RegulonDB RegulonDB 10.7: Regulon Form
   
   


CRP,CpxR,EnvY,Fur,IHF,OmpR,PhoB,RstA regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
CpxR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): CpxR response regulator, DNA-binding transcriptional dual regulator CpxR, YiiA
Gene name(s): cpxR
Functional conformation(s): CpxR , CpxR-Phosphorylated
Coregulator(s): AcrR, BaeR, BasR, CRP, CpxR, Cra, CsgD, CysB, EnvY, Fis, FliZ, Fur, GadE, H-NS, IHF, Lrp, MarA, MarR, MlrA, MqsA, NsrR, OmpR, PdhR, PhoB, RcdA, RcsAB, RcsB, Rob, RstA, SoxS, TyrR, YjjQ, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
CRP Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): Cap, Csm, DNA-binding transcriptional dual regulator CRP, GurB
Gene name(s): crp
Functional conformation(s): CRP , CRP-cAMP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CRP-Sxy, CaiF, ChbR, ComR, CpxR, Cra, CreB, CsgD, CspA, CsqR, CusR, CytR, DcuR, DeoR, DgoR, DksA-ppGpp, DnaA, DpiA, DsdC, EbgR, EnvY, EvgA, ExuR, FNR, FadR, FeaR, FhlA, Fis, FlhDC, FliZ, FucR, Fur, GadE, GadE-RcsB, GadW, GadX, GalR, GalS, GatR, GcvA, GlaR, GlcC, GlpR, GlrR, GntR, GutM, H-NS, HU, HdfR, HipB, HprR, HyfR, HypT, IHF, IclR, IdnR, LacI, LeuO, LexA, LrhA, Lrp, LsrR, MalI, MalT, MarA, MarR, MatA, McbR, MelR, MetJ, MhpR, Mlc, MlrA, ModE, MprA, MqsA, MurR, Nac, NadR, NagC, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PhoB, PhoP, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsAB, RcsB, RcsB-BglJ, RhaR, RhaS, Rob, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YiaJ, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PhoB Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator PhoB, PhoB response regulator, PhoT
Gene name(s): phoB
Functional conformation(s): PhoB , PhoB-Phosphorylated
Coregulator(s): ArgP, AscG, CRP, CpxR, CusR, EnvY, FNR, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HprR, IHF, Nac, NsrR, OmpR, PhoB, PrpR, QseB, RcdA, RstA, RutR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
EnvY      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional activator EnvY, envelope protein; thermoregulation of porin biosynthesis
Gene name(s): envY
Functional conformation(s): EnvY
Coregulator(s): CRP, CpxR, EnvY, Fur, IHF, Lrp, OmpR, PhoB, RstA, YjjQ
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
RstA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional regulator RstA, RstA response regulator, UrpT
Gene name(s): rstA
Functional conformation(s): RstA , RstA-Phosphorylated
Coregulator(s): BasR, CRP, CpxR, Cra, CsgD, EnvY, FNR, Fis, FliZ, Fur, H-NS, IHF, MlrA, MqsA, NarL, OmpR, PhoB, RcdA, RcsAB, RstA, 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, 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:
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-P , OmpR
Coregulator(s): AcrR, ArcA, BasR, CRP, CadC, CpxR, Cra, CsgD, EnvY, FNR, FadR, Fis, FliZ, Fur, GadE-RcsB, GadX, H-NS, HU, HdfR, IHF, LeuO, LrhA, Lrp, MarA, MatA, MlrA, MprA, MqsA, NhaR, OmpR, PhoB, PhoP, QseB, RcdA, RcsAB, Rob, RstA, SoxS, YjjQ, ppGpp
TRANSCRIPTION FACTOR: Info
Name:
Fur Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator Fur
Gene name(s): fur
Functional conformation(s): Fur , Fur-Mn2+ , Fur-Fe2+
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CdaR, CpxR, Cra, CusR, EnvY, FNR, Fis, FliZ, Fur, GadE, GadX, H-NS, HdfR, HprR, HypT, IHF, IscR, LrhA, Lrp, MarA, MatA, MetR, MntR, ModE, MqsA, Nac, NagC, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsAB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,CpxR,EnvY,Fur,IHF,OmpR,PhoB,RstA Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator CpxR repressor EnvY activator Fur activator IHF dual OmpR dual PhoB activator RstA repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator ompFp ompF 987134 987155 -52.5 tttgaaaccaAATCTTTATCTTTGTAGCACTTtcacggtagc [AIBSCS]
[GEA]
[1]
CRP-cAMP activator ompFp ompF 987174 987195 -92.5 aagttccttaAATTTTACTTTTGGTTACATATtttttctttt [AIBSCS]
[GEA]
[1]
CRP-cAMP activator ompFp ompF 987203 987224 -121.5 gtctctatggAAATATGACGGTGTTCACAAAGttccttaaat [AIBSCS]
[GEA]
[1]
IHF activator ompFp ompF 987194 987206 -108.0 cggtgttcacAAAGTTCCTTAAAttttactttt [APIORCISFBSCS]
[BCE]
[2]
OmpR-P activator ompFp ompF 987173 987192 -90.5 ttccttaaatTTTACTTTTGGTTACATATTttttcttttt [APIORCISFBSCS]
[BPP]
[GEA]
[SM]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
OmpR-P activator ompFp ompF 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg [AIBSCS]
[BPP]
[GEA]
[SM]
[11]
[3]
[12]
[4]
[5]
[6]
[13]
[7]
[8]
[14]
[9]
[10]
OmpR-P repressor ompFp ompF 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt [APIORCISFBSCS]
[BCE]
[BPP]
[GEA]
[SM]
[11]
[3]
[4]
[5]
[15]
[6]
[2]
[7]
[8]
[9]
[10]
CpxR-Phosphorylated repressor ompFp ompF 987514 987530 -429.5 ttttctgtcaAGTTATCTGTTTGTTAAgtcaagcaat [AIBSCS]
[BPP]
[GEA]
[16]
[17]
CpxR-Phosphorylated repressor ompFp ompF 987458 987472 -373.0 cgatcatcctGTTACGGAATATTACattgcaacat [AIBSCS]
[BPP]
[GEA]
[16]
[17]
CpxR-Phosphorylated repressor ompFp ompF 987153 987169 -68.5 acatatttttTCTTTTTGAAACCAAATctttatcttt [AIBSCS]
[BPP]
[GEA]
[16]
[17]
CpxR-Phosphorylated repressor ompFp ompF 987178 987192 -93.0 ttccttaaatTTTACTTTTGGTTACatattttttc [AIBSCS]
[BPP]
[GEA]
[16]
[17]
IHF repressor ompFp ompF 987262 987274 -176.0 aatataaggaAATCATATAAATAgattaaaatt [APIORCISFBSCS]
[BCE]
[2]
IHF repressor ompFp ompF 987148 987160 -62.0 ttctttttgaAACCAAATCTTTAtctttgtagc [APIORCISFBSCS]
[BCE]
[2]
RstA-Phosphorylated repressor ompFp ompF 987176 987192 -92.0 ttccttaaatTTTACTTTTGGTTACATattttttctt [APIORCISFBSCS]
[NAS]
[18]
OmpR-P repressor ompFp ompF 987453 987472 -370.5 cgatcatcctGTTACGGAATATTACATTGCaacatttacg [BPP]
[GEA]
[12]
[15]
[13]
[14]
[10]
OmpR-P repressor ompFp ompF 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg [AIBSCS]
[BPP]
[GEA]
[SM]
[11]
[3]
[12]
[4]
[5]
[6]
[13]
[7]
[8]
[14]
[9]
[10]
PhoB-Phosphorylated activator ompFp ompF         [GEA] [19]
Fur-Fe2+ activator ompFp ompF         [GEA] [1]
OmpR-P activator ompFp ompF 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt [APIORCISFBSCS]
[BCE]
[BPP]
[GEA]
[SM]
[11]
[3]
[4]
[5]
[15]
[6]
[2]
[7]
[8]
[9]
[10]
EnvY activator ompFp ompF         [IMP] [20]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BCE] Binding of cellular extracts
[BPP] Binding of purified proteins
[SM] Site mutation
[NAS] Non-traceable author statement
[IMP] Inferred from mutant phenotype
Reference(s): [1] Zhang Z., et al., 2005
[2] Ramani N., et al., 1992
[3] Forst SA., et al., 1989
[4] Lan CY., et al., 1998
[5] Mattison K., et al., 2002
[6] Qin L., et al., 2001
[7] Rampersaud A., et al., 1989
[8] Sato M., et al., 2000
[9] Tsung K., et al., 1989
[10] Yoshida T., et al., 2006
[11] Forst S., et al., 1995
[12] Huang KJ., et al., 1994
[13] Rampersaud A., et al., 1994
[14] Slauch JM., et al., 1991
[15] Oshima T., et al., 2002
[16] Batchelor E., et al., 2005
[17] Raivio TL., et al., 2013
[18] Ogasawara H., et al., 2007
[19] Marzan LW., et al., 2013
[20] Lundrigan MD., et al., 1984



