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:

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:

PhoB	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator PhoB, PhoB response regulator, PhoT

Gene name(s):

phoB

Functional conformation(s):

PhoB , PhoB-phosphorylated

Coregulator(s):

AlpA, ArgP, AscG, CRP, CpxR, CusR, EnvY, FNR, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HprR, IHF, Nac, NsrR, OmpR, PhoB, PrpR, QseB, RcdA, RstA, RutR

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

GadX	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator GadX, YhiX

Gene name(s):

gadX

Functional conformation(s):

GadX

Coregulator(s):

AdiY, AraC, ArcA, CRP, CadC, CspA, EvgA, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, Lrp, MarA, MqsA, NagC, NtrC, OmpR, PhoB, PhoP, RcsB, RutR, SdiA, TorR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

GadW	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator GadW, YhiW

Gene name(s):

gadW

Functional conformation(s):

GadW

Coregulator(s):

AdiY, ArcA, CRP, EvgA, FNR, Fis, FliZ, GadE, GadE-RcsB, GadW, GadX, H-NS, Lrp, MarA, PhoB, PhoP, RcsB, RutR, SdiA, TorR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

GadE	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional activator GadE, YhiE, YhiT, acid-responsive regulator of gadA and gadBC

Gene name(s):

gadE

Functional conformation(s):

GadE

Coregulator(s):

AdiY, ArcA, ArgR, CRP, CadC, CpxR, Cra, CusR, EvgA, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HdfR, HprR, IHF, Lrp, MarA, MatA, Nac, NsrR, OmpR, PdhR, PhoB, PhoP, PurR, RcsAB, RcsB, Rob, RutR, TorR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

RutR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator RutR, YcdC

Gene name(s):

rutR

Functional conformation(s):

RutR , RutR-thymine , RutR-uracil

Coregulator(s):

ArcA, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, IHF, NemR, NtrC, PepA, PhoB, PhoP, PurR, RutR

Summary:

TF Summary ...[more]

REGULATION EXERTED BY FNR,GadE,GadW,GadX,H-NS,PhoB,RutR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
FNR repressor GadE activator GadW repressor GadX activator H-NS repressor PhoB activator RutR repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
RutR	repressor	gadXp	gadW , gadX	3666654	3666674	-824.5	ggtgttcaacGTTGACTACCTGGGTGGTCAAattggtactt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
FNR	repressor	gadXp	gadW , gadX	3665992	3666005	-159.5	aagggattatTTGCTTACTATTAAtttccctgtg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
H-NS	repressor	gadXp	gadW , gadX

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[1] Shimada T., et al., 2007 [2] Constantinidou C., et al., 2006

Reference(s)
[1] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57
[2] 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
[3] Giangrossi M., Zattoni S., Tramonti A., De Biase D., Falconi M., 2005, Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli., J Biol Chem 280(22):21498-505
[4] Hommais F., Krin E., Laurent-Winter C., Soutourina O., Malpertuy A., Le Caer JP., Danchin A., Bertin P., 2001, Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS., Mol Microbiol 40(1):20-36
[5] Ma Z., Richard H., Tucker DL., Conway T., Foster JW., 2002, Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW)., J Bacteriol 184(24):7001-12
[6] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72
[7] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82
[8] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71