RegulonDB RegulonDB 10.10: Regulon Form
   
   


ArcA,CRP,Cra,IHF,IclR regulon in Escherichia coli K-12 genome


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:
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:
IclR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional repressor IclR
Gene name(s): iclR
Functional conformation(s): IclR-glyoxylate , IclR , IclR-pyruvate
Coregulator(s): ArcA, CRP, Cra, FadR, IHF, IclR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Cra Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator Cra, FruC, FruR, Shl
Gene name(s): cra
Functional conformation(s): Cra-β-D-fructofuranose 1-phosphate , Cra
Coregulator(s): AcrR, ArcA, BasR, BetI, BolA, BtsR, CRP, CpxR, Cra, CsgD, CusR, DcuR, DksA, FNR, Fis, FliZ, Fur, GadE, GlcC, GntR, H-NS, HprR, IHF, IclR, KdgR, Lrp, MarA, MarR, Mlc, MlrA, MqsA, NagC, NarL, NarP, OmpR, PdhR, PrpR, RcdA, RcsAB, Rob, RstA, SgrR, SoxS, TyrR, ppGpp
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,Cra,IHF,IclR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA repressor CRP repressor Cra activator IHF activator IclR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Cra activator aceBp aceB , aceA , aceK 4215227 4215244 -166.5 tgatagtcgaTCGTTAAGCGATTCAGCAccttacctca [GEA] [1]
[2]
IHF activator aceBp aceB , aceA , aceK 4215324 4215336 -72.0 ttcatattgtTATCAACAAGTTAtcaagtattt [GEA] [3]
IHF activator aceBp aceB , aceA , aceK 4215237 4215249 -159.0 tcgttaagcgATTCAGCACCTTAcctcaggcac [GEA] [3]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215258 4215264 -141.0 tacctcaggcACCTTCGggtgcctttt [GEA] [4]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215268 4215274 -131.0 accttcgggtGCCTTTTttatttccga [GEA] [4]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215277 4215283 -122.0 tgccttttttATTTCCGaaacgtacct [GEA] [4]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215295 4215301 -104.0 aacgtacctcAGCAGGTgaataaattt [GEA] [4]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215346 4215352 -53.0 atcaagtattTTTAATTaaaatggaaa [GEA] [5]
[4]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215357 4215372 -38.0 ttaattaaaaTGGAAATTGTTTTTGAttttgcattt [GEA] [5]
[4]
CRP-cyclic-AMP repressor aceBp aceB , aceA , aceK 4215361 4215382 -30.5 ttaaaatggaAATTGTTTTTGATTTTGCATTTtaaatgagta [GEA] [6]
IclR-pyruvate repressor aceBp aceB , aceA , aceK 4215373 4215379 -26.0 ttgtttttgaTTTTGCAttttaaatga [GEA] [5]
[4]
ArcA-phosphorylated repressor aceBp aceB , aceA , aceK

Evidence: [GEA] Gene expression analysis
Reference(s): [1] Ramseier TM., et al., 1993
[2] Son YJ., et al., 2011
[3] Resnik E., et al., 1996
[4] Yamamoto K., et al., 2003
[5] Pan B., et al., 1996
[6] Zhang Z., et al., 2005



Reference(s)    

 [1] Ramseier TM., Negre D., Cortay JC., Scarabel M., Cozzone AJ., Saier MH., 1993, In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium., J Mol Biol 234(1):28-44

 [2] Son YJ., Phue JN., Trinh LB., Lee SJ., Shiloach J., 2011, The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth., Microb Cell Fact 10:52

 [3] Resnik E., Pan B., Ramani N., Freundlich M., LaPorte DC., 1996, Integration host factor amplifies the induction of the aceBAK operon of Escherichia coli by relieving IclR repression., J Bacteriol 178(9):2715-7

 [4] Yamamoto K., Ishihama A., 2003, Two different modes of transcription repression of the Escherichia coli acetate operon by IclR., Mol Microbiol 47(1):183-94

 [5] Pan B., Unnikrishnan I., LaPorte DC., 1996, The binding site of the IclR repressor protein overlaps the promoter of aceBAK., J Bacteriol 178(13):3982-4

 [6] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [7] Iuchi S., Lin EC., 1988, arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways., Proc Natl Acad Sci U S A 85(6):1888-92

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