Reference(s)    

 [1] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [2] Ramani N., Huang L., Freundlich M., 1992, In vitro interactions of integration host factor with the ompF promoter-regulatory region of Escherichia coli., Mol Gen Genet 231(2):248-55

 [3] Forst SA., Delgado J., Inouye M., 1989, DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity., J Bacteriol 171(6):2949-55

 [4] Lan CY., Igo MM., 1998, Differential expression of the OmpF and OmpC porin proteins in Escherichia coli K-12 depends upon the level of active OmpR., J Bacteriol 180(1):171-4

 [5] 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

 [6] 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

 [7] Rampersaud A., Norioka S., Inouye M., 1989, Characterization of OmpR binding sequences in the upstream region of the ompF promoter essential for transcriptional activation., J Biol Chem 264(31):18693-700

 [8] Sato M., Machida K., Arikado E., Saito H., Kakegawa T., Kobayashi H., 2000, Expression of outer membrane proteins in Escherichia coli growing at acid pH., Appl Environ Microbiol 66(3):943-7

 [9] 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

 [10] 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

 [11] Forst S., Kalve I., Durski W., 1995, Molecular analysis of OmpR binding sequences involved in the regulation of ompF in Escherichia coli., FEMS Microbiol Lett 131(2):147-51

 [12] Huang KJ., Schieberl JL., Igo MM., 1994, A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene., J Bacteriol 176(5):1309-15

 [13] Rampersaud A., Harlocker SL., Inouye M., 1994, The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation., J Biol Chem 269(17):12559-66

 [14] Slauch JM., Silhavy TJ., 1991, cis-acting ompF mutations that result in OmpR-dependent constitutive expression., J Bacteriol 173(13):4039-48

 [15] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [16] Batchelor E., Walthers D., Kenney LJ., Goulian M., 2005, The Escherichia coli CpxA-CpxR envelope stress response system regulates expression of the porins ompF and ompC., J Bacteriol 187(16):5723-31

 [17] Raivio TL., Leblanc SK., Price NL., 2013, The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity., J Bacteriol 195(12):2755-67

 [18] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9

 [19] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [20] Lundrigan MD., Earhart CF., 1984, Gene envY of Escherichia coli K-12 affects thermoregulation of major porin expression., J Bacteriol 157(1):262-8


RegulonDB