RegulonDB RegulonDB 10.8: Regulon Form
   
   


CRP,NagC 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]

REGULATION EXERTED BY CRP,NagC Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP dual NagC repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator nagBp umpH , nagC , nagA , nagB 703802 703823 -104.5 gagtgtgtgaAAATTTAATTCGTATCGCAAATtaaacgcgtg [APIORCISFBSCS]
[BPP]
[1]
CRP-cAMP activator nagBp umpH , nagC , nagA , nagB 703768 703789 -70.5 aacgcgtgtcTTTTGTGAGTTTTGTCACCAAAtatcgttatt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[1]
[3]
[4]
[5]
NagC repressor nagBp umpH , nagC , nagA , nagB 703798 703820 -101.0 tgtgtgaaaaTTTAATTCGTATCGCAAATTAAAcgcgtgtctt [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[6]
[2]
[1]
[3]
[4]
NagC repressor nagBp umpH , nagC , nagA , nagB 703704 703726 -7.0 aaccagaaaaCTTATTTTATCATTCAAAAAATCaggtcggatt [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[6]
[2]
[1]
[3]
[4]
CRP-cAMP activator nagEp nagE 703802 703823 -27.5 cacgcgtttaATTTGCGATACGAATTAAATTTtcacacactc [APIORCISFBSCS]
[BPP]
[1]
CRP-cAMP activator nagEp nagE 703768 703789 -61.5 aataacgataTTTGGTGACAAAACTCACAAAAgacacgcgtt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[1]
[3]
[4]
[5]
NagC repressor nagEp nagE 703704 703726 -125.0 aatccgacctGATTTTTTGAATGATAAAATAAGttttctggtt [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[6]
[2]
[1]
[3]
[4]
NagC repressor nagEp nagE 703798 703820 -31.0 aagacacgcgTTTAATTTGCGATACGAATTAAAttttcacaca [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[6]
[2]
[1]
[3]
[4]
CRP-cAMP repressor nagEp nagE 703802 703823 -27.5 cacgcgtttaATTTGCGATACGAATTAAATTTtcacacactc [APIORCISFBSCS]
[BPP]
[1]
CRP-cAMP repressor nagBp umpH , nagC , nagA , nagB 703802 703823 -104.5 gagtgtgtgaAAATTTAATTCGTATCGCAAATtaaacgcgtg [APIORCISFBSCS]
[BPP]
[1]
CRP-cAMP repressor nagEp nagE 703768 703789 -61.5 aataacgataTTTGGTGACAAAACTCACAAAAgacacgcgtt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[1]
[3]
[4]
[5]
CRP-cAMP repressor nagBp umpH , nagC , nagA , nagB 703768 703789 -70.5 aacgcgtgtcTTTTGTGAGTTTTGTCACCAAAtatcgttatt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[1]
[3]
[4]
[5]
CRP activator NagC repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator ptsHp5 ptsH , ptsI , crr 2533427 2533448 -60.5 ttaggtgcttTTTTGTGGCCTGCTTCAAACTTtcgcccctcc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[7]
NagC repressor chiPp chiP , chiQ 708203 708225 -22.0 gaaagagattGATAATTCGCGTCGCGAAAAATAgtctgttcct [AIBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[8]
[9]
NagC repressor ptsHp5 ptsH , ptsI , crr 2533502 2533524 16.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg [AIBSCS] [8]
NagC repressor chiPp chiP , chiQ 707980 708004 -244.0 cggcgtttttTCTGCTTTTCTTCGCGAATTAATTCcgcttcgcaa [BPP]
[GEA]
[9]
CRP-cAMP activator chiPp chiP , chiQ 708158 708174 -70.5 catcaaaataTGTGCGGTTGCTCATGTtcttacattc [APIORCISFBSCS] [9]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BPP] Binding of purified proteins
[BCE] Binding of cellular extracts
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[SM] Site mutation
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Plumbridge J., et al., 1991
[2] Plumbridge J. 2001
[3] Plumbridge J., et al., 1993
[4] Plumbridge J., et al., 1998
[5] Rogers MJ., et al., 1988
[6] Fernandez M., et al., 2019
[7] Tanaka Y., et al., 1999
[8] Oberto J. 2010
[9] Plumbridge J., et al., 2014



Reference(s)    

 [1] Plumbridge J., Kolb A., 1991, CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli., J Mol Biol 217(4):661-79

 [2] Plumbridge J., 2001, DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli., Nucleic Acids Res 29(2):506-14

 [3] Plumbridge J., Kolb A., 1993, DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo., Mol Microbiol 10(5):973-81

 [4] Plumbridge J., Kolb A., 1998, DNA bending and expression of the divergent nagE-B operons., Nucleic Acids Res 26(5):1254-60

 [5] Rogers MJ., Ohgi T., Plumbridge J., Soll D., 1988, Nucleotide sequences of the Escherichia coli nagE and nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and for glucosamine-6-phosphate deaminase., Gene 62(2):197-207

 [6] Fernandez M., Plumbridge J., 2019, Complex synergistic amino acid-nucleotide interactions contribute to the specificity of NagC operator recognition and induction., Microbiology 165(7):792-803

 [7] Tanaka Y., Kimata K., Inada T., Tagami H., Aiba H., 1999, Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli., Genes Cells 4(7):391-9

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

 [9] Plumbridge J., Bossi L., Oberto J., Wade JT., Figueroa-Bossi N., 2014, Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella., Mol Microbiol 92(4):648-58


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