RegulonDB RegulonDB 11.1: Regulon Form
   
   


ArcA,CRP,CaiF,FNR,H-NS regulon in Escherichia coli K-12 genome


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-[4Fe-4S]2+ reduced , FNR-[2Fe-2S]2+ oxidized
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, BtsR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadE-RcsB, 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 , CRP-cyclic-AMP
Coregulator(s): AaeR, AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BolA, 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, FrlR, 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, PlaR, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsAB, RcsB, RcsB-BglJ, RhaR, RhaS, Rob, RspR, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, 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, BolA, BtsR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CreB, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MalT, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsAB, RcsB, RcsB-BglJ, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, 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, BtsR, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadE-RcsB, 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:
CaiF Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional activator CaiF
Gene name(s): caiF
Functional conformation(s): CaiF-L-carnitine , CaiF
Coregulator(s): ArcA, CRP, CaiF, FNR, H-NS
Summary: TF Summary ...[more]

REGULATION EXERTED BY ArcA,CRP,CaiF,FNR,H-NS Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA activator CRP activator CaiF activator FNR activator H-NS repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
ArcA-phosphorylated activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 41981 41995 50.0 tatattaaatGTTAACAAAAATAAAacaaacggga [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
ArcA-phosphorylated activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42003 42017 28.0 cgtccacgagGTTAATAATAATTATattaaatgtt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
ArcA-phosphorylated activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42131 42145 -101.0 cagagcataaCAAACTGATTATTAAtcaaaattaa [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
ArcA-phosphorylated activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42121 42135 -91.0 caaactgattATTAATCAAAATTAAcgaaaaaacg [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
CRP-cyclic-AMP activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42068 42090 -41.5 acccgaaacaAAAATGTGATACCAATCACAGAAtacagcttat [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [2]
[3]
[4]
[5]
FNR activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42121 42134 -90.5 aaactgattaTTAATCAAAATTAAcgaaaaaacg [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [6]
[7]
FNR activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42072 42085 -41.5 aaacaaaaatGTGATACCAATCACagaatacagc [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [6]
[7]
CaiF-L-carnitine activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42181 42196 -151.5 tgttttatggATCACCAATATTGAAAgtcagatgtt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
CaiF-L-carnitine activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42238 42253 -208.5 tgttaagttcCTCACCAATATTGAAAacacggcgta [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
CaiF-L-carnitine activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42257 42272 -227.5 taaatccaacTTTCAATATTGTTAAGttcctcacca [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
CaiF-L-carnitine activator caiTp caiE , caiD , caiC , caiB , caiA , caiT 42200 42215 -170.5 aaaaagaaatTTTCAATATTGTTTTAtggatcacca [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
H-NS repressor caiTp caiE , caiD , caiC , caiB , caiA , caiT

Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [1] Liu X., et al., 2004
[2] Buchet A., et al., 1998
[3] Buchet A., et al., 1999
[4] Eichler K., et al., 1994
[5] Tsai MJ., et al., 2018
[6] Constantinidou C., et al., 2006
[7] Salmon K., et al., 2003



Reference(s)    

 [1] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [2] Buchet A., Eichler K., Mandrand-Berthelot MA., 1998, Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region., J Bacteriol 180(10):2599-608

 [3] Buchet A., Nasser W., Eichler K., Mandrand-Berthelot MA., 1999, Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator., Mol Microbiol 34(3):562-75

 [4] Eichler K., Bourgis F., Buchet A., Kleber HP., Mandrand-Berthelot MA., 1994, Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli., Mol Microbiol 13(5):775-86

 [5] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [6] 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

 [7] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

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