601827	267	The mechanism which the cell employs to repress pfl expression with nitrate clearly involves NarL and NarP , but a further factor ( s ) which dictates whether repression is strong or weak , perhaps in response to the intracellular redox status , must be involved .
+7854119	11	The nrf promoter can be activated by either NarP or NarL in response to nitrite but is repressed by NarL in response to nitrate .
+8437517	14	Mutations in the putative NarL - binding site at the nirB promoter decrease FNR - dependent anaerobic induction , suggesting that NarL acts as a helper to FNR during transcription activation .
+10537212	12	This latter result indicated that ArcA suppresses anaerobic hyb expression and that a further factor , which remains to be identified , is involved in controlling anaerobic induction of operon expression .
+11004182	11	While either NarL or NarP was able to induce nrfA - lacZ expression in response to low levels of nitrate , only NarL could repress at high nitrate levels .
+11004182	29	In contrast , NarL is reported to repress nrfA expression in response to nitrate , whereas NarP cannot ( 14 – 16 , 23 , 24 ) .
+11004182	105	From prior batch culture experiments , both NarL and NarP were reported to activate nirB - lacZ in response to nitrate ( 23 , 24 ) .
+11004182	106	The chemostat experiments ( Fig . 3A ) also demonstrate that NarL or NarP can function independently of each other to induce nirB expression in response to nitrate .
+11004182	130	During batch cell culture conditions , nitrite was reported to induce nrfA expression via either the NarL or NarP response regulator proteins , while only nitrate was reported to cause repression of nrfA expression and only by NarL ( 14 , 16 , 24 ) .
+11004182	139	First , either NarL or NarP can activate nrfA - lacZ expression in response to added nitrate .
+11004182	308	During anaerobiosis , the Fnr protein ( F ) binds at its consensus recognition site , centered at 42 , to activate nirB operon expression .
+12923080	26	The nitrate induction of fdnG expression occurs at the level of transcription control , where NarL is a strong activator and NarP is a weak activator ( 11 , 20 ) .
+12923080	169	The nitrate - dependent repression of fdhF - lacZ expression shown in Fig . 3B was confirmed by batch culture experiments in which NarL negatively regulated gene expression .
+13129959	184	In the 146 strain , which retains the ModE protein binding site , ( napF - lacZ ) expression was induced during growth with added molybdate , and this induction required the modE allele ( data not shown ) .
+15978080	11	Summary Expression from the Escherichia coli nrf operon promoter is activated by the anaerobically triggered transcription factor , FNR , and by the nitrate / nitrite ioncontrolled response regulators , NarL or NarP , but is repressed by the IHF and Fis proteins .
+7643383	8	Expression of the aeg - 46.5 operon NY 14853 - 8101 , USA ( anaerobically expressed gene at 46.5 minutes on the genetic map ) is induced during anaerobic growth by the global transcriptional regulatory protein Fnr .
+7643383	9	aeg - 46.5 operon expression is further induced by the NarP protein in response to nitrate or nitrite and this induction is antagonized by NarL .
+7643383	227	A NarP / NarL site centered at – 44.5 bp Our results demonstrate that the symmetrical region centered at position 44.5 ( Choe & Reznikoff , 1993 ) is essential for NarP - dependent nitrate and nitrite activation of aeg - 46.5 operon expression .
+8501030	15	We found that the primary signal for NarP - dependent aeg - 46.5 operon induction is nitrite rather than nitrate .
+9335308	207	The dps promoter is activated by OxyR during growth and by IHF and s in stationary phase .
+9852003	12	The dcuB gene is strongly activated anaerobically by FNR , repressed in the presence of nitrate by NarL , and subject to cyclic AMP receptor protein ( CRP ) - mediated catabolite repression .
+9852003	45	Expression of fumB is also induced anaerobically ( 1.5 - or 5 - fold ) in a manner which is dependent on both FNR and ArcA ( 41 , 44 ) .
+9852003	183	This demonstrates that NarL has the major role in nitrate - induced repression of dcuB expression ( Fig . 5Dii ) .
+15995204	198	This indicates that the NarX - NarL system is solely responsible for nitrate repression of these four operons ( dcuB - fumB , aspA , frdABCD , and dcuSR ) involved in fumarate respiration .
+15995204	222	Expression from a monocopy ( dcuS - lacZ ) operon fusion revealed three - to fourfold repression by nitrate ( Table 2 ) , virtually all of which can be attributed to the NarX - NarL regulatory system rather than the paralogous NarQ - NarP system ( data not shown ) .
+16261196	189	In agreement with these findings , the nitrate - and nitrite - induced transcription from the hcp promoter in E . coli was found to depend on the response regulator proteins NarL and NarP [ 45 ] .
+19245365	12	NarLdependent activation at both the yeaR and ogt promoters is decreased in rich medium and this depends on Fis , a nucleoidassociated protein .
+19245365	231	We suggest that the induction of ogt by NarL alone in response to external nitrate provides a prophylactic insurance policy against possible genotoxic effects arising from nitrate metabolism .
+10850996	36	E - mail : m . h . j . bennik @ ato . wag - ur . nl . have shown that overexpression of Rob ( or its N - terminal domain alone ) activates transcription of sodA ( encoding manganese - containing superoxide dismutase ) , fumC ( encoding fumarase C ) , inaA ( encoding a weak acid - inducible protein ) , and micF ( gene for an antisense RNA repressing the outer membrane porin OmpF ) .
+10850996	216	Other genes reported to be activated by Rob in vitro ( fpr , fumC , micF , nfo , sodA , and zwf ) ( 15 ) or by Rob overexpression in vivo ( fumC , inaA , micF , and sodA ) ( 5 ) were not found in our study ; thus , it appears that the mutagenesis and screening procedure was not saturating .
+9409145	203	With arabinose , AraC activates transcription from the promoters of the catabolic operons ( Fig . 3 ) .
+9409145	1172	Genetic definition of the Escherichia coli zwf “ Soxbox , ” the DNA binding site for SoxS - mediated induction of glucose 6 - phosphate dehydrogenase in response to superoxide .
+24272778	16	E . coli AraC activates transcription of the araBAD , araFGH , araE , and araJ transcripts in the presence of its inducer , L - arabinose ( 5 ) .
+24272778	213	Thus , ydeNM is a novel AraC - regulated operon that is directly repressed by AraC in an arabinose - dependent manner .
+24272778	351	At the araC - araBAD intergenic region , AraC forms a repression loop in the absence of arabinose due to the dimerization of distally bound AraC monomers .
+20023096	46	We found that this repression is AraC dependent and is most likely due to binding by arabinose - bound AraC to the xylose promoters , with consequent inhibition of gene expression .
+20023096	117	When bound with arabinose , AraC activates the transcription of the araBAD , araE , and araFGH operons and represses transcription from the araC operon .
+8516313	35	When arabinose is added , the subunit that formerly contacted araO2 releases and shifts to the araI2 half - site , from which it activates transcription from the araBAD promoter ( PBAD ) ( 19 ) , results that extend a prior observation that the presence of arabinose can extend the region of aral2 that AraC protects from DNase I digestion ( 20 ) .
+1744033	132	The facts that arabinose induces the substantial transcription of araJ messenger ( 11 ) and that this transcription is regulated by CAP and AraC ( 11 , 18 ) are , however , consistent with araJ actually being translated and serving some purpose in the arabinose metabolism of E . coli .
+1447222	17	In the presence of arabinose , AraC protein activates the expression of the araBAD , araFGH , and araE promoters ( 6 - 10 ) .
