RegulonDB RegulonDB 10.8: Regulon Form
   
   


ArcA,CRP,FNR,Fis,Fur,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:
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 , CRP-cAMP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CRP-Sxy, 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, GadE-RcsB, 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, RcsAB, RcsB, RcsB-BglJ, 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:
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:
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,CRP,FNR,Fis,Fur,PdhR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
ArcA activator CRP activator FNR dual Fis activator Fur repressor PdhR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator grcAp1 grcA 2716553 2716574 -40.5 atgtgtggttTTTATTGATTTAAATCAAAGATtcaagggtgt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
ArcA-Phosphorylated activator grcAp1 grcA 2716615 2716629 -99.0 ttcacacccgCATAAGTTGATGTAAaacaataaaa [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
ArcA-Phosphorylated activator grcAp1 grcA 2716598 2716612 -82.0 tgatgtaaaaCAATAAAATCCATTTgcgaccatac [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
PdhR repressor grcAp1 grcA 2716499 2716515 17.0 actcaagcaaCAATGGTTTTACCAATTggccgcgaca [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[2]
Fis activator grcAp1 grcA 2716675 2716689 -159.0 acaaaatcatGCTCATTTTTTAGACttaaacgagt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
Fis activator grcAp1 grcA 2716633 2716647 -117.0 aatgtaaattGGTAAAATTTCACACccgcataagt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
Fis activator grcAp1 grcA 2716526 2716540 -10.0 aagggtgtttGAGGAGTATATATACactcaagcaa [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[3]
FNR activator grcAp1 grcA 2716557 2716570 -40.5 gtggtttttaTTGATTTAAATCAAagattcaagg [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[2]
FNR repressor grcAp1 grcA 2716610 2716623 -93.5 cccgcataagTTGATGTAAAACAAtaaaatccat [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[4]
[7]
[5]
[2]
FNR repressor grcAp1 grcA 2716557 2716570 -40.5 gtggtttttaTTGATTTAAATCAAagattcaagg [BPP]
[CV(CHIP-SV/SM)]
[GEA]
[SM]
[4]
[5]
[6]
[2]
Fur-Fe2+ repressor grcAp1 grcA         [GEA] [7]

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.
[BPP] Binding of purified proteins
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[SM] Site mutation
Reference(s): [1] Zheng D., et al., 2004
[2] Wyborn NR., et al., 2002
[3] Bradley MD., et al., 2007
[4] Green J., et al., 1998
[5] Marshall FA., et al., 2001
[6] Shalel-Levanon S., et al., 2005
[7] Kumar R., et al., 2011



Reference(s)    

 [1] 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

 [2] Wyborn NR., Messenger SL., Henderson RA., Sawers G., Roberts RE., Attwood MM., Green J., 2002, Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products., Microbiology 148(Pt 4):1015-26

 [3] 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

 [4] Green J., Baldwin ML., Richardson J., 1998, Downregulation of Escherichia coli yfiD expression by FNR occupying a site at -93.5 involves the AR1-containing face of FNR., Mol Microbiol 29(4):1113-23

 [5] Marshall FA., Messenger SL., Wyborn NR., Guest JR., Wing H., Busby SJ., Green J., 2001, A novel promoter architecture for microaerobic activation by the anaerobic transcription factor FNR., Mol Microbiol 39(3):747-53

 [6] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions., Biotechnol Bioeng 92(2):147-59

 [7] 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


RegulonDB