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:

FNR	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional dual regulator FNR, NirA, NirR, OssA, OxrA

Gene name(s):

fnr

Functional conformation(s):

FNR , FNR-[4Fe-4S]²⁺ reduced , FNR-[2Fe-2S]²⁺ oxidized

Coregulator(s):

AcrR, AdiY, ArcA, ArgP, ArgR, BtsR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlpR, H-NS, HdfR, HprR, HyfR, HypT, IHF, LeuO, Lrp, MalT, MarA, MetR, MlrA, ModE, Nac, NagC, NarL, NarP, NfeR, NikR, NorR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PhoP, PurR, PuuR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, TdcA, TdcR, TorR, YeiL, 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-cyclic-AMP , CRP

Coregulator(s):

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, 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:

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:

ArcA	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

External-Two-component systems

Synonym(s):

ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein

Gene name(s):

arcA

Functional conformation(s):

ArcA-phosphorylated , ArcA

Coregulator(s):

AdiY, AppY, ArcA, BetI, BtsR, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, 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:

SoxR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional dual regulator SoxR, MarC

Gene name(s):

soxR

Functional conformation(s):

SoxR , SoxR-[2Fe-2S]³⁺ oxydized , SoxR-[2Fe-2S]²⁺ reduced

Coregulator(s):

AcrR, ArcA, BasR, CRP, FNR, Fur, IHF, MarA, PhoP, Rob, SoxR, SoxS, TyrR

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:

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-Mn²⁺ , Fur-Fe²⁺ , Fur

Coregulator(s):

AcrR, AdiY, ArcA, ArgP, ArgR, AscG, 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 ArcA,CRP,FNR,Fur,IHF,MarA,Rob,SoxR,SoxS

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
ArcA repressor CRP activator FNR repressor Fur repressor IHF repressor MarA activator Rob activator SoxR activator SoxS activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
CRP-cyclic-AMP	activator	sodAp	sodA	4100649	4100671	-99.5	acggcattaaGTGGGTGATTTGCTTCACATCTCgggcattttc	[GEA]	[1] [2] [3]
MarA	activator	sodAp	sodA	4100709	4100728	-40.5	tacgaaaagtACGGCATTGATAATCATTTTcaatatcatt		[4] [5] [6]
SoxS	activator	sodAp	sodA	4100705	4100724	-44.0	cccttacgaaAAGTACGGCATTGATAATCAttttcaatat	[GEA] [RSE]	[7] [6] [8] [9]
ArcA-phosphorylated	repressor	sodAp	sodA	4100714	4100728	-38.0	aaagtacggcATTGATAATCATTTTcaatatcatt		[10]
ArcA-phosphorylated	repressor	sodAp	sodA	4100731	4100745	-21.0	atcattttcaATATCATTTAATTAActataatgaa		[10]
ArcA-phosphorylated	repressor	sodAp	sodA	4100742	4100756	-10.0	tatcatttaaTTAACTATAATGAACcaactgctta		[10]
IHF	repressor	sodAp	sodA	4100685	4100697	-68.0	cattttcctgCAAAACCATACCCttacgaaaag
IHF	repressor	sodAp	sodA	4100705	4100717	-48.0	cccttacgaaAAGTACGGCATTGataatcattt
IHF	repressor	sodAp	sodA	4100729	4100741	-24.0	taatcattttCAATATCATTTAAttaactataa
IHF	repressor	sodAp	sodA	4100752	4100764	-1.0	ttaactataaTGAACCAACTGCTtacgcggcat
Fur-Fe²⁺	repressor	sodAp	sodA	4100708	4100726	-42.0	ttacgaaaagTACGGCATTGATAATCATTttcaatatca	[GEA]	[11] [12]
Fur-Fe²⁺	repressor	sodAp	sodA	4100714	4100732	-36.0	aaagtacggcATTGATAATCATTTTCAATatcatttaat	[GEA]	[11] [12]
Fur-Fe²⁺	repressor	sodAp	sodA	4100720	4100738	-30.0	cggcattgatAATCATTTTCAATATCATTtaattaacta	[GEA]	[11] [12]
FNR	repressor	sodAp	sodA	4100715	4100728	-37.5	aagtacggcaTTGATAATCATTTTcaatatcatt	[GEA]	[13] [14] [12]
Fur-Fe²⁺	repressor	sodAp	sodA	4100717	4100735	-33.0	gtacggcattGATAATCATTTTCAATATCatttaattaa	[GEA]	[12] [15]
Rob	activator	sodAp	sodA	4100709	4100728	-40.5	tacgaaaagtACGGCATTGATAATCATTTTcaatatcatt		[16]
SoxR	activator	sodAp	sodA	4100758	4100775	9.0	ataatgaaccAACTGCTTACGCGGCATTaacaatcggc	[RSE]	[9]

Evidence:

[GEA] Gene expression analysis
[RSE] RNA-seq evidence

Reference(s):

[1] Tsai MJ., et al., 2018
[2] Via P., et al., 1996
[3] Zheng D., et al., 2004
[4] Jair KW., et al., 1995
[5] Martin RG., et al., 1999
[6] Martin RG., et al., 2011
[7] Jair KW., et al., 1996
[8] Pomposiello PJ., et al., 2001
[9] Seo SW., et al., 2015
[10] Tardat B., et al., 1993
[11] Chen Z., et al., 2007
[12] Kumar R., et al., 2011
[13] Hassan HM., et al., 1992
[14] Iuchi S., et al., 1994
[15] Niederhoffer EC., et al., 1990
[16] Ariza RR., et al., 1995

Reference(s)
[1] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951
[2] Via P., Badia J., Baldoma L., Obradors N., Aguilar J., 1996, Transcriptional regulation of the Escherichia coli rhaT gene., Microbiology 142 ( Pt 7):1833-40
[3] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93
[4] Jair KW., Martin RG., Rosner JL., Fujita N., Ishihama A., Wolf RE., 1995, Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters., J Bacteriol 177(24):7100-4
[5] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41
[6] Martin RG., Rosner JL., 2011, Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli., J Bacteriol 193(2):506-15
[7] Jair KW., Fawcett WP., Fujita N., Ishihama A., Wolf RE., 1996, Ambidextrous transcriptional activation by SoxS: requirement for the C-terminal domain of the RNA polymerase alpha subunit in a subset of Escherichia coli superoxide-inducible genes., Mol Microbiol 19(2):307-17
[8] Pomposiello PJ., Bennik MH., Demple B., 2001, Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate., J Bacteriol 183(13):3890-902
[9] 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
[10] Tardat B., Touati D., 1993, Iron and oxygen regulation of Escherichia coli MnSOD expression: competition between the global regulators Fur and ArcA for binding to DNA., Mol Microbiol 9(1):53-63
[11] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77
[12] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3
[13] Hassan HM., Sun HC., 1992, Regulatory roles of Fnr, Fur, and Arc in expression of manganese-containing superoxide dismutase in Escherichia coli., Proc Natl Acad Sci U S A 89(8):3217-21
[14] Iuchi S., Aristarkhov A., Dong JM., Taylor JS., Lin EC., 1994, Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase., J Bacteriol 176(6):1695-701
[15] Niederhoffer EC., Naranjo CM., Bradley KL., Fee JA., 1990, Control of Escherichia coli superoxide dismutase (sodA and sodB) genes by the ferric uptake regulation (fur) locus., J Bacteriol 172(4):1930-8
[16] Ariza RR., Li Z., Ringstad N., Demple B., 1995, Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein., J Bacteriol 177(7):1655-61