RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


AcrR,H-NS,HU,IHF,Lrp,MarA,OmpR,Rob,SoxS regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
Rob Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): CbpB, DNA-binding transcriptional dual regulator Rob, RobA, right origin-binding protein
Gene name(s): rob
Functional conformation(s): Rob
Coregulator(s): AcrR, ArcA, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, Fur, GadE, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS
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, 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:
SoxS Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator SoxS, regulation of superoxide response regulon
Gene name(s): soxS
Functional conformation(s): SoxS
Coregulator(s): AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, Fur, H-NS, HU, IHF, Lrp, MarA, MarR, Mlc, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS, Zur
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-leucine
Coregulator(s): AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
MarA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): CfxB, DNA-binding transcriptional dual regulator MarA, InaR, NfxC, NorB, SoxQ
Gene name(s): marA
Functional conformation(s): MarA
Coregulator(s): AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, PurR, PutA, RcsB, Rob, SoxR, SoxS, TorR, YdeO
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
AcrR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional repressor AcrR, YbaH
Gene name(s): acrR
Functional conformation(s): AcrR-ethidium , AcrR , AcrR-Proflavin , AcrR-R6G
Coregulator(s): AcrR, CRP, CpxR, Cra, EnvR, FNR, Fis, FliZ, Fur, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, MarR, MatA, MprA, OmpR, PhoP, QseB, RcsB, Rob, SoxR, SoxS, 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, 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:
HU      Tractordb tool
Connectivity class Local Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator HU, HUalpha;beta;
Gene name(s): hupB, hupA
Functional conformation(s): HU
Coregulator(s): AcrR, CRP, GalR, GalS, H-NS, HU, IHF, Lrp, MarA, OmpR, Rob, SoxS, TrpR, TyrR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
OmpR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): Cry, DNA-binding transcriptional dual regulator OmpR, Kmt, OmpB, OmpR response regulator
Gene name(s): ompR
Functional conformation(s): OmpR , OmpR-P
Coregulator(s): AcrR, ArcA, BasR, CRP, CadC, CpxR, Cra, CsgD, EnvY, FNR, FadR, Fis, FliZ, Fur, GadE, GadX, H-NS, HU, HdfR, IHF, LeuO, LrhA, Lrp, MarA, MatA, MlrA, MprA, MqsA, NhaR, OmpR, PhoB, PhoP, QseB, RcdA, RcsB, Rob, RstA, SoxS, YjjQ, ppGpp

REGULATION EXERTED BY AcrR,H-NS,HU,IHF,Lrp,MarA,OmpR,Rob,SoxS Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AcrR repressor H-NS repressor HU activator IHF repressor Lrp repressor MarA activator OmpR activator Rob activator SoxS activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Rob activator micFp micF 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac [BPP]
[GEA]
[HIBSCS]
[1]
SoxS activator micFp micF 2313036 2313055 -38.5 gtatttgacaGCACTGAATGTCAAAACAAAaccttcactc [BCE]
[BPP]
[CEUMA]
[IHBCE]
[RE]
[2]
[3]
[4]
SoxS activator micFp micF 2312955 2312974 -119.5 aagattattgCGGAATGGCGAAATAAGCACctaacatcaa [BCE]
[BPP]
[CEUMA]
[IHBCE]
[RE]
[2]
[3]
[4]
IHF repressor micFp micF 2313006 2313018 -72.0 tcaaggttaaAATCAATAACTTAttcttaagta [BCE]
[BPP]
[GEA]
[HIBSCS]
[5]
Lrp repressor micFp micF 2313163 2313177 87.5 gatgcctcgcATTCGGTTTTTTTTAcccttcttta [BPP]
[GEA]
[2]
[6]
[7]
Lrp-leucine repressor micFp micF 2313199 2313210 122.0 acacttttcaTTATTCTGTGCTaccacagaaa [BPP]
[GEA]
[2]
[7]
Lrp repressor micFp micF 2313134 2313148 58.5 tgaatgtctgTTTACCCCTATTTCAaccggatgcc [BPP]
[GEA]
[2]
[6]
[7]
Lrp repressor micFp micF 2313103 2313117 27.5 attaactttaTTTATTACCGTCATTcatttctgaa [BPP]
[GEA]
[2]
[6]
[7]
AcrR repressor micFp micF 2313112 2313135 41.0 atttattaccGTCATTCATTTCTGAATGTCTGTTtacccctatt [AIBSCS] [8]
OmpR-P activator micFp micF 2312909 2312928 -165.5 tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa [BPP]
[GEA]
[HIBSCS]
[SM]
[9]
[10]
[11]
[12]
OmpR-P activator micFp micF 2312888 2312907 -186.5 taaaacttttAAGATGTTTCATTTATCGCTatagatgttt [BPP]
[GEA]
[HIBSCS]
[SM]
[9]
[10]
[11]
[12]
OmpR-P activator micFp micF 2312868 2312887 -206.5 atccaacacgAATATGATACTAAAACTTTTaagatgtttc [BPP]
[GEA]
[HIBSCS]
[SM]
[9]
[10]
[13]
[12]
HU activator micFp micF         [GEA] [14]
H-NS repressor micFp micF         [GEA] [15]
[2]
MarA activator micFp micF 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[2]
[16]
[1]
[8]

