RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


AdiY,ArcA,CRP,FNR,Fis,GadE,GadW,GadX,H-NS,RcsB,TorR,ppGpp regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
Fis Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator Fis, Nbp, site-specific DNA inversion stimulation factor
Gene name(s): fis
Functional conformation(s): Fis
Coregulator(s): AcrR, AdiY, AppY, ArcA, ArgP, BasR, CRP, CpxR, Cra, CreB, CspA, CusR, CytR, DeoR, DksA, DksA-ppGpp, DnaA, FNR, FadR, Fis, FlhDC, FliZ, Fur, GadE, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
FNR Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator FNR, NirA, NirR, OssA, OxrA
Gene name(s): fnr
Functional conformation(s): FNR , FNR-[2Fe-2S]2+ oxidized
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadW, GadX, GcvA, GlpR, H-NS, HdfR, HprR, HyfR, HypT, IHF, LeuO, Lrp, MalT, MarA, MetR, MlrA, ModE, Nac, NagC, NarL, NarP, NfeR, NikR, NorR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PhoP, PurR, PuuR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, TdcA, TdcR, TorR, YeiL, ppGpp
Summary: TF Summary ...[more]
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:
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:
ArcA Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class External-Two-component systems
Synonym(s): ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein
Gene name(s): arcA
Functional conformation(s): ArcA-Phosphorylated , ArcA
Coregulator(s): AdiY, AppY, ArcA, BetI, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, 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:
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:
AdiY      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional activator AdiY
Gene name(s): adiY
Functional conformation(s): AdiY
Coregulator(s): AdiY, ArcA, ArgR, CRP, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HdfR, IHF, Lrp, Nac, RcsB, TorR, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY AdiY,ArcA,CRP,FNR,Fis,GadE,GadW,GadX,H-NS,RcsB,TorR,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AdiY activator ArcA activator CRP repressor FNR repressor Fis repressor GadE activator GadW dual GadX activator H-NS repressor RcsB repressor TorR repressor ppGpp activation    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP repressor gadAp gadX , gadA 3667659 3667680 -62.5 cgtttttctgCTTAGGATTTTGTTATTTAAATtaagcctgta [GEA]
[HIBSCS]
[1]
Fis repressor gadAp gadX , gadA 3667745 3667764 -147.0 aacagcaatgTTTGGGCGATTTTTATTACGataataaagt [AIBSCS]
[GEA]
[2]
Fis repressor gadAp gadX , gadA 3667716 3667735 -118.0 gataataaagTCTGTTTTTAATATTATCATgttaaatgtt [AIBSCS]
[GEA]
[2]
Fis repressor gadAp gadX , gadA 3667692 3667711 -94.0 tatcatgttaAATGTTTATATTATAAAAAGtcgtttttct [AIBSCS]
[GEA]
[2]
Fis repressor gadAp gadX , gadA 3667616 3667635 -18.0 ccttgcttccATTGCGGATAAATCCTACTTttttattgcc [AIBSCS]
[GEA]
[2]
GadX activator gadAp gadX , gadA 3667608 3667627 -10.5 ccattgcggaTAAATCCTACTTTTTTATTGccttcaaata [BPP]
[GEA]
[3]
[4]
[5]
[6]
[7]
FNR repressor gadAp gadX , gadA 3667590 3667603 11.5 ttattgccttCAAATAAATTTAAGgagttcgaaa [AIBSCS]
[GEA]
[8]
RcsB-Pasp56 repressor gadAp gadX , gadA 3667619 3667632 -18.5 tgcttccattGCGGATAAATCCTActtttttatt [BPP]
[GEA]
[IHBCE]
[SM]
[9]
[10]
[11]
GadE-RcsB activator gadAp gadX , gadA 3667660 3667680 -62.5 cgtttttctgCTTAGGATTTTGTTATTTAAAttaagcctgt [BPP]
[CEUMA]
[GEA]
[HIBSCS]
[IHBCE]
[RE]
[SM]
[9]
[1]
[10]
[12]
[13]
[14]
[15]
[16]
[5]
GadX activator gadAp gadX , gadA 3667719 3667738 -121.5 tacgataataAAGTCTGTTTTTAATATTATcatgttaaat [BPP]
[GEA]
[HIBSCS]
[3]
[4]
[17]
[5]
[6]
[7]
GadX activator gadAp gadX , gadA 3667629 3667648 -31.5 taagcctgtaATGCCTTGCTTCCATTGCGGataaatccta [BPP]
[GEA]
[3]
[4]
[5]
[6]
[7]
GadW dual gadAp gadX , gadA 3667698 3667717 -100.5 taatattatcATGTTAAATGTTTATATTATaaaaagtcgt [BPP]
[GEA]
[HIBSCS]
[4]
[17]
[5]
[7]
GadW dual gadAp gadX , gadA 3667676 3667695 -78.0 tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta [BPP]
[GEA]
[4]
[7]
GadW dual gadAp gadX , gadA 3667655 3667674 -57.5 tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc [BPP]
[GEA]
[4]
[7]
GadX activator gadAp gadX , gadA 3667676 3667695 -78.0 tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta [BPP]
[GEA]
[3]
[4]
[5]
[6]
[7]
GadX activator gadAp gadX , gadA 3667655 3667674 -57.5 tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc [BPP]
[GEA]
[3]
[4]
[5]
[6]
[7]
H-NS repressor gadAp gadX , gadA         [BPP]
[GEA]
[3]
[4]
[6]
GadW dual gadAp gadX , gadA 3667719 3667738 -121.5 tacgataataAAGTCTGTTTTTAATATTATcatgttaaat [BPP]
[GEA]
[HIBSCS]
[4]
[17]
[5]
[7]
GadW dual gadAp gadX , gadA 3667719 3667738 -121.5 tacgataataAAGTCTGTTTTTAATATTATcatgttaaat [BPP]
[GEA]
[HIBSCS]
[4]
[17]
[5]
[7]
GadW dual gadAp gadX , gadA 3667698 3667717 -100.5 taatattatcATGTTAAATGTTTATATTATaaaaagtcgt [BPP]
[GEA]
[HIBSCS]
[4]
[17]
[5]
[7]
ArcA-Phosphorylated activator gadAp gadX , gadA         [AIBSCS]
[GEA]
[18]
AdiY activator gadAp gadX , gadA         [BPP] [19]
GadW dual gadAp gadX , gadA 3667676 3667695 -78.0 tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta [BPP]
[GEA]
[4]
[7]
GadW dual gadAp gadX , gadA 3667655 3667674 -57.5 tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc [BPP]
[GEA]
[4]
[7]
GadX activator gadAp gadX , gadA 3667698 3667717 -100.5 taatattatcATGTTAAATGTTTATATTATaaaaagtcgt [BPP]
[GEA]
[HIBSCS]
[3]
[4]
[17]
[5]
[6]
[7]
TorR-Pasp repressor gadAp gadX , gadA 3667530 3667539 73.5 cagaactactCGATTCACGTtttggcgcaa [AIBSCS]
[GEA]
[20]
TorR-Pasp repressor gadAp gadX , gadA 3667725 3667734 -122.5 ataataaagtCTGTTTTTAAtattatcatg [AIBSCS]
[GEA]
[20]

