RegulonDB RegulonDB 10.8: Regulon Form
   
   


FNR,Fis,FlhDC,IHF,NarL,NarP,NsrR 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:
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:
NsrR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional repressor NsrR, YjeB
Gene name(s): nsrR
Functional conformation(s): NsrR-[2Fe-2S]reduced , NsrR-[2Fe-2S]2+ oxidized , NsrR-nitric oxide , NsrR
Coregulator(s): ArcA, CRP, CpxR, CsgD, CytR, DksA, DksA-ppGpp, DsdC, FNR, FeaR, FhlA, Fis, FlhDC, Fur, GadE, H-NS, IHF, IscR, Lrp, MatA, MetR, ModE, Nac, NarL, NarP, NorR, NsrR, OxyR, PdhR, PhoB, QseB, SutR, 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]
TRANSCRIPTION FACTOR: Info
Name:
FlhDC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): FlhDC DNA-binding transcriptional dual regulator
Gene name(s): flhC, flhD
Functional conformation(s): FlhDC
Coregulator(s): ArcA, BtsR, CRP, CsgD, DpiA, FNR, FhlA, Fis, FlhDC, GalR, GalS, GlpR, H-NS, IHF, MatA, ModE, NarL, NarP, NsrR, SutR
Summary: TF Summary ...[more]

REGULATION EXERTED BY FNR,Fis,FlhDC,IHF,NarL,NarP,NsrR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR activator Fis repressor FlhDC activator IHF dual NarL dual NarP activator NsrR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
IHF activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287538 4287550 -127.0 tgattaattcTTTGAGGAACATGcagttatgca [AIBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[1]
[2]
[3]
NarP-Phosphorylated activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287584 4287599 -79.0 gaggaagataCTGACTAACTCTAAAGtggtatttta [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[7]
[8]
[9]
NarP-Phosphorylated activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287593 4287608 -70.0 actgactaacTCTAAAGTGGTATTTTacatgcactt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[7]
[8]
[9]
NarL-Phosphorylated activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287613 4287628 -50.0 tattttacatGCACTTACAATTGATTaaagacaaca [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[6]
[7]
[8]
[9]
IHF repressor nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287610 4287622 -55.0 tggtattttaCATGCACTTACAAttgattaaag [BPP]
[GEA]
[1]
[4]
[5]
NarL-Phosphorylated repressor nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287641 4287656 -22.0 agacaacattCACAGTGTGGTTATTTgttacacata [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[6]
[7]
[8]
[9]
Fis repressor nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287649 4287663 -15.0 ttcacagtgtGGTTATTTGTTACACataggggcga [BPP]
[GEA]
[1]
[4]
[5]
FNR activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287623 4287636 -41.5 gcacttacaaTTGATTAAAGACAAcattcacagt [BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[5]
[6]
NsrR repressor nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287545 4287556 -121.0 ttctttgaggAACATGCAGTTAtgcatgctgt [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[10]
[11]
NarL-Phosphorylated repressor nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287613 4287628 -50.0 tattttacatGCACTTACAATTGATTaaagacaaca [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[6]
[7]
[8]
[9]
NarL-Phosphorylated activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287593 4287608 -70.0 actgactaacTCTAAAGTGGTATTTTacatgcactt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[7]
[8]
[9]
FlhDC activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG         [GEA] [12]
NsrR repressor nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287599 4287617 -63.0 taactctaaaGTGGTATTTTACATGCACTtacaattgat [APIORCISFBSCS]
[BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[13]
[11]
NarL-Phosphorylated activator nrfAp nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG 4287584 4287599 -79.0 gaggaagataCTGACTAACTCTAAAGtggtatttta [AIBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[7]
[8]
[9]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[GEA] Gene expression analysis
[SM] Site mutation
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BCE] Binding of cellular extracts
Reference(s): [1] Browning DF., et al., 2004
[2] Browning DF., et al., 2006
[3] Sclavi B., et al., 2007
[4] Browning DF., et al., 2002
[5] Browning DF., et al., 2005
[6] Darwin AJ., et al., 1997
[7] Rabin RS., et al., 1993
[8] Tyson KL., et al., 1994
[9] Wang H., et al., 2000
[10] Filenko N., et al., 2007
[11] Partridge JD., et al., 2009
[12] Pruss BM., et al., 2001
[13] Browning DF., et al., 2010



Reference(s)    

 [1] Browning DF., Beatty CM., Sanstad EA., Gunn KE., Busby SJ., Wolfe AJ., 2004, Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF., Mol Microbiol 51(1):241-54

 [2] Browning DF., Lee DJ., Wolfe AJ., Cole JA., Busby SJ., 2006, The Escherichia coli K-12 NarL and NarP proteins insulate the nrf promoter from the effects of integration host factor., J Bacteriol 188(21):7449-56

 [3] Sclavi B., Beatty CM., Thach DS., Fredericks CE., Buckle M., Wolfe AJ., 2007, The multiple roles of CRP at the complex acs promoter depend on activation region 2 and IHF., Mol Microbiol 65(2):425-40

 [4] Browning DF., Beatty CM., Wolfe AJ., Cole JA., Busby SJ., 2002, Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region., Mol Microbiol 43(3):687-701

 [5] Browning DF., Grainger DC., Beatty CM., Wolfe AJ., Cole JA., Busby SJ., 2005, Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression., Mol Microbiol 57(2):496-510

 [6] 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

 [7] 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

 [8] Tyson KL., Cole JA., Busby SJ., 1994, Nitrite and nitrate regulation at the promoters of two Escherichia coli operons encoding nitrite reductase: identification of common target heptamers for both NarP- and NarL-dependent regulation., Mol Microbiol 13(6):1045-55

 [9] Wang H., Gunsalus RP., 2000, The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite., J Bacteriol 182(20):5813-22

 [10] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol 189(12):4410-7

 [11] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [12] Pruss BM., Liu X., Hendrickson W., Matsumura P., 2001, FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions., FEMS Microbiol Lett 197(1):91-7

 [13] Browning DF., Lee DJ., Spiro S., Busby SJ., 2010, Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site., J Bacteriol 192(14):3824-8


RegulonDB