RegulonDB RegulonDB 10.8: Regulon Form
   
   


FNR,Fis,NarL 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:
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-[4Fe-4S]2+ reduced , FNR-[2Fe-2S]2+ oxidized , FNR
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:
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]

REGULATION EXERTED BY FNR,Fis,NarL Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR activator Fis repressor NarL repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarL-Phosphorylated repressor dmsAp1 dmsA , dmsB , dmsC 940788 940803 -27.0 ataccgaacaATAATTACTCCTCACTtacacgtaat [BCE]
[BPP]
[1]
[2]
NarL-Phosphorylated repressor dmsAp1 dmsA , dmsB , dmsC 940808 940823 -7.0 ctcacttacaCGTAATACTACTTTCGagtgaaaatc [BCE]
[BPP]
[1]
[2]
NarL-Phosphorylated repressor dmsAp1 dmsA , dmsB , dmsC 940829 940844 15.0 tttcgagtgaAAATCTACCTATCTCTttgattttca [APIORCISFBSCS]
[BPP]
[1]
[2]
Fis repressor dmsAp1 dmsA , dmsB , dmsC 940783 940797 -33.0 ctttgataccGAACAATAATTACTCctcacttaca [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
Fis repressor dmsAp1 dmsA , dmsB , dmsC 940821 940840 8.0 aatactacttTCGAGTGAAAATCTACCTATctctttgatt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
Fis repressor dmsAp1 dmsA , dmsB , dmsC 940874 940888 59.0 atgtatacaaGCCTATATAGCGAACtgctatagaa [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
FNR activator dmsAp1 dmsA , dmsB , dmsC 940775 940788 -41.5 ttgtctccctTTGATACCGAACAAtaattactcc [BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[1]
[4]
[5]
[2]

Evidence: [BCE] Binding of cellular extracts
[BPP] Binding of purified proteins
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[AIBSCS] Automated inference based on similarity to consensus sequences
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[SM] Site mutation
Reference(s): [1] Bearson SM., et al., 2002
[2] Tyson KL., et al., 1993
[3] Bradley MD., et al., 2007
[4] Lamberg KE., et al., 2000
[5] Melville SB., et al., 1996



Reference(s)    

 [1] Bearson SM., Albrecht JA., Gunsalus RP., 2002, Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions., BMC Microbiol 2(1):13

 [2] Tyson KL., Bell AI., Cole JA., Busby SJ., 1993, Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL., Mol Microbiol 7(1):151-7

 [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] Lamberg KE., Kiley PJ., 2000, FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3., Mol Microbiol 38(4):817-27

 [5] Melville SB., Gunsalus RP., 1996, Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes., Proc Natl Acad Sci U S A 93(3):1226-31


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