RegulonDB RegulonDB 11.1: Regulon Form
   
   


AppY,ArcA,Fis,IscR,NarL,NarP,YdeO 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:
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:
IscR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator IscR, YfhP
Gene name(s): iscR
Functional conformation(s): IscR-a [2Fe-2S] iron-sulfur cluster , IscR
Coregulator(s): AppY, ArcA, Fis, Fur, IHF, IscR, NarL, NarP, NrdR, NsrR, OxyR, YdeO
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 , NarL-phosphorylated
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:
NarP Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator NarP, nitrate/nitrite response regulator NarP
Gene name(s): narP
Functional conformation(s): NarP , NarP-phosphorylated
Coregulator(s): AppY, ArcA, CRP, Cra, EvgA, FNR, FhlA, Fis, FlhDC, H-NS, IHF, IscR, ModE, NagC, NarL, NarP, NorR, NsrR, OxyR, PhoP, RcsB, UvrY, YdeO
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
YdeO Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator YdeO
Gene name(s): ydeO
Functional conformation(s): YdeO
Coregulator(s): AppY, ArcA, CRP, EvgA, Fis, FliZ, GadE, GadE-RcsB, GadW, GadX, H-NS, IscR, MarA, NarL, NarP, PhoP, RcsB, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
AppY      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DLP12 prophage; DNA-binding transcriptional activator AppY
Gene name(s): appY
Functional conformation(s): AppY
Coregulator(s): AppY, ArcA, Fis, IscR, NarL, NarP, YdeO
Summary: TF Summary ...[more]

REGULATION EXERTED BY AppY,ArcA,Fis,IscR,NarL,NarP,YdeO Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AppY activator ArcA activator Fis repressor IscR repressor NarL repressor NarP repressor YdeO activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
ArcA-phosphorylated activator hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031910 1031924 -67.0 aaaaataggtCCATTTTTATCGCTAaaagataaat [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
IscR repressor hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031930 1031954 -42.0 cgctaaaagaTAAATCCACACAGTTTGTATTGTTTtgtgcaaaag [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [2]
NarP-phosphorylated repressor hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031982 1031997 7.0 acgctttattAACAATACTTTCTGGCgacgtgcgcc [EXP-IEP-GENE-EXPRESSION-ANALYSIS]  
NarP-phosphorylated repressor hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031966 1031981 -10.0 gtgcaaaagtTTCACTACGCTTTATTaacaatactt [EXP-IEP-GENE-EXPRESSION-ANALYSIS]  
Fis repressor hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031956 1031970 -21.0 gtattgttttGTGCAAAAGTTTCACtacgctttat [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
IscR repressor hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031933 1031957 -39.0 taaaagataaATCCACACAGTTTGTATTGTTTTGTgcaaaagttt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [4]
ArcA-phosphorylated activator hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031966 1031988 -7.5 gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [4]
YdeO activator hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF 1031912 1031935 -61.0 aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [5]
AppY activator hyaAp hyaA , hyaB , hyaC , hyaD , hyaE , hyaF

Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [1] Richard DJ., et al., 1999
[2] Giel JL., et al., 2006
[3] Bradley MD., et al., 2007
[4] Nesbit AD., et al., 2012
[5] Yamanaka Y., et al., 2014



Reference(s)    

 [1] Richard DJ., Sawers G., Sargent F., McWalter L., Boxer DH., 1999, Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli., Microbiology 145 ( Pt 10):2903-12

 [2] Giel JL., Rodionov D., Liu M., Blattner FR., Kiley PJ., 2006, IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli., Mol Microbiol 60(4):1058-75

 [3] 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

 [4] Nesbit AD., Fleischhacker AS., Teter SJ., Kiley PJ., 2012, ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli., J Bacteriol 194(24):6892-9

 [5] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [6] King PW., Przybyla AE., 1999, Response of hya expression to external pH in Escherichia coli., J Bacteriol 181(17):5250-6

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