+1447222	27	In the absence of arabinose , AraC protein represses araBAD transcription by a mechanism involving cooperative binding of AraC protein to two AraC binding sites at a distance , resulting in formation of a DNA loop ( 15 - 19 , 39 , 40 ) .
+19906180	207	Interestingly , many other transporters for amino acids such as the uptake genes for arginine ( artPIQM ) , serine ( sdaC ) , alanine ( cycA ) and proline ( proY ) , and the export gene for leucine ( leuE ) are also regulated reciprocally by Lrp and leucine ( Kutukova et al . , 2005 ; Cho et al . , 2008 ) .
+19906180	209	In contrast , several transporters for aromatic amino acids ( brnQ , ilvKHMGF and ilvJHMGF ) appear to be regulated by the concerted mode , their expression is downregulated by Lrp and leucine potentiates this effect ( Cho et al . , 2008 ) .
+17504942	37	Our results indicate that whereas ArgP activates argO transcription in the presence of Arg through the process of RNA polymerase ( RNAP ) recruitment ( Ptashne and Gann 1997 ; Browning and Busby 2004 ) , the mechanism by which Lys addition phenocopies an argP mutation is not simply by preventing the binding of ArgP to the argO operator but instead by reversible trapping of the recruited RNAP at the promoter in a novel molecular complex that is proficient for neither productive nor abortive transcription .
+18502871	151	There is a strict correlation between the presence of ArgP and a high level of lysine - repressed dapB transcription , provided that the dapB regulatory region contains the necessary cis - acting upstream sequences .
+15150242	191	( iii ) The transcription of yggA in vivo is ArgP dependent and is induced by exogenous Arg or Arg - Ala ( and also by an argR mutation ) , whereas the addition of Lys or Lys - Ala phenocopies the effect of an argP null mutation ; furthermore , yggA expression is rendered constitutive in an argP d strain .
+15150242	194	Therefore , a straightforward interpretation of our results , as further discussed below , is that ( i ) ArgP is a transcriptional activator of yggA , ( ii ) ArgP ’ s activator function is enhanced by Arg and inhibited by Lys , and ( iii ) yggA encodes an Arg ( and CAN ) exporter in E . coli .
+21890697	8	ArgP mediates lysine ( Lys ) repression of argO , dapB , and gdhA in vivo , for which two alternative mechanisms have been identified : at the dapB and gdhA regulatory regions , ArgP binding is reduced upon the addition of Lys , whereas at argO , RNA polymerase is trapped at the step of promoter clearance by Lys - bound ArgP .
+21890697	41	Our results indicate that negative regulation involving Lys as coeffector is mediated by ArgP and that the target genes include argO , lysP , lysC , asd , dapB , dapD , lysA , and gdhA .
+21890697	168	In the case of argO , ArgP mediates its transcriptional activation by Arg , as well as its repression by Lys ( 7 , 26 , 32 , 37 ) ; the latter is achieved by a mechanism involving the active trapping at the argO promoter by ArgP of RNA polymerase , which is then prevented from being released to engage in productive transcription ( 26 ) .
+21890697	171	These include lysP , lysC , lysA , dapD , and asd ( in addition to argO , dapB , and gdhA ) , all of which exhibited ArgP - mediated repression upon Lys supplementation in vivo , as well as ArgP binding to the corresponding cis regulatory regions in vitro .
+21441513	322	ArgP of E . coli is also responsible for the lysine - dependent regulation of dapB , which encodes one of the enzymes of the diaminopimelate and lysine biosynthesis pathway ( 2 ) , and argO , which encodes the arginine exporter ArgO ( 24 , 30 ) .
+15066032	168	Further evidence that growth on chitin is limiting for induction of NagC is shown by the analysis of the effect of chitin and chitobiose on induction of a NagC - regulated nagB – lacZ fusion .
+18028317	31	In the presence of chitobiose , ChbR , along with CRP , activates transcription from the chb promoter ( Plumbridge and Pellegrini , 2004 ) .
+15659677	8	P1 controls eda induction on gluconate and is regulated by GntR .
+15659677	9	P2 controls eda induction on glucuronate and galacturonate and is regulated by KdgR .
+12618441	229	Taken together , GntH seems to repress the expression of the gntKU and gntT genes , and the repression occurs even in the presence of gluconate , which could be physiologically important , as discussed below .
+12618441	314	In contrast to the case for GntR , the GntI genes in the presence of cloned GntH were negligibly induced by gluconate ( Table 3 ; Fig . 5 ) .
+14593252	6	The results presented allow us to speculate that GntR initiates expression of the GntII genes , followed by their large induction by GntH when cells were grown in gluconate minimum medium .
+14593252	28	Bausch et al . [ 1998 ] provided biochemical evidence that the idnD and idnO genes in GntII encode idonate dehydrogenase , oxidizing idonate to 5 - ketogluconate and 5 - ketogluconate reductase , reducing 5 - ketogluconate to gluconate , respectively , and that the GntII system is induced by GntH in the presence of idonate or 5 - ketogluconate .
+18346968	259	Expression of the E . coli K - 12 melAB genes , which encode products essential for melibiose metabolism , depends on transcription activation by MelR and CRP , and is triggered by melibiose ( 7,9 ) .
+10747919	7	Busby § , and Tomofusa Tsuchiya ¶ From the Department of Microbiology , Faculty of Pharmaceutical Sciences , Okayama University , Tsushima , Okayama , 700 – 8530 Japan and the § School of Biosciences , The University of Birmingham , Edgbaston , Birmingham B15 2TT , United Kingdom MelR is an Escherichia coli transcription factor that activates expression of the melAB operon in response to the presence of melibiose in the environment .
+16621812	8	Busby * School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , United Kingdom Received 29 December 2005 / Accepted 10 February 2006 Transcription of the Escherichia coli melAB operon is regulated by the MelR protein , an AraC family member whose activity is modulated by the binding of melibiose .
+16621812	36	It has been proposed ( 30 ) that repression requires the formation of a DNA loop that is stabilized by MelR binding at site R and site 2 and that the presence of melibiose breaks this loop , resulting in derepression of pmelR , occupation of site 2 , and induction of pmelAB ( Fig . 1 ) .
+16621812	103	Table 3 lists - galactosidase activity measurements , which showed that pmelAB activity is very low in the absence of melibiose and that melibiose triggers a 50 - fold increase in pmelAB activity that is MelR dependent .
+16621812	200	When triggered by melibiose , wild - type MelR requires the assistance of CRP to activate transcription at pmelAB ( 31 ) .
+16621812	226	This model is supported by genetic analyses , notably , mutations that alter amino acids in the AraC N - terminal arm that result in AraC - dependent activation of paraBAD in the absence of arabinose ( 19 , 21 , 22 , 34 , 35 ) .
+10760179	91	Results in Fig . 3 show that , in each case , the single base substitution in the Site R MelR - binding site results in a significant reduction in MelR - dependent repression of the melR promoter in both the absence and presence of melibiose .
+11742992	57	Hence , in the absence of MelR , CRP does not activate transcription at the melAB promoter whereas , in the presence of MelR , CRP activates transcription ~ 10 - fold ( Figure 1C ) .
+8729576	199	In spite of such high similarity , Fnr is associated not with the transport system but with the switching of respiration styles ; i . e . under the anaerobic condition , Fnr activates the transcription of anaerobic enzyme genes , repressing the transcription of oxidase gene ( Spiro & Guest , 1991 ) , together with ArcA , one of the response regulators in Group 1 , that represses the transcription of aerobic respiration enzyme genes ( Iuchi et al . , 1990 ; Iuchi & Lin , 1993 ) .
