RegulonDB RegulonDB 10.7: Regulon Form
   
   


CpxR,EnvY,IHF,Lrp,OmpR,YjjQ 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:
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, 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:
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:
YjjQ Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional repressor YjjQ
Gene name(s): yjjQ
Functional conformation(s): YjjQ
Coregulator(s): AcrR, CRP, CpxR, EnvY, FliZ, Fur, H-NS, HdfR, IHF, LrhA, Lrp, MatA, OmpR, 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, 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

REGULATION EXERTED BY CpxR,EnvY,IHF,Lrp,OmpR,YjjQ Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CpxR activator EnvY activator IHF repressor Lrp repressor OmpR activator YjjQ repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CpxR-Phosphorylated activator ompCp1 ompC 2313174 2313188 -351.0 tgaaaagtgtGTAAAGAAGGGTAAAaaaaaccgaa [AIBSCS]
[BPP]
[GEA]
[1]
CpxR-Phosphorylated activator ompCp1 ompC 2312957 2312971 -134.0 atgttaggtgCTTATTTCGCCATTCcgcaataatc [AIBSCS]
[BPP]
[GEA]
[1]
CpxR-Phosphorylated activator ompCp1 ompC 2312920 2312931 -95.0 aagttcccttGCATTTACATTTtgaaacatct [AIBSCS]
[BPP]
[GEA]
[1]
OmpR-P activator ompCp1 ompC 2312909 2312928 -88.5 ttcccttgcaTTTACATTTTGAAACATCTAtagcgataaa [APIORCISFBSCS]
[BPP]
[GEA]
[SM]
[2]
[3]
[4]
[5]
[6]
OmpR-P activator ompCp1 ompC 2312888 2312907 -67.5 aaacatctatAGCGATAAATGAAACATCTTaaaagtttta [APIORCISFBSCS]
[BPP]
[GEA]
[SM]
[2]
[3]
[4]
[5]
[6]
OmpR-P activator ompCp1 ompC 2312868 2312887 -47.5 gaaacatcttAAAAGTTTTAGTATCATATTcgtgttggat [APIORCISFBSCS]
[BPP]
[GEA]
[SM]
[2]
[3]
[4]
[7]
[6]
Lrp repressor ompCp1 ompC 2313199 2313213 -376.0 gtttttctgtGGTAGCACAGAATAAtgaaaagtgt [BPP]
[GEA]
[8]
[9]
Lrp repressor ompCp1 ompC 2313163 2313177 -340.5 taaagaagggTAAAAAAAACCGAATgcgaggcatc [BPP]
[GEA]
[8]
[9]
Lrp repressor ompCp1 ompC 2313134 2313148 -311.5 ggcatccggtTGAAATAGGGGTAAAcagacattca [BPP]
[GEA]
[8]
[9]
Lrp repressor ompCp1 ompC 2313103 2313117 -280.5 ttcagaaatgAATGACGGTAATAAAtaaagttaat [BPP]
[GEA]
[8]
[9]
Lrp repressor ompCp1 ompC 2312822 2312836 2.0 tttggggagaATGGACTTGCCGACTgattaatgag [BPP]
[GEA]
[8]
[9]
Lrp-leucine repressor ompCp1 ompC 2312761 2312772 64.5 gcaaataaagGCATATAACAGAgggttaataa [BPP]
[GEA]
[8]
[9]
Lrp repressor ompCp1 ompC 2312738 2312752 86.0 gagggttaatAACATGAAAGTTAAAgtactgtccc [BPP]
[GEA]
[8]
[9]
Lrp repressor ompCp1 ompC 2312852 2312866 -29.5 tatcatattcGTGTTGGATTATTCTgcatttttgg [AIBSCS]
[BPP]
[GEA]
[8]
[9]
[10]
IHF repressor ompCp1 ompC 2313006 2313018 -182.0 tacttaagaaTAAGTTATTGATTttaaccttga [APIORCISFBSCS]
[BCE]
[BPP]
[GEA]
[11]
YjjQ repressor ompCp1 ompC 2312887 2312901 -64.0 ctatagcgatAAATGAAACATCTTAaaagttttag [AIBSCS]
[GEA]
[12]
EnvY activator ompCp1 ompC         [IMP] [13]
[14]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[SM] Site mutation
[BCE] Binding of cellular extracts
[IMP] Inferred from mutant phenotype
Reference(s): [1] Batchelor E., et al., 2005
[2] Coyer J., et al., 1990
[3] Mattison K., et al., 2002
[4] Oshima T., et al., 2002
[5] Tsung K., et al., 1989
[6] Yoshida T., et al., 2006
[7] Qin L., et al., 2001
[8] Ernsting BR., et al., 1992
[9] Ferrario M., et al., 1995
[10] Fraenkel YM., et al., 1995
[11] Huang L., et al., 1990
[12] Wiebe H., et al., 2015
[13] Lundrigan MD., et al., 1984
[14] Otsuka J., et al., 1996



Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] Fraenkel YM., Mandel Y., Friedberg D., Margalit H., 1995, Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon., Comput Appl Biosci 11(4):379-87

 [11] 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

 [12] Wiebe H., Gurlebeck D., Gross J., Dreck K., Pannen D., Ewers C., Wieler LH., Schnetz K., 2015, YjjQ Represses Transcription of flhDC and Additional Loci in Escherichia coli., J Bacteriol 197(16):2713-20

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

 [14] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol 178(2):183-204


RegulonDB