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-In contrast , the E89D variant was less active than WT MarA for fpr and completely inactive ( indistinguishable from the control plasmid ) for mdtG .

-E89G was approximately twice as active as WT MarA for fpr and 4-fold more active for mdtG although for both promoters it was considerably less active than E89A .

-( The activations shown here are greater than those apparent in Table 2 because the expression of the plasmids carrying MarA , SoxS , and their mutants is not entirely shut off by lacI q so that the increases expressed in Table 2 appear smaller .

-If , as outlined above and presented in greater detail in the Discussion , steric interference with the phosphate between positions 12 and 13 and the glutamic-acid side chain at position 89 is responsible for the very poor activation of promoters such as fpr , then it would be predicted that binding of WT MarA to the fpr marbox would be enhanced if that phosphate were absent .

-We therefore compared the binding affinity of WT MarA to either a 36-bp double-stranded DNA containing the marbox sequence of fpr or with dsDNA of the same sequence and length but prepared so that the phosphate linkage between positions 12 and 13 of the marbox was eliminated ( see Materials and Methods ) .

-Again  , MarA bound very poorly to the fpr marbox  .

-Of the seven class I promoters examined , MarA ( Q91A ) activated the acrAB , marRAB , and zwf promoters to similar extents as WT MarA but activated acnA , fpr , mdtG , and poxB to only 60 % or less of MarA WT levels  .

-For the nine class II promoters , MarA ( Q91A ) significantly reduced the activation of fumC , inaA , micF , pqiA , and ybjC but had no significant effect on nfsB , mdaB , sodA , oryhbW .

-Indeed , nfsB and sodA are among the promoters that Q91A activated to the same extent as WT MarA .

-Among the class I promoters that exhibited measurable binding to MarA , MarA ( Q91A ) showed no greater binding or activation for acrAB , a modest reduction in activation and binding for mdtG and zwf , and a reduction in binding but not in activation for marRAB .

-Although not observed in these experiments , a more detailed analysis of the binding of MarA ( Q91A ) to the micF marbox  showed a very small reduction in binding concomitant with the reduced ability of MarA ( Q91A ) to activate the class II micF promoter  .

-We have shown here that the MarA glutamic-acid residue E89 is responsible for decreasing the binding of WT MarA relative to SoxS for the class I marbox promoters , acnA , mdtG , fpr , and zwf , thereby decreasing the relative activation of these promoters and hence the resistance engendered to superoxides by MarA .

-x First published online 19 November 2009 Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgPmmi 6950 1513 .

-This shows that whereas both NagC and ChbR appear to act as repressors for the chbB operon in the absence of the inducing sugar chitobiose , ChbR is necessary for induction and so behaves as a dual-function repressor -- activator .

-Identification of the DNAbinding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in-vivo DNA footprinting .

-MelR is a member of the AraC-XylS family of bacterial gene regulatory proteins  and our previous studies have shown that MelR , together with the cyclic AMP receptor protein , CRP , regulates expression of the melAB operon that encodes products essential for melibiose metabolism  .

-For example , the nitrate reductase genes narGHJI are regulated exclusively by NarL and are not responsive to NarP as observed here for cydD , while nitrate induction of the fdnGHI operon is regulated predominantly by NarL but is also responsive in part to NarP  .

-Under identical experimental conditions as for argO , the regulatory regions of the other ArgP-regulated genes ( asd , dapB , dapD , gdhA , lysA , lysC , and lysP ) were also bound by ArgP , with apparent K d s ranging from 55 nM to 170 nM ; in all these cases ( unlike the situation with argO ) , the addition of Lys was associated with an increase in the apparent K d , indicating that ArgP binding in these instances is Lys-sensitive .

-Given that the activation by full-length , chromosomally expressed RhaS at rhaBAD is approximately 33-fold higher than that of chromosomally expressed RhaR at rhaSR , comparable efficiencies of activation by the CTDs to their full-length counterparts would have resulted in His 6-RhaR-CTD activating rhaSR by approximately 30-fold .

-This observation not only allows us to understand how a modest mutation in O NC2 can affect fimB expression whereas the D3 mutation does not , but it also supports our prior assertion that NanR activates fimB expression without NagC  .

-These latter results , together with the experiments described here showing that MetJ binds to this region of DNA , strongly suggest that the-8 to + 27 region is involved in metE repression .

-Thus , it appears that NarL and NarP adopt overlapping mechanisms to inhibit ydhY -- T expression .

-Some of these operons are regulated by the NarL protein alone , such as the narG and frdA operons , whereas expression of the nirB ( encoding NADH-dependent nitrite reductase ) , nrfA and fdnG operons is controlled by both the NarL and NarP proteins .

-The ArgP protein enhances the expression of the argK gene To test the biological activity of the ArgP protein on the arginine transport system , the amounts of mRNA synthesized by a 502 bp KpnI-EcoRV DNA fragment containing the N terminus and the control region of the argK gene was investigated .

-RESULTS Oligomerization of DnaA Protein to the dnaA Promoter -- Sequence-specific DNA binding of DnaA protein to the dnaA promoter region  was studied in detail using a combined gel-shift and chemical footprinting assay to determine the extent of DNA binding to the region flanking the consensus DNA-binding site , the DnaA box .

-An alternative explanation is that repression occurs by the ' roadblock ' mechanism described for PurR repression of the purB promoter  .

-The experiments in Fig. 2a -- c suggest that the binding of Rob to the robboxes of the fumC , micF , and inaA promoters occludes the binding of 70 R4 to the 35 hexamer of these class II promoters , as is also the case during SoxS-dependent activation of the fumC and micF promoters .

-ß-Galactosidase activity Promoter Mutated site minus NO 3 plus NO 3 Fold induction ogt100 93 + 1 439 + 12 4.7 ogt102 NarL I 92 + 5 107 + 6 1.2 ogt104 NarL II 56 + 2 87 + 3 1.6 the yeaR promoter is repressed by the binding of NsrR to a target that overlaps the 10 hexamer element  [ 12,31,32 ] .

-Besides , MarA activates fumC , fpr , nfo and other genes possibly involved in response to the oxidative-stress .

-Nitrate-and nitrite-mediated expression of the hcp is dependent on NarL and NarP Sequence analysis of the hcp regulatory region suggested that it contains a binding site for FNR and also binding sites for nitrite-and nitrate-activated regulators , NarL and NarP  .

-Therefore , arafl is essential for both repression and activation and acts as a switch to allow both the repressor and the activator forms of the AraC protein to control the araBAD promoter .

-As hmpA and ytfE encode a nitric-oxide reductase and a mechanism to repair iron-sulfur centers damaged by nitric-oxide , the demonstration that hcp-hcr , hmpA , and ytfE are the three transcripts most tightly regulated by NsrR highlights the possibility that the hybrid cluster protein , HCP , might also be part of a defense mechanism against reactive nitrogen stress .

-3901-3905 , June 1987 Microbiology The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli ( frd gene/tor gene/regulation ) S. Thus the D3 region is not apparently required for NanR to activate fimB expression in the wildtype background , and it could contain specific sequences that inhibit this .

-Another example is the NarL/NarP-and FNR-stimulated expression of nirB and nrf genes , which are repressed by Fis and IHF  .

-These results show that constitutive and inducible expression of the chromosomal MarA was able to upregulate nfnB expression in contrast with the lack of activation mediated by constitutive expression of the chromosomal SoxS and Rob proteins .

-Transcription activation at the Escherichia coli melAB promoter : interactions of MelR with its DNA target site and with domain 4 of the RNA polymerase sigma subunit .

-Orientation of MelR bound at site R Wade et al.  showed that MelR-binding site R is essential for MelR-dependent repression of the melR A MelR RNA-1 B TB23 TB23 TB22 TB22 MelR + + % Relative Intensity 150 100 50 0 TB23 MelR + MelR TB22 Figure 2 .

