RegulonDB RegulonDB 10.8: Regulon Form
   
   


Fis,H-NS,IHF,MntR,OxyR regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
Fis Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator Fis, Nbp, site-specific DNA inversion stimulation factor
Gene name(s): fis
Functional conformation(s): Fis
Coregulator(s): AcrR, AdiY, AppY, ArcA, ArgP, BasR, CRP, CpxR, Cra, CreB, CspA, CusR, CytR, DeoR, DksA, DksA-ppGpp, DnaA, FNR, FadR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, MazE-MazF, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, RcsB-BglJ, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, ppGpp
Summary: TF Summary ...[more]
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, BtsR, CRP, CadC, CaiF, CdaR, CpxR, Cra, 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, 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:
OxyR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator OxyR, MomR, Mor, bifunctional regulatory protein sensor for oxidative stress
Gene name(s): oxyR
Functional conformation(s): OxyR
Coregulator(s): CRP, ExuR, FNR, Fis, Fur, H-NS, IHF, IscR, MarA, MetJ, MetR, MntR, NarL, NarP, NsrR, OxyR, Rob, SoxS, UxuR, Zur
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, 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, PspF, PurR, QseB, RcdA, RcsAB, 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:
MntR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): MntR-Mn2+ DNA-binding transcriptional dual regulator
Gene name(s): mntR
Functional conformation(s): MntR-Mn2+ , MntR-Cd2+ , MntR
Coregulator(s): Fis, Fur, H-NS, IHF, MntR, OxyR
Summary: TF Summary ...[more]

REGULATION EXERTED BY Fis,H-NS,IHF,MntR,OxyR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
Fis repressor H-NS repressor IHF activator MntR repressor OxyR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF activator dpsp dps 849042 849054 -98.5 tatatctaacTCATTGAATCTTTattagttttg [APIORCISFBSCS] [1]
OxyR activator dpsp dps 848986 849002 -44.0 ctattagtgtGATAGGAACAGCCAGAAtagcggaaca [APIORCISFBSCS] [1]
H-NS repressor dpsp dps 848943 848953 3.5 tatacttaatCTCGTTAATTActgggacata [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
OxyR activator dpsp dps 849008 849024 -66.0 ttgtttttcaCGCTTGTTACCACTATTagtgtgatag [APIORCISFBSCS] [1]
MntR repressor dpsp dps 848957 848978 -17.5 gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
Fis repressor dpsp dps 848969 848983 -26.0 agccagaataGCGGAACACATAGCCggtgctatac [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[3]
Fis repressor dpsp dps 848953 848967 -10.0 cacatagccgGTGCTATACTTAATCtcgttaatta [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[3]
OxyR activator dpsp dps 848959 848975 -17.0 tagcggaacaCATAGCCGGTGCTATACttaatctcgt [CEUMA]
[IHBCE]
[RE]
[4]

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
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
Reference(s): [1] Altuvia S., et al., 1994
[2] Grainger DC., et al., 2008
[3] Yamamoto K., et al., 2011
[4] Seo SW., et al., 2015



Reference(s)    

 [1] Altuvia S., Almiron M., Huisman G., Kolter R., Storz G., 1994, The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase., Mol Microbiol 13(2):265-72

 [2] Grainger DC., Goldberg MD., Lee DJ., Busby SJ., 2008, Selective repression by Fis and H-NS at the Escherichia coli dps promoter., Mol Microbiol 68(6):1366-77

 [3] Yamamoto K., Ishihama A., Busby SJ., Grainger DC., 2011, The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein., J Bacteriol 193(6):1477-80

 [4] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99


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