RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


CRP,Cra,FNR,Fis,H-NS,IHF,NarL,NarP 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, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, 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 , FNR-[2Fe-2S]2+ oxidized
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, 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:
CRP Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): Cap, Csm, DNA-binding transcriptional dual regulator CRP, GurB
Gene name(s): crp
Functional conformation(s): CRP-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CaiF, ChbR, ComR, CpxR, Cra, CreB, CsgD, CspA, CsqR, CusR, CytR, DcuR, DeoR, DgoR, DksA-ppGpp, DnaA, DpiA, DsdC, EbgR, EnvY, EvgA, ExuR, FNR, FadR, FeaR, FhlA, Fis, FlhDC, FliZ, FucR, Fur, GadE, GadW, GadX, GalR, GalS, GatR, GcvA, GlaR, GlcC, GlpR, GlrR, GntR, GutM, H-NS, HU, HdfR, HipB, HprR, HyfR, HypT, IHF, IclR, IdnR, LacI, LeuO, LexA, LrhA, Lrp, LsrR, MalI, MalT, MarA, MarR, MatA, McbR, MelR, MetJ, MhpR, Mlc, MlrA, ModE, MprA, MqsA, MurR, Nac, NadR, NagC, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PhoB, PhoP, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsB, RhaR, RhaS, Rob, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YiaJ, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
H-NS      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): BglY, Cur, DNA-binding protein HLP-II (HU, BH2, HD, NS), DNA-binding transcriptional dual regulator H-NS, Drc, DrdX, Drs, FimG, Hns, HnsA, Irk, MsyA, OsmZ, PilG, TopS, TopX, VirR
Gene name(s): hns
Functional conformation(s): H-NS
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, BasR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsB, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, TorR, UvrY, YdeO, YjjQ, 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-Phosphorylated , NarL
Coregulator(s): AppY, ArcA, CRP, Cra, DcuR, DpiA, EvgA, FNR, FhlA, Fis, FlhDC, H-NS, IHF, IscR, Lrp, ModE, NagC, NarL, NarP, NikR, NorR, NsrR, OxyR, PhoP, RcsB, RstA, 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-Phosphorylated , NarP
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:
Cra Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator Cra, FruC, FruR, Shl
Gene name(s): cra
Functional conformation(s): Cra , Cra-β-D-fructofuranose 1-phosphate , Cra-β-D-fructose 1,6-bisphosphate
Coregulator(s): AcrR, ArcA, BasR, BetI, CRP, CpxR, Cra, CsgD, CusR, DksA, FNR, Fis, FliZ, Fur, GadE, GlcC, GntR, H-NS, HprR, IHF, IclR, KdgR, Lrp, MarA, MarR, Mlc, MlrA, MqsA, NagC, NarL, NarP, OmpR, PdhR, PrpR, RcdA, RcsB, Rob, RstA, SgrR, SoxS, TyrR, 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, 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, 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, RcsB, 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 CRP,Cra,FNR,Fis,H-NS,IHF,NarL,NarP Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP repressor Cra repressor FNR activator Fis repressor H-NS repressor IHF dual NarL activator NarP activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarP-Phosphorylated activator nirBp nirB , nirD , nirC , cysG 3493905 3493920 -74.0 tacaaatcagCAATATACCCATTAAGgagtatataa [BCE]
[BPP]
[GEA]
[SM]
[1]
[2]
[3]
[4]
NarP-Phosphorylated activator nirBp nirB , nirD , nirC , cysG 3493914 3493929 -65.0 gcaatataccCATTAAGGAGTATATAaaggtgaatt [BCE]
[BPP]
[GEA]
[SM]
[1]
[2]
[3]
[4]
CRP-cAMP repressor nirBp nirB , nirD , nirC , cysG 3493680 3493701 -296.5 acgctgtcgtCTTTGTGATGTGCTTCCTGTTAggtttcgtca [AIBSCS]
[GEA]
[5]
CRP-cAMP repressor nirBp nirB , nirD , nirC , cysG 3493935 3493956 -41.5 atataaaggtGAATTTGATTTACATCAATAAGcggggttgct [AIBSCS]
[GEA]
[5]
IHF activator nirBp nirB , nirD , nirC , cysG 3493866 3493878 -115.0 catgaaatatCAGACAATTCCGTgacttaagaa [BPP]
[GEA]
[HIBSCS]
[1]
[6]
IHF repressor nirBp nirB , nirD , nirC , cysG 3493893 3493905 -88.0 taagaaaattTATACAAATCAGCaatataccca [BCE]
[BPP]
[GEA]
[7]
[1]
[6]
Cra repressor nirBp nirB , nirD , nirC , cysG 3493963 3493980 -15.5 taagcggggtTGCTGAATCGTTAAGGTAggcggtaata [BCE]
[GEA]
[HIBSCS]
[1]
[8]
Fis repressor nirBp nirB , nirD , nirC , cysG 3493883 3493897 -97.0 ttccgtgactTAAGAAAATTTATACaaatcagcaa [BPP]
[HIBSCS]
[1]
Fis repressor nirBp nirB , nirD , nirC , cysG 3494002 3494016 23.0 aaaagaaatcGAGGCAAAAATGAGCaaagtcagac [AIBSCS]
[BPP]
[7]
[1]
Fis repressor nirBp nirB , nirD , nirC , cysG 3493838 3493852 -142.0 cgctcattttGTCTATTTTTTGCACaaacatgaaa [BPP]
[GEA]
[HIBSCS]
[1]
[6]
[9]
FNR activator nirBp nirB , nirD , nirC , cysG 3493939 3493952 -41.5 aaaggtgaatTTGATTTACATCAAtaagcggggt [BPP]
[GEA]
[HIBSCS]
[SM]
[1]
[6]
[10]
[11]
[3]
NarL-Phosphorylated activator nirBp nirB , nirD , nirC , cysG 3493914 3493929 -65.0 gcaatataccCATTAAGGAGTATATAaaggtgaatt [BCE]
[BPP]
[GEA]
[SM]
[1]
[2]
[3]
[4]
NarL-Phosphorylated activator nirBp nirB , nirD , nirC , cysG 3493905 3493920 -74.0 tacaaatcagCAATATACCCATTAAGgagtatataa [BCE]
[BPP]
[GEA]
[SM]
[1]
[2]
[3]
[4]
H-NS repressor nirBp nirB , nirD , nirC , cysG         [BPP]
[GEA]
[7]
[1]