-Similar to the results of metE expression , MetR greatly stimulates the synthesis of MetH using plasmid pQN1011 as template  .

-Separate contributions of UhpA and CAP to activation of transcription of the uhpT promoter of Escherichia coli .

-Summary Expression from the Escherichia coli nrfA promoter ( pnrfA ) is activated by both the FNR protein ( an anaerobically triggered transcription activator ) and the NarL or NarP proteins ( transcription activators triggered by nitrite and nitrate ) .

-One obvious difference between the synthetic promoter and the napF operon promoter is that transcription from the latter is also activated by the NarP protein bound to a site centered at position 44.5 .

-NarL-mediated repression of the frdA promoter is achieved by NarL binding over a large region centred near the transcription start site and including the FNR site  .

-The microarray data for the other promoters that are apparently activated by NsrR must be evaluated cautiously , however , because few of these transcripts encode proteins known or suspected to be involved in the response to RNS , and most of the differences were much smaller ( typically two-to threefold apparent activation ) than the 30-fold repression of ytfE , the 14-fold repression of hmpA , and the up-to-15-fold repression of hcp .

-As at the yeaR promoter , nitrate-dependent induction can be repressed by Fis that binds to a single site overlapping the upstream DNA site for NarL .

-This was indeed suggested by Détiollaz et al.  on the basis that IHF sites replacing CAP sites allowed activation of the malT promoter , albeit less than with CAP .

-It accepts a methyl group from methylphosphotriesters and then acts as a transcriptional activator of the ada operon AdiY Escherichia coli SP : P33234 Transcriptional activator of the adiA gene for 253 32 , 237 biodegradative acid-induced arginine decarboxylase AfrR Escherichia coli TE : Q07681 Probable transcriptional activator of the 272 258 afrABRS operon for expression of AF/R1 fimbria in E. coli RDEC-1 , a rabbit pathogen AggR Escherichia coli SP : P43464 Transcriptional activator of the aggA gene for 265 183 aggregative adherence fimbria I ( AAF/I ) expression in enteroaggregative E. coli strains AppY Escherichia coli SP : P05052 Transcriptional activator of the cyxAB , hyaAB-243 12 , 131 CDEF and appA operons during the deceleration phase of growth AraC Citrobacter freundii SP : P11765 Regulator of several operons involved in the 281 30 transport and catabolism of L-arabinose ( similar to E. coli AraC ) AraC Escherichia coli SP : P03021 Activator of the expression of the araBAD , 292 174 , 238 , 248 , 266 araFGH and araE operons , which are involved in the transport and catabolism of L-arabinose .

-The NarL and NarP proteins are each able to activate expression of the nirB and nrfA operons by interaction with common DNA-binding sites .

-The NarL/NarP protein binding sites required for activation of the nirB and nrfA operons are located further upstream  than that of the aeg-46 .5 operon  .

-Coeffectors of ArgP in yggA regulation .

-The identification of NagC as an activator of fimB expression indicated that the expression of the recombinase would be inhibited by GlcNAc .

-In conclusion , MelR and CRP bind to the melAB promoter co-operatively to adjacent sites in order to activate transcription in a co-dependent manner .

-Like MalE-SoxS , MarA ( i ) activated the transcription of zwf , fpr , fumC , micF , nfo , and sodA ; ( ii ) required a 21-bp '' soxbox '' sequence to activate zwf transcription ; and ( iii ) was '' ambidextrous , '' i. e. , required the C-terminal domain of the a subunit of RNA polymerase for activation of zwf but not fumC or micF .

-Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP ( cAMP ) - cAMP receptor protein complex .

-They demonstrated that acnA has two promoters , P1 and P2 , the latter being regulated by SoxS , FNR , CRP and ArcA .

-This domain alone could activate transcription of araBAD up to 15 % as well as full-length AraC when alone or to the same level as fulllength AraC when fused to an unrelated dimerization domain  .

-We found that Rob ( i ) activates the transcription of zwf , fpr , fumC , micF , nfo , and sodA , ( ii ) requires a 21-bp soxbox-marbox-robbox sequence to activate zwf transcription , ( iii ) protects the soxbox/marbox/robbox from attack by DNase I , ( iv ) is ambidextrous , i. e. , requires the C-terminal domain of the a subunit of RNA polymerase for activation of zwf but not fumC or micF , ( v ) bends zwf and fumC DNA , and ( vi ) binds zwf and fumC DNA as a monomer .

-These indicate that DnaA and IciA proteins independently bind to their respective binding sites on the dnaA # 1996 Blackwell Science Ltd , Molecular Microbiology , 19 , 389 -- 396392 Y. Schematic representation of regulation of araBAD and araC promoters by CAP , P1 , and P2 .

-This work is a first step in studying the mechanism ( s ) by which AraC regulates transcription at the araE promoter , p E , and at p FGH .

-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 ) .

-The mechanism of transcriptional activation of micF and ompC by OmpR as well as a role of IHF in this activation need to be better understood .

-At the same time , it is noteworthy that two of the genes that are most prominently regulated by ArgP , argO and lysP , are both also regulated by the leucineresponsive general transcriptional regulator Lrp  .

-The Rob homologs MarA and SoxS can activate transcription of a broad range of genes in-vivo  , including sodA , fumC , micF , zwf , and inaA , suggesting broadly overlapping activities of these three regulators .

- Systematic mutagenesis of the DNA binding sites for SoxS in the zwf and fpr promoters of Escherichia coli : identifying nucleotides required for DNA binding and transcription activation .

-Although a similar arrangement of sites around the transcription initiation regions of other genes of the gal regulon might have suggested that they all are regulated by a similar mechanism to galE  , the results presented in this paper demonstrate that repression of the galP gene , is mediated by a distinctly different nucleoprotein complex involving NagC as well as GalR and GalS and including at least 280 bp of DNA .

-These data clearly indicate that the hcp promoter is activated by FNR and repressed by NsrR .

-Transcriptional repression of the dnaA gene of Escherichia coli by DnaA protein .

-We identified eight genes and confirmed that seven are transcriptionally activated by normal expression of Rob from the chromosomal rob gene ( inaA , marR , aslB , ybaO , mdlA , yfhD , and ybiS ) .

-Thus , the dmsA promoter is repressed by NarL binding to multiple sites spread across 80 bp covering the entire promoter  .

-We conclude that RhaR positively regulates transcription from the promoters pl , p2 and p3 , and that RhaS may regulate p1 and p3 weakly .

-The shaded boxes denote 22 bp DNA sites for CRP : one site centered at position 241.5 is responsible for the activation of the melR promoter , while the other , centered at position 2155.5 is involved in activation of the melAB promoter .

-For example , the galETK operon is regulated by three factors GalR , CAP and the nucleoid-associated protein HU .

-Research Article J Mol Microbiol Biotechnol 2003 ; 6 : 41 -- 56 DOI : 10.1159 / 000073407 Dual Control by Regulators , GntH and GntR , of the GntII Genes for Gluconate Metabolism in Escherichia coli Ryouichi Tsunedomi Hanae Izu Takuya Kawai Mamoru Yamada Department of Biological Chemistry , Faculty of Agriculture , Yamaguchi University , Yamaguchi , Japan Key Words Gluconate metabolism W Gntll W gntR W gntH W Divergent promoter W Expressional regulation Abstract Escherichia coli possesses two systems , GntI and GntII , for gluconate uptake and catabolism , whose genes are regulated by GntR as a repressor and GntH as an activator , respectively .

-Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX , but the effect of the Mlc protein is stronger .

