RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


FliZ,GadE,GadW,GadX,H-NS,Lrp,MarA,PhoP,RcsB,TorR regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
H-NS      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): BglY, Cur, DNA-binding protein HLP-II (HU, BH2, HD, NS), DNA-binding transcriptional dual regulator H-NS, Drc, DrdX, Drs, FimG, Hns, HnsA, Irk, MsyA, OsmZ, PilG, TopS, TopX, VirR
Gene name(s): hns
Functional conformation(s): H-NS
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, BasR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsB, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, TorR, UvrY, YdeO, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
RcsB Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional activator RcsB, RcsB response regulator
Gene name(s): rcsB
Functional conformation(s): RcsB-Pasp56
Coregulator(s): AcrR, AdiY, ArcA, BasR, CRP, CpxR, Cra, CsgD, EvgA, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, GlrR, H-NS, HdfR, IHF, LeuO, LexA, LrhA, Lrp, MarA, MatA, MlrA, MqsA, NagC, NarL, NarP, NhaR, NtrC, OmpR, PhoP, QseB, RcdA, RcsB, RstA, StpA, TorR, UvrY, YdeO, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Lrp Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Sensing external and internal signals
Synonym(s): AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA
Gene name(s): lrp
Functional conformation(s): Lrp , Lrp-leucine
Coregulator(s): AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
MarA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): CfxB, DNA-binding transcriptional dual regulator MarA, InaR, NfxC, NorB, SoxQ
Gene name(s): marA
Functional conformation(s): MarA
Coregulator(s): AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, PurR, PutA, RcsB, Rob, SoxR, SoxS, TorR, YdeO
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
GadX Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator GadX, YhiX
Gene name(s): gadX
Functional conformation(s): GadX
Coregulator(s): AdiY, AraC, ArcA, CRP, CadC, CspA, EvgA, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, Lrp, MarA, MqsA, NagC, NtrC, OmpR, PhoB, PhoP, RcsB, RutR, SdiA, TorR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
GadW Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator GadW, YhiW
Gene name(s): gadW
Functional conformation(s): GadW
Coregulator(s): AdiY, ArcA, CRP, EvgA, FNR, Fis, FliZ, GadE, GadW, GadX, H-NS, Lrp, MarA, PhoB, PhoP, RcsB, RutR, SdiA, TorR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PhoP Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator PhoP, PhoP response regulator
Gene name(s): phoP
Functional conformation(s): PhoP , PhoP-Phosphorylated
Coregulator(s): AcrR, ArcA, ArgR, BasR, CRP, CysB, EnvR, EvgA, FNR, FadR, FliZ, GadE, GadW, GadX, H-NS, HypT, Lrp, MalT, MarA, MetJ, MprA, NagC, NarL, NarP, NtrC, OmpR, PdhR, PhoP, PurR, RbsR, RcsB, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, UvrY, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
GadE Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional activator GadE, YhiE, YhiT, acid-responsive regulator of gadA and gadBC
Gene name(s): gadE
Functional conformation(s): GadE
Coregulator(s): AdiY, ArcA, ArgR, CRP, CadC, CpxR, Cra, CusR, EvgA, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HdfR, HprR, IHF, Lrp, MarA, MatA, Nac, NsrR, OmpR, PdhR, PhoB, PhoP, PurR, RcsB, Rob, RutR, TorR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
TorR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator TorR, TorR response regulator
Gene name(s): torR
Functional conformation(s): TorR-TorI , TorR-Pasp
Coregulator(s): AdiY, ArcA, CRP, FNR, Fis, FliZ, GadE, GadW, GadX, H-NS, Lrp, MarA, NarL, PhoP, RcsB, TorR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
FliZ      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional regulator FliZ, YedH
Gene name(s): fliZ
Functional conformation(s): FliZ
Coregulator(s): AcrR, AdiY, BasR, CRP, CpxR, Cra, CsgD, EvgA, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HdfR, IHF, LrhA, Lrp, MarA, MatA, MlrA, MqsA, OmpR, PhoP, QseB, RcdA, RcsB, RstA, RutR, TorR, YdeO, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY FliZ,GadE,GadW,GadX,H-NS,Lrp,MarA,PhoP,RcsB,TorR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FliZ repressor GadE activator GadW dual GadX dual H-NS repressor Lrp repressor MarA repressor PhoP activator RcsB activator TorR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
MarA repressor hdeAp yhiD , hdeB , hdeA 3656820 3656839 -39.0 tgattttgatATTTTCCATCAACATGACATatacagaaaa [APPH]
[GEA]
[HIBSCS]
[SM]
[1]
H-NS repressor hdeAp yhiD , hdeB , hdeA 3656902 3656916 -118.0 tgcagtcgatTTAATAAAAATTTCCtaattgcagt [BPP]
[GEA]
[HIBSCS]
[2]
[3]
[4]
Lrp-leucine repressor hdeAp yhiD , hdeB , hdeA 3656802 3656817 -18.0 catgacatatACAGAAAACCAGGTTAtaacctcagt [AIBSCS]
[GEA]
[5]
Lrp-leucine repressor hdeAp yhiD , hdeB , hdeA 3656839 3656854 -55.0 tgaaataaaaATATCTGATTTTGATAttttccatca [AIBSCS]
[GEA]
[5]
Lrp-leucine repressor hdeAp yhiD , hdeB , hdeA 3656848 3656863 -64.0 tcattgtattGAAATAAAAATATCTGattttgatat [AIBSCS]
[GEA]
[5]
Lrp-leucine repressor hdeAp yhiD , hdeB , hdeA 3656881 3656896 -97.0 tttcctaattGCAGTATCTGATGCATctgtaactca [AIBSCS]
[GEA]
[5]
Lrp-leucine repressor hdeAp yhiD , hdeB , hdeA 3656900 3656915 -116.0 gcagtcgattTAATAAAAATTTCCTAattgcagtat [AIBSCS]
[GEA]
[5]
Lrp-leucine repressor hdeAp yhiD , hdeB , hdeA 3656943 3656958 -159.0 aaatcccctgCTATCAATCTATGCCAaaaacgcgtc [AIBSCS]
[GEA]
[5]
GadW dual hdeAp yhiD , hdeB , hdeA 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[5]
[6]
[7]
GadX dual hdeAp yhiD , hdeB , hdeA 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat [AIBSCS]
[GEA]
[5]
[7]
PhoP-Phosphorylated activator hdeAp yhiD , hdeB , hdeA 3656815 3656831 -32.0 atattttccaTCAACATGACATATACAgaaaaccagg [BPP]
[GEA]
[HIBSCS]
[8]
GadE activator hdeAp yhiD , hdeB , hdeA 3656899 3656918 -117.5 aatgcagtcgATTTAATAAAAATTTCCTAAttgcagtatc [AIBSCS]
[BPP]
[CEUMA]
[GEA]
[HIBSCS]
[IHBCE]
[RE]
[9]
[10]
[5]
[11]
[7]
GadX dual hdeAp yhiD , hdeB , hdeA 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[9]
[5]
[6]
[7]
GadW dual hdeAp yhiD , hdeB , hdeA 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[5]
[6]
[7]
GadX dual hdeAp yhiD , hdeB , hdeA 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat [AIBSCS]
[GEA]
[5]
[7]
GadW dual hdeAp yhiD , hdeB , hdeA 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat [AIBSCS]
[GEA]
[5]
[7]
GadX dual hdeAp yhiD , hdeB , hdeA 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[9]
[5]
[6]
[7]
GadW dual hdeAp yhiD , hdeB , hdeA 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat [AIBSCS]
[GEA]
[5]
[7]
GadX dual hdeAp yhiD , hdeB , hdeA 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat [BPP]
[GEA]
[HIBSCS]
[9]
[5]
[6]
[7]
GadW dual hdeAp yhiD , hdeB , hdeA 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat [BPP]
[GEA]
[HIBSCS]
[5]
[6]
[7]
FliZ repressor hdeAp yhiD , hdeB , hdeA 3656757 3656812 8.0 catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat [BPP]
[GEA]
[12]
GadW dual hdeAp yhiD , hdeB , hdeA 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat [BPP]
[GEA]
[HIBSCS]
[5]
[6]
[7]
RcsB-Pasp56 activator hdeAp yhiD , hdeB , hdeA         [GEA] [13]
GadX dual hdeAp yhiD , hdeB , hdeA 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat [BPP]
[GEA]
[HIBSCS]
[9]
[5]
[6]
[7]
GadE activator hdeAp yhiD , hdeB , hdeA 3656773 3656792 9.5 ataacctcagTGTCGAAATTGATTCGTGACggctctttca [CEUMA]
[IHBCE]
[RE]
[11]
TorR-Pasp activator hdeAp yhiD , hdeB , hdeA 3656814 3656823 -27.5 catcaacatgACATATACAGaaaaccaggt [AIBSCS]
[GEA]
[14]
[5]
TorR-Pasp activator hdeAp yhiD , hdeB , hdeA 3656838 3656847 -51.5 aaaatatctgATTTTGATATtttccatcaa [AIBSCS]
[GEA]
[5]

Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[BPP] Binding of purified proteins
[AIBSCS] Automated inference based on similarity to consensus sequences
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
Reference(s): [1] Schneiders T., et al., 2004
[2] De Biase D., et al., 1999
[3] Shin M., et al., 2005
[4] Yoshida T., et al., 1993
[5] Ruiz C., et al., 2008
[6] Tramonti A., et al., 2008
[7] Tucker DL., et al., 2003
[8] Zwir I., et al., 2005
[9] Hommais F., et al., 2004
[10] Itou J., et al., 2009
[11] Seo SW., et al., 2015
[12] Pesavento C., et al., 2012
[13] Johnson MD., et al., 2011
[14] Bordi C., et al., 2003



Reference(s)    

 [1] Schneiders T., Barbosa TM., McMurry LM., Levy SB., 2004, The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA., J Biol Chem 279(10):9037-42

 [2] De Biase D., Tramonti A., Bossa F., Visca P., 1999, The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system., Mol Microbiol 32(6):1198-211

 [3] Shin M., Song M., Rhee JH., Hong Y., Kim YJ., Seok YJ., Ha KS., Jung SH., Choy HE., 2005, DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping., Genes Dev 19(19):2388-98

 [4] Yoshida T., Ueguchi C., Yamada H., Mizuno T., 1993, Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant., Mol Gen Genet 237(1-2):113-22

 [5] Ruiz C., McMurry LM., Levy SB., 2008, Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli., J Bacteriol 190(4):1290-7

 [6] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82

 [7] Tucker DL., Tucker N., Ma Z., Foster JW., Miranda RL., Cohen PS., Conway T., 2003, Genes of the GadX-GadW regulon in Escherichia coli., J Bacteriol 185(10):3190-201

 [8] Zwir I., Shin D., Kato A., Nishino K., Latifi T., Solomon F., Hare JM., Huang H., Groisman EA., 2005, Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica., Proc Natl Acad Sci U S A 102(8):2862-7

 [9] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [10] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

 [11] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [12] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93

 [13] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [14] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol 48(1):211-23


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