RegulonDB RegulonDB 10.8: Regulon Form
   
   


CRP,NagC,NanR 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 , 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:
NagC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator NagC, NagR, transcriptional repressor of nag (N-acetylglucosamine) operon
Gene name(s): nagC
Functional conformation(s): NagC , NagC-N-acetyl-D-glucosamine 6-phosphate
Coregulator(s): AraC, BasR, CRP, ChbR, Cra, DksA, DksA-ppGpp, EvgA, FNR, Fur, GadX, GalR, GalS, H-NS, IHF, LexA, Mlc, NagC, NanR, NarL, NarP, PhoP, RcsB, UvrY, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
NanR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator NanR, YhcK
Gene name(s): nanR
Functional conformation(s): NanR-NANA , NanR
Coregulator(s): BasR, CRP, DksA, DksA-ppGpp, Fis, H-NS, IHF, NagC, NanR, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,NagC,NanR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator NagC repressor NanR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator nanCp nanS , nanM , nanC 4539979 4540000 -61.5 gatcgacataTTTTGTGACACGAATTGCAAATctggttttgt [AIBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
NagC repressor nanCp nanS , nanM , nanC 4540194 4540216 -277.0 aaccaggaaaCATATTTCATGATGAGAATTATGctcagcctga [AIBSCS]
[APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM]
[2]
[3]
[4]
NagC repressor nanCp nanS , nanM , nanC 4539982 4540004 -65.0 aaaagatcgaCATATTTTGTGACACGAATTGCAaatctggttt [AIBSCS]
[APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[1]
[3]
[4]
NanR repressor nanCp nanS , nanM , nanC 4539920 4539925 6.5 caggtataaaGGTGCAccaagatagt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/GS)]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/GS)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[CV(GEA/SM/GS)]
[GEA]
[GS]
[SM]
[1]
[5]
[6]
[7]
[3]
[4]
NanR repressor nanCp nanS , nanM , nanC 4539937 4539942 -11.5 tttttgatctGGTATAacaggtataa [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/GS)]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/GS)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[CV(GEA/SM/GS)]
[GEA]
[GS]
[SM]
[1]
[5]
[6]
[7]
[3]
[4]
NanR repressor nanCp nanS , nanM , nanC 4539928 4539933 -2.5 tggtataacaGGTATAaaggtgcacc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/GS)]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/GS)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[CV(GEA/SM/GS)]
[GEA]
[GS]
[SM]
[1]
[5]
[6]
[7]
[3]
[4]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[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.
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[SM] Site mutation
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[CV(CHIP-SV/GEA/GS)] cross validation(CHIP-SV/GEA/GS)
[CV(GEA/GS)] cross validation(GEA/GS)
[CV(GEA/SM/GS)] cross validation(GEA/SM/GS)
[GS] genomic SELEX
Reference(s): [1] Condemine G., et al., 2005
[2] Oberto J. 2010
[3] Sohanpal BK., et al., 2004
[4] Sohanpal BK., et al., 2007
[5] El-Labany S., et al., 2003
[6] Kalivoda KA., et al., 2013
[7] Shimada T., et al., 2018



Reference(s)    

 [1] Condemine G., Berrier C., Plumbridge J., Ghazi A., 2005, Function and expression of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli., J Bacteriol 187(6):1959-65

 [2] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

 [3] Sohanpal BK., El-Labany S., Lahooti M., Plumbridge JA., Blomfield IC., 2004, Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12., Proc Natl Acad Sci U S A 101(46):16322-7

 [4] Sohanpal BK., Friar S., Roobol J., Plumbridge JA., Blomfield IC., 2007, Multiple co-regulatory elements and IHF are necessary for the control of fimB expression in response to sialic acid and N-acetylglucosamine in Escherichia coli K-12., Mol Microbiol 63(4):1223-36

 [5] El-Labany S., Sohanpal BK., Lahooti M., Akerman R., Blomfield IC., 2003, Distant cis-active sequences and sialic acid control the expression of fimB in Escherichia coli K-12., Mol Microbiol 49(4):1109-18

 [6] Kalivoda KA., Steenbergen SM., Vimr ER., 2013, Control of the Escherichia coli sialoregulon by transcriptional repressor NanR., J Bacteriol 195(20):4689-701

 [7] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936


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