Evidence: [BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[BCE] Binding of cellular extracts
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
[AIBSCS] Automated inference based on similarity to consensus sequences
[SM] Site mutation
Reference(s): [1] Kwon HJ., et al., 2000
[2] Delihas N., et al., 2001
[3] Li Z., et al., 1994
[4] Seo SW., et al., 2015
[5] Huang L., et al., 1990
[6] Ernsting BR., et al., 1992
[7] Ferrario M., et al., 1995
[8] Rodionov DA., et al., 2001
[9] Coyer J., et al., 1990
[10] Mattison K., et al., 2002
[11] Tsung K., et al., 1989
[12] Yoshida T., et al., 2006
[13] Qin L., et al., 2001
[14] Painbeni E., et al., 1997
[15] Deighan P., et al., 2000
[16] Gillette WK., et al., 2000



Reference(s)    

 [1] Kwon HJ., Bennik MH., Demple B., Ellenberger T., 2000, Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA., Nat Struct Biol 7(5):424-30

 [2] Delihas N., Forst S., 2001, MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors., J Mol Biol 313(1):1-12

 [3] Li Z., Demple B., 1994, SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA., J Biol Chem 269(28):18371-7

 [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

 [5] Huang L., Tsui P., Freundlich M., 1990, Integration host factor is a negative effector of in vivo and in vitro expression of ompC in Escherichia coli., J Bacteriol 172(9):5293-8

 [6] Ernsting BR., Atkinson MR., Ninfa AJ., Matthews RG., 1992, Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli., J Bacteriol 174(4):1109-18

 [7] Ferrario M., Ernsting BR., Borst DW., Wiese DE., Blumenthal RM., Matthews RG., 1995, The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF., J Bacteriol 177(1):103-13

 [8] Rodionov DA., Gelfand MS., Mironov AA., Rakhmaninova AB., 2001, Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria., J Mol Microbiol Biotechnol 3(2):319-24

 [9] Coyer J., Andersen J., Forst SA., Inouye M., Delihas N., 1990, micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change., J Bacteriol 172(8):4143-50

 [10] Mattison K., Oropeza R., Byers N., Kenney LJ., 2002, A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC., J Mol Biol 315(4):497-511

 [11] Tsung K., Brissette RE., Inouye M., 1989, Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting., J Biol Chem 264(17):10104-9

 [12] Yoshida T., Qin L., Egger LA., Inouye M., 2006, Transcription regulation of ompF and ompC by a single transcription factor, OmpR., J Biol Chem 281(25):17114-23

 [13] Qin L., Yoshida T., Inouye M., 2001, The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli., Proc Natl Acad Sci U S A 98(3):908-13

 [14] Painbeni E., Caroff M., Rouviere-Yaniv J., 1997, Alterations of the outer membrane composition in Escherichia coli lacking the histone-like protein HU., Proc Natl Acad Sci U S A 94(13):6712-7

 [15] Deighan P., Free A., Dorman CJ., 2000, A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability., Mol Microbiol 38(1):126-39

 [16] Gillette WK., Martin RG., Rosner JL., 2000, Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation., J Mol Biol 299(5):1245-55


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