-In vitro , ArgP binds the lysP regulatory region with a K d of around 55 nM and the binding affinity is diminished upon the addition of Lys  , suggesting that Lys represses lysP in-vivo by engendering the loss of ArgP binding to the lysP operator region .

-For the nirBDC and nrfABCDEFG operons , Fnr protein , bound near position 41.5 , activates transcription maximally only when phospho-NarL or-NarP protein is bound further upstream to block inhibition by other proteins  .

-These results indicated that ArgP is responsible for the transcriptional activation of lysP in the absence of lysine .

-In our previous study  , we reported that repression of the melR promoter by MelR was unaffected by point mutations in either site 1 or site 1 0 .

- FNR dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3 .

-Expression of acrZ is coregulated with acrAB and tolC by the MarA , Rob , and SoxS transcription factors .

-Moreover , a common inverted repeat sequence coincided with the defined here NsrR recognition motif was shown to be involved in NsrR-mediated repression of the ytfE gene .

-At the nirB promoter ( pnirB ) , it has been shown that IHF and Fis drive the promoter DNA into an inhibitory architecture , which represses FNR-dependent transcription .

-An isorepressor , GalS , has also been identified as © 2008 The Authors Journal compilation © 2008 Blackwell Publishing LtdNagC , GalR and GalS repression at galP 147 Fig. 1 .

-Deletion of crp  resulted in a level of expression from each fusion that was similar to the expression from ( rhaS-lacZ ) 90 in the crp strain background , supporting our hypothesis that full rhaSR activation requires CRP .

-This suggests that Fnr and NarP may act synergistically to activate napF operon expression .

-Negative regulation of aeg-46 .5 operon expression by the NarL protein In addition to its function as a transcriptional activator , the NarL protein negatively regulates expression of the frdA , dmsA and nrfA operons in response to nitrate availability .

-Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator .

-Our analysis revealed that inaA , marRAB , aslB , ybaO , mdlA , yfhD , and ybiS were transcriptionally activated by constitutive levels of Rob , while galT expression was repressed .

-NarL-phosphate must bind to multiple upstream sites to activate transcription from the narG promoter of Escherichia coli .

-However , narG and frdA operon expression is regulated by the NarL protein alone  , suggesting that the NarL binding sites in these control regions are not efficiently recognized by the NarP protein .

-Furthermore , as NagC binding to O NC1 prevents CRP-dependent activation of nanC  , this study should enhance our understanding of the regulation of this gene as well .

-The Escherichia coli Ada protein can interact with two distinct determinants in the 70 subunit of RNA polymerase according to promoter architecture : identification of the target of Ada activation at the alkA promoter .

-Also , DnaA protein functions as a transcriptional repressor for the expression of other genes including rpoH  , mioC  , the guaBA operon  , and uvrB  , while the expression of the nrd gene appeared to be enhanced by DnaA protein  .

-Transposon mutagenesis experiments aimed at defining the Rob regulon revealed eight Rob-regulated targets , namely inaA , marRAB , aslB , ybaO , mdlA , yfhD , ybiS , and galT  , some of which are also known members of the mar and sox regulons  .

-Results illustrated in Figure 5B show that MelR-dependent repression of the melR promoter is unaffected when CRP binding at this target is prevented .

-Northern blotting analysis indicated that RbsR represses the purHD operon for de novo synthesis of purine nucleotide but activates the add and udk genes involved in the salvage pathway of purine nucleotide synthesis .

-Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP ( cAMP ) - cAMP receptor protein complex .

-The Ada protein has two activation domains , one of which is an AraC/XylS family domain which is required to activate transcription of the alkA operon  .

-In the first point , such a case has been reported in the galETK ( M ) operon concerning galactose utilization , which is regulated by GalR and GalS [ Weickert and Adhya , 1993a b ] , but its molecular mechanism is clearly different from that of the GntII gene regulation .

-Although a 26-bp near-perfect palindromic region from 102 to 77 exists upstream of argO ( see Fig. 1A ) , neither its deletion  nor that of an overlapping 1260 GENES & DEVELOPMENT upstream region from 115 to 90  led to any significant loss of either ArgP binding to argO in-vitro ( Fig. 2B ) or to Arg-and Lys-modulated transcriptional regulation in-vivo ( Fig. 1B , top panel ) .

-Summary Expression of the narK gene of Escherichia coli , like the narGHJI operon , is positively regulated by two frans-acting factors : Fnr , which is activated by anaerobic conditions , and NarL , which is activated by the presence of nitrate .

-Here , we found that Lrp binds to several sites at the lysP control region and is able to potentiate the transcriptional activation mediated by ArgP when lysine becomes limiting .

-NsrR : sixth protein to regulate transcription factor at P nrfA .

-MelR is essential for induction of the melAB operon that is responsible for melibiose metabolism .

-Clearly there is a component ( 13-to 20-fold ) to the activation by CRP at rhaSR that is independent of both-CTD and RhaR and hence does not function by the same mechanism used at simple class I CRP-dependent promoters , nor does it function through cooperative binding with RhaR .

-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 .

-In the present study , we first identified two positively charged amino-acids in 70 , K593 and R599 , and three negatively charged amino-acids in RhaR , D276 , E284 , and D285 , that were important for RhaR-mediated transcription activation of the rhaSR operon .

- Transcription activation at the Escherichia coli melAB promoter : the role of MelR and the cyclic AMP receptor protein .

-A common phenotype associated with transcriptional activation of micF by Rob , SoxS and MarA is multiple antibiotic resistance .

-Since both Lrp and ArgP stimulate argO expression and bind to overlapping targets in the argO control region , we were interested in analysing potential interferences in the action of these transcriptional activators on argO expression , in response to environmental conditions .

-The fact that most Fnrdependent promoters have the latter architecture may be due to the fact that many of them are also activated by the NarL protein ( e. g. , the narG , fdnG , nrfA , and nirB promoters ) .

-Microarray analysis revealed that NsrR represses nine operons encoding 20 genes in Escherichia coli MG1655 , including the hmpA , ytfE , and ygbA genes that were previously shown to be regulated by NsrR .

-Studies of the araBAD promoter , p BAD , show that to activate transcription the AraC protein binding site must overlap the 35 region of the promoter by 4 bp   .

-Activation by Lrp interferes with the previously demonstrated activation of the argO promoter by ArgP .

-The finding of only one MetR binding site suggests that the binding of MetR to this region may be responsible for both the activation of expression of metE as well as the autoregulation of metR  .

-Sufficiency of Rob for in-vitro transcriptional activation of zwf , fpr , fumC , micF , nfo , and sodA , promoters known to be activated by MalE-SoxS and MarA .

-DISCUSSION The napF operon exhibits a unique pattern of expression and a unique control region architecture in comparison to other characterized E. coli Fnr-and Nar-regulated operons .

-We previously demonstrated that in-vitro transcriptional activation by MarA at the zwf promoter requires interaction with the carboxy-terminal domain of the a subunit of RNA polymerase  and inferred that MarA activates the mar promoter by enhancing the binding of RNA polymerase  .

-At low to intermediate levels of nitrate  NarP appeared to antagonize the ability of NarL to activate fdnG operon expression .

-Although most NarLdependent promoters are also co-dependent on a second transcription factor , FNR protein , two targets , the yeaR and ogt promoters , are activated by NarL alone with no involvement of FNR .

-FNR can only activate transcription at the E. coli nirB promoter when the FIS and IHF repressors are removed by the binding of NarL or NarP  .

-Thus , stimulation of b1452 was dependent on MarA and a region  identified as a potential binding site for the activators .

-The strong upregulation of nfnB by the plasmidspecified MarA observed in this study contrasts with the reported weaker upregulation of NfnB activity and nfnB expression by SoxS  .

-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  .

