RegulonDB RegulonDB 10.8: Regulon Form
   
   


FNR,Fis,IHF,NarL,RstA 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:
RstA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional regulator RstA, RstA response regulator, UrpT
Gene name(s): rstA
Functional conformation(s): RstA , RstA-Phosphorylated
Coregulator(s): BasR, BtsR, CRP, CpxR, Cra, CsgD, EnvY, FNR, Fis, FliZ, Fur, H-NS, IHF, MlrA, MqsA, NarL, OmpR, PhoB, RcdA, RcsAB, RstA, ppGpp
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,RstA Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR activator Fis repressor IHF activator NarL activator RstA activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279720 1279735 -79.0 cctaaaggggTATCTTAGGAATTTACtttatttttc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279728 1279743 -71.0 ggtatcttagGAATTTACTTTATTTTtcatccccat [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279742 1279757 -57.0 ttactttattTTTCATCCCCATCACTcttgatcgtt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279591 1279606 -208.0 gagccattaaTATGTTACCCATGGGGaatactcctt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
[3]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279710 1279725 -89.0 tgttaattatCCTAAAGGGGTATCTTaggaatttac [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[1]
[2]
[3]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279614 1279629 -185.0 gggaatactcCTTAATACCCATCTGCataaaaatct [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[1]
[2]
[3]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279698 1279713 -101.0 ttatgtggtgGCTGTTAATTATCCTAaaggggtatc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[1]
[2]
[6]
[3]
IHF activator narGp narG , narH , narJ , narI 1279676 1279688 -125.0 aaacgtcttaATTTACAGTCTGTtatgtggtgg [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[2]
[7]
[8]
NarL-Phosphorylated activator narGp narG , narH , narJ , narI 1279604 1279619 -195.0 gttacccatgGGGAATACTCCTTAATacccatctgc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[1]
[2]
[3]
RstA-Phosphorylated activator narGp narG , narH , narJ , narI 1279523 1279539 -276.0 ctttttttatGCGTCATTTAGTTACAAcatactaatg [APIORCISFBSCS] [9]
[10]
Fis repressor narGp narG , narH , narJ , narI 1279697 1279711 -103.0 gttatgtggtGGCTGTTAATTATCCtaaaggggta [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[11]
Fis repressor narGp narG , narH , narJ , narI 1279734 1279748 -66.0 ttaggaatttACTTTATTTTTCATCcccatcactc [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[11]
FNR activator narGp narG , narH , narJ , narI 1279759 1279772 -41.5 cccatcactcTTGATCGTTATCAAttcccacgct [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[12]
[13]
[14]
[15]

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/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[SM] Site mutation
[BCE] Binding of cellular extracts
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Li J., et al., 1994
[2] Rabin RS., et al., 1992
[3] Stewart V. 1982
[4] Darwin AJ., et al., 1996
[5] Darwin AJ., et al., 1997
[6] Rabin RS., et al., 1993
[7] Schroder I., et al., 1993
[8] Zhang X., et al., 1996
[9] Ogasawara H., et al., 2007
[10] Oshima T., et al., 2002
[11] Bradley MD., et al., 2007
[12] Eiglmeier K., et al., 1989
[13] Lamberg KE., et al., 2000
[14] Li SF., et al., 1988
[15] 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] Rabin RS., Collins LA., Stewart V., 1992, In vivo requirement of integration host factor for nar (nitrate reductase) operon expression in Escherichia coli K-12., Proc Natl Acad Sci U S A 89(18):8701-5

 [3] Stewart V., 1982, Requirement of Fnr and NarL functions for nitrate reductase expression in Escherichia coli K-12., J Bacteriol 151(3):1320-5

 [4] Darwin AJ., Li J., Stewart V., 1996, Analysis of nitrate regulatory protein NarL-binding sites in the fdnG and narG operon control regions of Escherichia coli K-12., Mol Microbiol 20(3):621-32

 [5] Darwin AJ., Tyson KL., Busby SJ., Stewart V., 1997, Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement., Mol Microbiol 25(3):583-95

 [6] Rabin RS., Stewart V., 1993, Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12., J Bacteriol 175(11):3259-68

 [7] Schroder I., Darie S., Gunsalus RP., 1993, Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor., J Biol Chem 268(2):771-4

 [8] Zhang X., DeMoss JA., 1996, Structure modification induced in the narG promoter by binding of integration host factor and NARL-P., J Bacteriol 178(13):3971-3

 [9] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9

 [10] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [11] 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

 [12] Eiglmeier K., Honore N., Iuchi S., Lin EC., Cole ST., 1989, Molecular genetic analysis of FNR-dependent promoters., Mol Microbiol 3(7):869-78

 [13] 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

 [14] Li SF., DeMoss JA., 1988, Location of sequences in the nar promoter of Escherichia coli required for regulation by Fnr and NarL., J Biol Chem 263(27):13700-5

 [15] 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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