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
[IHBCE] Inferred by a human based on computational evidence
[SM] Site mutation
[CEUMA] ChIP-exo evidence used in manual assertion
[RE] RNA-seq evidence
Reference(s): [1] Castanie-Cornet MP., et al., 2001
[2] Bradley MD., et al., 2007
[3] Giangrossi M., et al., 2005
[4] Ma Z., et al., 2002
[5] Tramonti A., et al., 2006
[6] Tramonti A., et al., 2002
[7] Tucker DL., et al., 2003
[8] Constantinidou C., et al., 2006
[9] Castanie-Cornet MP., et al., 2010
[10] Castanie-Cornet MP., et al., 2007
[11] Krin E., et al., 2010
[12] Hommais F., et al., 2004
[13] Itou J., et al., 2009
[14] Johnson MD., et al., 2011
[15] Ma Z., et al., 2003
[16] Seo SW., et al., 2015
[17] Tramonti A., et al., 2008
[18] Salmon KA., et al., 2005
[19] Krin E., et al., 2010
[20] Bordi C., et al., 2003



Reference(s)    

 [1] Castanie-Cornet MP., Foster JW., 2001, Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes., Microbiology 147(Pt 3):709-15

 [2] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [3] Giangrossi M., Zattoni S., Tramonti A., De Biase D., Falconi M., 2005, Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli., J Biol Chem 280(22):21498-505

 [4] Ma Z., Richard H., Tucker DL., Conway T., Foster JW., 2002, Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW)., J Bacteriol 184(24):7001-12

 [5] Tramonti A., De Canio M., Delany I., Scarlato V., De Biase D., 2006, Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli., J Bacteriol 188(23):8118-27

 [6] Tramonti A., Visca P., De Canio M., Falconi M., De Biase D., 2002, Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system., J Bacteriol 184(10):2603-13

 [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] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [9] Castanie-Cornet MP., Cam K., Bastiat B., Cros A., Bordes P., Gutierrez C., 2010, Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE., Nucleic Acids Res 38(11):3546-54

 [10] Castanie-Cornet MP., Treffandier H., Francez-Charlot A., Gutierrez C., Cam K., 2007, The glutamate-dependent acid resistance system in Escherichia coli: essential and dual role of the His-Asp phosphorelay RcsCDB/AF., Microbiology 153(Pt 1):238-46

 [11] 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

 [12] 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

 [13] 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

 [14] 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

 [15] Ma Z., Gong S., Richard H., Tucker DL., Conway T., Foster JW., 2003, GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12., Mol Microbiol 49(5):1309-20

 [16] 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

 [17] 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

 [18] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [19] 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

 [20] 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


RegulonDB