+9484892	119	To confirm that the different levels of expression in the glucose and glycerol media are caused by cAMP / CAP activation , the expression of the manX – lacZ and borG – lacZ fusions was measured in a cya strain ( TP2006 ) .
+15743943	134	There is no obvious 35 promoter sequence , but a potential CAP site is detectable on the sequence ( Fig . 1A ) , centered at position 61.5 , which is consistent with the strong catabolite repression observed with the nanC fusion .
+9469834	117	However , cAMP caused a large ( 15 - fold ) stimulation of nagE and a 2.5 - fold stimulation of nagB when the CAP site was located at its functional distance .
+24593230	151	In the absence of chitosugars ( uninduced ) the chb , chiP and nag operons are repressed by NagC .
+24593230	184	This suggested that ChiX pairing with the RNA sequence from the chbB - chbC intercistronic spacer – the very mechanism responsible for ChiX inactivation during chitobiose induction – downregulates chbC expression under uninduced conditions .
+1629153	254	The FNR protein is required for fdnGHI and narGHJI operon expression during anaerobic growth , and the NARL protein is required for induction by nitrate ( 4 ; for a review , see reference 25 ) .
+7601827	217	For example , nitrate induction of the narGHJI operon ( 21 ) and the narK gene ( 12 ) is controlled exclusively by NarL , while induction of the fdnGHI operon is controlled principally by NarL , but NarP also effects a degree of control ( observed with a narL mutant ) ( 21 ) .
+7601827	218	Expression of the dmsABC and the frdABCD operons is repressed in the presence of nitrate , and this repression is dependent on the NarL protein ( 8 , 10 , 21 , 28 ) .
+2168848	36	We found that expression of the fdnCHI operon was induced anaerobically by nitrate , and required fnr ’ and narL + .
+12079504	26	These studies define the molecular interactions of Fnr and NarL at the dmsABC P1 promoter that together provide for the oxygen and nitrate regulated expression of this respiratory pathway operon .
+12079504	33	Likewise , the poor match of the Fnr site at the promoter for the fumarate reductase gene , frdA to the consensus Fnr sequence may account for the relatively weak anaerobic induction for this respiratory operon [ 14 ] .
+12079504	42	The 114 - fold anaerobic activation seen for the wild - type dmsA promoter was reduced to about 35 - fold in each of the two mutants ( Figure 1 ) , indicating that the position of the Fnr site at the wild - type dmsA promoter is important for controlling optimal dmsA gene expression .
+12079504	137	+ 40 + 30 + 20 + 10 + 1 - 10 - 20 - 30 - 40 - 50 dmsA Conclusions This study investigated the effects of sequence changes in the Fnr - recognition site on the anaerobic activation of dmsA - lacZ expression as well as examined the NarL recognition sites wi
+13129959	9	The napF operon control region exhibits unusual organization of DNA binding sites for the transcription regulators Fnr and NarP , which activate transcription in response to anaerobiosis and nitrate , respectively .
+7643383	36	Nitrate and nitrite induction of the nirB operon and nitrite induction of nrfA operon expression is mediated to differing extents by the NarL and NarP proteins ( Rabin & Stewart , 1993 ; Tyson et al . , 1993 , 1994 ) .
+7643383	43	Previous experiments suggest that the nitrate and nitrite induction of aeg - 46.5 operon expression is mediated solely by the NarP protein , in contrast to all other nitrate and / or nitrite - inducible operons studied to date that are efficiently activated by the NarL protein alone or by both the NarL and NarP proteins ( Rabin & Stewart , 1993 ) .
+7643383	44	The NarP - dependent nitrate and nitrite induction of aeg - 46.5 operon expression is increased in a narL null strain .
+7643383	83	Also , the effects of control region deletions from 275 to 68 on the nitrate and nitrite induction ratios of aeg - 46.5 operon expression ( Table 1 ) may be an indirect result of the effect on Fnr - dependent regulation .
+9696769	126	When wild - type Fnr was expressed from a multicopy plasmid , ( napF - lacZ ) expression was induced approximately sixfold by anaerobiosis ( Table 1 ) .
+9696769	133	Deletion , mutational , and footprint analyses had indicated that napF operon expression in vivo is induced weakly by either Fnr or NarP alone and strongly by Fnr and NarP together .
+9696769	172	MBP - NarL antagonizes activation of the napF promoter by Fnr ( D154A ) and MBP - NarP in vitro .
+9696769	181	DISCUSSION The napF promoter is one of several regulated by Fnr in response to anaerobiosis and by NarL or NarP in response to nitrate and nitrite .
+15995204	56	Additionally , nitrate , acting via the NarL response regulator , represses the transcription of the frdA and dcuB - fumB operons ( Fig . 1C ) ( 18 , 22 , 27 , 53 ) .
+17720788	287	Recent studies have documented NsrR and Fnr regulation of ytfE ( dnrN ) gene expression patterns similar to those reported here for the yeaR - yoaG operon : NsrR - dependent induction by nitrite and nitric oxide ( or compounds that generate nitric oxide ) and enhanced expression in fnr null strains ( 6 , 20 , 24 ) .
+18227264	222	Consistent with the hypothesis that YdhY – T has a role in anaerobic metabolism , gel retardation , footprinting , sitedirected mutagenesis and transcript - mapping experiments showed that the oxygen - responsive transcription factor FNR directly activates transcription of ydhY – T under anaerobic conditions by binding at a site located at position 242.5 relative to the transcript start , confirming and extending earlier work that shows that ydhY is expressed from a class II FNR - dependent promoter ( Kang et al . , 2005 ) .
+22101843	123	Thus , the expression of the citCDEFXGT gene cluster of E . coli depends on CitA / CitB , and the system confers induction by citrate in the absence of oxygen and nitrate .
+11073923	7	EGAN * Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66045 Received 21 August 2000 / Accepted 18 September 2000 The Escherichia coli rhaSR operon encodes two AraC family transcription activators , RhaS and RhaR , and is activated by RhaR in the presence of L - rhamnose . - Galactosidase assays of various rhaS - lacZ promoter fusions combined with mobility shift assays indicated that a cyclic AMP receptor protein ( CRP ) site located at 111.5 is also required for full activation of rhaSR expression .
+11073923	214	This result indicates that in the presence of RhaR , - CTD can contribute to transcription activation at rhaSR , perhaps by interaction with DNA and / or RhaR .
+17513476	21	The RhaS protein functions to activate transcription of two of the operons in the Escherichia coli L - rhamnose regulon in response to the availability of L - rhamnose ( 11 , 40 ) .
+18227264	223	Furthermore , ydhY – T expression is regulated by the NarXL and NarPQ nitrate - and nitriteresponsive two - component systems , confirming the results of previous transcription - profiling studies ( Constantinidou et al . , 2006 ) .
+24593230	45	In the presence of chitobiose / triose , a metabolite of chitobiose , probably monodeacetylated chitobiose - 6P ( Verma and Mahadevan , 2012 ) , causes the ChbR regulatory protein to activate transcription of the chb operon .
+22101843	281	Nevertheless , CitA is required for the maximal induction of dcuB - lacZ by citrate ( but not by fumarate ) as shown here and earlier ( 25 ) , and DcuS / DcuR is required for the maximal expression of citC - lacZ .
+15667305	11	Nitrate - and nitriteinduced transcription from the hcp promoter was activated by the response regulator proteins NarL and NarP .
+1560456	11	AraC protein bound at the aral site immediately adjacent to the RNA polymerase binding site of the pBAX ) promoter stimulates transcription of the araBAD genes in the presence of arabinose ( Lee et al . , 1974 ; Hahn et al . , 1986 ; Martin et al . , 1986 ) .
