RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CRP,Fis,XylR 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, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, 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-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, 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, 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, RcsB, 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:
XylR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator XylR
Gene name(s): xylR
Functional conformation(s): XylR , XylR-xylose
Coregulator(s): AraC, CRP, Fis, XylR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,Fis,XylR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator Fis repressor XylR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator xylFp xylF , xylG , xylH , xylR 3730878 3730900 -180.5 gataattcacAAGTGTGCGCTCGCTCGCAAAATaaaatggaat [AIBSCS]
[GEA]
[HIBSCS]
[1]
[2]
[3]
XylR-xylose activator xylFp xylF , xylG , xylH , xylR 3730999 3731016 -61.5 tcaagaaataAACCAAAAATCGTAATCGaaagataaaa [BPP]
[GEA]
[HIBSCS]
[1]
[2]
XylR-xylose activator xylFp xylF , xylG , xylH , xylR 3731020 3731037 -40.5 gtaatcgaaaGATAAAAATCTGTAATTGttttcccctg [BPP]
[GEA]
[HIBSCS]
[1]
[2]
Fis repressor xylFp xylF , xylG , xylH , xylR 3731081 3731100 22.0 gtttatcgcgGTGATTGTTACTTATTAAAActgtcctcta [AIBSCS]
[GEA]
[4]
[5]
Fis repressor xylFp xylF , xylG , xylH , xylR 3730978 3730997 -82.0 aagtaagatcTCGGTCATAAATCAAGAAATaaaccaaaaa [AIBSCS]
[GEA]
[4]
Fis repressor xylFp xylF , xylG , xylH , xylR 3730985 3731004 -75.0 atctcggtcaTAAATCAAGAAATAAACCAAaaatcgtaat [AIBSCS]
[GEA]
[4]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
Reference(s): [1] Laikova ON., et al., 2001
[2] Song S., et al., 1997
[3] Tsai MJ., et al., 2018
[4] Bradley MD., et al., 2007
[5] Xu J., et al., 1995



Reference(s)    

 [1] Laikova ON., Mironov AA., Gelfand MS., 2001, Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria., FEMS Microbiol Lett 205(2):315-22

 [2] Song S., Park C., 1997, Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator., J Bacteriol 179(22):7025-32

 [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] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [5] Xu J., Johnson RC., 1995, Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli., J Bacteriol 177(4):938-47


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