RegulonDB RegulonDB 10.8: Regulon Form
   
   


FNR,Fis,IHF,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]
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, 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 FNR,Fis,IHF,NarL Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR activator Fis repressor IHF activator NarL activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarL-Phosphorylated activator narKp1 narK 1277821 1277836 -103.0 taatttttatGAAGTCACTGTACTCActatgggtaa [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277857 1277872 -67.0 tgataaatatCAATGATAGATAAAGTtatcttatcg [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277844 1277859 -80.0 tcactatgggTAATGATAAATATCAAtgatagataa [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277834 1277849 -90.0 gtcactgtacTCACTATGGGTAATGAtaaatatcaa [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277770 1277785 -154.0 tcgctttacaTCGGTAAGGGTAGGGAttttacagca [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277764 1277779 -160.0 ggttagtcgcTTTACATCGGTAAGGGtagggatttt [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277747 1277762 -177.0 ctccttatttGCCGTGTGGTTAGTCGctttacatcg [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277710 1277725 -214.0 ctattggctgAAGTATACCCATACCCggaaagagtt [APIORCISFBSCS]
[BPP]
[1]
NarL-Phosphorylated activator narKp1 narK 1277730 1277745 -194.0 atacccggaaAGAGTTACTCCTTATTtgccgtgtgg [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM]
[2]
[1]
NarL-Phosphorylated activator narKp1 narK 1277826 1277841 -98.0 tttatgaagtCACTGTACTCACTATGggtaatgata [APIORCISFBSCS]
[BPP]
[2]
[1]
IHF activator narKp1 narK 1277796 1277808 -130.0 ttttacagcaCCGTGAAAAATCTcataattttt [BPP]
[GEA]
[3]
[1]
Fis repressor narKp1 narK 1277880 1277899 -43.0 agttatcttaTCGTTTGATTTACATCAAATtgcctttagc [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[4]
FNR activator narKp1 narK 1277846 1277859 -79.5 actatgggtaATGATAAATATCAAtgatagataa [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[5]
FNR activator narKp1 narK 1277884 1277897 -41.5 atcttatcgtTTGATTTACATCAAattgccttta [BCE]
[BPP]
[CV(CHIP-SV/SM)]
[SM]
[2]
[6]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BPP] Binding of purified proteins
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[SM] Site mutation
[GEA] Gene expression analysis
[AIBSCS] Automated inference based on similarity to consensus sequences
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[BCE] Binding of cellular extracts
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
Reference(s): [1] Li J., et al., 1994
[2] Bonnefoy V., et al., 1992
[3] Kolesnikow T., et al., 1992
[4] Bradley MD., et al., 2007
[5] Walker MS., et al., 1992
[6] Melville SB., et al., 1996



Reference(s)    

 [1] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [2] Bonnefoy V., DeMoss JA., 1992, Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli., Mol Microbiol 6(23):3595-602

 [3] Kolesnikow T., Schroder I., Gunsalus RP., 1992, Regulation of narK gene expression in Escherichia coli in response to anaerobiosis, nitrate, iron, and molybdenum., J Bacteriol 174(22):7104-11

 [4] 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

 [5] Walker MS., DeMoss JA., 1992, Role of alternative promoter elements in transcription from the nar promoter of Escherichia coli., J Bacteriol 174(4):1119-23

 [6] 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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