+10601201	180	The CRP K52N mutant possesses a third activating region , designated AR3 ( small black triangle ) , that has been proposed to contact the subunit ( see text ) . contrast to CRP , which effectively activated the wild - type fucPIK promoter only in the presence of fucose but failed to activate the IS5 - disrupted promoter in the presence or absence of fucose , as previously reported ( 8 ) .
+8501030	154	These results show that the NarP protein activates F ( aeg - 46.5 - lacZ ) expression in response to nitrate and nitrite and that the NarL protein antagonizes this activation .
+19376854	246	waaY promoter is also induced by antibiotics through the mar system .
+24272778	349	Although arabinose - dependent repression by AraC has not been observed before , there are clear parallels with arabinose - dependent activation of araBAD transcription .
+12079504	41	To evaluate how the spacing between the Fnr binding site and the start of dmsA transcription alters the anaerobic activation of dmsA - lacZ expression , single basepair insertions were introduced at position - 35 ( ?JA448 and ?JA449 ) .
+11004182	140	Second , NarL can repress nrfA - lacZ expression when nitrate is present , whereas NarP cannot ( compare the NarL NarP strain to the NarL NarP strain and to the wild - type strain ) .
+12923080	226	NarP thus performs a unique role to fine - tune fdnG operon expression by delaying the ability of NarL to activate when nitrate levels are low .
+12618441	332	In the model , gluconate is first imported by gluconate permease , GntP , as demonstrated ( 15 ) , and interacts with the GntR molecule to induce the GntI system genes .
+12079504	138	The data illustrates that Fnr is responsible for the 100 - fold anaerobic activation of dmsA expression .
+8010957	12	MelR activity can be triggered by the inclusion of melibiose in the growth medium ; the role of MelR is to activate transcription initiation at the melAB promoter ( pmelAB ) in response to melibiose or , possibly , some other metabolite .
+18502871	152	Interestingly , lysine is known to virtually abolish transcription activation of argO , a bona fide ArgP target .
+17449618	193	A major protection mechanism against NO in the cytoplasm is provided by flavorubredoxin and its reductase , NorVW , which are synthesized in response to NO activation of the transcription activator NorR ( 15 , 20 , 22 ) .
+9409145	310	Transcription initiation from P melAB is stimulated by the MelR regulator with melibiose .
+7643383	12	A sequence with similarity to the Fnr - binding site consensus , centered at position 64.5 , was essential for Fnr - dependent anaerobic induction of aeg - 46.5 operon expression .
+7854119	185	The resuits in Tabie 7 confirm that expression from pnrf was totally FNR dependent and induced during anaerobic growth .
+16621812	213	This strong repression is relieved by melibiose and , thus , melibiose toggles MelR between two alternative states , one that activates pmelAB and one that represses pmelR ( Fig . 1B ) .
+8655507	225	An excellent CAP - binding site ( 19 ) is centered at bp 70 with respect to the transcriptional start site of the gntK gene , explaining the phenomenon of glucose catabolite repression observed in Northern blot analysis .
+9852003	59	The results show that the dcuB gene is expressed exclusively under anaerobic conditions in a manner that is FNR dependent and that it is repressed by NarL in the presence of nitrate and is subject to CRP - mediated catabolite repression .
+2543976	73	If the MetR protein synthesized from pRSE562 was responsible for the observed increase in MetH synthesis , the MetJ protein and AdoMet , if added to the first incubation , should inhibit the increase by preventing MetR synthesis .
+20023096	211	Based on our results with the arabinose transporter deletion strains , arabinose likely inhibits xylose gene expression by one of two mechanisms : either ( i ) arabinose - bound AraC binds to the P xylA promoter and prevents it from being activated by xylose - bound XylR or ( ii ) arabinose directly binds XylR and inhibits its activity .
+10537212	116	In the narL narP double null mutant , nitrate repression of hyb expression was relieved and anaerobic regulation after growth in the absence of nitrate was similar to that observed in the wild - type strain ( Table 3 ) .
+12079504	4	Expression of the dmsABC genes that encode the membrane - associated DMSO / TMAO reductase is positively regulated during anaerobic conditions by the Fnr protein and negatively regulated by the NarL protein when nitrate is present .
+24593230	141	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 chitobiose ( Figueroa - Bossi et al . , 2009 ) .
+19376854	13	waaY expression was also regulated by MarA ( multiple - antibiotic resistance regulator ) , which shares a binding site ( soxbox ) with SoxS , and was induced by salicylate , a nonoxidative compound .
+10760178	33	Interestingly , AraC - dependent transcription initiation at the araBAD promoter is increased by the cyclic AMP receptor protein ( CRP ) , a well - characterized global regulator , controlled by cyclic AMP ( cAMP ) , that activates the expression of a number of genes in response to a variety of stresses , including glucose starvation ( reviewed by Kolb et al . , 1993 ) .
+10760179	149	The presence of melibiose triggers a conformational change in MelR such that the dimer now occupies Site 2 and Site 2 0 and activation of the melAB promoter ensues .
+19906180	138	DNase I footprinting of Lrp binding to the argO control region ( top strand revealed ) without and with 7 mM L - leucine in the binding buffer .
+7643383	266	In an anaerobic environment the Fnr protein ( F ) is active and binds to the – 64.5 site to induce aeg - 46.5 operon expression .
+12618441	14	These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate , allowing the organism to switch from the GntI to the GntII system .
+10537212	253	Effects of s and the transcriptional activator AppY on induction of the Escherichia coli hya and cbd – appA operons in response to carbon and phosphate starvation .
+2543976	142	One explanation for this discrepancy is that the purified MetR protein ( 20 ) may be partly inactive so that the amount needed for activation of metE and metH expression in vitro appears higher than actually required .
+12586421	241	( 2002 ) The NorR protein of Escherichia coli activates expression of the £ avorubredoxin gene norV in response to reactive nitrogen species .
+12079504	31	To our knowledge , this " consensus " Fnr - dependent dmsA promoter exhibits the highest anaerobic induction of any Fnr - regulated E . coli promoter examined .
+17720788	256	However , sequence inspection failed to reveal an apparent Fnr protein binding site in the yeaR - yoaG operon control region ( Fig . 1A ) ( 12 , 40 ) , and microarray analysis revealed Fnr - independent induction of yeaR transcription in response to nitrite ( 12 ) .
+12079504	27	Results and Discussion Effect of cis - acting mutations in the Fnr binding site on anaerobic induction of dmsA - lacZ expression To investigate the effects of sequence changes in the dmsA Fnr - recognition site on the anaerobic activation of dmsAlacZ expression , site - directed mutagenesis and ß - galactosidase assays were performed ( Figure 1 ) .
+3041410	19	In the presence of arabinose , AraC protein bound at the araI site , which is immediately adjacent to the RNA polymerase binding site of the PBAD promoter , stimulates transcription of the araBAD genes ( Fig . 1 ) .
+11004182	31	In contrast , only NarL is reported to activate nirB in response to nitrite ( 23 , 24 ) .
+24272778	9	We demonstrate arabinose - dependent repression of ydeNM by AraC , in contrast to the well - described arabinose - dependent activation of other target genes .

+SmtB is a metal - dependent repressor of the cyanobacterial metallothionein gene smtA : identification of a Zn inhibited DNA - protein complex .
+ygeA and polB are positively regulated by AraC and arabinose due to partial read - through of Rho - independent terminators ( Fig . 2 , 4 , and 5 ) .
+In this study , we show for the first time that the operator sequence is indeed the binding site for the negative regulator GntR and that gluconate is the true inducer of gntT , by inactivation of GntR binding to the operator .
