RegulonDB RegulonDB 10.8: Regulon Form
   
   


CRP,DksA-ppGpp,Fis,IHF,ppGpp regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
Fis Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator Fis, Nbp, site-specific DNA inversion stimulation factor
Gene name(s): fis
Functional conformation(s): Fis
Coregulator(s): AcrR, AdiY, AppY, ArcA, ArgP, BasR, CRP, CpxR, Cra, CreB, CspA, CusR, CytR, DeoR, DksA, DksA-ppGpp, DnaA, FNR, FadR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, MazE-MazF, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, RcsB-BglJ, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, 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:
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, 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, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YiaJ, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,DksA-ppGpp,Fis,IHF,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP dual DksA-ppGpp inhibition Fis repressor IHF activator ppGpp inhibition    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator dusBp dusB , fis 3410068 3410089 -167.5 cataaagaaaAATTGAGAACTTACTCAAATTTctttgagtgt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
CRP-cAMP activator dusBp dusB , fis 3409983 3410004 -252.5 acgcggggcgAAGTGCGAGCAAGCTCACAAAAggcacgtaaa [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
IHF activator dusBp dusB , fis 3410126 3410138 -114.0 tttctaatatGATGATTTTTATGagtaattatc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[2]
[3]
CRP-cAMP activator dusBp dusB , fis 3410172 3410193 -63.0 tttaaatgcaATTCTTTGATCCATCTCAGAGGattggtcaaa [BPP]
[GEA]
[4]
Fis repressor dusBp dusB , fis 3410018 3410032 -221.0 acgtaaatttGCCGATTATTTACGCaaatttgcgt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[5]
[6]
[3]
Fis repressor dusBp dusB , fis 3410096 3410110 -143.0 atttctttgaGTGTAAATTTTAGTCactattttct [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[5]
[6]
[3]
Fis repressor dusBp dusB , fis 3410138 3410152 -101.0 tgatttttatGAGTAATTATCGCACcacgctcatt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[5]
[6]
[3]
Fis repressor dusBp dusB , fis 3410264 3410278 26.0 gtcacagtatGGTCATTTCTTAACTcatgcgcatc [APIORCISFBSCS]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[3]
Fis repressor dusBp dusB , fis 3410156 3410170 -83.0 atcgcaccacGCTCATTTTAAATGCaattctttga [APIORCISFBSCS]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[3]
Fis repressor dusBp dusB , fis 3410197 3410211 -42.0 tcagaggattGGTCAAAGTTTGGCCtttcatctcg [APIORCISFBSCS]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[7]
[3]
CRP-cAMP repressor dusBp dusB , fis 3410172 3410193 -63.0 tttaaatgcaATTCTTTGATCCATCTCAGAGGattggtcaaa [BPP]
[GEA]
[4]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BPP] Binding of purified proteins
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[SM] Site mutation
Reference(s): [1] Zheng D., et al., 2004
[2] Nasser W., et al., 2002
[3] Pratt TS., et al., 1997
[4] Nasser W., et al., 2001
[5] Ball CA., et al., 1992
[6] Hengen PN., et al., 1997
[7] Ninnemann O., et al., 1992



Reference(s)    

 [1] 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

 [2] Nasser W., Rochman M., Muskhelishvili G., 2002, Transcriptional regulation of fis operon involves a module of multiple coupled promoters., EMBO J 21(4):715-24

 [3] Pratt TS., Steiner T., Feldman LS., Walker KA., Osuna R., 1997, Deletion analysis of the fis promoter region in Escherichia coli: antagonistic effects of integration host factor and Fis., J Bacteriol 179(20):6367-77

 [4] Nasser W., Schneider R., Travers A., Muskhelishvili G., 2001, CRP modulates fis transcription by alternate formation of activating and repressing nucleoprotein complexes., J Biol Chem 276(21):17878-86

 [5] Ball CA., Osuna R., Ferguson KC., Johnson RC., 1992, Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli., J Bacteriol 174(24):8043-56

 [6] Hengen PN., Bartram SL., Stewart LE., Schneider TD., 1997, Information analysis of Fis binding sites., Nucleic Acids Res 25(24):4994-5002

 [7] Ninnemann O., Koch C., Kahmann R., 1992, The E.coli fis promoter is subject to stringent control and autoregulation., EMBO J 11(3):1075-83


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