-We show in this study that strains with null mutations in either argP or yggA exhibit abnormally increased sensitivities to CAN ( Can ss ) and that ArgP is a transcriptional regulator of yggA that mediates the latter 's induction by Arg .

-CAT fusion analysis revealed that the operon has a promoter for gntR and another for gntKU , and that the gntR gene is constitutively expressed , while that of gntKU is regulated positively by the cAMP-CRP complex and negatively by GntR .

-The same concentration and batch of MarA protein , on the other hand , repressed both purA and hdeA  .

-Also , both half-sites of the Fnr recognition sequence at dmsA are required for Fnrdependent expression and are similar in their ability to activate dmsA transcription .

-RhaR regulates transcription of rhaSR by binding promoter DNA spanning 32 to 82 relative to the rhaSR transcription start site .

-Compared with other operons regulated by NagC , nagE-BACD and glmUS , it is very likely that the repression complex involves an interaction between NagC bound to its two sites , NagC1 and NagC2 , so that a DNA loop is formed .

-Altogether , these data indicate that ArgP is able to activate transcription from the dapB promoter , provided that some sequences upstream of 81 are present , and is necessary for lysine to repress dapB expression .

-ArgP and cadBA regulation .

-© 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd , Molecular Microbiology , 63 , 1223 -- 1236Regulation of fimB by Neu 5Ac and GlcNAc 1229 lower level of fimB expression , as would be expected if it prevents activation by both NagC and NanR .

-Together , these results indicate that Lrp upregulates expression of cadBA .

-( B ) Transcription activation by RhaS expressed from the chromosome in SME1048 ( wild-type rhaSR ) .

-The three activators may have different quantitative effects on particular promoters , for example SoxS activates fpr to a much greater extent than does MarA .

-174 , No. 15 Localization of Upstream Sequence Elements Required for Nitrate and Anaerobic Induction of fdn ( Formate Dehydrogenase-N ) Operon Expression in Escherichia coli K-12 JING LI ' AND VALLEY STEWART ' 2 * Sections of Microbiology ' and Genetics & Development , 2 Cornell University , Ithaca , New York 14853-8101 Received 25 March 1992/Accepted 19 May 1992 Two transcriptional activators , the FNR and NARL proteins , are required for induction of the fdnGHI operon , encoding Escherichia coli formate dehydrogenase-N .

-GntR represses the GntI genes gntKU and gntT , whereas GntH was previously suggested to be an activator for the GntII genes gntV and idnDO-gntWH .

-Taken together , our results argue that residues Thr158 , Pro160 , Gln164 and Lys166 of CRP participate in transcription activation at the melAB promoter : these residues identify a surface of CRP that overlaps with AR1  .

-At the moment we do not know how NagC activates the fimB promoter , but two general scenarios seem most plausible .

-To determine whether ArgP directly regulates lysP transcription , we tested binding of ArgP to the lysP promoter/control region .

-We investigated whether DnaA protein and RNA polymerase can coexist at the dnaA promoter by gel-shift and footprinting analyses and whether a direct protein-protein interaction between DnaA protein and RNA polymerase is the mechanism of inhibition of transcription .

-Although there is no simple rationale for why the yeaR and ogt promoters are also repressed by Fis , we suggest that rapidly growing cells may opt out of certain stress responses , and we speculate that RNS may be a small risk in these conditions compared with other stresses .

-Concluding remarks The hcp gene has been shown to be regulated by FNR , NarL and NarP proteins .

-Although DnaA protein , at concentrations of 75 ng and greater , reduced transcription from rpmH promoter 1P , repression was preferential for the dnaA promoters .

-Two other regulators , OmpR and CpxR , activate nanC expression , although a direct control has not been proven .

-It is interesting to note that the three central operators , galOE2 , OE3 and OE4 , which have higher affinity for GalS than GalR , all have A/T at positions 8 of the operators ( Fig. 1B ) which is also the case for the mglB and galS operators ( Weickert and Adhya , 1993a , b ) which are preferentially regulated by GalS .

-the activation of t , he lac promoter and arnC ' B. 4 I ) 1 ) ~ CRP is similar in that CRT ' shows the S ~ IIIP orientation tlependcnce in both operons : as in nrtc ( ` H ~ ~ lO , CRT ' can partially activate the lnc promoter when its distance from the promoter is increased by 11 base-pairs , but not by five base-pairs , both in uiuo  and in r * itro ( St. raney et n / .

-Among functions that could contribute to cellular resistance to environmental agents , Rob enhances expression of mdlA , which encodes a multiple-drug-resistance-like ATP-binding component of a transport system  , and strongly enhances expression of micF , the antisense RNA that downregulates the outer membrane porin OmpF .

-Other unknowns are how OmpR activates micF transcription while binding at far upstream sequences , i. e. in the-156 to-216 region ( Figure 4 ( a ) ) .

-MarA upregulates expression of nfnB Both oxygen-insensitive nitroreductases nfsA and nfnB were shown to be upregulated by constitutive expression of MarA from plasmid pAS10  .

-gave a single retarded band of mobility similar to that observed with purified His 6-ArgP protein , whereas crude extracts devoid of ArgP gave no retarded band ( Fig. 3B ; see also Fig. 5A ) , indicating that no protein other than ArgP is able to bind significantly to the dapB promoter region .

-The results of this analysis confirm this assertion , and show additionally that NagC is also better able to We previously presented evidence suggesting that the D2 region , and hence NanR and NagC , could activate fimB expression by blocking the inhibitory effect of additional cis-acting element ( s ) positioned closer to nanC  .

-The mechanism of IciA protein stimulation of transcription from dnaA promoter 1P in the presence of inhibitory amounts of DnaA protein was examined .

-Alternatively,-CTD residues 321 , 322 , and 323 were defective at a rhaBAD promoter fusion that was activated only by the RhaS protein .

-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 .

-However , it is clear that they allow coordination of nanC and fimB expression , since NanR and NagC repress one and activate the other of these divergently arranged genes .

-The artPIQM operon is , besides being downregulated by Lrp  , also repressed by ArgR  .

-Indeed , the GalS isorepressor was discovered because , in the absence of GalR , there was some residual repression of the galE gene .

-Mutational analysis of the nirB and nrfA operon control regions has identified cis-acting regions that are required for both NarL and NarP-dependent induction  .

-The results described above indicated that ArgP binds the lysP regulatory region to mediate its nearly 35-fold transcriptional activation and that the absence of such ArgP binding either in argP mutants or upon Lys supplementation in argP strains results in very low levels of lysP expression .

-NagC repression is critical in maintaining chiP mRNA levels low enough , relative to ChiX , to allow full silencing by this sRNA .

-Considering the in-vivo and in-vitro data presented in this work , the mechanism by which ArgP regulates argO transcription  , and the known capacity of Lrp to alter the shape of the DNA by inducing bending and wrapping  , a model for lysP regulation in which binding of Lrp to the lysP control region may favor and/or stabilize the ArgP-RNA polymerase-DNA complexes or introduce DNA conformational changes is conceivable .

-NorR usually regulates cytoplasmic NO reductase norVW and sometimes another membrane-bound NO reductase ( norB ) and the NO dioxygenase hmp .

-In addition , the PQ-or SoxSresponsive genes gatABD , gltA , nfnB , and ybjC were recently shown to be activated by constitutive expression of MarA  .

-© 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd , Molecular Microbiology , 71 , 146 -- 157NagC , GalR and GalS repression at galP 149 corresponds to the strength of the galactose-derepressed galP promoter and implies that the long fusion is better repressed than the short fusion .

-Despite overlapping regulation by SoxS , MarA , and Rob , the three systems exhibit differential control in terms of both the strength of their effects on individual genes and activation of some promoters uniquely ( e. g. , zwf by SoxS or MarA but not by Rob ) .