+To investigate the role of the CRP and adenylate cyclase in catabolite repression of the gntT gene by glucose and gluconate , crp and cya null mutations were transduced into the strain carrying the chromosomal gntT : : lacZ fusion .
+COLI 1787 Downloaded from http : / / jb . asm . org / FIG . 2 — Continued . on January 11 , 2016 by Instituto de Biotecnologia , UNAM the gntK expression was repressed by GntR in the absence of gluconate .
+OmpR can activate or repress the ompF gene depending on osmolarity conditions and the strength of the promoter ( 30 ) .
+After a 1 - h induction of MarA by IPTG , a decline was seen in the levels of transcripts of purA ( Fig . 1A ) and hdeA ( Fig . 1B ) .
+For instance , Rob has been shown to bind and activate the zwf promoter in vitro but whole cell zwf regulation cannot be activated by Rob , although the gene responds to SoxS and MarA ( Ariza et al . , 1995 ; Jair et al . , 1995 1996a ; b ) .
+For example , both the AcrAB efflux pump and micF induced - decreases in OmpF porin are turned on in response to oxidative stress or weak acids .
+The addition of MetJ and AdoMet to incubations containing MetR also results in a 75 % inhibition of metE expression but no effect on MetH expression ( line 2 vs . line 4 ) .
+Binding of NagC and Mlc to nagE operators in vivo As Mlc showed a stronger affinity for the nagE operator than NagC , it seemed possible that Mlc might be able to regulate the nagE promoter in the absence of NagC in vivo . ThreenagE – lacZ fusions were tested : the standard ‘ loop - forming ’ nagBE – lacZ fusion , whose expression is repressed by NagC binding co - operatively to the nagE and nagB operators ; and two single operator nagE – lacZ fusions , missing the nagB promoter / operator , but carrying the same nagE – lacZ junction .
+To verify that Mlc does bind preferentially to the nagE operator in vivo , the effect of plasmids overproducing either Mlc or NagC was tested in a strain mutated for both mlc and nagC . Plasmids expressing either NagC or Mlc produce considerable repression of the nagBE – lacZ looped fusion , reducing expression 88 - and 56 - fold ( Table 2 ) .
+Therefore , expression of nuo is regulated by O2 and nitrate via ArcA , NarL , FNR and IHF at sites within the - 277 region , and by other factors including C4 dicarboxyiates at a site between - 277 and - 899 .
+RESULTS Maximal nitrate repression of pfl expression is dependent on functional NarL , NarP , NarX , and NarQ proteins .
+The mechanism which the cell employs to repress pfl expression with nitrate clearly involves NarL and NarP , but a further factor ( s ) which dictates whether repression is strong or weak , perhaps in response to the intracellular redox status , must be involved .
+The nrf promoter can be activated by either NarP or NarL in response to nitrite but is repressed by NarL in response to nitrate .
+Mutations in the putative NarL - binding site at the nirB promoter decrease FNR - dependent anaerobic induction , suggesting that NarL acts as a helper to FNR during transcription activation .
+This latter result indicated that ArcA suppresses anaerobic hyb expression and that a further factor , which remains to be identified , is involved in controlling anaerobic induction of operon expression .
+While either NarL or NarP was able to induce nrfA - lacZ expression in response to low levels of nitrate , only NarL could repress at high nitrate levels .
+In contrast , NarL is reported to repress nrfA expression in response to nitrate , whereas NarP cannot ( 14 – 16 , 23 , 24 ) .
+From prior batch culture experiments , both NarL and NarP were reported to activate nirB - lacZ in response to nitrate ( 23 , 24 ) .
+The chemostat experiments ( Fig . 3A ) also demonstrate that NarL or NarP can function independently of each other to induce nirB expression in response to nitrate .
+During batch cell culture conditions , nitrite was reported to induce nrfA expression via either the NarL or NarP response regulator proteins , while only nitrate was reported to cause repression of nrfA expression and only by NarL ( 14 , 16 , 24 ) .
+First , either NarL or NarP can activate nrfA - lacZ expression in response to added nitrate .
+During anaerobiosis , the Fnr protein ( F ) binds at its consensus recognition site , centered at 42 , to activate nirB operon expression .
+The nitrate induction of fdnG expression occurs at the level of transcription control , where NarL is a strong activator and NarP is a weak activator ( 11 , 20 ) .
+The nitrate - dependent repression of fdhF - lacZ expression shown in Fig . 3B was confirmed by batch culture experiments in which NarL negatively regulated gene expression .
+In the 146 strain , which retains the ModE protein binding site , ( napF - lacZ ) expression was induced during growth with added molybdate , and this induction required the modE allele ( data not shown ) .
+Summary Expression from the Escherichia coli nrf operon promoter is activated by the anaerobically triggered transcription factor , FNR , and by the nitrate / nitrite ioncontrolled response regulators , NarL or NarP , but is repressed by the IHF and Fis proteins .
+Expression of the aeg - 46.5 operon NY 14853 - 8101 , USA ( anaerobically expressed gene at 46.5 minutes on the genetic map ) is induced during anaerobic growth by the global transcriptional regulatory protein Fnr .
+aeg - 46.5 operon expression is further induced by the NarP protein in response to nitrate or nitrite and this induction is antagonized by NarL .
+A NarP / NarL site centered at – 44.5 bp Our results demonstrate that the symmetrical region centered at position 44.5 ( Choe & Reznikoff , 1993 ) is essential for NarP - dependent nitrate and nitrite activation of aeg - 46.5 operon expression .
+We found that the primary signal for NarP - dependent aeg - 46.5 operon induction is nitrite rather than nitrate .
+The dps promoter is activated by OxyR during growth and by IHF and s in stationary phase .
+The dcuB gene is strongly activated anaerobically by FNR , repressed in the presence of nitrate by NarL , and subject to cyclic AMP receptor protein ( CRP ) - mediated catabolite repression .
+Expression of fumB is also induced anaerobically ( 1.5 - or 5 - fold ) in a manner which is dependent on both FNR and ArcA ( 41 , 44 ) .
+This demonstrates that NarL has the major role in nitrate - induced repression of dcuB expression ( Fig . 5Dii ) .
+This indicates that the NarX - NarL system is solely responsible for nitrate repression of these four operons ( dcuB - fumB , aspA , frdABCD , and dcuSR ) involved in fumarate respiration .
+Expression from a monocopy ( dcuS - lacZ ) operon fusion revealed three - to fourfold repression by nitrate ( Table 2 ) , virtually all of which can be attributed to the NarX - NarL regulatory system rather than the paralogous NarQ - NarP system ( data not shown ) .
+In agreement with these findings , the nitrate - and nitrite - induced transcription from the hcp promoter in E . coli was found to depend on the response regulator proteins NarL and NarP [ 45 ] .
+NarLdependent activation at both the yeaR and ogt promoters is decreased in rich medium and this depends on Fis , a nucleoidassociated protein .
+We suggest that the induction of ogt by NarL alone in response to external nitrate provides a prophylactic insurance policy against possible genotoxic effects arising from nitrate metabolism .
+E - mail : m . h . j . bennik @ ato . wag - ur . nl . have shown that overexpression of Rob ( or its N - terminal domain alone ) activates transcription of sodA ( encoding manganese - containing superoxide dismutase ) , fumC ( encoding fumarase C ) , inaA ( encoding a weak acid - inducible protein ) , and micF ( gene for an antisense RNA repressing the outer membrane porin OmpF ) .
