RegulonDB RegulonDB 10.8: Regulon Form
   
   


ArgP,CRP,FNR,Fur,Nac regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
ArgP Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator ArgP, IciA
Gene name(s): argP
Functional conformation(s): ArgP-lysine , ArgP-arginine , ArgP
Coregulator(s): ArgP, CRP, DnaA, FNR, Fis, Fur, H-NS, Lrp, LysR, Nac, NrdR, PhoB, 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-[4Fe-4S]2+ reduced , FNR-[2Fe-2S]2+ oxidized , FNR
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-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:
Nac Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator Nac
Gene name(s): nac
Functional conformation(s): Nac
Coregulator(s): AdiY, ArgP, ArgR, AsnC, CRP, CytR, FNR, Fur, GadE, HdfR, IHF, Lrp, Nac, NsrR, NtrC, PhoB, PurR, QseB
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Fur Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator Fur
Gene name(s): fur
Functional conformation(s): Fur-Mn2+ , Fur , Fur-Fe2+
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CdaR, CpxR, Cra, CusR, EnvY, FNR, Fis, FliZ, Fur, GadE, GadX, H-NS, HdfR, HprR, HypT, IHF, IscR, LrhA, Lrp, MarA, MatA, MetR, MntR, ModE, MqsA, Nac, NagC, NarL, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsAB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY ArgP,CRP,FNR,Fur,Nac Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArgP activator CRP repressor FNR activator Fur dual Nac repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP repressor gdhAp1 gdhA 1842265 1842286 -32.5 gggtcattttTTTCTTGCTTACCGTCACATTCttgatggtat [APIORCISFBSCS] [1]
Nac repressor gdhAp1 gdhA 1842345 1842359 45.0 agcacaatcgTATTAATATATAAGGgttttatatc [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
Nac repressor gdhAp1 gdhA 1842220 1842234 -81.0 tcgcatttggTTATGAGATTACTCTcgttattaat [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
Nac repressor gdhAp1 gdhA 1842276 1842290 -25.0 ttcttgcttaCCGTCACATTCTTGAtggtatagtc [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
Nac repressor gdhAp1 gdhA 1842325 1842339 25.0 cacatgacatAAACAACATAAGCACaatcgtatta [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
ArgP activator gdhAp1 gdhA 1842219 1842238 -79.5 atcgcatttgGTTATGAGATTACTCTCGTTattaatttgc [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[3]
[4]
Fur-Fe2+ activator gdhAp1 gdhA         [GEA] [5]
Fur-Fe2+ repressor gdhAp1 gdhA         [GEA] [5]
FNR activator gdhAp1 gdhA         [GEA] [5]
ArgP activator gdhAp1 gdhA 1842239 1842258 -59.5 tactctcgttATTAATTTGCTTTCCTGGGTcatttttttc [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[4]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[BPP] Binding of purified proteins
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[SM] Site mutation
Reference(s): [1] Riba L., et al., 1988
[2] Camarena L., et al., 1998
[3] Marbaniang CN., et al., 2011
[4] Nguyen Le Minh P., et al., 2018
[5] Kumar R., et al., 2011



Reference(s)    

 [1] Riba L., Becerril B., Servin-Gonzalez L., Valle F., Bolivar F., 1988, Identification of a functional promoter for the Escherichia coli gdhA gene and its regulation., Gene 71(2):233-46

 [2] Camarena L., Poggio S., Garcia N., Osorio A., 1998, Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein., FEMS Microbiol Lett 167(1):51-6

 [3] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [4] Nguyen Le Minh P., Velazquez Ruiz C., Vandermeeren S., Abwoyo P., Bervoets I., Charlier D., 2018, Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli., Microbiol Res 206:141-158

 [5] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3


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