-Similarly , at the FNR-activated NarL-repressed dmsA promoter NarL protects a large region that includes the sites for both FNR and RNA polymerase binding  .

-For the marbox transversion mutants  which are insensitive to stimulation by Rob , the presence of Rob increases the transcription of the chromosomal marRAB promoter and therefore only increases the repression of the mutant fusions .

-In a nagC strain , the threefold increase in chbB -- lacZ expression compared with the wild type is , as expected , eliminated by the NagC plasmid .

-This shows that we had failed to identify MelR mutants with improved specificity for the changed KK433 MelR-binding sequences ; mutants with specificity for the KK433 sequence would have given lower levels of activation with the wild-type melAB promoter .

-As shown previously  , purified DnaA protein repressed transcription from the dnaA promoters , 1P and 2P ( Fig. 5A ) .

-Therefore , the 22 heptamer site is a critical site for mediating NarL repression of nrfA gene expression .

-In contrast , the repression of both soxS and rob by SoxS , Rob , or MarA occurs via a yet to be identified binding site ( s ) within the sox and rob promoter regions  .

-Since we have shown previously that MalE-SoxS and MarA are sufficient for the in-vitro transcriptional activation of the zwf , fpr , fumC , micF , nfo , and sodA promoters ( i. e. , additional factors are not required )  , we conducted similar studies with purified Rob protein .

-The mutation in nagO1 behaved as expected : expression was higher in glycerol , giving a © 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd , Molecular Microbiology , 71 , 146 -- 157NagC , GalR and GalS repression at galP 151 value comparable to the nagC mutation and expression was strongly increased by growth on galactose .

-Since the results above suggested that the argO regulatory region upstream of 89 is not required for ArgP binding , we tested fragments with increasing length of downstream sequence in the EMSA experiments .

-Strikingly , all induction is lost with the JK14 fragment , showing that MelR binding to Site 1 and Site 1 0 is essential for activation of the melAB promoter .

-MarA activates the expression of diverse genes , including acrAB , micF , mlr-1 , -2 , and-3 , slp , and inaA , which endow cells with resistance  .

-We show here that MarA directly represses both purA and hdeA .

-NagC is best characterized as a repressor  , although the regulator does activate one of the glmUS operon promoters albeit by binding at the more conventional position of-47 relative to the transcriptional start site  .

-Based on data from in-vitro studies , Celis suggested that wild-type ArgP both represses its own transcription and activates that of argK ; he also sought to explain the Can r phenotype associated with the argP d mutation on the assumption that it is a loss-of-function ( that is , dominant-negative ) allele whose product is unable to efficiently activate the genes involved in Arg uptake , including argK  .

-However , in-vitro experiments show IHF to repress ompC transcription from two of its three promoters .

-Many Cel + strains carry mutations in nagC The NagC repressor that regulates the nag operon involved in N-acetylglucosamine metabolism was also shown to regulate the chb operon  .

-The impact of DcuR on citC expression might be due to a transcriptional activation of citAB by DcuR , as discussed below .

-nanC expression was predicted to be regulated by the two-component regulatory system CpxR-CpxA by transcriptome analysis  .

-Thus , the melR promoter is not efficiently repressed by MelR and MelR is overexpressed .

-acrZ is regulated by MarA , Rob , and SoxS .

-Role of CRP in activation of the melAB promoter The results from the in-vitro studies reported above suggest that CRP interacts directly at the melAB promoter .

-It should be noted ( lanes 1-4 ) that although plasmid pRSE562 directs the synthesis of the MetR protein there is still a large stimulation of metE expression by added MetR protein .

-NarX and/or NarQ sensors , both NarL and NarP are phosphorylated where either response regulator can then activate nrfA gene expression .

-These results fit with a model in which ArgP contributes to enhanced transcription of dapB when lysine becomes limiting .

-Measurements of b-galactosidase activities in the resulting transformants indicated that none of the single base changes in MelR binding site 2 significantly affected MelR-dependent activation of the JK22 melAB promoter ( data not shown ) .

-Both intact Rob and the N-terminal fragment activated expression of stress genes ( inaA , fumC , sodA ) but with a pattern distinct from that found for SoxS and MarA .

-In silico analyses and experimental verification of potential binding sites for Lrp in the argO control region The formation of multiple Lrp -- argO operator complexes with a different apparent stoichiometry suggests the existence of several binding sites for Lrp in the argO control region .

-Q 2000 Blackwell Science Ltd , Molecular Microbiology , 36 , 211 ± 222Activation at the E. coli melAB promoter 219 which transcription activation at the melAB promoter is absolutely dependent on the occupation of Site 2 0 by MelR .

-For example , binding of Lrp to the isolated strong binding site 2 of the ilvIH control region occurred in the nM range  but , in contrast , binding to site 2 of the pap operon could not be detected by EMSA , although this site was successfully used for the growth of co-crystals  .

-RhaR activates transcription of the operon that encodes the two activator proteins , rhaSR  .

-Role of multiple CytR binding sites on cooperativity , competition , and induction at the Escherichia coli udp promoter .

-RhaR activates transcription of rhaSR , and RhaS activates transcription of the operon that encodes the L-rhamnose catabolic enzymes , rhaBAD , as well as the operon that encodes the L-rhamnose transport protein , rhaT .

-We identified amino-acid-residues in the C-terminal domain of 70 and in RhaR that are important for RhaR-mediated transcription activation at the rhaSR promoter .

-c The Authors Journal compilation c 2009 Biochemical SocietyTranscription activation by Escherichia coli NarL protein 251 Figure 1 NarL regulates the E. coli yeaR promoter ( A ) This Figure shows the E. coli K-12 yeaR promoter sequence from positions 64 to + 86 with respect to the transcription start site   .

-This results in the formation of a repression loop and the repression of the araC promoter by AraC  .

-Expression of the operon , consisting of marR , marA , and marB , is normally repressed by MarR but can be induced by diverse compounds such as tetracycline , chloramphenicol , menadione , and salicylates  .

-The fact that the same level of CRP-dependent transcription activation is seen in-vitro with both RNAP preparations argues that CRP activates transcription at the melAB promoter independently of aCTD .

- 420 , 249 -- 257 ( Printed in Great Britain ) doi : 10.1042 / BJ20090183 249 Competition between NarL-dependent activation and Fis-dependent repression controls expression from the Escherichia coli yeaR and ogt promoters Derrick J. Effect of excess ChbR and NagC on repression of the chbB -- lacZ fusion .

-wild type nagC chbR pTZ ( NagC ) 48 ± 6 47 ± 3 83 ± 4 pTZ ( Mlc ) 42 ± 4 62 ± 3 56 ± 4 pTZ ( ChbR ) 2.3 ± 0.2 32 ± 2 2.8 ± 0.5 pTZ control .

-Scanning-replacement mutagenesis of the region separating O NC1 from O NC2 and the effect of IHF on fimB expression Although the results described above show that O NC1 and O NC2 function together , the distance between the centre of the two operators  is longer than for any other NagC-regulated operon .

-Mutagenesis of the Fnr recognition sequence at the dmsA promoter region confirmed the contribution of Fnr in the 100-fold activation of dmsABC expression and explored the DNA sequence and spacing requirements for the Fnr recognition site at the P1 promoter .

-These studies also show that the cyclic AMP receptor protein ( CRP ) interacts with the melAB promoter and increases MelR-dependent transcription activation .

-Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli .

-NagC represses nagE , encoding the N-acetylglucosamine-specific transporter , while Mlc represses three PTS operons , ptsG , manXYZ and ptsHIcrr , involved in the uptake of glucose .

-A greater extent of derepression results from mutation of the external operator site by comparison to the internal operator site mutants , suggesting that binding of GntR to the external site results in a stronger repression of the gntT gene .