+Other genes reported to be activated by Rob in vitro ( fpr , fumC , micF , nfo , sodA , and zwf ) ( 15 ) or by Rob overexpression in vivo ( fumC , inaA , micF , and sodA ) ( 5 ) were not found in our study ; thus , it appears that the mutagenesis and screening procedure was not saturating .
+With arabinose , AraC activates transcription from the promoters of the catabolic operons ( Fig . 3 ) .
+Genetic definition of the Escherichia coli zwf “ Soxbox , ” the DNA binding site for SoxS - mediated induction of glucose 6 - phosphate dehydrogenase in response to superoxide .
+E . coli AraC activates transcription of the araBAD , araFGH , araE , and araJ transcripts in the presence of its inducer , L - arabinose ( 5 ) .
+Thus , ydeNM is a novel AraC - regulated operon that is directly repressed by AraC in an arabinose - dependent manner .
+At the araC - araBAD intergenic region , AraC forms a repression loop in the absence of arabinose due to the dimerization of distally bound AraC monomers .
+We found that this repression is AraC dependent and is most likely due to binding by arabinose - bound AraC to the xylose promoters , with consequent inhibition of gene expression .
+When bound with arabinose , AraC activates the transcription of the araBAD , araE , and araFGH operons and represses transcription from the araC operon .
+When arabinose is added , the subunit that formerly contacted araO2 releases and shifts to the araI2 half - site , from which it activates transcription from the araBAD promoter ( PBAD ) ( 19 ) , results that extend a prior observation that the presence of arabinose can extend the region of aral2 that AraC protects from DNase I digestion ( 20 ) .
+The facts that arabinose induces the substantial transcription of araJ messenger ( 11 ) and that this transcription is regulated by CAP and AraC ( 11 , 18 ) are , however , consistent with araJ actually being translated and serving some purpose in the arabinose metabolism of E . coli .
+In the presence of arabinose , AraC protein activates the expression of the araBAD , araFGH , and araE promoters ( 6 - 10 ) .
+In the absence of arabinose , AraC protein represses araBAD transcription by a mechanism involving cooperative binding of AraC protein to two AraC binding sites at a distance , resulting in formation of a DNA loop ( 15 - 19 , 39 , 40 ) .
+Interestingly , many other transporters for amino acids such as the uptake genes for arginine ( artPIQM ) , serine ( sdaC ) , alanine ( cycA ) and proline ( proY ) , and the export gene for leucine ( leuE ) are also regulated reciprocally by Lrp and leucine ( Kutukova et al . , 2005 ; Cho et al . , 2008 ) .
+In contrast , several transporters for aromatic amino acids ( brnQ , ilvKHMGF and ilvJHMGF ) appear to be regulated by the concerted mode , their expression is downregulated by Lrp and leucine potentiates this effect ( Cho et al . , 2008 ) .
+Our results indicate that whereas ArgP activates argO transcription in the presence of Arg through the process of RNA polymerase ( RNAP ) recruitment ( Ptashne and Gann 1997 ; Browning and Busby 2004 ) , the mechanism by which Lys addition phenocopies an argP mutation is not simply by preventing the binding of ArgP to the argO operator but instead by reversible trapping of the recruited RNAP at the promoter in a novel molecular complex that is proficient for neither productive nor abortive transcription .
+There is a strict correlation between the presence of ArgP and a high level of lysine - repressed dapB transcription , provided that the dapB regulatory region contains the necessary cis - acting upstream sequences .
+( iii ) The transcription of yggA in vivo is ArgP dependent and is induced by exogenous Arg or Arg - Ala ( and also by an argR mutation ) , whereas the addition of Lys or Lys - Ala phenocopies the effect of an argP null mutation ; furthermore , yggA expression is rendered constitutive in an argP d strain .
+Therefore , a straightforward interpretation of our results , as further discussed below , is that ( i ) ArgP is a transcriptional activator of yggA , ( ii ) ArgP ’ s activator function is enhanced by Arg and inhibited by Lys , and ( iii ) yggA encodes an Arg ( and CAN ) exporter in E . coli .
+ArgP mediates lysine ( Lys ) repression of argO , dapB , and gdhA in vivo , for which two alternative mechanisms have been identified : at the dapB and gdhA regulatory regions , ArgP binding is reduced upon the addition of Lys , whereas at argO , RNA polymerase is trapped at the step of promoter clearance by Lys - bound ArgP .
+Our results indicate that negative regulation involving Lys as coeffector is mediated by ArgP and that the target genes include argO , lysP , lysC , asd , dapB , dapD , lysA , and gdhA .
+In the case of argO , ArgP mediates its transcriptional activation by Arg , as well as its repression by Lys ( 7 , 26 , 32 , 37 ) ; the latter is achieved by a mechanism involving the active trapping at the argO promoter by ArgP of RNA polymerase , which is then prevented from being released to engage in productive transcription ( 26 ) .
+These include lysP , lysC , lysA , dapD , and asd ( in addition to argO , dapB , and gdhA ) , all of which exhibited ArgP - mediated repression upon Lys supplementation in vivo , as well as ArgP binding to the corresponding cis regulatory regions in vitro .
+ArgP of E . coli is also responsible for the lysine - dependent regulation of dapB , which encodes one of the enzymes of the diaminopimelate and lysine biosynthesis pathway ( 2 ) , and argO , which encodes the arginine exporter ArgO ( 24 , 30 ) .
+Further evidence that growth on chitin is limiting for induction of NagC is shown by the analysis of the effect of chitin and chitobiose on induction of a NagC - regulated nagB – lacZ fusion .
+In the presence of chitobiose , ChbR , along with CRP , activates transcription from the chb promoter ( Plumbridge and Pellegrini , 2004 ) .
+P1 controls eda induction on gluconate and is regulated by GntR .
+P2 controls eda induction on glucuronate and galacturonate and is regulated by KdgR .
+Taken together , GntH seems to repress the expression of the gntKU and gntT genes , and the repression occurs even in the presence of gluconate , which could be physiologically important , as discussed below .
+In contrast to the case for GntR , the GntI genes in the presence of cloned GntH were negligibly induced by gluconate ( Table 3 ; Fig . 5 ) .
+The results presented allow us to speculate that GntR initiates expression of the GntII genes , followed by their large induction by GntH when cells were grown in gluconate minimum medium .
+Bausch et al . [ 1998 ] provided biochemical evidence that the idnD and idnO genes in GntII encode idonate dehydrogenase , oxidizing idonate to 5 - ketogluconate and 5 - ketogluconate reductase , reducing 5 - ketogluconate to gluconate , respectively , and that the GntII system is induced by GntH in the presence of idonate or 5 - ketogluconate .
+Expression of the E . coli K - 12 melAB genes , which encode products essential for melibiose metabolism , depends on transcription activation by MelR and CRP , and is triggered by melibiose ( 7,9 ) .
+Busby § , and Tomofusa Tsuchiya ¶ From the Department of Microbiology , Faculty of Pharmaceutical Sciences , Okayama University , Tsushima , Okayama , 700 – 8530 Japan and the § School of Biosciences , The University of Birmingham , Edgbaston , Birmingham B15 2TT , United Kingdom MelR is an Escherichia coli transcription factor that activates expression of the melAB operon in response to the presence of melibiose in the environment .
+Busby * School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , United Kingdom Received 29 December 2005 / Accepted 10 February 2006 Transcription of the Escherichia coli melAB operon is regulated by the MelR protein , an AraC family member whose activity is modulated by the binding of melibiose .
+It has been proposed ( 30 ) that repression requires the formation of a DNA loop that is stabilized by MelR binding at site R and site 2 and that the presence of melibiose breaks this loop , resulting in derepression of pmelR , occupation of site 2 , and induction of pmelAB ( Fig . 1 ) .
