RegulonDB RegulonDB 11.1: Regulon Form
   
   


H-NS,IHF,Lrp,QseB 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, BolA, BtsR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CreB, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MalT, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsAB, RcsB, RcsB-BglJ, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, TorR, UvrY, YdeO, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Lrp Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Sensing external and internal signals
Synonym(s): AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA
Gene name(s): lrp
Functional conformation(s): Lrp , Lrp-L-leucine
Coregulator(s): AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, QseB, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
QseB Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional activator QseB, QseB response regulator, YgiX
Gene name(s): qseB
Functional conformation(s): QseB-Phosphorylated , QseB
Coregulator(s): AcrR, BasR, CRP, FliZ, Fur, H-NS, HdfR, IHF, LrhA, Lrp, MatA, Nac, NsrR, OmpR, PhoB, QseB, RcsAB, YjjQ
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, BolA, BtsR, 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, HipAB, 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, PlaR, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY H-NS,IHF,Lrp,QseB Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
H-NS activator IHF activator Lrp activator QseB activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF activator fimAp fimA , fimI , fimC , fimD , fimF , fimG , fimH 4542764 4542776 77.0 aaaaagcatcTAACTGTTTGATAtgtaaattat [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
[2]
[3]
[4]
Lrp activator fimAp fimA , fimI , fimC , fimD , fimF , fimG , fimH 4542859 4542873 173.0 gacgcatcttCCTCATTCTTCTCTCcaaaaaccac [EXP-IEP-RNA-SEQ] [5]
[6]
Lrp activator fimAp fimA , fimI , fimC , fimD , fimF , fimG , fimH 4542921 4542935 235.0 aagataacaaTAGAATATTAAGCCAacaaataaac [EXP-IEP-RNA-SEQ] [7]
[5]
[6]
Lrp activator fimAp fimA , fimI , fimC , fimD , fimF , fimG , fimH 4542890 4542904 204.0 ccacctcatgCAATATAAACATCTAtaaataaaga [EXP-IEP-MICROARRAY]
[EXP-IEP-RNA-SEQ] 		[8]
[7]
[5]
[6]
IHF activator fimAp fimA , fimI , fimC , fimD , fimF , fimG , fimH 4542636 4542648 -52.0 aggtttgattTAACTTATTGATAataaagttaa [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
[2]
[3]
[4]
H-NS activator fimAp fimA , fimI , fimC , fimD , fimF , fimG , fimH

Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence
[EXP-IEP-MICROARRAY] high throughput expression microarray evidence
Reference(s): [1] Blomfield IC., et al., 1997
[2] Dorman CJ., et al., 1987
[3] Dove SL., et al., 1996
[4] Kulasekara HD., et al., 1999
[5] Kroner GM., et al., 2019
[6] Roesch PL., et al., 1998
[7] Gally DL., et al., 1994
[8] Cho BK., et al., 2008



Reference(s)    

 [1] Blomfield IC., Kulasekara DH., Eisenstein BI., 1997, Integration host factor stimulates both FimB- and FimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in Escherichia coli., Mol Microbiol 23(4):705-17

 [2] Dorman CJ., Higgins CF., 1987, Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases., J Bacteriol 169(8):3840-3

 [3] Dove SL., Dorman CJ., 1996, Multicopy fimB gene expression in Escherichia coli: binding to inverted repeats in vivo, effect on fimA gene transcription and DNA inversion., Mol Microbiol 21(6):1161-73

 [4] Kulasekara HD., Blomfield IC., 1999, The molecular basis for the specificity of fimE in the phase variation of type 1 fimbriae of Escherichia coli K-12., Mol Microbiol 31(4):1171-81

 [5] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [6] Roesch PL., Blomfield IC., 1998, Leucine alters the interaction of the leucine-responsive regulatory protein (Lrp) with the fim switch to stimulate site-specific recombination in Escherichia coli., Mol Microbiol 27(4):751-61

 [7] Gally DL., Rucker TJ., Blomfield IC., 1994, The leucine-responsive regulatory protein binds to the fim switch to control phase variation of type 1 fimbrial expression in Escherichia coli K-12., J Bacteriol 176(18):5665-72

 [8] Cho BK., Barrett CL., Knight EM., Park YS., Palsson BO., 2008, Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli., Proc Natl Acad Sci U S A 105(49):19462-7

 [9] Schembri MA., Olsen PB., Klemm P., 1998, Orientation-dependent enhancement by H-NS of the activity of the type 1 fimbrial phase switch promoter in Escherichia coli., Mol Gen Genet 259(3):336-44

 [10] Gou Y., Liu W., Wang JJ., Tan L., Hong B., Guo L., Liu H., Pan Y., Zhao Y., 2019, CRISPR-Cas9 knockout of qseB induced asynchrony between motility and biofilm formation in Escherichia coli., Can J Microbiol 65(9):691-702

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