RegulonDB RegulonDB 10.10: Regulon Form
   
   


CRP,GntR,IdnR 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-cyclic-AMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BolA, 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, FrlR, 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, PlaR, 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, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
GntR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional repressor GntR
Gene name(s): gntR
Functional conformation(s): GntR , GntR-D-gluconate
Coregulator(s): CRP, Cra, GntR, IdnR, KdgR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
IdnR      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator IdnR, GntH, YjgS
Gene name(s): idnR
Functional conformation(s): IdnR-5-dehydro-D-gluconate , IdnR-Idonate , IdnR
Coregulator(s): CRP, GntR, IdnR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,GntR,IdnR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator GntR repressor IdnR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cyclic-AMP activator gntKp gntU , gntK 3577703 3577724 -68.5 ttaagcccacAAATTTGAAGTAGCTCACACTTatacacttaa [GEA] [1]
IdnR-5-dehydro-D-gluconate repressor gntKp gntU , gntK 3577623 3577638 15.5 ttaccgataaCAGTTACCCGTAACATttttaattct [GEA] [2]
IdnR-5-dehydro-D-gluconate repressor gntKp gntU , gntK 3577636 3577651 2.5 cggctggacaATGTTACCGATAACAGttacccgtaa [GEA] [2]
GntR repressor gntKp gntU , gntK 3577621 3577640 15.5 tgttaccgatAACAGTTACCCGTAACATTTttaattcttg [GEA] [2]
GntR repressor gntKp gntU , gntK 3577634 3577653 2.5 tccggctggaCAATGTTACCGATAACAGTTacccgtaaca [GEA] [1]
[2]
CRP activator GntR repressor IdnR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cyclic-AMP activator idnKp idnK 4494466 4494488 -120.5 aactgtcattATTTGTGATGAAGATCACGTCAGaaaattgtta [GEA] [3]
[4]
[5]
CRP-cyclic-AMP activator idnKp idnK 4494516 4494537 -70.5 atgttacgcaTAACGTGATGTGCCTTGTAATTcttatcagta [GEA] [3]
[5]
GntR repressor idnKp idnK 4494504 4494523 -83.5 tgttacattaCTATGTTACGCATAACGTGAtgtgccttgt [GEA] [5]
GntR repressor idnKp idnK 4494484 4494503 -103.5 tgaagatcacGTCAGAAAATTGTTACATTActatgttacg [GEA] [5]
GntR repressor idnKp idnK 4494534 4494553 -53.5 tgtgccttgtAATTCTTATCAGTAGAAATAaaaaaacgtg [GEA] [5]
CRP-cyclic-AMP activator idnDp idnR , idnT , idnO , idnD 4494516 4494537 -91.5 tactgataagAATTACAAGGCACATCACGTTAtgcgtaacat [GEA] [3]
[5]
IdnR-5-dehydro-D-gluconate activator idnDp idnR , idnT , idnO , idnD 4494506 4494521 -78.5 aaggcacatcACGTTATGCGTAACATagtaatgtaa [GEA] [6]
[5]
CRP-cyclic-AMP activator idnDp idnR , idnT , idnO , idnD 4494466 4494488 -41.5 taacaattttCTGACGTGATCTTCATCACAAATaatgacagtt [GEA] [3]
[4]
[5]
GntR repressor idnDp idnR , idnT , idnO , idnD 4494534 4494553 -108.5 cacgttttttTATTTCTACTGATAAGAATTacaaggcaca [GEA] [5]
GntR repressor idnDp idnR , idnT , idnO , idnD 4494484 4494503 -58.5 cgtaacatagTAATGTAACAATTTTCTGACgtgatcttca [GEA] [5]
GntR repressor idnDp idnR , idnT , idnO , idnD 4494504 4494523 -78.5 acaaggcacaTCACGTTATGCGTAACATAGtaatgtaaca [GEA] [5]
IdnR activator idnKp idnK 4494506 4494521 -83.5 ttacattactATGTTACGCATAACGTgatgtgcctt [GEA] [6]
[5]

Evidence: [GEA] Gene expression analysis
Reference(s): [1] Izu H., et al., 1997
[2] Tsunedomi R., et al., 2003
[3] Bausch C., et al., 2004
[4] Tsai MJ., et al., 2018
[5] Tsunedomi R., et al., 2003
[6] Bausch C., et al., 1998



Reference(s)    

 [1] Izu H., Adachi O., Yamada M., 1997, Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli., J Mol Biol 267(4):778-93

 [2] Tsunedomi R., Izu H., Kawai T., Matsushita K., Ferenci T., Yamada M., 2003, The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli., J Bacteriol 185(6):1783-95

 [3] Bausch C., Ramsey M., Conway T., 2004, Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli., J Bacteriol 186(5):1388-97

 [4] 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

 [5] Tsunedomi R., Izu H., Kawai T., Yamada M., 2003, Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli., J Mol Microbiol Biotechnol 6(1):41-56

 [6] Bausch C., Peekhaus N., Utz C., Blais T., Murray E., Lowary T., Conway T., 1998, Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli., J Bacteriol 180(14):3704-10


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