+Table 3 lists - galactosidase activity measurements , which showed that pmelAB activity is very low in the absence of melibiose and that melibiose triggers a 50 - fold increase in pmelAB activity that is MelR dependent .
+When triggered by melibiose , wild - type MelR requires the assistance of CRP to activate transcription at pmelAB ( 31 ) .
+This model is supported by genetic analyses , notably , mutations that alter amino acids in the AraC N - terminal arm that result in AraC - dependent activation of paraBAD in the absence of arabinose ( 19 , 21 , 22 , 34 , 35 ) .
+Results in Fig . 3 show that , in each case , the single base substitution in the Site R MelR - binding site results in a significant reduction in MelR - dependent repression of the melR promoter in both the absence and presence of melibiose .
+Hence , in the absence of MelR , CRP does not activate transcription at the melAB promoter whereas , in the presence of MelR , CRP activates transcription ~ 10 - fold ( Figure 1C ) .
+In spite of such high similarity , Fnr is associated not with the transport system but with the switching of respiration styles ; i . e . under the anaerobic condition , Fnr activates the transcription of anaerobic enzyme genes , repressing the transcription of oxidase gene ( Spiro & Guest , 1991 ) , together with ArcA , one of the response regulators in Group 1 , that represses the transcription of aerobic respiration enzyme genes ( Iuchi et al . , 1990 ; Iuchi & Lin , 1993 ) .
+To confirm that the different levels of expression in the glucose and glycerol media are caused by cAMP / CAP activation , the expression of the manX – lacZ and borG – lacZ fusions was measured in a cya strain ( TP2006 ) .
+There is no obvious 35 promoter sequence , but a potential CAP site is detectable on the sequence ( Fig . 1A ) , centered at position 61.5 , which is consistent with the strong catabolite repression observed with the nanC fusion .
+However , cAMP caused a large ( 15 - fold ) stimulation of nagE and a 2.5 - fold stimulation of nagB when the CAP site was located at its functional distance .
+In the absence of chitosugars ( uninduced ) the chb , chiP and nag operons are repressed by NagC .
+This suggested that ChiX pairing with the RNA sequence from the chbB - chbC intercistronic spacer – the very mechanism responsible for ChiX inactivation during chitobiose induction – downregulates chbC expression under uninduced conditions .
+The FNR protein is required for fdnGHI and narGHJI operon expression during anaerobic growth , and the NARL protein is required for induction by nitrate ( 4 ; for a review , see reference 25 ) .
+For example , nitrate induction of the narGHJI operon ( 21 ) and the narK gene ( 12 ) is controlled exclusively by NarL , while induction of the fdnGHI operon is controlled principally by NarL , but NarP also effects a degree of control ( observed with a narL mutant ) ( 21 ) .
+Expression of the dmsABC and the frdABCD operons is repressed in the presence of nitrate , and this repression is dependent on the NarL protein ( 8 , 10 , 21 , 28 ) .
+We found that expression of the fdnCHI operon was induced anaerobically by nitrate , and required fnr ’ and narL + .
+These studies define the molecular interactions of Fnr and NarL at the dmsABC P1 promoter that together provide for the oxygen and nitrate regulated expression of this respiratory pathway operon .
+Likewise , the poor match of the Fnr site at the promoter for the fumarate reductase gene , frdA to the consensus Fnr sequence may account for the relatively weak anaerobic induction for this respiratory operon [ 14 ] .
+The 114 - fold anaerobic activation seen for the wild - type dmsA promoter was reduced to about 35 - fold in each of the two mutants ( Figure 1 ) , indicating that the position of the Fnr site at the wild - type dmsA promoter is important for controlling optimal dmsA gene expression .
++ 40 + 30 + 20 + 10 + 1 - 10 - 20 - 30 - 40 - 50 dmsA Conclusions This study investigated the effects of sequence changes in the Fnr - recognition site on the anaerobic activation of dmsA - lacZ expression as well as examined the NarL recognition sites wi
+The napF operon control region exhibits unusual organization of DNA binding sites for the transcription regulators Fnr and NarP , which activate transcription in response to anaerobiosis and nitrate , respectively .
+Nitrate and nitrite induction of the nirB operon and nitrite induction of nrfA operon expression is mediated to differing extents by the NarL and NarP proteins ( Rabin & Stewart , 1993 ; Tyson et al . , 1993 , 1994 ) .
+Previous experiments suggest that the nitrate and nitrite induction of aeg - 46.5 operon expression is mediated solely by the NarP protein , in contrast to all other nitrate and / or nitrite - inducible operons studied to date that are efficiently activated by the NarL protein alone or by both the NarL and NarP proteins ( Rabin & Stewart , 1993 ) .
+The NarP - dependent nitrate and nitrite induction of aeg - 46.5 operon expression is increased in a narL null strain .
+Also , the effects of control region deletions from 275 to 68 on the nitrate and nitrite induction ratios of aeg - 46.5 operon expression ( Table 1 ) may be an indirect result of the effect on Fnr - dependent regulation .
+When wild - type Fnr was expressed from a multicopy plasmid , ( napF - lacZ ) expression was induced approximately sixfold by anaerobiosis ( Table 1 ) .
+Deletion , mutational , and footprint analyses had indicated that napF operon expression in vivo is induced weakly by either Fnr or NarP alone and strongly by Fnr and NarP together .
+MBP - NarL antagonizes activation of the napF promoter by Fnr ( D154A ) and MBP - NarP in vitro .
+DISCUSSION The napF promoter is one of several regulated by Fnr in response to anaerobiosis and by NarL or NarP in response to nitrate and nitrite .
+Additionally , nitrate , acting via the NarL response regulator , represses the transcription of the frdA and dcuB - fumB operons ( Fig . 1C ) ( 18 , 22 , 27 , 53 ) .
+Recent studies have documented NsrR and Fnr regulation of ytfE ( dnrN ) gene expression patterns similar to those reported here for the yeaR - yoaG operon : NsrR - dependent induction by nitrite and nitric oxide ( or compounds that generate nitric oxide ) and enhanced expression in fnr null strains ( 6 , 20 , 24 ) .
+Consistent with the hypothesis that YdhY – T has a role in anaerobic metabolism , gel retardation , footprinting , sitedirected mutagenesis and transcript - mapping experiments showed that the oxygen - responsive transcription factor FNR directly activates transcription of ydhY – T under anaerobic conditions by binding at a site located at position 242.5 relative to the transcript start , confirming and extending earlier work that shows that ydhY is expressed from a class II FNR - dependent promoter ( Kang et al . , 2005 ) .
+Thus , the expression of the citCDEFXGT gene cluster of E . coli depends on CitA / CitB , and the system confers induction by citrate in the absence of oxygen and nitrate .
+EGAN * Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66045 Received 21 August 2000 / Accepted 18 September 2000 The Escherichia coli rhaSR operon encodes two AraC family transcription activators , RhaS and RhaR , and is activated by RhaR in the presence of L - rhamnose . - Galactosidase assays of various rhaS - lacZ promoter fusions combined with mobility shift assays indicated that a cyclic AMP receptor protein ( CRP ) site located at 111.5 is also required for full activation of rhaSR expression .
+This result indicates that in the presence of RhaR , - CTD can contribute to transcription activation at rhaSR , perhaps by interaction with DNA and / or RhaR .
+The RhaS protein functions to activate transcription of two of the operons in the Escherichia coli L - rhamnose regulon in response to the availability of L - rhamnose ( 11 , 40 ) .
