RegulonDB RegulonDB 10.8: Regulon Form
   
   


ArcA,FNR,Fis,Fur,IHF,NsrR,PdhR 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:
ArcA Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class External-Two-component systems
Synonym(s): ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein
Gene name(s): arcA
Functional conformation(s): ArcA , ArcA-Phosphorylated
Coregulator(s): AdiY, AppY, ArcA, BetI, BtsR, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PdhR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): AceC, DNA-binding transcriptional dual regulator PdhR, GenA, YacB
Gene name(s): pdhR
Functional conformation(s): PdhR , PdhR-pyruvate
Coregulator(s): ArcA, BasR, BtsR, CRP, CpxR, Cra, CusR, FNR, Fis, Fur, GadE, GlcC, HprR, HypT, IHF, MraZ, NsrR, PdhR, PhoP
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:
Fur Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator Fur
Gene name(s): fur
Functional conformation(s): Fur-Mn2+ , Fur , Fur-Fe2+
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CdaR, CpxR, Cra, CusR, EnvY, FNR, Fis, FliZ, Fur, GadE, GadX, H-NS, HdfR, HprR, HypT, IHF, IscR, LrhA, Lrp, MarA, MatA, MetR, MntR, ModE, MqsA, Nac, NagC, NarL, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsAB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY ArcA,FNR,Fis,Fur,IHF,NsrR,PdhR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA repressor FNR repressor Fis dual Fur repressor IHF repressor NsrR repressor PdhR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
ArcA-Phosphorylated repressor ndhp ndh 1166052 1166066 68.0 aaccattaatTAACAATTGGTTAATaaatttaagg [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
ArcA-Phosphorylated repressor ndhp ndh 1166050 1166064 66.0 ataaccattaATTAACAATTGGTTAataaatttaa [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
ArcA-Phosphorylated repressor ndhp ndh 1166041 1166055 57.0 gctatgttaaTAACCATTAATTAACaattggttaa [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
ArcA-Phosphorylated repressor ndhp ndh 1166036 1166050 52.0 taagagctatGTTAATAACCATTAAttaacaattg [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
ArcA-Phosphorylated repressor ndhp ndh 1166020 1166034 36.0 gtaacctgttGTTAATTAAGAGCTAtgttaataac [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
ArcA-Phosphorylated repressor ndhp ndh 1165928 1165942 -57.0 cttttcagcaACAAAACTTGATTAAcatcaatttt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
IHF repressor ndhp ndh 1166011 1166023 26.0 ttcattgctgTAACCTGTTGTTAattaagagct [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
IHF repressor ndhp ndh 1165969 1165981 -17.0 accaatgcacCATTCATGTTATTctcaatagcg [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
IHF repressor ndhp ndh 1165928 1165940 -58.0 cttttcagcaACAAAACTTGATTaacatcaatt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[3]
PdhR repressor ndhp ndh 1165949 1165965 -35.0 ttaacatcaaTTTTGGTATGACCAATGcaccattcat [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[4]
Fis activator ndhp ndh 1165913 1165927 -72.0 ggtaaagtcgCCTATCTTTTCAGCAacaaaacttg [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM]
[5]
[6]
Fis activator ndhp ndh 1165862 1165876 -123.0 cacaaattcgCTCAAATAATAAACAataaactctg [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM]
[5]
[6]
Fis repressor ndhp ndh 1166035 1166049 51.0 ttaagagctaTGTTAATAACCATTAattaacaatt [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/SM)]
[SM]
[5]
[6]
FNR repressor ndhp ndh 1165935 1165948 -50.5 gcaacaaaacTTGATTAACATCAAttttggtatg [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[7]
[6]
[8]
[9]
FNR repressor ndhp ndh 1165891 1165904 -94.5 actctgttttTTGATCTCACCCGGtaaagtcgcc [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[SM]
[7]
[6]
[8]
[9]
Fur-Fe2+ repressor ndhp ndh         [GEA] [8]
NsrR repressor ndhp ndh 1165992 1166003 6.0 ctcaatagcgAAGAACATTTTCattgctgtaa [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[10]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BCE] Binding of cellular extracts
[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)
[SM] Site mutation
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
Reference(s): [1] Liu X., et al., 2004
[2] Rolfe MD., et al., 2012
[3] Green J., et al., 1997
[4] Ogasawara H., et al., 2007
[5] Green J., et al., 1996
[6] Jackson L., et al., 2004
[7] Green J., et al., 1994
[8] Kumar R., et al., 2011
[9] Salmon K., et al., 2003
[10] Partridge JD., et al., 2009



Reference(s)    

 [1] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [2] Rolfe MD., Ocone A., Stapleton MR., Hall S., Trotter EW., Poole RK., Sanguinetti G., Green J., 2012, Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations., Open Biol 2(7):120091

 [3] Green J., Anjum MF., Guest JR., 1997, Regulation of the ndh gene of Escherichia coli by integration host factor and a novel regulator, Arr., Microbiology 143 ( Pt 9):2865-75

 [4] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41

 [5] Green J., Anjum MF., Guest JR., 1996, The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis., Mol Microbiol 20(5):1043-55

 [6] Jackson L., Blake T., Green J., 2004, Regulation of ndh expression in Escherichia coli by Fis., Microbiology 150(Pt 2):407-13

 [7] Green J., Guest JR., 1994, Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors., Mol Microbiol 12(3):433-44

 [8] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [9] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [10] 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


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