-The fourth promoter predicted to be regulated by NsrR was P hcp , the promoter of a two-gene operon encoding the hybrid cluster protein , HCP , and its reductase , HCR .

-During the course of this work , it became apparent that GntR might affect gntT expression by a mechanism that is independent of negative control by operator binding as well as activation by cAMP-CRP .

-To confirm that the nfnB activation observed in the array study was specifically mediated by MarA rather than by a cell stress response to the constitutive expression of the protein from a multicopy number plasmid , Northern blot analysis was performed on cells in which MarA production was inducible .

-To investigate further the involvement of Fis in catabolite-repression , the expression of an nrf : : lac fusion was compared in cells with and without a functional fis gene .

-Auto-activation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli .

-The extent of AraC stimulation of araBAD is at least 25-fold larger .

-Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli .

-CRP binding upstream of the E. coli malK promoter repositions three molecules of MalT on the DNA such that they are able to activate transcription  .

-Thus , NanR and NagC appear to activate fimB expression independently .

-The expression of xylF is negatively regulated by Fis and RpoS at the transcriptional level  , and a putative regulator , xylR , was found downstream of xylFGH .

-An important observation was that purified MarA was able to activate transcription in-vitro of nfnB .

-The napF operon provides the only known example of a promoter activated by NarP but not NarL .

-So far , our results demonstrate that ArgP directly binds to the lysP promoter/control region and that the T-N 11-A sequence located close to the RNA polymerase binding site is important for binding and crucial for lysP transcription .

-Similarly , incubation of the pnrf97 EcoRI -- HindIII fragment with Fis binds to the nrfA -- acs intergenic region and represses transcription At the E. coli nirB promoter , transcription initiation is repressed by the association of the nucleoid-associated factors , Fis and IHF  .

-Thus MarA is able to repress the rob promoter after the preformed open complex clears the promoter .

-Given that cyclic AMP receptor protein ( CRP ) , the second activator required for full rhaBAD expression , can not activate rhaBAD expression in a rhaS strain , it was of interest to test whether CRP could activate transcription in combination with RhaS-CTD .

-Note that the magnitude of the effect of CRP on activation of the melAB promoter in the in-vitro transcription experiment ( Fig. 2B ) is less than might have been expected from the footprinting and in-vivo experiments  .

-The expression of ptsG is controlled by Mlc binding to two operators upstream of two promoters , both of which are subject to Mlc repression .

-In a similar experiment with a rob + mar strain , excess MarA stimulated mar transcription of a wild-type mar : : lacZ fusion by only 1.6-fold  .

-This indicates that ( i ) the 70 NarL heptamer site is essential for NarL to function as an activator of nrfA expression and that ( ii ) other sites are used for NarL to repress expression independently of the 70 site , in contrast to prior interpretations ( see Discussion ) .

-A plasmid carrying the mlc gene expressed from its own promoter ( pMlc2 , a gift from S. Ichihara ) produced a 10-fold repression of the manX -- lacZ fusion , while a plasmid in which Mlc was under the control of the lac promoter , pTZ ( Mlc ) , reduced expression of the fusion to less than measurable values  .

-Fis represses the ogt promoter by displacing upstream-bound NarL To investigate a role of Fis at the ogt promoter , expression of the ogt : : lac fusion was compared in strain JCB387 and in the fis mutant derivative , JCB3871 .

-In the same experiment we also examined the expression of hdeA , which had been observed in another macroarray study to be repressed upon MarA induction in cells  .

-In the second part of the present study , we selected another E. coli promoter , the ogt promoter , that transcriptome analysis  had predicted to be activated by NarL alone , and we have used biochemical and genetic analysis to compare its expression and organization with the yeaR promoter .

-The major conclusions are that : ( i ) both Lrp and ArgP stimulate P argO in an effector-dependent manner , but to a different extent , ( ii ) the two regulators behave as competitive activators , and ( iii ) ArgP is intrinsically a more potent activator for P argO as compared with Lrp .

-Thus , not only does IHF stimulate both FimB and FimE recombination , as well as activate fimbrial expression in phase ON cells , but it is now clear that it enhances fimB expression too .

-This results in the repression of transcription , suggesting that the extent of oligomerization of DnaA proteins over two dnaA promoters contributes to the autoregulation of expression of the dnaA gene .

-Concomitant with upregulation of tolC , EvgA upregulated several multidrug resistance genes ( acrAB , emrKY , mdfA and yhiUV ) and showed increased antibiotic resistance that was fully dependent on TolC but only partially dependent on AcrA .

-An additional 50-fold activation of rhaBAD expression occurs when CRP occupies its binding site centered at 92.5 , which places CRP adjacent to RhaS  .

-The treB treC operon is negatively regulated by TreR , whose gene treR is located upstream of treB but is not part of the operon .

-ExuR regulates expression of the uxaCA , uxaB and exuT operons involved in galacturonate catabolism .

-MelRdependent activation of the melAB promoter requires the binding of MelR subunits to four 18 bp sites and the binding of a single CRP dimer to a low-affinity target sequence  .

-These results suggest that the DNA region between 90 and 128 is important for activation at rhaSR and that putative CRP sites 2 , 3 , and/or 4 may be functional CRP sites .

-This complex binding pattern and its Lrp concentration-dependent profile strongly suggest the cooperative binding of Lrp dimers to multiple binding sites in the argO control region and the formation of complexes with a different stoichiometry .

-To confirm the role of ArgP in the regulation of lysP transcription , the argP gene was cloned into plasmid pBAD24 under the control of the arabinose-inducible promoter  .

-476-480 , January 1989 Biochemistry In vivo DNA loops in araCBAD : Size limits and helical repeat ( supercoiling/twist/periodicity / linking number deficit/looping energetics ) DONG-HEE LEE AND ROBERT F. SCHLEIF Biochemistry Department , Brandeis University , Waltham , MA 02254 Communicated by Alexander Rich , October 14 , 1988 ABSTRACT Formation of a DNA loop by AraC proteins bound at the aral and araO2 sites , whose center-to-center distance is 211 base pairs , is necessary for repression of the araBAD promoter , PBAD , of Escherichia coli .

-This is likely due to the greater extent of activation by SoxS of promoters involved in superoxide defense , e. g. , acnA , fpr , zwf , fumC , and sodA .

-Optimal MelR-dependent repression of the melR promoter depends on upstream sequences Transcription initiation of the melR promoter is dependent on the binding of CRP to a 22 bp DNA site centered at position 241.5 , but sequences further upstream are not essential  .

-Taken together , these results support a model in which O NC2 enhances the binding of NagC to O NC1 , with the two sites functioning jointly to control fimB expression .

-P1 drives cotranscription of edd and eda and is induced by growth on gluconate  ; P1 appears to be controlled by GntR  , although binding of GntR to the P1 regulatory region was not established prior to this work .

-Transcriptional co-activation at the ansB promoters : involvement of the activating regions of CRP and FNR when bound in tandem .

-We did not detect any significant differences in RNAP association , suggesting that under these growth-conditions , AraC does not regulate expression of a transcript that initiates within dcp .

-However , placing the NanR , IHF and NagC binding sites closer to the fimB promoter enhances the ability of the regulators to activate fimB expression .

-Further studies showed that the melR promoter is a typical Class II CRPdependent promoter , activated by a single dimer of CRP , that binds to a 22 bp DNA site centred at position 241.5 with respect to the transcription start point  .

- DNA binding sites for the Mlc and NagC proteins : regulation of nagE , encoding the N-acetylglucosamine specific transporter in Escherichia coli .

-Indeed , the effect of the mutation in OE5 was similar to © 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd , Molecular Microbiology , 71 , 146 -- 157NagC , GalR and GalS repression at galP 153 that in the weakly binding OE2 and OE3 sites ( a mutation in OE4 has not yet been tested ) .

