RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CsgD,FlhDC,H-NS,IHF,MatA,NsrR,SutR 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:
CsgD Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator CsgD
Gene name(s): csgD
Functional conformation(s): CsgD
Coregulator(s): BasR, CRP, CpxR, Cra, CsgD, DksA-ppGpp, FlhDC, FliZ, H-NS, IHF, MatA, MlrA, MqsA, NsrR, OmpR, RcdA, RcsB, RstA, SutR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
NsrR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional repressor NsrR, YjeB
Gene name(s): nsrR
Functional conformation(s): NsrR-nitric oxide , NsrR-[2Fe-2S]2+ oxidized , NsrR
Coregulator(s): ArcA, CRP, CpxR, CsgD, CytR, DksA, DksA-ppGpp, DsdC, FNR, FeaR, FhlA, Fis, FlhDC, Fur, GadE, H-NS, IHF, IscR, Lrp, MatA, MetR, ModE, Nac, NarL, NarP, NorR, NsrR, OxyR, PdhR, PhoB, QseB, SutR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
MatA      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator MatA, EcpR, YkgK
Gene name(s): ecpR
Functional conformation(s): MatA
Coregulator(s): AcrR, CRP, CsgD, FlhDC, FliZ, Fur, GadE, H-NS, HdfR, IHF, LrhA, MatA, NsrR, OmpR, QseB, RcsB, SutR, YjjQ
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
SutR      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator SutR, YdcN
Gene name(s): sutR
Functional conformation(s): SutR
Coregulator(s): CsgD, FlhDC, H-NS, IHF, MatA, NsrR, SutR
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]
TRANSCRIPTION FACTOR: Info
Name:
FlhDC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): FlhDC DNA-binding transcriptional dual regulator
Gene name(s): flhC, flhD
Functional conformation(s): FlhDC
Coregulator(s): ArcA, CRP, CsgD, DpiA, FNR, FhlA, Fis, FlhDC, GalR, GalS, GlpR, H-NS, IHF, MatA, ModE, NarL, NarP, NsrR, SutR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CsgD,FlhDC,H-NS,IHF,MatA,NsrR,SutR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CsgD repressor FlhDC activator H-NS activator IHF repressor MatA repressor NsrR repressor SutR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
FlhDC activator fliAp1 tcyJ , fliZ , fliA 2001878 2001894 -67.0 gaatttacctGTAACCCCCAAATAACCcctcatttca [BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
[4]
[5]
FlhDC activator fliAp1 tcyJ , fliZ , fliA 2001849 2001865 -38.0 tcatttcaccCACTAATCGTCCGATTAaaaaccctgc [BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
[4]
[6]
[5]
CsgD repressor fliAp1 tcyJ , fliZ , fliA 2001823 2001837 -10.5 aaaccctgcaGAAACGGATAATCATgccgataact [AIBSCS]
[BPP]
[7]
H-NS activator fliAp1 tcyJ , fliZ , fliA         [GEA]
[IMP]
[8]
MatA repressor fliAp1 tcyJ , fliZ , fliA         [BPP] [9]
SutR repressor fliAp1 tcyJ , fliZ , fliA         [AIBSCS]
[BPP]
[GEA]
[10]
NsrR repressor fliAp1 tcyJ , fliZ , fliA 2002021 2002032 -207.0 cctacaagttGAATTGCAATTTattgaatttg [GEA]
[HIBSCS]
[11]
IHF repressor fliAp1 tcyJ , fliZ , fliA 2002014 2002030 -202.5 tacaagttgaATTGCAATTTATTGAATttgcacattt [GEA]
[IHBCE]
[SM]
[12]
NsrR repressor fliAp1 tcyJ , fliZ , fliA 2001808 2001819 7.0 taatcatgccGATAACTCATATaacgcagggc [GEA]
[HIBSCS]
[SM]
[11]
IHF repressor fliAp1 tcyJ , fliZ , fliA 2001998 2002014 -186.5 atttattgaaTTTGCACATTTTTGTAGgccggataag [GEA]
[IHBCE]
[SM]
[12]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[AIBSCS] Automated inference based on similarity to consensus sequences
[IMP] Inferred from mutant phenotype
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Brandi A., et al., 2016
[2] Ikebe T., et al., 1999
[3] Lee YY., et al., 2011
[4] Liu X., et al., 1994
[5] Stafford GP., et al., 2005
[6] Liu X., et al., 1996
[7] Dudin O., et al., 2014
[8] Bertin P., et al., 1994
[9] Lehti TA., et al., 2012
[10] Yamamoto K., et al., 2015
[11] Partridge JD., et al., 2009
[12] Amores GR., et al., 2017



Reference(s)    

 [1] Brandi A., Giangrossi M., Giuliodori AM., Falconi M., 2016, An Interplay among FIS, H-NS, and Guanosine Tetraphosphate Modulates Transcription of the Escherichia coli cspA Gene under Physiological Growth Conditions., Front Mol Biosci 3:19

 [2] Ikebe T., Iyoda S., Kutsukake K., 1999, Promoter analysis of the class 2 flagellar operons of Salmonella., Genes Genet Syst 74(4):179-83

 [3] Lee YY., Barker CS., Matsumura P., Belas R., 2011, Refining the Binding of the Escherichia coli Flagellar Master Regulator, FlhD4C2, on a Base-Specific Level., J Bacteriol 193(16):4057-68

 [4] Liu X., Matsumura P., 1994, The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons., J Bacteriol 176(23):7345-51

 [5] Stafford GP., Ogi T., Hughes C., 2005, Binding and transcriptional activation of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2., Microbiology 151(Pt 6):1779-88

 [6] Liu X., Matsumura P., 1996, Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli., Mol Microbiol 21(3):613-20

 [7] Dudin O., Geiselmann J., Ogasawara H., Ishihama A., Lacour S., 2014, Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation., J Bacteriol 196(3):707-15

 [8] Bertin P., Terao E., Lee EH., Lejeune P., Colson C., Danchin A., Collatz E., 1994, The H-NS protein is involved in the biogenesis of flagella in Escherichia coli., J Bacteriol 176(17):5537-40

 [9] Lehti TA., Bauchart P., Dobrindt U., Korhonen TK., Westerlund-Wikstrom B., 2012, The fimbriae activator MatA switches off motility in Escherichia coli by repression of the flagellar master operon flhDC., Microbiology 158(Pt 6):1444-55

 [10] Yamamoto K., Nakano M., Ishihama A., 2015, Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli., Microbiology 161(Pt 1):99-111

 [11] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [12] Amores GR., de Las Heras A., Sanches-Medeiros A., Elfick A., Silva-Rocha R., 2017, Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli., Sci Rep 7(1):16768


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