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 , 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:

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:

NarL	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator NarL, FrdR, NarR, nitrate/nitrite response regulator NarL

Gene name(s):

narL

Functional conformation(s):

NarL , NarL-phosphorylated

Coregulator(s):

AppY, ArcA, CRP, Cra, DcuR, DpiA, EvgA, FNR, FhlA, Fis, FlhDC, Fur, H-NS, IHF, IscR, Lrp, ModE, NagC, NarL, NarP, NikR, NorR, NsrR, OxyR, PhoP, RcsB, RstA, SoxS, TorR, UvrY, YdeO

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-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 ArcA,CRP,FNR,Fur,NarL,SoxS

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
ArcA repressor CRP repressor FNR dual Fur activator NarL repressor SoxS repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
FNR	activator	ompWp	ompW	1313903	1313916	-81.5	aacttctaaaTTAATCCAGATCAAtaaagggtga	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2]
CRP-cyclic-AMP	repressor	ompWp	ompW	1313941	1313957	-42.5	tcatatgtaaTGTGATCTATGTAGGATcatttgttac	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
ArcA-phosphorylated	repressor	ompWp	ompW	1313983	1314001	1.5	tgtaggtataTTCGTCACGTTTTTATAACcataacgacg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
NarL-phosphorylated	repressor	ompWp	ompW	1313965	1313981	-18.5	gatcatttgtTACTCCAATGTAGGTATattcgtcacg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
FNR	repressor	ompWp	ompW	1313858	1313871	-126.5	tatttaaaaaTTGATTTAAATCACattaaccagg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Fur-Fe²⁺	activator	ompWp	ompW

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[1] Constantinidou C., et al., 2006 [2] Xiao M., et al., 2016

Reference(s)
[1] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15
[2] Xiao M., Lai Y., Sun J., Chen G., Yan A., 2016, Transcriptional Regulation of the Outer Membrane Porin Gene ompW Reveals its Physiological Role during the Transition from the Aerobic to the Anaerobic Lifestyle of Escherichia coli., Front Microbiol 7:799
[3] Zhang P., Ye Z., Ye C., Zou H., Gao Z., Pan J., 2019, OmpW is positively regulated by iron via Fur, and negatively regulated by SoxS contribution to oxidative stress resistance in Escherichia coli., Microb Pathog 138:103808