-Combined , the effector modulated activation of argO transcription by ArgP and Lrp must ensure an adapted and fine-tuned synthesis of the transporter in response to environmental conditions .

-Figure 4 shows autoradiographs from electromobility-shift assays designed to investigate how NarL represses FNR-dependent activation of the ynfE promoter .

-In the second part of the present study , we investigated the E. coli ogt promoter , which Constantinidou et al.  had also found to be induced by NarL independently of FNR .

-It should be remembered that nagE encodes the GlcNAc-specific PTS transporter and the genes for two other PTS transporters ( ptsG and manXYZ ) plus the genes for the central components of the PTS ( ptsHIcrr ) have been shown to be regulated by Mlc  .

-ArgP binds a site upstream of the dapB promoter .

-Taking these results together with those presented above , it is concluded that the cooperative interaction of NagC bound to O NC1 and O NC2 , with IHF bound to the site identified in this work , forms a nucleoprotein complex that activates fimB expression .

-Repression of the Escherichia coli melR promoter by MelR : evidence that efficient repression requires the formation of a repression loop .

-The promoter for the MarA-activated gene nfnB  , also mixed with gnd DNA , was tested in parallel as a positive control for MarA activity .

-Transcriptional co-activation at the ansB promoters : involvement of the activating regions of CRP and FNR when bound in tandem .

-Furthermore , even the finding of Celis  that argK is a target for transcriptional activation by ArgP may need to be reexamined , given that ( i ) there is a discrepancy between the expected argK runoff transcript size  determined from the promoter mapping data published by Celis et al. in an earlier paper  and that reported by him  for ArgP activation experiments  and ( ii ) the promoter ( for argK ) mapped by his group  is within the argK coding region per the genome sequence published by Blattner et al.  ( GenBank accession number AE000375 , wherein argK is annotated ygfD ) .

-Mechanism of activation by CRP at rhaSR .

-These observations indicate that the inhibition of binding of RNA polymerase to the dnaA promoters is dependent upon the oligomerization of DnaA protein to regions flanking the DnaA box and that the binding of one or two DnaA monomers to the DnaA box is not sufficient for occlusion of RNA polymerase from the dnaA promoters .

-Previously , overexpression of Rob was shown to induce multiple antibiotic and superoxide resistance phenotypes  , to activate expression of fumC , inaA , and sodA in-vivo  , and to activate the transcription of six mar/soxRS regulon promoters in-vitro by mechanisms that are strikingly similar to that of MarA and SoxS  .

-When RNAP was added to the rob promoter at 0 ° C prior to MarA addition and then transfer to 37 ° C , MarA inhibited rob transcription ( see Fig. 6B ) .

-Both gntT and gntKU are regulated positively by the cyclic AMP ( cAMP ) - cAMP receptor protein ( CRP ) complex and negatively by GntR ; one GntR-binding element for gntK has been proposed  , and two GntR-binding elements for gntT were experimentally defined  .

-Purified His 6-tagged ArgP protein binds with an apparent K d of 35 nM to the dapB promoter in a gel retardation assay , provided that sequences up to 103 are present .

-In the presence of 200 nM MarA , there was a 5 -- 6-fold activation in nfnB transcription , as expected  .

-This demonstrated that either NarL or NarP is required to activate transcription from the hcp promoter .

- DnaA protein regulates transcription of the rpoH gene of Escherichia coli .

-It is important to note that the molecular mechanisms of lysinedependent regulation by ArgP differ between argO and dapB  .

-Taken together , our results suggest that CRP site 3 is the major site required for CRP activation of rhaSR expression .

-The expression of both fusions was increased by growth on galactose and to a lesser extent by growth on GlcNAc , supporting the hypothesis that NagC is involved in repression of galP  .

-Occlusion of RNA Polymerase by Oligomerization of DnaA Protein over the dnaA Promoter of Escherichia coli *  Yong Sun Lee § ¶ and Deog Su Hwang From the Institute for Molecular Biology and Genetics and the § Department of Microbiology , Seoul National University , Seoul 151-742 , Korea DnaA protein , the initiator protein for initiation of Escherichia coli chromosomal replication , has been shown to repress its own expression from two dnaA promoters , 1P and 2P .

-These results together indicated that marbox 3 , and particularly its RE2 , was critical for repression of hdeA by MarA .

-However , this idea was contradicted when a single mutation at position 16 ( C to G ) of RE 2 , which has been shown to establish direct contacts with the second of two HTH motifs of MarA  , eliminated MarA-mediated activation of the nfnB gene .

-Molecular Microbiology  36  , 223 ± 229 Repression of the Escherichia coli melR promoter by MelR : evidence that efficient repression requires the formation of a repression loop Joseph T .

-While the soxS gene is under the redox-regulated , positive control of SoxR , marA is under negative control by MarR , a repressor whose DNA-binding activity is regulated by the binding of small molecules with toxic effects  .

- Transcription activation at the Escherichia coli melAB promoter : the role of MelR and the cyclic AMP receptor protein .

-The physiological significance of the repression of purA and hdeA by MarA is not known .

-MelR stimulates transcription initiation at the melAB promoter by binding to four sites centered at positions 120.5 , 100.5 , 62.5 , and 42.5 upstream of the transcript start point .

-Expression of the E. coli argO gene is activated by ArgP , also known as IciA , which is a transcriptional activator of the LysR type transcriptional regulator family  .

-Q 2000 Blackwell Science Ltd , Molecular Microbiology , 36 , 211 ± 222Activation at the E. coli melAB promoter 213 in-vitro and that this activation is dependent on MelR and melibiose .

-Transcription activation at the Escherichia coli melAB promoter : interactions of MelR with its DNA target site and with domain 4 of the RNA polymerase sigma subunit .

-These results establish the unconventional napF operon control region architecture , in which the major promoter P1 is activated by the Fnr protein bound to a site centered at 64.5 with respect to the transcription initiation site , working in conjunction with the phospho-NarP protein bound to a site centered at 44.5 .

-The relative degrees of repression of the ydhY -- lacZ fusion in the presence of nitrite ( approximately twofold ) or nitrate ( ~ 13-fold ) suggest that NarL-mediated inhibition of FNR recruitment is a key component of the regulation of the ydhY -- T promoter , and that NarP-mediated inhibition of RNA polymerase binding is partially overcome by the ability of FNR to recruit RNA polymerase .

-To determine whether the purified MarA protein affected gene expression , we tested its ability to activate the in-vitro transcription of zwf , sodA , micF , and fumC , genes known to be under mar control in-vivo , and of fpr and nfo , genes not known to be regulated by mar in-vivo but activated by SoxS in-vivo and by MalE-SoxS in-vitro .

-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 .

-Expression of hdeA was repressed by induced expression of MarA ( see Ref .

-We found that purified MarA was sufficient in-vitro to repress transcription of both purA and hdeA .

-MelR carrying each of the single substitutions is less able to repress the melR promoter , while MelR carrying some combinations of substitutions is completely unable to repress the melR promoter .

-Moreover , they found that Rob overexpression activates expression of fumC , sodA , and inaA ( unknown function ) , but not zwf , and that purified Rob forms DNA-protein complexes with DNA fragments containing the micF , sodA , nfo , and zwf promoters  .

- Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly .

-Given the proximity of this binding site to the start site for transcription , these results suggest a model where AraC sterically inhibits the binding of XylR and RNA polymerase to the P xylA promoter , consistent with our experimental results .

-Presumably , uninduced levels of MarA and/or SoxS mediate a low-level induction of the inaA gene ; the lower basal level of inaA expression in Dmar strains was noted earlier  .

-RhaS activates transcription from rhaBAD , and transcription from the rhaS gene is controlled by RhaR  .

