RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
CRP Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): Cap, Csm, DNA-binding transcriptional dual regulator CRP, GurB
Gene name(s): crp
Functional conformation(s): CRP-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CaiF, ChbR, ComR, CpxR, Cra, CreB, CsgD, CspA, CsqR, CusR, CytR, DcuR, DeoR, DgoR, DksA-ppGpp, DnaA, DpiA, DsdC, EbgR, EnvY, EvgA, ExuR, FNR, FadR, FeaR, FhlA, Fis, FlhDC, FliZ, FucR, Fur, GadE, GadW, GadX, GalR, GalS, GatR, GcvA, GlaR, GlcC, GlpR, GlrR, GntR, GutM, H-NS, HU, HdfR, HipB, HprR, HyfR, HypT, IHF, IclR, IdnR, LacI, LeuO, LexA, LrhA, Lrp, LsrR, MalI, MalT, MarA, MarR, MatA, McbR, MelR, MetJ, MhpR, Mlc, MlrA, ModE, MprA, MqsA, MurR, Nac, NadR, NagC, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PhoB, PhoP, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsB, RhaR, RhaS, Rob, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YiaJ, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
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:
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:
EvgA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional activator EvgA, EvgA response regulator
Gene name(s): evgA
Functional conformation(s): EvgA-Phosphorylated , EvgA
Coregulator(s): CRP, EvgA, FNR, FliZ, GadE, GadW, GadX, H-NS, NagC, NarL, NarP, PhoP, RcsB, UvrY, YdeO
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]
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 CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP repressor EvgA activator FliZ repressor GadE activator GadW activator GadX activator H-NS repressor YdeO activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
GadE activator gadEp gadE , gadF , mdtE , mdtF 3658137 3658156 -198.5 caaacgttaaCTTTTTGTTTGCTATTTACAagctgataac [BPP]
[GEA]
[1]
GadE activator gadEp gadE , gadF , mdtE , mdtF 3658272 3658291 -63.5 taaagttcttATAGGCGTTTACTATATTGAacaacgattc [BPP]
[GEA]
[HIBSCS]
[1]
[2]
GadE activator gadEp gadE , gadF , mdtE , mdtF 3658305 3658324 -30.5 acgattcggaCAAGGATGTAAATAATGAAAaggatgacat [BPP]
[GEA]
[1]
CRP-cAMP repressor gadEp gadE , gadF , mdtE , mdtF 3658315 3658336 -19.5 caaggatgtaAATAATGAAAAGGATGACATATtcgaaacgat [BPP]
[HIBSCS]
[3]
GadX activator gadEp gadE , gadF , mdtE , mdtF 3657761 3657780 -574.5 aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa [GEA]
[HIBSCS]
[4]
[5]
[6]
[7]
[2]
GadX activator gadEp gadE , gadF , mdtE , mdtF 3657740 3657759 -595.5 ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat [GEA]
[HIBSCS]
[4]
[5]
[6]
[7]
[2]
GadW activator gadEp gadE , gadF , mdtE , mdtF 3657740 3657759 -595.5 ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat [AIBSCS]
[GEA]
[6]
[7]
YdeO activator gadEp gadE , gadF , mdtE , mdtF         [BPP]
[GEA]
[1]
GadW activator gadEp gadE , gadF , mdtE , mdtF 3657761 3657780 -574.5 aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa [GEA]
[HIBSCS]
[6]
[7]
EvgA-Phosphorylated activator gadEp gadE , gadF , mdtE , mdtF         [BPP]
[GEA]
[1]
H-NS repressor gadEp gadE , gadF , mdtE , mdtF         [BPP] [8]
FliZ repressor gadEp gadE , gadF , mdtE , mdtF 3658325 3658383 9.5 aataatgaaaAGGATGACATATTCGAAACGATAACGGCTAAGGAGCAAGTTATGATTTTTCTCATGACGaaagattctt [BPP]
[GEA]
[SM]
[9]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[AIBSCS] Automated inference based on similarity to consensus sequences
[SM] Site mutation
Reference(s): [1] Ma Z., et al., 2004
[2] Tucker DL., et al., 2003
[3] Hirakawa H., et al., 2006
[4] Nishino K., et al., 2008
[5] Sayed AK., et al., 2009
[6] Sayed AK., et al., 2007
[7] Tramonti A., et al., 2008
[8] Krin E., et al., 2010
[9] Pesavento C., et al., 2012



Reference(s)    

 [1] Ma Z., Masuda N., Foster JW., 2004, Characterization of EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli., J Bacteriol 186(21):7378-89

 [2] 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

 [3] Hirakawa H., Inazumi Y., Senda Y., Kobayashi A., Hirata T., Nishino K., Yamaguchi A., 2006, N-acetyl-d-glucosamine induces the expression of multidrug exporter genes, mdtEF, via catabolite activation in Escherichia coli., J Bacteriol 188(16):5851-8

 [4] Nishino K., Senda Y., Yamaguchi A., 2008, The AraC-family regulator GadX enhances multidrug resistance in Escherichia coli by activating expression of mdtEF multidrug efflux genes., J Infect Chemother 14(1):23-9

 [5] Sayed AK., Foster JW., 2009, A 750 bp sensory integration region directs global control of the Escherichia coli GadE acid resistance regulator., Mol Microbiol 71(6):1435-50

 [6] Sayed AK., Odom C., Foster JW., 2007, The Escherichia coli AraC-family regulators GadX and GadW activate gadE, the central activator of glutamate-dependent acid resistance., Microbiology 153(Pt 8):2584-92

 [7] 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

 [8] 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

 [9] 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


RegulonDB