RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


FNR,Fur,H-NS regulon in Escherichia coli K-12 genome


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:
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:
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-Fe2+ , Fur-Mn2+ , Fur
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, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY FNR,Fur,H-NS Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR activator Fur repressor H-NS activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
H-NS activator fesp fes , ybdZ , entF , fepE 612679 612693 -0.5 tatcaataatATTATCAATATATTTctgcaatcaa [GEA] [1]
Fur-Fe2+ repressor fesp fes , ybdZ , entF , fepE 612657 612675 -21.0 cgctattgcaAATGCAAATAGTTATCAATaatattatca [BPP]
[GEA]
[HIBSCS]
[2]
[3]
[4]
[5]
Fur-Fe2+ repressor fesp fes , ybdZ , entF , fepE 612676 612694 -2.0 agttatcaatAATATTATCAATATATTTCtgcaatcaat [BPP]
[GEA]
[HIBSCS]
[2]
[3]
[4]
Fur-Fe2+ repressor fesp fes , ybdZ , entF , fepE 612663 612681 -15.0 tgcaaatgcaAATAGTTATCAATAATATTatcaatatat [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[2]
[3]
[4]
[5]
Fur-Fe2+ repressor fesp fes , ybdZ , entF , fepE 612669 612687 -9.0 tgcaaatagtTATCAATAATATTATCAATatatttctgc [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[2]
[3]
[4]
[5]
Fur-Fe2+ repressor fesp fes , ybdZ , entF , fepE 612650 612668 -28.0 gccattacgcTATTGCAAATGCAAATAGTtatcaataat [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[2]
[6]
[7]
[3]
[4]
[8]
[5]
FNR activator fesp fes , ybdZ , entF , fepE 612537 612550 -143.5 aactgtcgggCATGGTCGTCATCAacacgacgca [AIBSCS]
[GEA]
[9]

Evidence: [GEA] Gene expression analysis
[BPP] Binding of purified proteins
[HIBSCS] Human inference based on similarity to consensus sequences
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] White-Ziegler CA., et al., 2007
[2] Chen Z., et al., 2007
[3] Kumar R., et al., 2011
[4] Newman DL., et al., 1999
[5] Zhang Z., et al., 2005
[6] Escolar L., et al., 1998
[7] Hunt MD., et al., 1994
[8] Vassinova N., et al., 2000
[9] Constantinidou C., et al., 2006



Reference(s)    

 [1] White-Ziegler CA., Malhowski AJ., Young S., 2007, Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12., J Bacteriol 189(15):5429-40

 [2] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

 [3] 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

 [4] Newman DL., Shapiro JA., 1999, Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development., Mol Microbiol 33(1):18-32

 [5] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [6] Escolar L., Perez-Martin J., de Lorenzo V., 1998, Coordinated repression in vitro of the divergent fepA-fes promoters of Escherichia coli by the iron uptake regulation (Fur) protein., J Bacteriol 180(9):2579-82

 [7] Hunt MD., Pettis GS., McIntosh MA., 1994, Promoter and operator determinants for fur-mediated iron regulation in the bidirectional fepA-fes control region of the Escherichia coli enterobactin gene system., J Bacteriol 176(13):3944-55

 [8] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-82

 [9] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15


RegulonDB