RegulonDB RegulonDB 10.7: Regulon Form
   
   


AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB 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, GadE-RcsB, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, MazE-MazF, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, RcsB-BglJ, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, 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 , CRP-cAMP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CRP-Sxy, 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, GadE-RcsB, 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, RcsAB, RcsB, RcsB-BglJ, 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:
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 , RcsB-Pasp56
Coregulator(s): AdiY, ArcA, CRP, CadC, CpxR, EvgA, FNR, Fis, FliZ, GadE, GadE-RcsB, GadW, GadX, GlrR, H-NS, LeuO, LexA, Lrp, MarA, NagC, NarL, NarP, NhaR, NtrC, OmpR, PhoB, PhoP, RcsB, RcsB-BglJ, Rob, StpA, TorR, UvrY, 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, GadE-RcsB, 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, GadE-RcsB, 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, GadE-RcsB, GadW, GadX, H-NS, HdfR, HprR, IHF, Lrp, MarA, MatA, Nac, NsrR, OmpR, PdhR, PhoB, PhoP, PurR, RcsAB, RcsB, Rob, RutR, TorR, YdeO, 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, GadE-RcsB, GadW, GadX, H-NS, HdfR, IHF, Lrp, Nac, 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, RcsAB, RcsB, RstA, RutR, TorR, YdeO, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AdiY activator CRP repressor Fis repressor FliZ repressor GadE activator GadW dual GadX activator RcsB activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
GadE activator gadBp gadC , gadB 1572125 1572144 -62.5 ataaataacaTTAGGATTTTGTTATTTAAAcacgagtcct [APIORCISFBSCS]
[BPP]
[CEUMA]
[GEA]
[IHBCE]
[RE]
[1]
[2]
[3]
[4]
[5]
[6]
CRP-cAMP repressor gadBp gadC , gadB 1572125 1572146 -63.5 cgataaataaCATTAGGATTTTGTTATTTAAAcacgagtcct [APIORCISFBSCS]
[GEA]
[1]
Fis repressor gadBp gadC , gadB 1572170 1572184 -105.0 gtttttcaatGAAAAAATATTATTCgcgtaatatc [AIBSCS]
[GEA]
[7]
Fis repressor gadBp gadC , gadB 1572124 1572138 -59.0 aacattaggaTTTTGTTATTTAAACacgagtcctt [AIBSCS]
[GEA]
[7]
Fis repressor gadBp gadC , gadB 1572092 1572106 -27.0 ctttgcacttGCTTACTTTATCGATaaatcctact [AIBSCS]
[GEA]
[7]
Fis repressor gadBp gadC , gadB 1572029 1572043 37.0 agtttaaaatGGATAAGAAGCAAGTaacggattta [AIBSCS]
[GEA]
[7]
GadX activator gadBp gadC , gadB 1572080 1572099 -17.5 cttgcttactTTATCGATAAATCCTACTTTtttaatgcga [BPP]
[GEA]
[8]
[9]
[5]
[10]
[6]
GadX activator gadBp gadC , gadB 1572102 1572121 -39.5 atttaaacacGAGTCCTTTGCACTTGCTTActttatcgat [BPP]
[GEA]
[8]
[9]
[5]
[10]
[6]
GadX activator gadBp gadC , gadB 1572182 1572201 -119.5 gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat [BPP]
[GEA]
[8]
[9]
[5]
[10]
[6]
GadX activator gadBp gadC , gadB 1572294 1572313 -231.5 ataataatcaAGTACTAATAGTGATATTTTaaggtctgat [APIORCISFBSCS]
[BPP]
[CEUMA]
[GEA]
[IHBCE]
[RE]
[9]
[4]
[11]
[5]
GadX activator gadBp gadC , gadB 1572273 1572292 -210.5 tgatattttaAGGTCTGATTTTTACGTGATaattcaggag [APIORCISFBSCS]
[BPP]
[GEA]
[9]
[11]
[5]
GadW activator gadBp gadC , gadB 1572161 1572180 -98.5 ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa [BPP]
[GEA]
[9]
[5]
[6]
RcsB-Pasp56 activator gadBp gadC , gadB 1572130 1572144 -64.5 ataaataacaTTAGGATTTTGTTATttaaacacga [APIORCISFBSCS]
[GEA]
[12]
[13]
GadW repressor gadBp gadC , gadB 1572182 1572201 -119.5 gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat [BPP]
[GEA]
[9]
[5]
[6]
GadW repressor gadBp gadC , gadB 1572161 1572180 -98.5 ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa [BPP]
[GEA]
[9]
[5]
[6]
GadW repressor gadBp gadC , gadB 1572273 1572292 -210.5 tgatattttaAGGTCTGATTTTTACGTGATaattcaggag [APIORCISFBSCS]
[BPP]
[GEA]
[9]
[11]
[5]
[6]
GadW activator gadBp gadC , gadB 1572294 1572313 -231.5 ataataatcaAGTACTAATAGTGATATTTTaaggtctgat [APIORCISFBSCS]
[BPP]
[GEA]
[9]
[11]
[5]
[6]
GadW activator gadBp gadC , gadB 1572182 1572201 -119.5 gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat [BPP]
[GEA]
[9]
[5]
[6]
GadW activator gadBp gadC , gadB 1572273 1572292 -210.5 tgatattttaAGGTCTGATTTTTACGTGATaattcaggag [APIORCISFBSCS]
[BPP]
[GEA]
[9]
[11]
[5]
[6]
AdiY activator gadBp gadC , gadB         [BPP] [14]
FliZ repressor gadBp gadC , gadB         [BPP]
[GEA]
[15]
[16]
GadX activator gadBp gadC , gadB 1572161 1572180 -98.5 ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa [BPP]
[GEA]
[8]
[9]
[5]
[10]
[6]
GadW repressor gadBp gadC , gadB 1572294 1572313 -231.5 ataataatcaAGTACTAATAGTGATATTTTaaggtctgat [APIORCISFBSCS]
[BPP]
[GEA]
[9]
[11]
[5]
[6]
GadX activator gadBp gadC , gadB 1572330 1572349 -268.0 ctatttttatGTAATAATTTTATAAATGCGttcaaaataa [CEUMA]
[IHBCE]
[RE]
[4]
GadX activator gadBp gadC , gadB 1572246 1572265 -184.0 gataattcagGAGACACAGAATGCGCATAAaaataacagc [CEUMA]
[IHBCE]
[RE]
[4]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BPP] Binding of purified proteins
[CEUMA] ChIP-exo evidence used in manual assertion
[GEA] Gene expression analysis
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Castanie-Cornet MP., et al., 2001
[2] Itou J., et al., 2009
[3] Ma Z., et al., 2003
[4] Seo SW., et al., 2015
[5] Tramonti A., et al., 2006
[6] Tucker DL., et al., 2003
[7] Bradley MD., et al., 2007
[8] Giangrossi M., et al., 2005
[9] Ma Z., et al., 2002
[10] Tramonti A., et al., 2002
[11] Tramonti A., et al., 2008
[12] Castanie-Cornet MP., et al., 2007
[13] Johnson MD., et al., 2011
[14] Krin E., et al., 2010
[15] Pesavento C., et al., 2008
[16] Pesavento C., et al., 2012



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] 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

 [3] 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

 [4] 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

 [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] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [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] 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

 [15] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46

 [16] 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


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