RegulonDB RegulonDB 10.8: Regulon Form
   
   


FNR,IHF,PhoB 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-[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:
PhoB Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator PhoB, PhoB response regulator, PhoT
Gene name(s): phoB
Functional conformation(s): PhoB , PhoB-Phosphorylated
Coregulator(s): ArgP, AscG, CRP, CpxR, CusR, EnvY, FNR, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HprR, IHF, Nac, NsrR, OmpR, PhoB, PrpR, QseB, RcdA, RstA, RutR
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 FNR,IHF,PhoB Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR activator IHF activator PhoB activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF activator pstSp phoU , pstB , pstA , pstC , pstS 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc [BPP]
[GEA]
[1]
[2]
[3]
PhoB-Phosphorylated activator pstSp phoU , pstB , pstA , pstC , pstS 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct [APIORCISFBSCS]
[BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[7]
PhoB-Phosphorylated activator pstSp phoU , pstB , pstA , pstC , pstS 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat [APIORCISFBSCS]
[BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[6]
FNR activator pstSp phoU , pstB , pstA , pstC , pstS         [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[8]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BCE] Binding of cellular extracts
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[SM] Site mutation
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Spira B., et al., 1999
[2] Taschner NP., et al., 2004
[3] Taschner NP., et al., 2006
[4] Kimura S., et al., 1989
[5] Makino K., et al., 1988
[6] Marzan LW., et al., 2013
[7] Otsuka J., et al., 1996
[8] Salmon K., et al., 2003



Reference(s)    

 [1] Spira B., Yagil E., 1999, The integration host factor (IHF) affects the expression of the phosphate-binding protein and of alkaline phosphatase in Escherichia coli., Curr Microbiol 38(2):80-5

 [2] Taschner NP., Yagil E., Spira B., 2004, A differential effect of sigmaS on the expression of the PHO regulon genes of Escherichia coli., Microbiology 150(Pt 9):2985-92

 [3] Taschner NP., Yagil E., Spira B., 2006, The effect of IHF on sigmaS selectivity of the phoA and pst promoters of Escherichia coli., Arch Microbiol 185(3):234-7

 [4] Kimura S., Makino K., Shinagawa H., Amemura M., Nakata A., 1989, Regulation of the phosphate regulon of Escherichia coli: characterization of the promoter of the pstS gene., Mol Gen Genet 215(3):374-80

 [5] Makino K., Shinagawa H., Amemura M., Kimura S., Nakata A., Ishihama A., 1988, Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro., J Mol Biol 203(1):85-95

 [6] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [7] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol 178(2):183-204

 [8] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55


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