Evidence: [BCE] Binding of cellular extracts
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[SM] Site mutation
[AIBSCS] Automated inference based on similarity to consensus sequences
[HIBSCS] Human inference based on similarity to consensus sequences
Reference(s): [1] Browning DF., et al., 2004
[2] Darwin AJ., et al., 1997
[3] Tyson KL., et al., 1993
[4] Wang H., et al., 2000
[5] Zheng D., et al., 2004
[6] Browning DF., et al., 2008
[7] Browning DF., et al., 2000
[8] Tyson K., et al., 1997
[9] Wu H., et al., 1998
[10] Eiglmeier K., et al., 1989
[11] Jayaraman PS., et al., 1988



Reference(s)    

 [1] Browning DF., Cole JA., Busby SJ., 2004, Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter., Mol Microbiol 53(1):203-15

 [2] 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

 [3] 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

 [4] 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

 [5] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [6] Browning DF., Cole JA., Busby SJ., 2008, Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter., J Bacteriol 190(21):7258-67

 [7] Browning DF., Cole JA., Busby SJ., 2000, Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly., Mol Microbiol 37(5):1258-69

 [8] Tyson K., Busby S., Cole J., 1997, Catabolite regulation of two Escherichia coli operons encoding nitrite reductases: role of the Cra protein., Arch Microbiol 168(3):240-4

 [9] Wu H., Tyson KL., Cole JA., Busby SJ., 1998, Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors., Mol Microbiol 27(2):493-505

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

 [11] Jayaraman PS., Gaston KL., Cole JA., Busby SJ., 1988, The nirB promoter of Escherichia coli: location of nucleotide sequences essential for regulation by oxygen, the FNR protein and nitrite., Mol Microbiol 2(4):527-30


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