-Transcription activation at the Escherichia coli melAB promoter : interactions of MelR with the C-terminal domain of the RNA polymerase alpha subunit .

-Transcriptional activation by MarA , SoxS and Rob of two tolC promoters using one binding site : a complex promoter configuration for tolC in Escherichia coli .

-This scenario is plausible , because ArgP and Lrp competitively activate argO  .

-These results argue that different conformational states of MelR are responsible for activation of the melAB promoter and repression of the melR promoter .

-The ArgP protein represses its own synthesis Sequences consistent with the consensus for E. coli promoters  have not been found upstream of the start codon for the iciA ( argP ) gene  .

-marA expression is repressed by MarR and is derepressed by the interaction of MarR with various phenolic compounds such as salicylate .

-Thus , if the model proposed above is correct , it seems probable that NanR must make contact with RNA polymerase , or another regulatory factor bound closer to the promoter , in order to activate fimB expression in the wild-type background as well .

-Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP .

-Two approaches were used to confirm that NsrR is this sixth factor that regulates P nrfA .

-This study demonstrates that MarA can repress the expression of the rob gene both in-vivo and in-vitro via a marbox sequence located within its promoter .

-This resembles the known co-regulation of acrAB and tolC by the transcriptional factor MarA .

-These results appear to be consistent with those from the experiments with lacZ operon fusions , as shown in Table 4 , and it is likely that the binding of GntR to a single element ( the R1 sequence ) is capable of decreasing the transcription of the gntKU genes .

-We hypothesize that CRP binding to some or all of these sites may influence transcription activation at rhaSR .

-In the intact cell , transcription of purA was decreased in cells constitutively producing MarA  .

-This change confers partial CRP independence on the melR promoter ( data not shown ) and also causes a small reduction in MelR-dependent repression .

-The most intensely examined operon is araBAD , where AraC is required for repression and activation of BAD transcription  .

-For example , nitrate induction of the narGHJI operon  and the narK gene  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 )  .

-Thus , maximum activation of the mar regulon promoter inaA depends on the autostimulatory effect of MarA on the mar operon .

-One of the ara loops , that involving AraC bound at araO2 and araI , was previously shown to generate repression of araBAD ( 5-7 ) .

-For instance , Rob has been shown to bind and activate the zwf promoter in-vitro but whole-cell zwf regulation can not be activated by Rob , although the gene responds to SoxS and MarA  .

-According to the results described here , Lrp participates in the activation of cadBA under inducing conditions .

-One of the more striking points in each model is that the NarP protein is nonessential ( i. e. , not a major player ) and that it can function as an antagonist of NarL in its ability to activate nirB or nrfA operon expression .

-To further investigate ArgP-mediated activation of dapB transcription , we purified His-tagged ArgP protein  and used it to perform EMSE .

-To investigate how IHF activates fimB expression further , the IHF binding site mutation described above was combined with those in O NC1 , O NC2 and O NR alone , and O NC1 O NR in combination , and the expression of the FimB -- LacZ chimera was measured  .

-In the case of the ydbC promoter , the differences in transcript levels between the two transformants were at least as great as those for the NsrRrepressed genes , making P ydbE a prime candidate for direct activation by NsrR .

-However , under inducing conditions , the P cadBA activity in the lrp : : Km r mutant strain was 2-fold lower than that in the parent strain , suggesting that Lrp stimulates expression of cadBA .

-twofold lower in the arcA mutant ( JRG3841 ) , indicating that ArcA plays no more than a minor role in regulating dcuB expression in response to oxygen ( Fig. 5B ) and that ArcA is not responsible for the FNR-independent mechanism of anaerobic activation of dcuB transcription .

-To test this hypothesis further , and to examine the effect of operator-to-promoter distance on NagC activation , the effect of deleting the 274 bp region ( D7 ) described above on fimB expression was also analysed  .

-In the case of the ytfE promoter , repression by NsrR is the dominant regulatory mechanism , though there is also some evidence for anaerobic repression by FNR , as reported previously  .

-Our results indicate that the repression of transcription from the two dnaA promoters ( 1P and 2P ) by DnaA protein is promoted by the oligomerization of DnaA protein over dnaA promoters 1P and 2P and that this binding directly prevents RNA polymerase binding to the two promoters .

-Discussion We showed in earlier work that fimB expression , and hence the OFF-to-ON phase switching of type 1 fimbriation , is activated by NanR and NagC and hence repressed Fig. 9 .

-2 When the two dnaA promoters were repressed by DnaA protein , IciA protein was able to restore transcription from the 1P promoter with little effect on transcription from the 2P promoter  .

-RNA polymerase binding to the region containing dnaA promoter 1P  was inhibited by DnaA protein  .

-More recently , ArgP was shown to bind to an approximately 60-bp-long sequence partially overlapping the argO promoter  .

-Our previous experiments have shown that when both dnaA promoters 1P and 2P were repressed by DnaA protein , IciA protein specifically activated transcription from dnaA promoter 1P , while dnaA promoter 2P was still repressed  .

-Recently , a direct regulatory connection between oxidative-stress and iron metabolism was shown by Zheng et al. , who demonstrated the transcriptional activation of fur by SoxS and OxyR  .

-The enhanced ability of Fnr to activate dmsABC gene expression is possibly , by analogy to Crp , due to increased affinity of Fnr at the consensus versus the native non-consensus Fnr recognition sequence at dmsA .

-There are two NagC operator sites upstream of gimU The perfect inverse correlation between the induction of nag and repression of glm genes posed the question as to whether the regulation of glmU expression involved the NagC protein .

-Recent studies  have shown that the occupation of site 2 by MelR is the most crucial for the activation of the melAB promoter , but that , of the four target sites , site 2 binds MelR most weakly .

-Autoradiographs of EMSA analyses of Lrp binding to the argO control region without and with 7 mM L-leucine in the binding buffer respectively .

-It was shown that to activate transcription in P araBAD , the AraC protein binding site must overlap the 35 region of the promoter by 4 bp  .

-In vitro activation of the transcription of araBAD operon by AraC activator .

-Studies of araE transcription in-vitro confirm the results in-vivo and show that promoter activity is directly stimulated by AraC and CRP  .

-Our conclusion runs contrary to that of Han et al.  , who overproduced IciA ( ArgP ) and employed an RNase protection assay to show that nrdA transcription is ArgP regulated in-vivo .

-DNA-protein recognition : demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor .

-Finally , at the ( rhaB-lacZ ) 110 fusion , which contains the CRP site required for full rhaBAD activation as well as the full RhaS binding site , there was a twofold contribution to activation by CRP when in combination with RhaS-CTD and a fivefold contribution to activation4990 WICKSTRUM ET AL. .

-J. For example , MarA binds tightly to the marRAB promoter in-vitro yet stimulates transcription by only ~ 3-fold ; no significant binding to inaA can be demonstrated by gel shift experiments , yet transcription is stimulated > 5-fold .

-In summary , these results demonstrate that gntT is positively regulated by CRP .

-Dominant-negative AraC mutants that fail to activate transcription of araBAD were selected , and their interactions with specific bases of the binding site were probed with chemically modified DNA .

-Curiously , Barbosa and Levy  found elevated gatA and gatC transcription due to MarA expression , and Pomposiello and colleagues  found elevated gatA , gatB and gatD upon treating cells with paraquat , and elevated gatZ , gatA , gatB , gatC and gatD upon treating cells with salicylate .

-Recently , the implication of Lrp in the regulation of the gene encoding the arginine exporter ( argO ) was reported .

-Miller et al.  have found that SoxS activates mar transcription in-vivo , and we have recently found a marbox sequence in the promoter region upstream of marRAB which binds MarA and enables either purified MalE-SoxS or MarA to activate transcription of marRAB in-vitro  .