RegulonDB

TRANSCRIPTION FACTOR:

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, FadR, Fis, Fur, GadE-RcsB, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS, 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, BolA, BtsR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CreB, 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, MalT, 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:

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, NarL, 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-L-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:

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, BluR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HU, IHF, LacI, 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-Proflavin , AcrR-R6G , AcrR-ethidium , AcrR

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, RcsAB, 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, 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:

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):

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-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

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	micFp1	micF	2313034	2313053	-40.0	aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
SoxS	activator	micFp1	micF	2313036	2313055	-38.5	gtatttgacaGCACTGAATGTCAAAACAAAaccttcactc	[EXP-IEP-RNA-SEQ]	[2] [3] [4]
SoxS	activator	micFp1	micF	2312955	2312974	-119.5	aagattattgCGGAATGGCGAAATAAGCACctaacatcaa	[EXP-IEP-RNA-SEQ]	[2] [3] [4]
IHF	repressor	micFp1	micF	2313006	2313018	-72.0	tcaaggttaaAATCAATAACTTAttcttaagta	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]
Lrp	repressor	micFp1	micF	2313163	2313177	87.5	gatgcctcgcATTCGGTTTTTTTTAcccttcttta	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2] [6] [7]
Lrp-L-leucine	repressor	micFp1	micF	2313199	2313210	122.0	acacttttcaTTATTCTGTGCTaccacagaaa	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2] [7]
Lrp	repressor	micFp1	micF	2313134	2313148	58.5	tgaatgtctgTTTACCCCTATTTCAaccggatgcc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2] [6] [7]
Lrp	repressor	micFp1	micF	2313103	2313117	27.5	attaactttaTTTATTACCGTCATTcatttctgaa	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2] [6] [7]
AcrR	repressor	micFp1	micF	2313112	2313135	41.0	atttattaccGTCATTCATTTCTGAATGTCTGTTtacccctatt		[8]
OmpR-phosphorylated	activator	micFp1	micF	2312909	2312928	-165.5	tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9] [10] [11] [12] [13] [14]
OmpR-phosphorylated	activator	micFp1	micF	2312888	2312907	-186.5	taaaacttttAAGATGTTTCATTTATCGCTatagatgttt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9] [11] [12] [13] [14]
OmpR-phosphorylated	activator	micFp1	micF	2312868	2312887	-206.5	atccaacacgAATATGATACTAAAACTTTTaagatgtttc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9] [11] [12] [15] [14]
HU	activator	micFp1	micF

Evidence:

[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

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] Gerken H., et al., 2020
[11] Mattison K., et al., 2002
[12] Miyake Y., et al., 2020
[13] Tsung K., et al., 1989
[14] Yoshida T., et al., 2006
[15] Qin L., et al., 2001

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] Gerken H., Vuong P., Soparkar K., Misra R., 2020, Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli., mBio 11(3)
[11] 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
[12] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661
[13] 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
[14] 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
[15] 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
[16] 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
[17] 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
[18] 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