RegulonDB

TRANSCRIPTION FACTOR:

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:

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,MarA,SoxR,SoxS

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
ArcA repressor CRP activator CRP unknown FNR repressor Fur repressor MarA activator SoxR activator SoxS activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
MarA	activator	fumCp2	fumC	1686746	1686765	-46.5	ttccagcagaTACAACTCACACAATGCACCcgctgtgtga	[GEA]	[1] [2]
SoxS	activator	fumCp2	fumC	1686681	1686700	19.5	ggtttttttaCATGGCACGAAAGACCAAACatttgttatc	[GEA] [RSE]	[3] [4] [2] [5]
CRP-cyclic-AMP	activator	fumCp2	fumC	1686752	1686774	-53.5	aatgacttctTCCAGCAGATACAACTCACACAAtgcacccgct	[GEA]	[6]
CRP-cyclic-AMP	unknown	fumCp2	fumC	1687183	1687205	-484.5	cgattatcgtCGGTCGTGATATTGCTCACGCCAaactgaaaga	[GEA]	[6]
Fur-Fe²⁺	repressor	fumCp2	fumC

Evidence:	[GEA] Gene expression analysis [RSE] RNA-seq evidence
Reference(s):	[1] Gillette WK., et al., 2000 [2] Pomposiello PJ., et al., 2001 [3] Benov L., et al., 2002 [4] Jair KW., et al., 1995 [5] Seo SW., et al., 2015 [6] Chen YP., et al., 2012

Reference(s)
[1] 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
[2] 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
[3] Benov L., Fridovich I., 2002, Induction of the soxRS regulon of Escherichia coli by glycolaldehyde., Arch Biochem Biophys 407(1):45-8
[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] 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
[6] Chen YP., Lin HH., Yang CD., Huang SH., Tseng CP., 2012, Regulatory role of cAMP receptor protein over Escherichia coli fumarase genes., J Microbiol 50(3):426-33
[7] 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
[8] Fuentes AM., Diaz-Mejia JJ., Maldonado-Rodriguez R., Amabile-Cuevas CF., 2001, Differential activities of the SoxR protein of Escherichia coli: SoxS is not required for gene activation under iron deprivation., FEMS Microbiol Lett 201(2):271-5