RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CRP,CytR,DeoR,Fis,ModE regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
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, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, 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-MoO42-, ModR
Gene name(s): modE
Functional conformation(s): ModE-MoO42- , 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-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, 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, 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, RcsB, 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:
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-Deoxyribose-5-phosphate , DeoR
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-cAMP dual deoCp2 deoC , deoA , deoB , deoD 4617174 4617195 -93.5 tgaaagtgaaTTATTTGAACCAGATCGCATTAcagtgatgca [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
CRP-cAMP activator deoCp2 deoC , deoA , deoB , deoD 4617227 4617248 -40.5 agatttccttAATTGTGATGTGTATCGAAGTGtgttgcggag [BPP]
[GEA]
[HIBSCS]
[SM]
[2]
[3]
[17]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[18]
ModE-MoO42- repressor deoCp2 deoC , deoA , deoB , deoD 4617231 4617254 -35.0 ttccttaattGTGATGTGTATCGAAGTGTGTTGCggagtagatg [BPP]
[GEA]
[HIBSCS]
[19]
DeoR repressor deoCp2 deoC , deoA , deoB , deoD 4617262 4617277 -8.0 tgcggagtagATGTTAGAATACTAACaaactcgcaa [HIBSCS]
[SM]
[1]
[14]
DeoR repressor deoCp2 deoC , deoA , deoB , deoD 4616962 4616977 -308.0 attgttttctGCTTCCAGTGCCAGAAaatggcgctt [HIBSCS]
[SM]
[1]
[14]
DeoR repressor deoCp2 deoC , deoA , deoB , deoD 4616383 4616398 -887.0 gtagccccctTTTGTGAAAATTTTATcatgcaccgg [HIBSCS]
[SM]
[1]
[14]
CytR repressor deoCp2 deoC , deoA , deoB , deoD 4617180 4617201 -87.5 tgaattatttGAACCAGATCGCATTACAGTGAtgcaaacttg [BPP]
[GEA]
[HIBSCS]
[SM]
[3]
[17]
[4]
[5]
[6]
[7]
[8]
[9]
[11]
[12]
[13]
CytR repressor deoCp2 deoC , deoA , deoB , deoD 4617208 4617227 -61.0 gtgatgcaaaCTTGTAAGTAGATTTCCTTAattgtgatgt [BPP]
[GEA]
[SM]
[2]
[3]
[20]
[17]
[4]
[5]
[6]
[7]
[8]
[9]
[11]
[12]
[13]
CytR repressor deoCp2 deoC , deoA , deoB , deoD 4617200 4617216 -70.5 gcattacagtGATGCAAACTTGTAAGTagatttcctt [BPP]
[GEA]
[HIBSCS]
[SM]
[3]
[17]
[4]
[5]
[6]
[7]
[8]
[9]
[11]
[12]
[13]
[18]
[21]
Fis activator deoCp2 deoC , deoA , deoB , deoD 4617169 4617183 -102.0 tcatttgaaaGTGAATTATTTGAACcagatcgcat [AIBSCS]
[GEA]
[22]
CRP-cAMP dual deoCp2 deoC , deoA , deoB , deoD 4617174 4617195 -93.5 tgaaagtgaaTTATTTGAACCAGATCGCATTAcagtgatgca [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[2]
[3]
[17]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
Reference(s): [1] Amouyal M., et al., 1989
[2] Brikun I., et al., 1996
[3] Chahla M., et al., 2003
[4] Mollegaard NE., et al., 1993
[5] Pedersen H., et al., 1991
[6] Perini LT., et al., 1996
[7] Shin M., et al., 2001
[8] Sogaard-Andersen L., et al., 1990
[9] Sogaard-Andersen L., et al., 1991
[10] Sogaard-Andersen L., et al., 1990
[11] Sogaard-Andersen L., et al., 1991
[12] Sogaard-Andersen L., et al., 1991
[13] Sogaard-Andersen L., et al., 1993
[14] Valentin-Hansen P., et al., 1986
[15] Valentin-Hansen P., et al., 1989
[16] Zheng D., et al., 2004
[17] Mayes DG. 1977
[18] Valentin-Hansen P. 1982
[19] Tao H., et al., 2005
[20] Gerlach P., et al., 1991
[21] Valentin-Hansen P., et al., 1986
[22] Gonzalez-Gil G., et al., 1996



Reference(s)    

 [1] Amouyal M., Mortensen L., Buc H., Hammer K., 1989, Single and double loop formation when deoR repressor binds to its natural operator sites., Cell 58(3):545-51

 [2] Brikun I., Suziedelis K., Stemmann O., Zhong R., Alikhanian L., Linkova E., Mironov A., Berg DE., 1996, Analysis of CRP-CytR interactions at the Escherichia coli udp promoter., J Bacteriol 178(6):1614-22

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] Valentin-Hansen P., Albrechtsen B., Love Larsen JE., 1986, DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor., EMBO J 5(8):2015-21

 [15] Valentin-Hansen P., Holst B., Josephsen J., Hammer K., Albrechtsen B., 1989, CRP/cAMP- and CytR-regulated promoters in Escherichia coli K12: the cdd promoter., Mol Microbiol 3(10):1385-90

 [16] 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

 [17] Mayes DG., 1977, A comparison of menstrual bleeding patterns associated with three IUD models: an example of reference period analysis., J Biosoc Sci 9(1):121-35

 [18] Valentin-Hansen P., 1982, Tandem CRP binding sites in the deo operon of Escherichia coli K-12., EMBO J 1(9):1049-54

 [19] 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

 [20] Gerlach P., Sogaard-Andersen L., Pedersen H., Martinussen J., Valentin-Hansen P., Bremer E., 1991, The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli K-12., J Bacteriol 173(17):5419-30

 [21] Valentin-Hansen P., Larsen JE., Hojrup P., Short SA., Barbier CS., 1986, Nucleotide sequence of the CytR regulatory gene of E. coli K-12., Nucleic Acids Res 14(5):2215-28

 [22] Gonzalez-Gil G., Bringmann P., Kahmann R., 1996, FIS is a regulator of metabolism in Escherichia coli., Mol Microbiol 22(1):21-9


RegulonDB