RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


BasR,DksA,DksA-ppGpp,H-NS,IHF,NagC,NanR,ppGpp regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
H-NS      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): BglY, Cur, DNA-binding protein HLP-II (HU, BH2, HD, NS), DNA-binding transcriptional dual regulator H-NS, Drc, DrdX, Drs, FimG, Hns, HnsA, Irk, MsyA, OsmZ, PilG, TopS, TopX, VirR
Gene name(s): hns
Functional conformation(s): H-NS
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, BasR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsB, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, TorR, UvrY, YdeO, YjjQ, 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 , NanR-NANA
Coregulator(s): BasR, CRP, DksA, DksA-ppGpp, Fis, H-NS, IHF, NagC, NanR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
BasR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): BasR response regulator, DNA-binding transcriptional dual regulator BasR, PmrA
Gene name(s): basR
Functional conformation(s): BasR-Phosphorylated
Coregulator(s): BasR, CRP, CpxR, Cra, CsgD, DksA, DksA-ppGpp, Fis, FliZ, H-NS, IHF, MarA, MlrA, MqsA, NagC, NanR, OmpR, PdhR, PhoP, PutA, QseB, RcdA, RcsB, RstA, SoxR, SoxS, ppGpp
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, 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, 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, RcsB, 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 BasR,DksA,DksA-ppGpp,H-NS,IHF,NagC,NanR,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
BasR activator DksA activation DksA-ppGpp activation H-NS repressor IHF activator NagC activator NanR activator ppGpp activation    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NagC activator fimBp2 fimB 4539982 4540004 -674.0 aaaccagattTGCAATTCGTGTCACAAAATATGtcgatctttt [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
NagC activator fimBp2 fimB 4540194 4540216 -462.0 tcaggctgagCATAATTCTCATCATGAAATATGtttcctggtt [AIBSCS]
[BPP]
[HIBSCS]
[SM]
[4]
[2]
[3]
NanR activator fimBp2 fimB 4539937 4539942 -727.5 ttatacctgtTATACCagatcaaaaa [BPP]
[GEA]
[GS]
[HIBSCS]
[SM]
[1]
[5]
[6]
[7]
[2]
[3]
NanR activator fimBp2 fimB 4539920 4539925 -744.5 actatcttggTGCACCtttatacctg [BPP]
[GEA]
[GS]
[HIBSCS]
[SM]
[1]
[5]
[6]
[7]
[2]
[3]
NanR activator fimBp2 fimB 4539928 4539933 -736.5 ggtgcaccttTATACCtgttatacca [BPP]
[GEA]
[GS]
[HIBSCS]
[SM]
[1]
[5]
[6]
[7]
[2]
[3]
IHF activator fimBp2 fimB 4540085 4540097 -576.0 agatcttagtTTAACTATTTGTTttataaataa [BPP]
[HIBSCS]
[SM]
[3]
BasR-Phosphorylated activator fimBp2 fimB 4540616 4540635 -41.5 ttgaacgaatATTAAATTTTGCTGAATTTTttatgttgat [BPP]
[HIBSCS]
[8]
H-NS repressor fimBp2 fimB         [BPP]
[GEA]
[9]
[10]
[11]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[GS] genomic SELEX
Reference(s): [1] Condemine G., et al., 2005
[2] Sohanpal BK., et al., 2004
[3] Sohanpal BK., et al., 2007
[4] Oberto J. 2010
[5] El-Labany S., et al., 2003
[6] Kalivoda KA., et al., 2013
[7] Shimada T., et al., 2018
[8] Ogasawara H., et al., 2012
[9] Donato GM., et al., 1999
[10] Donato GM., et al., 1997
[11] Olsen PB., et al., 1998



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] 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

 [3] 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

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

 [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

 [8] Ogasawara H., Shinohara S., Yamamoto K., Ishihama A., 2012, Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli., Microbiology 158(Pt 6):1482-92

 [9] Donato GM., Kawula TH., 1999, Phenotypic analysis of random hns mutations differentiate DNA-binding activity from properties of fimA promoter inversion modulation and bacterial motility., J Bacteriol 181(3):941-8

 [10] Donato GM., Lelivelt MJ., Kawula TH., 1997, Promoter-specific repression of fimB expression by the Escherichia coli nucleoid-associated protein H-NS., J Bacteriol 179(21):6618-25

 [11] Olsen PB., Schembri MA., Gally DL., Klemm P., 1998, Differential temperature modulation by H-NS of the fimB and fimE recombinase genes which control the orientation of the type 1 fimbrial phase switch., FEMS Microbiol Lett 162(1):17-23


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