+Furthermore , ydhY – T expression is regulated by the NarXL and NarPQ nitrate - and nitriteresponsive two - component systems , confirming the results of previous transcription - profiling studies ( Constantinidou et al . , 2006 ) .
+In the presence of chitobiose / triose , a metabolite of chitobiose , probably monodeacetylated chitobiose - 6P ( Verma and Mahadevan , 2012 ) , causes the ChbR regulatory protein to activate transcription of the chb operon .
+Nevertheless , CitA is required for the maximal induction of dcuB - lacZ by citrate ( but not by fumarate ) as shown here and earlier ( 25 ) , and DcuS / DcuR is required for the maximal expression of citC - lacZ .
+Nitrate - and nitriteinduced transcription from the hcp promoter was activated by the response regulator proteins NarL and NarP .
+AraC protein bound at the aral site immediately adjacent to the RNA polymerase binding site of the pBAX ) promoter stimulates transcription of the araBAD genes in the presence of arabinose ( Lee et al . , 1974 ; Hahn et al . , 1986 ; Martin et al . , 1986 ) .
+The CRP K52N mutant possesses a third activating region , designated AR3 ( small black triangle ) , that has been proposed to contact the subunit ( see text ) . contrast to CRP , which effectively activated the wild - type fucPIK promoter only in the presence of fucose but failed to activate the IS5 - disrupted promoter in the presence or absence of fucose , as previously reported ( 8 ) .
+These results show that the NarP protein activates F ( aeg - 46.5 - lacZ ) expression in response to nitrate and nitrite and that the NarL protein antagonizes this activation .
+waaY promoter is also induced by antibiotics through the mar system .
+Although arabinose - dependent repression by AraC has not been observed before , there are clear parallels with arabinose - dependent activation of araBAD transcription .
+To evaluate how the spacing between the Fnr binding site and the start of dmsA transcription alters the anaerobic activation of dmsA - lacZ expression , single basepair insertions were introduced at position - 35 ( ?JA448 and ?JA449 ) .
+Second , NarL can repress nrfA - lacZ expression when nitrate is present , whereas NarP cannot ( compare the NarL NarP strain to the NarL NarP strain and to the wild - type strain ) .
+NarP thus performs a unique role to fine - tune fdnG operon expression by delaying the ability of NarL to activate when nitrate levels are low .
+In the model , gluconate is first imported by gluconate permease , GntP , as demonstrated ( 15 ) , and interacts with the GntR molecule to induce the GntI system genes .
+The data illustrates that Fnr is responsible for the 100 - fold anaerobic activation of dmsA expression .
+MelR activity can be triggered by the inclusion of melibiose in the growth medium ; the role of MelR is to activate transcription initiation at the melAB promoter ( pmelAB ) in response to melibiose or , possibly , some other metabolite .
+Interestingly , lysine is known to virtually abolish transcription activation of argO , a bona fide ArgP target .
+A major protection mechanism against NO in the cytoplasm is provided by flavorubredoxin and its reductase , NorVW , which are synthesized in response to NO activation of the transcription activator NorR ( 15 , 20 , 22 ) .
+Transcription initiation from P melAB is stimulated by the MelR regulator with melibiose .
+A sequence with similarity to the Fnr - binding site consensus , centered at position 64.5 , was essential for Fnr - dependent anaerobic induction of aeg - 46.5 operon expression .
+The resuits in Tabie 7 confirm that expression from pnrf was totally FNR dependent and induced during anaerobic growth .
+This strong repression is relieved by melibiose and , thus , melibiose toggles MelR between two alternative states , one that activates pmelAB and one that represses pmelR ( Fig . 1B ) .
+An excellent CAP - binding site ( 19 ) is centered at bp 70 with respect to the transcriptional start site of the gntK gene , explaining the phenomenon of glucose catabolite repression observed in Northern blot analysis .
+The results show that the dcuB gene is expressed exclusively under anaerobic conditions in a manner that is FNR dependent and that it is repressed by NarL in the presence of nitrate and is subject to CRP - mediated catabolite repression .
+If the MetR protein synthesized from pRSE562 was responsible for the observed increase in MetH synthesis , the MetJ protein and AdoMet , if added to the first incubation , should inhibit the increase by preventing MetR synthesis .
+Based on our results with the arabinose transporter deletion strains , arabinose likely inhibits xylose gene expression by one of two mechanisms : either ( i ) arabinose - bound AraC binds to the P xylA promoter and prevents it from being activated by xylose - bound XylR or ( ii ) arabinose directly binds XylR and inhibits its activity .
+In the narL narP double null mutant , nitrate repression of hyb expression was relieved and anaerobic regulation after growth in the absence of nitrate was similar to that observed in the wild - type strain ( Table 3 ) .
+Expression of the dmsABC genes that encode the membrane - associated DMSO / TMAO reductase is positively regulated during anaerobic conditions by the Fnr protein and negatively regulated by the NarL protein when nitrate is present .
+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 chitobiose ( Figueroa - Bossi et al . , 2009 ) .
+waaY expression was also regulated by MarA ( multiple - antibiotic resistance regulator ) , which shares a binding site ( soxbox ) with SoxS , and was induced by salicylate , a nonoxidative compound .
+Interestingly , AraC - dependent transcription initiation at the araBAD promoter is increased by the cyclic AMP receptor protein ( CRP ) , a well - characterized global regulator , controlled by cyclic AMP ( cAMP ) , that activates the expression of a number of genes in response to a variety of stresses , including glucose starvation ( reviewed by Kolb et al . , 1993 ) .
+The presence of melibiose triggers a conformational change in MelR such that the dimer now occupies Site 2 and Site 2 0 and activation of the melAB promoter ensues .
+DNase I footprinting of Lrp binding to the argO control region ( top strand revealed ) without and with 7 mM L - leucine in the binding buffer .
+In an anaerobic environment the Fnr protein ( F ) is active and binds to the – 64.5 site to induce aeg - 46.5 operon expression .
+These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate , allowing the organism to switch from the GntI to the GntII system .
+Effects of s and the transcriptional activator AppY on induction of the Escherichia coli hya and cbd – appA operons in response to carbon and phosphate starvation .
+One explanation for this discrepancy is that the purified MetR protein ( 20 ) may be partly inactive so that the amount needed for activation of metE and metH expression in vitro appears higher than actually required .
+( 2002 ) The NorR protein of Escherichia coli activates expression of the £ avorubredoxin gene norV in response to reactive nitrogen species .
+To our knowledge , this " consensus " Fnr - dependent dmsA promoter exhibits the highest anaerobic induction of any Fnr - regulated E . coli promoter examined .
+However , sequence inspection failed to reveal an apparent Fnr protein binding site in the yeaR - yoaG operon control region ( Fig . 1A ) ( 12 , 40 ) , and microarray analysis revealed Fnr - independent induction of yeaR transcription in response to nitrite ( 12 ) .
+Results and Discussion Effect of cis - acting mutations in the Fnr binding site on anaerobic induction of dmsA - lacZ expression To investigate the effects of sequence changes in the dmsA Fnr - recognition site on the anaerobic activation of dmsAlacZ expression , site - directed mutagenesis and ß - galactosidase assays were performed ( Figure 1 ) .
+In the presence of arabinose , AraC protein bound at the araI site , which is immediately adjacent to the RNA polymerase binding site of the PBAD promoter , stimulates transcription of the araBAD genes ( Fig . 1 ) .
+In contrast , only NarL is reported to activate nirB in response to nitrite ( 23 , 24 ) .
+We demonstrate arabinose - dependent repression of ydeNM by AraC , in contrast to the well - described arabinose - dependent activation of other target genes .