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:

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:

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-ethidium , AcrR , AcrR-Proflavin , AcrR-R6G

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:

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 AcrR,FNR,Fur,SoxR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
AcrR repressor FNR repressor Fur repressor SoxR repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
SoxR	repressor	soxRp	soxR	4277440	4277457	2.5	gagtataattCCTCAAGTTAACTTGAGGtaaagcgatt	[GEA] [RSE]	[1] [2] [3]
AcrR	repressor	soxRp	soxR	4277444	4277454	2.5	ataattcctcAAGTTAACTTGaggtaaagcg	[GEA]	[4]
Fur-Fe²⁺	repressor	soxRp	soxR

Evidence:	[GEA] Gene expression analysis [RSE] RNA-seq evidence
Reference(s):	[1] Hidalgo E., et al., 1995 [2] Hidalgo E., et al., 1998 [3] Seo SW., et al., 2015 [4] Lee JO., et al., 2014

Reference(s)
[1] Hidalgo E., Bollinger JM., Bradley TM., Walsh CT., Demple B., 1995, Binuclear [2Fe-2S] clusters in the Escherichia coli SoxR protein and role of the metal centers in transcription., J Biol Chem 270(36):20908-14
[2] Hidalgo E., Leautaud V., Demple B., 1998, The redox-regulated SoxR protein acts from a single DNA site as a repressor and an allosteric activator., EMBO J 17(9):2629-36
[3] 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
[4] Lee JO., Cho KS., Kim OB., 2014, Overproduction of AcrR increases organic solvent tolerance mediated by modulation of SoxS regulon in Escherichia coli., Appl Microbiol Biotechnol 98(20):8763-73
[5] 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