RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


GadE,GadW,GadX,H-NS,MarA,YdeO 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:
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:
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:
YdeO Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator YdeO
Gene name(s): ydeO
Functional conformation(s): YdeO
Coregulator(s): AppY, ArcA, CRP, EvgA, Fis, FliZ, GadE, GadW, GadX, H-NS, IscR, MarA, NarL, NarP, PhoP, RcsB, YdeO, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY GadE,GadW,GadX,H-NS,MarA,YdeO Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
GadE activator GadW repressor GadX activator H-NS repressor MarA repressor YdeO activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
MarA repressor slpp slp , dctR 3653964 3653983 39.0 tagtaacatgAACATGACAAAAGGTGCACTcatcctcagc [GEA]
[HIBSCS]
[1]
[2]
GadW repressor slpp slp , dctR 3653866 3653885 -60.5 atcagacaggTTTACGTTACTATCAGGCATatcacctcag [AIBSCS]
[GEA]
[3]
[4]
GadX activator slpp slp , dctR 3653845 3653864 -81.5 ctaaacagaaAGGATATAAACATCAGACAGgtttacgtta [BPP]
[CEUMA]
[GEA]
[HIBSCS]
[IHBCE]
[RE]
[5]
[3]
[4]
YdeO activator slpp slp , dctR 3653884 3653909 -40.0 actatcaggcATATCACCTCAGAATCAGATGAAAACtataaagaaa [BPP]
[GEA]
[IHBCE]
[6]
GadW repressor slpp slp , dctR 3653845 3653864 -81.5 ctaaacagaaAGGATATAAACATCAGACAGgtttacgtta [GEA]
[HIBSCS]
[3]
[4]
H-NS repressor slpp slp , dctR         [BPP] [7]
GadE-RcsB activator slpp slp , dctR         [BPP]
[GEA]
[8]
[9]
GadX activator slpp slp , dctR 3653866 3653885 -60.5 atcagacaggTTTACGTTACTATCAGGCATatcacctcag [AIBSCS]
[BPP]
[GEA]
[3]
[4]
GadX activator slpp slp , dctR 3653942 3653961 17.0 ttttaatattTGTTGATAAGGATAGTAACAtgaacatgac [CEUMA]
[IHBCE]
[RE]
[5]
GadX activator slpp slp , dctR 3653923 3653942 -3.0 aaagaaatatCTATTATGGTTTTAATATTTgttgataagg [CEUMA]
[IHBCE]
[RE]
[5]
GadX activator slpp slp , dctR 3653856 3653875 -70.5 ggatataaacATCAGACAGGTTTACGTTACtatcaggcat [CEUMA]
[IHBCE]
[RE]
[5]

Evidence: [GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
Reference(s): [1] Price GP., et al., 2000
[2] Seoane AS., et al., 1995
[3] Tramonti A., et al., 2008
[4] Tucker DL., et al., 2003
[5] Seo SW., et al., 2015
[6] Yamanaka Y., et al., 2014
[7] Krin E., et al., 2010
[8] Johnson MD., et al., 2011
[9] Krin E., et al., 2010



Reference(s)    

 [1] Price GP., St John AC., 2000, Purification and analysis of expression of the stationary phase-inducible slp lipoprotein in Escherichia coli: role of the Mar system., FEMS Microbiol Lett 193(1):51-6

 [2] Seoane AS., Levy SB., 1995, Identification of new genes regulated by the marRAB operon in Escherichia coli., J Bacteriol 177(3):530-5

 [3] 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

 [4] 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

 [5] 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

 [6] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [7] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [8] 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

 [9] Krin E., Danchin A., Soutourina O., 2010, RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli., Res Microbiol 161(5):363-371


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