RegulonDB RegulonDB 10.10: Regulon Form
   
   


CRP,ExuR,FNR 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-cyclic-AMP , CRP
Coregulator(s): 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, 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:
ExuR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional repressor ExuR, negative regulator of exu regulon, exuT, uxaAC, and uxuB
Gene name(s): exuR
Functional conformation(s): ExuR , ExuR-α-D-galacturonate, α-D-glucuronate , ExuR-α-D-glucuronate
Coregulator(s): CRP, DpiA, ExuR, FNR, OxyR, UxuR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,ExuR,FNR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator ExuR repressor FNR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
ExuR repressor uxaCp2 uxaA , uxaC 3244850 3244867 -1.5 ctttgagagtAATTTTTTTAACTACGTTtattgatcta   [1]
[2]
ExuR repressor uxaCp2 uxaA , uxaC 3244874 3244891 -25.5 cgcggcctgcAGCGAGATTTACCACTTTgagagtaatt   [1]
ExuR repressor uxaCp2 uxaA , uxaC 3244795 3244812 54.5 cggactctggAAATTGGTGTGATAACTTtgtcagcatc   [1]
CRP-cyclic-AMP activator uxaCp2 uxaA , uxaC 3244952 3244974 -105.5 atacaactttAAAAGGTGAGAGCCATCACAAATgtgggaatat [GEA] [1]
[2]
[3]
ExuR repressor uxaCp2 uxaA , uxaC 3244976 3244993 -127.5 ggcagaaagaTAACTTGTCATACAACTTtaaaaggtga [GEA] [4]
[2]
FNR activator uxaCp2 uxaA , uxaC

Evidence: [GEA] Gene expression analysis
Reference(s): [1] Medina-Rivera A., et al., 2011
[2] Rodionov DA., et al., 2000
[3] Tsai MJ., et al., 2018
[4] Mata-Gilsinger M., et al., 1983



Reference(s)    

 [1] Medina-Rivera A., Abreu-Goodger C., Thomas-Chollier M., Salgado H., Collado-Vides J., van Helden J., 2011, Theoretical and empirical quality assessment of transcription factor-binding motifs., Nucleic Acids Res 39(3):808-24

 [2] Rodionov DA., Mironov AA., Rakhmaninova AB., Gelfand MS., 2000, Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria., Mol Microbiol 38(4):673-83

 [3] 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

 [4] Mata-Gilsinger M., Ritzenthaler P., Blanco C., 1983, Characterization of the operator sites of the exu regulon in Escherichia coli K-12 by operator-constitutive mutations and repressor titration., Genetics 105(4):829-42

 [5] 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

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