RegulonDB RegulonDB 11.1: Regulon Form
   
   


ArcA,CRP,FNR,IHF,NarL 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:
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:
NarL Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator NarL, FrdR, NarR, nitrate/nitrite response regulator NarL
Gene name(s): narL
Functional conformation(s): NarL , NarL-phosphorylated
Coregulator(s): AppY, ArcA, CRP, Cra, DcuR, DpiA, EvgA, FNR, FhlA, Fis, FlhDC, Fur, H-NS, IHF, IscR, Lrp, ModE, NagC, NarL, NarP, NikR, NorR, NsrR, OxyR, PhoP, RcsB, RstA, SoxS, TorR, UvrY, YdeO
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
IHF Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator IHF
Gene name(s): ihfB, ihfA
Functional conformation(s): IHF
Coregulator(s): AcrR, AdiY, ArcA, ArgR, AtoC, BasR, BolA, BtsR, CRP, Cbl, CpxR, Cra, CsgD, CysB, DksA, DksA-ppGpp, EnvY, FNR, FadR, FhlA, Fis, FlhDC, FliZ, Fur, GadE, GlcC, GlpR, GlrR, H-NS, HU, HdfR, HipAB, HipB, IHF, IclR, IscR, LrhA, Lrp, MarA, MatA, MlrA, MntR, ModE, MprA, MqsA, Nac, NagC, NanR, NarL, NarP, NorR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PepA, PhoB, PlaR, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY ArcA,CRP,FNR,IHF,NarL Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA activator CRP activator FNR activator IHF activator NarL repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
ArcA-phosphorylated activator focAp1 pflB , focA 954492 954506 -6.0 ataatgctttGTTAGTATCTCGTCGccgacttaat [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
ArcA-phosphorylated activator focAp1 pflB , focA 954737 954751 -251.0 tataaggttaAATATCGGTAATTTGtatttaataa [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IEP-MICROARRAY] 		[1]
[2]
IHF activator focAp1 pflB , focA 954599 954611 -112.5 atttttatttGGATAATCAAATAtttactccgt [EXP-IEP-GENE-EXPRESSION-ANALYSIS]  
CRP-cyclic-AMP activator focAp1 pflB , focA 954523 954544 -40.5 aagccaggcgAGATATGATCTATATCAATTTCtcatctataa [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
[4]
NarL-phosphorylated repressor focAp1 pflB , focA 954725 954731 -235.0 atttgtatttAATAAATacgatcgata [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954838 954844 -348.0 aatgtaggctTAATGATtagtctgagt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954836 954842 -346.0 tgtaggcttaATGATTAgtctgagtta [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954776 954782 -286.0 catatatttgCATTAATaaaataattg [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954760 954766 -270.0 taaaataattGTAATTAtaaggttaaa [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954716 954722 -226.0 taataaatacGATCGATattgttactt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954642 954648 -152.0 ggaaaaaattCAACTCAtttgttaatt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954510 954516 -20.0 tttctcatctATAATGCtttgttagta [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
ArcA-phosphorylated activator focAp1 pflB , focA 954600 954614 -114.0 tttatttttaTTTGGATAATCAAATatttactccg [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IEP-MICROARRAY] 		[6]
[1]
[2]
[7]
[8]
[9]
NarL-phosphorylated repressor focAp1 pflB , focA 954591 954597 -101.0 aatcaaatatTTACTCCgtatttgcat [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954527 954533 -37.0 gatatgatctATATCAAtttctcatct [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
NarL-phosphorylated repressor focAp1 pflB , focA 954743 954749 -253.0 taaggttaaaTATCGGTaatttgtatt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
FNR activator focAp1 pflB , focA 954527 954540 -40.5 caggcgagatATGATCTATATCAAtttctcatct [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]

Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IEP-MICROARRAY] high throughput expression microarray evidence
Reference(s): [1] Drapal N., et al., 1995
[2] Federowicz S., et al., 2014
[3] Sawers G., et al., 1997
[4] Zheng D., et al., 2004
[5] Kaiser M., et al., 1995
[6] Drapal N., et al., 1995
[7] Sawers G. 1993
[8] Sawers G., et al., 1992
[9] Sirko A., et al., 1993



Reference(s)    

 [1] Drapal N., Sawers G., 1995, Promoter 7 of the Escherichia coli pfl operon is a major determinant in the anaerobic regulation of expression by ArcA., J Bacteriol 177(18):5338-41

 [2] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

 [3] Sawers G., Kaiser M., Sirko A., Freundlich M., 1997, Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition., Mol Microbiol 23(4):835-45

 [4] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [5] Kaiser M., Sawers G., 1995, Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP., J Bacteriol 177(13):3647-55

 [6] Drapal N., Sawers G., 1995, Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region., Mol Microbiol 16(3):597-607

 [7] Sawers G., 1993, Specific transcriptional requirements for positive regulation of the anaerobically inducible pfl operon by ArcA and FNR., Mol Microbiol 10(4):737-47

 [8] Sawers G., Suppmann B., 1992, Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins., J Bacteriol 174(11):3474-8

 [9] Sirko A., Zehelein E., Freundlich M., Sawers G., 1993, Integration host factor is required for anaerobic pyruvate induction of pfl operon expression in Escherichia coli., J Bacteriol 175(18):5769-77

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