RegulonDB

TRANSCRIPTION FACTOR:

Name:

Fis	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

TFs for DNA-bending

Synonym(s):

DNA-binding transcriptional dual regulator Fis, Nbp, site-specific DNA inversion stimulation factor

Gene name(s):

fis

Functional conformation(s):

Fis

Coregulator(s):

AcrR, AdiY, AppY, ArcA, ArgP, BasR, CRP, CpxR, Cra, CreB, CspA, CusR, CytR, DeoR, DksA, DksA-ppGpp, DnaA, FNR, FadR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, MazE-MazF, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, RcsB-BglJ, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

ModE	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External sensing using transported metabolites

Synonym(s):

ChlD, DNA-binding transcriptional dual regulator ModE, ModE-MoO₄^2-, ModR

Gene name(s):

modE

Functional conformation(s):

ModE-molybdate , ModE

Coregulator(s):

ArcA, CRP, CytR, DeoR, FNR, FhlA, Fis, FlhDC, Fur, IHF, Lrp, ModE, NarL, NarP, NsrR

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:

CytR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Sensing external and internal signals

Synonym(s):

DNA-binding transcriptional repressor CytR

Gene name(s):

cytR

Functional conformation(s):

CytR-cytidine , CytR

Coregulator(s):

CRP, CytR, DeoR, DnaA, Fis, ModE, Nac, NsrR

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

DeoR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional repressor DeoR, NucR, transcriptional repressor for deo operon, tsx, nupG

Gene name(s):

deoR

Functional conformation(s):

DeoR , DeoR-Deoxyribose-5-phosphate

Coregulator(s):

CRP, CytR, DeoR, Fis, ModE

Summary:

TF Summary ...[more]

REGULATION EXERTED BY CRP,CytR,DeoR,Fis,ModE

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
CRP dual CytR repressor DeoR repressor Fis activator ModE repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
CRP-cyclic-AMP	activator	deoCp2	deoC , deoA , deoB , deoD	4617174	4617195	-93.5	tgaaagtgaaTTATTTGAACCAGATCGCATTAcagtgatgca	[GEA]	[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]
CRP-cyclic-AMP	activator	deoCp2	deoC , deoA , deoB , deoD	4617227	4617248	-40.5	agatttccttAATTGTGATGTGTATCGAAGTGtgttgcggag	[GEA]	[1] [2] [3] [4] [6] [7] [8] [12] [9] [10]
ModE-molybdate	repressor	deoCp2	deoC , deoA , deoB , deoD	4617231	4617254	-35.0	ttccttaattGTGATGTGTATCGAAGTGTGTTGCggagtagatg	[GEA]	[13]
DeoR	repressor	deoCp2	deoC , deoA , deoB , deoD	4617262	4617277	-8.0	tgcggagtagATGTTAGAATACTAACaaactcgcaa
DeoR	repressor	deoCp2	deoC , deoA , deoB , deoD	4616962	4616977	-308.0	attgttttctGCTTCCAGTGCCAGAAaatggcgctt
DeoR	repressor	deoCp2	deoC , deoA , deoB , deoD	4616383	4616398	-887.0	gtagccccctTTTGTGAAAATTTTATcatgcaccgg
CytR	repressor	deoCp2	deoC , deoA , deoB , deoD	4617180	4617201	-87.5	tgaattatttGAACCAGATCGCATTACAGTGAtgcaaacttg	[GEA]	[1] [2] [3] [4] [5] [6] [7] [12] [9] [10]
CytR	repressor	deoCp2	deoC , deoA , deoB , deoD	4617208	4617227	-61.0	gtgatgcaaaCTTGTAAGTAGATTTCCTTAattgtgatgt	[GEA]	[1] [2] [3] [4] [5] [6] [7] [12] [9] [10]
CytR	repressor	deoCp2	deoC , deoA , deoB , deoD	4617200	4617216	-70.5	gcattacagtGATGCAAACTTGTAAGTagatttcctt	[GEA]	[1] [2] [3] [4] [5] [6] [7] [12] [9] [10]
Fis	activator	deoCp2	deoC , deoA , deoB , deoD	4617169	4617183	-102.0	tcatttgaaaGTGAATTATTTGAACcagatcgcat	[GEA]	[14]
CRP-cyclic-AMP	repressor	deoCp2	deoC , deoA , deoB , deoD	4617174	4617195	-93.5	tgaaagtgaaTTATTTGAACCAGATCGCATTAcagtgatgca	[GEA]	[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

