RegulonDB

TRANSCRIPTION FACTOR:

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, BolA, BtsR, 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-cyclic-AMP

Coregulator(s):

AaeR, AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BolA, 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, FrlR, 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, PlaR, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsAB, RcsB, RcsB-BglJ, RhaR, RhaS, Rob, RspR, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, 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):

AlpA, 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, BolA, BtsR, 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, BolA, 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, PlaR, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, 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-phosphorylated , OmpR

Coregulator(s):

AcrR, ArcA, BasR, BolA, BtsR, 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, NagC, 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-Fe²⁺ , Fur , Fur-Mn²⁺

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, NarL, 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-cyclic-AMP	activator	ompFp	ompF	987134	987155	-52.5	tttgaaaccaAATCTTTATCTTTGTAGCACTTtcacggtagc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
CRP-cyclic-AMP	activator	ompFp	ompF	987174	987195	-92.5	aagttccttaAATTTTACTTTTGGTTACATATtttttctttt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
CRP-cyclic-AMP	activator	ompFp	ompF	987203	987224	-121.5	gtctctatggAAATATGACGGTGTTCACAAAGttccttaaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
IHF	activator	ompFp	ompF	987194	987206	-108.0	cggtgttcacAAAGTTCCTTAAAttttactttt
OmpR-phosphorylated	activator	ompFp	ompF	987173	987192	-90.5	ttccttaaatTTTACTTTTGGTTACATATTttttcttttt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2] [3] [4] [5] [6] [7] [8] [9]
OmpR-phosphorylated	activator	ompFp	ompF	987133	987152	-50.5	gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[10] [2] [11] [3] [4] [5] [12] [6] [7] [13] [8] [9]
OmpR-phosphorylated	activator	ompFp	ompF	987153	987172	-70.5	gttacatattTTTTCTTTTTGAAACCAAATctttatcttt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[10] [2] [3] [4] [14] [5] [15] [6] [7] [8] [9]
IHF	repressor	ompFp	ompF	987262	987274	-176.0	aatataaggaAATCATATAAATAgattaaaatt
IHF	repressor	ompFp	ompF	987148	987160	-62.0	ttctttttgaAACCAAATCTTTAtctttgtagc
RstA-phosphorylated	repressor	ompFp	ompF	987176	987192	-92.0	ttccttaaatTTTACTTTTGGTTACATattttttctt	[AS-NAS]	[16]
OmpR-phosphorylated	repressor	ompFp	ompF	987453	987472	-370.5	cgatcatcctGTTACGGAATATTACATTGCaacatttacg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[11] [14] [12] [13] [9]
OmpR-phosphorylated	repressor	ompFp	ompF	987133	987152	-50.5	gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[10] [2] [11] [3] [4] [5] [12] [6] [7] [13] [8] [9]
PhoB-phosphorylated	activator	ompFp	ompF

Evidence:

[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[AS-NAS] Non-traceable author statement

Reference(s):

[1] Zhang Z., et al., 2005
[2] Forst SA., et al., 1989
[3] Lan CY., et al., 1998
[4] Mattison K., et al., 2002
[5] Qin L., et al., 2001
[6] Rampersaud A., et al., 1989
[7] Sato M., et al., 2000
[8] Tsung K., et al., 1989
[9] Yoshida T., et al., 2006
[10] Forst S., et al., 1995
[11] Huang KJ., et al., 1994
[12] Rampersaud A., et al., 1994
[13] Slauch JM., et al., 1991
[14] Oshima T., et al., 2002
[15] Ramani N., et al., 1992
[16] Ogasawara H., et al., 2007

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] 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
[3] 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
[4] 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
[5] 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
[6] 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
[7] 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
[8] 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
[9] 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
[10] 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
[11] 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
[12] 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
[13] Slauch JM., Silhavy TJ., 1991, cis-acting ompF mutations that result in OmpR-dependent constitutive expression., J Bacteriol 173(13):4039-48
[14] 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
[15] 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
[16] 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
[17] 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
[18] Lundrigan MD., Earhart CF., 1984, Gene envY of Escherichia coli K-12 affects thermoregulation of major porin expression., J Bacteriol 157(1):262-8
[19] 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
[20] 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