RegulonDB RegulonDB 11.1: Regulon Form
   
   


Fis,IHF,PepA,PurR,RutR 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, 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:
PurR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional repressor PurR
Gene name(s): purR
Functional conformation(s): PurR-Guanine , PurR , PurR-hypoxanthine
Coregulator(s): CRP, DnaA, FNR, Fis, Fur, GadE, GcvA, IHF, Lrp, MarA, MetR, Nac, PepA, PhoP, PurR, RbsR, RutR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PepA      Tractordb tool
Connectivity class Local Regulator
Synonym(s): CarP, PepA, XerB
Gene name(s): pepA
Functional conformation(s): PepA
Coregulator(s): Fis, IHF, PepA, PurR, RutR
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]
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, BolA, 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, PlaR, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY Fis,IHF,PepA,PurR,RutR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
Fis activator IHF dual PepA repressor PurR repressor RutR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF activator carAp1 carA , carB 29240 29252 -305.0 atttaatttaTTGATTATAAAGGgctttaattt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
[2]
[3]
PepA repressor carAp1 carA , carB 29459 29485 -79.0 ttttgtcgctTAATGCCTGTAAAACATGCATGAGCCAcaaaataata [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
[4]
PepA repressor carAp1 carA , carB 29365 29391 -173.0 aattttgaccATTTGGTCCACTTTTTTCTGCTCGTTTttatttcatg [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[3]
[4]
RutR activator carAp1 carA , carB 29359 29375 -184.0 aatgtaaattTTGACCATTTGGTCCACttttttctgc [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
[6]
Fis activator carAp1 carA , carB 29386 29405 -156.0 ttttttctgcTCGTTTTTATTTCATGCAATcttcttgctg [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
Fis activator carAp1 carA , carB 29439 29458 -103.0 cagaacaggtTAGATGATCTTTTTGTCGCTtaatgcctgt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
Fis activator carAp1 carA , carB 29461 29480 -81.0 ttgtcgcttaATGCCTGTAAAACATGCATGagccacaaaa [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
PurR-hypoxanthine repressor carAp1 carA , carB 29415 29430 -128.5 tcttcttgctGCGCAAGCGTTTTCCAgaacaggtta [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [8]
[3]
[4]
IHF repressor carAp1 carA , carB 29240 29252 -305.0 atttaatttaTTGATTATAAAGGgctttaattt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
[2]
[3]

Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Charlier D., et al., 1994
[2] Charlier D., et al., 1993
[3] Devroede N., et al., 2006
[4] Devroede N., et al., 2004
[5] Shimada T., et al., 2007
[6] Shimada T., et al., 2008
[7] Bradley MD., et al., 2007
[8] Cho BK., et al., 2011



Reference(s)    

 [1] Charlier D., Huysveld N., Roovers M., Glansdorff N., 1994, On the role of the Escherichia coli integration host factor (IHF) in repression at a distance of the pyrimidine specific promoter P1 of the carAB operon., Biochimie 76(10-11):1041-51

 [2] Charlier D., Roovers M., Gigot D., Huysveld N., Pierard A., Glansdorff N., 1993, Integration host factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2., Mol Gen Genet 237(1-2):273-86

 [3] Devroede N., Huysveld N., Charlier D., 2006, Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase., J Bacteriol 188(9):3236-45

 [4] Devroede N., Thia-Toong TL., Gigot D., Maes D., Charlier D., 2004, Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled., J Mol Biol 336(1):25-42

 [5] 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

 [6] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5

 [7] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [8] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

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