Evidence:

[GEA] Gene expression analysis

Reference(s):

[1] Chahla M., et al., 2003
[2] Mollegaard NE., et al., 1993
[3] Pedersen H., et al., 1991
[4] Perini LT., et al., 1996
[5] Shin M., et al., 2001
[6] Sogaard-Andersen L., et al., 1990
[7] Sogaard-Andersen L., et al., 1991
[8] Sogaard-Andersen L., et al., 1990
[9] Sogaard-Andersen L., et al., 1991
[10] Sogaard-Andersen L., et al., 1993
[11] Zheng D., et al., 2004
[12] Sogaard-Andersen L., et al., 1991
[13] Tao H., et al., 2005
[14] Gonzalez-Gil G., et al., 1996

Reference(s)
[1] Chahla M., Wooll J., Laue TM., Nguyen N., Senear DF., 2003, Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon., Biochemistry 42(13):3812-25
[2] Mollegaard NE., Rasmussen PB., Valentin-Hansen P., Nielsen PE., 1993, Characterization of promoter recognition complexes formed by CRP and CytR for repression and by CRP and RNA polymerase for activation of transcription on the Escherichia coli deoP2 promoter., J Biol Chem 268(23):17471-7
[3] Pedersen H., Sogaard-Andersen L., Holst B., Valentin-Hansen P., 1991, Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter., J Biol Chem 266(27):17804-8
[4] Perini LT., Doherty EA., Werner E., Senear DF., 1996, Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein., J Biol Chem 271(52):33242-55
[5] Shin M., Kang S., Hyun SJ., Fujita N., Ishihama A., Valentin-Hansen P., Choy HE., 2001, Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor., EMBO J 20(19):5392-9
[6] Sogaard-Andersen L., Martinussen J., Mollegaard NE., Douthwaite SR., Valentin-Hansen P., 1990, The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12., J Bacteriol 172(10):5706-13
[7] Sogaard-Andersen L., Mironov AS., Pedersen H., Sukhodelets VV., Valentin-Hansen P., 1991, Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli., Proc Natl Acad Sci U S A 88(11):4921-5
[8] Sogaard-Andersen L., Mollegaard NE., Douthwaite SR., Valentin-Hansen P., 1990, Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli., Mol Microbiol 4(9):1595-601
[9] Sogaard-Andersen L., Valentin-Hansen P., 1991, Restored DNA-binding of the cAMP-CRP activator complex reestablishes negative regulation by the CytR repressor in the deoP2 promoter in Escherichia coli., Mol Gen Genet 231(1):76-80
[10] Sogaard-Andersen L., Valentin-Hansen P., 1993, Protein-protein interactions in gene regulation: the cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor., Cell 75(3):557-66
[11] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93
[12] Sogaard-Andersen L., Pedersen H., Holst B., Valentin-Hansen P., 1991, A novel function of the cAMP-CRP complex in Escherichia coli: cAMP-CRP functions as an adaptor for the CytR repressor in the deo operon., Mol Microbiol 5(4):969-75
[13] Tao H., Hasona A., Do PM., Ingram LO., Shanmugam KT., 2005, Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli., Arch Microbiol 184(4):225-33
[14] Gonzalez-Gil G., Bringmann P., Kahmann R., 1996, FIS is a regulator of metabolism in Escherichia coli., Mol Microbiol 22(1):21-9