RegulonDB RegulonDB 10.8: Regulon Form
   
   


ArcA,NtrC,PhoP,RutR regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
ArcA Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class External-Two-component systems
Synonym(s): ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein
Gene name(s): arcA
Functional conformation(s): ArcA , ArcA-Phosphorylated
Coregulator(s): AdiY, AppY, ArcA, BetI, BtsR, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PhoP Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator PhoP, PhoP response regulator
Gene name(s): phoP
Functional conformation(s): PhoP , PhoP-Phosphorylated
Coregulator(s): AcrR, ArcA, ArgR, BasR, CRP, CysB, EnvR, EvgA, FNR, FadR, FliZ, GadE, GadW, GadX, H-NS, HypT, Lrp, MalT, MarA, MetJ, MprA, NagC, NarL, NarP, NtrC, OmpR, PdhR, PhoP, PurR, RbsR, RcsB, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, UvrY, 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]
TRANSCRIPTION FACTOR: Info
Name:
NtrC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator NtrC, GlnG, GlnT, NtrC response regulator
Gene name(s): glnG
Functional conformation(s): NtrC-Pasp
Coregulator(s): ArcA, ArgR, CRP, CysB, FNR, Fis, Fur, GadX, GlrR, IHF, Nac, NtrC, PhoP, RcsB, RutR, ppGpp

REGULATION EXERTED BY ArcA,NtrC,PhoP,RutR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA activator NtrC activator PhoP activator RutR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
ArcA-Phosphorylated activator rutAp rutG , rutF , rutE , rutD , rutC , rutB , rutA 1074116 1074130 -97.0 ctgttttgacCGTTTAGTCCACTTTttaccagata [AIBSCS]
[CV(GEA)]
[GEA]
[1]
PhoP-Phosphorylated activator rutAp rutG , rutF , rutE , rutD , rutC , rutB , rutA 1074125 1074140 -106.0 ttatgtgcaaCTGTTTTGACCGTTTAgtccactttt [AIBSCS]
[CV(GEA)]
[GEA]
[2]
RutR repressor rutAp rutG , rutF , rutE , rutD , rutC , rutB , rutA 1074120 1074138 -102.5 atgtgcaactGTTTTGACCGTTTAGTCCActttttacca [AIBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[3]
[4]
[5]
NtrC-Pasp activator rutAp rutG , rutF , rutE , rutD , rutC , rutB , rutA 1074142 1074158 -124.0 cgcgcacagaTGCATGTTTTATGTGCAactgttttga [AIBSCS]
[CV(GEA)]
[GEA]
[6]
NtrC-Pasp activator rutAp rutG , rutF , rutE , rutD , rutC , rutB , rutA 1074163 1074179 -145.0 ctcgaccttcTGCACTCTCATCGCGCAcagatgcatg [AIBSCS]
[CV(GEA)]
[GEA]
[6]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[CV(GEA)] cross validation(GEA)
[GEA] Gene expression analysis
[BPP] Binding of purified proteins
[CV(GEA/SM)] cross validation(GEA/SM)
[CV(SM)] cross validation(SM)
[SM] Site mutation
Reference(s): [1] Salmon KA., et al., 2005
[2] Monsieurs P., et al., 2005
[3] Nguyen Le Minh P., et al., 2015
[4] Shimada T., et al., 2007
[5] Shimada T., et al., 2008
[6] Zimmer DP., et al., 2000



Reference(s)    

 [1] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [2] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [3] Nguyen Le Minh P., de Cima S., Bervoets I., Maes D., Rubio V., Charlier D., 2015, Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli., FEBS Open Bio 5:76-84

 [4] 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

 [5] 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

 [6] 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


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