RegulonDB RegulonDB 10.9: Regulon Form
   
   


ArcA,FNR,IHF,NarL regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
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 , FNR-[4Fe-4S]2+ reduced , FNR-[2Fe-2S]2+ oxidized
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:
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-Phosphorylated , ArcA
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:
NarL Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator NarL, FrdR, NarR, nitrate/nitrite response regulator NarL
Gene name(s): narL
Functional conformation(s): NarL-Phosphorylated , NarL
Coregulator(s): AppY, ArcA, CRP, Cra, DcuR, DpiA, EvgA, FNR, FhlA, Fis, FlhDC, Fur, H-NS, IHF, IscR, Lrp, ModE, NagC, NarL, NarP, NikR, NorR, NsrR, OxyR, PhoP, RcsB, RstA, SoxS, TorR, UvrY, YdeO
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
IHF Weight Matrix      Tractordb tool
Connectivity class Global Regulator
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, 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]

REGULATION EXERTED BY ArcA,FNR,IHF,NarL Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA repressor FNR repressor IHF repressor NarL activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarL-Phosphorylated activator nuoAp2 nuoN , nuoM , nuoL , nuoK , nuoJ , nuoI , nuoH , nuoG , nuoF , nuoE , nuoC , nuoB , nuoA 2405281 2405287 -122.0 agggcattaaATGCTAATggtgttgata    
IHF repressor nuoAp2 nuoN , nuoM , nuoL , nuoK , nuoJ , nuoI , nuoH , nuoG , nuoF , nuoE , nuoC , nuoB , nuoA 2405222 2405234 -66.0 tttgttaaagTTGACAAAAGGTTAtagaaaggag   [1]
[2]
IHF repressor nuoAp2 nuoN , nuoM , nuoL , nuoK , nuoJ , nuoI , nuoH , nuoG , nuoF , nuoE , nuoC , nuoB , nuoA 2405230 2405242 -74.0 aagaaactttTGTTAAAGTTGACAaaaggttata   [1]
[2]
ArcA-Phosphorylated repressor nuoAp2 nuoN , nuoM , nuoL , nuoK , nuoJ , nuoI , nuoH , nuoG , nuoF , nuoE , nuoC , nuoB , nuoA 2405263 2405277 -108.0 atgctaatggTGTTGATATTATGTAAactaatgtga   [3]
[4]
[5]
IHF repressor nuoAp2 nuoN , nuoM , nuoL , nuoK , nuoJ , nuoI , nuoH , nuoG , nuoF , nuoE , nuoC , nuoB , nuoA 2405239 2405251 -83.0 actaatgtgaAGAAACTTTTGTTAaagttgacaa   [1]
[2]
FNR repressor nuoAp2 nuoN , nuoM , nuoL , nuoK , nuoJ , nuoI , nuoH , nuoG , nuoF , nuoE , nuoC , nuoB , nuoA 2405196 2405209 -40.5 agaaaggagtAAAAAACCACATCAAttagctgtat   [6]
[7]
ArcA repressor FNR repressor IHF repressor NarL repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF repressor ubiCp ubiC , ubiA 4252425 4252437 -12.0 ttgcgtattaGATCACTTAATTTGctttacatct   [8]
FNR repressor ubiCp ubiC , ubiA 4252436 4252449 -0.5 atcacttaatTTGCTTTACATCTCCcgtaaacact   [8]
NarL-Phosphorylated repressor ubiCp ubiC , ubiA

Reference(s): [1] Bongaerts J., et al., 1995
[2] Wackwitz B., et al., 1999
[3] Lynch AS., et al., 1996
[4] Salmon KA., et al., 2005
[5] Shalel-Levanon S., et al., 2005
[6] Kumar R., et al., 2011
[7] Salmon K., et al., 2003
[8] Soballe B., et al., 1997



Reference(s)    

 [1] Bongaerts J., Zoske S., Weidner U., Unden G., 1995, Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators., Mol Microbiol 16(3):521-34

 [2] Wackwitz B., Bongaerts J., Goodman SD., Unden G., 1999, Growth phase-dependent regulation of nuoA-N expression in Escherichia coli K-12 by the Fis protein: upstream binding sites and bioenergetic significance., Mol Gen Genet 262(4-5):876-83

 [3] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49

 [4] 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

 [5] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli., Metab Eng 7(5-6):364-74

 [6] 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

 [7] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [8] Soballe B., Poole RK., 1997, Aerobic and anaerobic regulation of the ubiCA operon, encoding enzymes for the first two committed steps of ubiquinone biosynthesis in Escherichia coli., FEBS Lett 414(2):373-6

 [9] Kwon O., Druce-Hoffman M., Meganathan R., 2005, Regulation of the ubiquinone (coenzyme Q) biosynthetic genes ubiCA in Escherichia coli., Curr Microbiol 50(4):180-9


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