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

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-cAMP

Coregulator(s):

AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, 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, 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, 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, YiaJ, YjjQ, ZraR, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

Nac	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator Nac

Gene name(s):

nac

Functional conformation(s):

Nac

Coregulator(s):

AdiY, ArgP, ArgR, AsnC, CRP, CytR, FNR, Fur, GadE, HdfR, IHF, Lrp, Nac, NsrR, NtrC, PhoB, PurR, QseB

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

Lrp	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

Sensing external and internal signals

Synonym(s):

AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA

Gene name(s):

lrp

Functional conformation(s):

Lrp-leucine , Lrp

Coregulator(s):

AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, QseB, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

ArgR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Sensing external and internal signals

Synonym(s):

DNA-binding transcriptional dual regulator ArgR, XerA

Gene name(s):

argR

Functional conformation(s):

ArgR , ArgR-L-arginine

Coregulator(s):

AdiY, ArgR, CRP, DksA-ppGpp, FNR, Fur, GadE, H-NS, HdfR, IHF, Lrp, Nac, NtrC, PhoP, 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:

HdfR	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator HdfR, YifA, YifD

Gene name(s):

hdfR

Functional conformation(s):

HdfR

Coregulator(s):

AcrR, AdiY, ArgR, CRP, FNR, FliZ, Fur, GadE, H-NS, HdfR, IHF, LrhA, Lrp, MatA, Nac, OmpR, QseB, RcsAB, YjjQ

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

AdiY	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional activator AdiY

Gene name(s):

adiY

Functional conformation(s):

AdiY

Coregulator(s):

AdiY, ArcA, ArgR, CRP, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HdfR, IHF, Lrp, Nac, RcsB, TorR, ppGpp

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, 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, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YiaJ, 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, 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 AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
AdiY activator ArgR repressor CRP repressor FNR repressor Fur repressor GadE activator HdfR activator IHF activator Lrp activator Nac repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
IHF	activator	gltBp	gltB , gltD , gltF	3354418	3354430	-85.0	ttttaatttcAGTCATTTAATAAagaattttgc	[BPP] [GEA]	[1] [2]
IHF	activator	gltBp	gltB , gltD , gltF	3354414	3354426	-89.0	tccattttaaTTTCAGTCATTTAataaagaatt	[BPP] [GEA]	[1] [2]
Lrp	activator	gltBp	gltB , gltD , gltF	3354350	3354364	-152.0	cctttatgacAGTCAGGAATTGACTgtttctctaa	[APIORCISFBSCS] [BPP] [CV(SM)] [SM]	[3] [2] [4]
Lrp	activator	gltBp	gltB , gltD , gltF	3354287	3354301	-215.0	caattaaggcAGTATAAAATGCTGGttttgtcgtc	[APIORCISFBSCS] [BPP] [CV(SM)] [SM]	[3] [2] [4]
Lrp	activator	gltBp	gltB , gltD , gltF	3354256	3354270	-246.0	aggcaaaaacAGTAGCATGAAACGTcattaccaat	[APIORCISFBSCS] [BPP] [CV(SM)] [SM]	[5] [2] [4]
CRP-cAMP	repressor	gltBp	gltB , gltD , gltF	3354433	3354454	-65.5	tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat	[APIORCISFBSCS] [BPP] [CV(GEA)] [CV(GEA)] [CV(GEA/SM)] [CV(SM)] [GEA] [SM]	[2]
Lrp-leucine	activator	gltBp	gltB , gltD , gltF	3354394	3354409	-108.0	ttttagccttAAAGATAAAATCCATTttaatttcag	[AIBSCS] [CV(GEA)] [GEA]	[6]
ArgR-L-arginine	repressor	gltBp	gltB , gltD , gltF	3354169	3354186	-331.5	aatcaaaattACCGAAATTTCATGCATAatcacataaa	[APIORCISFBSCS] [BPP] [CV(GEA)] [CV(GEA)] [GEA]	[7] [2]
ArgR-L-arginine	repressor	gltBp	gltB , gltD , gltF	3354148	3354165	-352.0	gcttttatcaACTGCATAATCAATCAAAattaccgaaa	[APIORCISFBSCS] [BPP] [CV(GEA)] [CV(GEA)] [GEA]	[7] [2]
FNR	repressor	gltBp	gltB , gltD , gltF	3354476	3354489	-26.5	agcttgccatTTGACCTGTATCAGctttcccgat	[AIBSCS] [CV(GEA)] [GEA]	[8] [9]
HdfR	activator	gltBp	gltB , gltD , gltF					[BPP]	[10]
AdiY	activator	gltBp	gltB , gltD , gltF					[BPP]	[10]
Nac	repressor	gltBp	gltB , gltD , gltF					[GEA]	[11]
GadE	activator	gltBp	gltB , gltD , gltF	3354215	3354234	-284.0	gcttatcttgTGTCAGATTTTTTTATCTCCtgatggattt	[BPP] [CEUMA] [CV(GEA)] [CV(GEA)] [GEA] [IHBCE] [RE]	[12] [13]
Fur-Fe²⁺	repressor	gltBp	gltB , gltD , gltF					[GEA]	[9]

Evidence:

[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(SM)] cross validation(SM)
[SM] Site mutation
[CV(GEA)] cross validation(GEA)
[CV(GEA/SM)] cross validation(GEA/SM)
[AIBSCS] Automated inference based on similarity to consensus sequences
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence

Reference(s):

[1] Paul L., et al., 2001
[2] Paul L., et al., 2007
[3] Oliver G., et al., 1987
[4] Wiese DE., et al., 1997
[5] Ernsting BR., et al., 1992
[6] Lintner RE., et al., 2008
[7] Cho S., et al., 2015
[8] Constantinidou C., et al., 2006
[9] Kumar R., et al., 2011
[10] Krin E., et al., 2010
[11] Zimmer DP., et al., 2000
[12] Hommais F., et al., 2004
[13] Seo SW., et al., 2015

Reference(s)
[1] Paul L., Blumenthal RM., Matthews RG., 2001, Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF., J Bacteriol 183(13):3910-8
[2] Paul L., Mishra PK., Blumenthal RM., Matthews RG., 2007, Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR., BMC Microbiol 7:2
[3] Oliver G., Gosset G., Sanchez-Pescador R., Lozoya E., Ku LM., Flores N., Becerril B., Valle F., Bolivar F., 1987, Determination of the nucleotide sequence for the glutamate synthase structural genes of Escherichia coli K-12., Gene 60(1):1-11
[4] Wiese DE., Ernsting BR., Blumenthal RM., Matthews RG., 1997, A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli., J Mol Biol 270(2):152-68
[5] Ernsting BR., Atkinson MR., Ninfa AJ., Matthews RG., 1992, Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli., J Bacteriol 174(4):1109-18
[6] Lintner RE., Mishra PK., Srivastava P., Martinez-Vaz BM., Khodursky AB., Blumenthal RM., 2008, Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio., BMC Microbiol 8:60
[7] Cho S., Cho YB., Kang TJ., Kim SC., Palsson B., Cho BK., 2015, The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli., Nucleic Acids Res 43(6):3079-88
[8] 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
[9] 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
[10] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273
[11] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9
[12] 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
[13] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970