RegulonDB RegulonDB 10.8: Regulon Form
   
   


FNR,NarL,NarP 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-[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]

REGULATION EXERTED BY FNR,NarL,NarP Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR dual NarL activator NarP repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarL-Phosphorylated activator fdnGp fdnG , fdnH , fdnI 1547264 1547279 -100.0 tttttctaccGCTATTGAGGTAGGTCaatttgcgaa [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
NarL-Phosphorylated activator fdnGp fdnG , fdnH , fdnI 1547255 1547270 -109.0 agtggtgcgtTTTTCTACCGCTATTGaggtaggtca [BCE]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[5]
[4]
NarL-Phosphorylated activator fdnGp fdnG , fdnH , fdnI 1547287 1547302 -77.0 gtcaatttgcGAAGGCGGATTATTTTgtggcaaaca [APIORCISFBSCS]
[BCE]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
NarL-Phosphorylated activator fdnGp fdnG , fdnH , fdnI 1547240 1547255 -124.0 actggcctgtCAGGCAGTGGTGCGTTtttctaccgc [APIORCISFBSCS]
[BCE]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[6]
[3]
[4]
FNR activator fdnGp fdnG , fdnH , fdnI 1547268 1547281 -97.5 tctaccgctaTTGAGGTAGGTCAAtttgcgaagg [APIORCISFBSCS]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[5]
FNR activator fdnGp fdnG , fdnH , fdnI 1547323 1547336 -42.5 gatgttctttTTGATTTCGCGCAAaaagattcag [APIORCISFBSCS]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[5]
[7]
NarP-Phosphorylated repressor fdnGp fdnG , fdnH , fdnI 1547264 1547279 -100.0 tttttctaccGCTATTGAGGTAGGTCaatttgcgaa [GEA]
[SM]
[2]
[4]
FNR repressor fdnGp fdnG , fdnH , fdnI 1547268 1547281 -97.5 tctaccgctaTTGAGGTAGGTCAAtttgcgaagg [APIORCISFBSCS]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[5]
NarP-Phosphorylated repressor fdnGp fdnG , fdnH , fdnI 1547255 1547270 -109.0 agtggtgcgtTTTTCTACCGCTATTGaggtaggtca [GEA]
[SM]
[2]
[4]
FNR activator NarL repressor NarP repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarP-Phosphorylated repressor ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754634 1754641 6.0 attttttctcCTAACCATaaaggattag [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[8]
NarP-Phosphorylated repressor ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754625 1754632 15.0 cctaaccataAAGGATTAgtttatcggc [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[8]
NarL-Phosphorylated repressor ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754650 1754665 -16.0 ttaagggctcAGAATAATCACATTATtttttctcct [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[8]
NarL-Phosphorylated repressor ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754676 1754691 -42.0 gtaattttaaTTGATAACGATCAATGttaagggctc [APIORCISFBSCS]
[CV(GEA)]
[GEA]
[8]
FNR activator ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754678 1754691 -42.5 gtaattttaaTTGATAACGATCAAtgttaagggc [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[9]
[8]
NarL-Phosphorylated repressor ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754629 1754644 6.0 attattttttCTCCTAACCATAAAGGattagtttat [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[8]
NarL-Phosphorylated repressor ydhYp ydhT , ydhU , ydhX , ydhW , ydhV , ydhY 1754620 1754635 15.0 tctcctaaccATAAAGGATTAGTTTAtcggcgttaa [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[8]

Evidence: [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(GEA)] cross validation(GEA)
[CV(GEA/SM)] cross validation(GEA/SM)
[CV(SM)] cross validation(SM)
[GEA] Gene expression analysis
[SM] Site mutation
[BCE] Binding of cellular extracts
Reference(s): [1] Berg BL., et al., 1990
[2] Darwin AJ., et al., 1997
[3] Rabin RS., et al., 1993
[4] Wang H., et al., 2003
[5] Li J., et al., 1992
[6] Li J., et al., 1994
[7] Spiro S., et al., 1991
[8] Partridge JD., et al., 2008
[9] Kang Y., et al., 2005



Reference(s)    

 [1] Berg BL., Stewart V., 1990, Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12., Genetics 125(4):691-702

 [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] 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

 [4] Wang H., Gunsalus RP., 2003, Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP., J Bacteriol 185(17):5076-85

 [5] Li J., Stewart V., 1992, Localization of upstream sequence elements required for nitrate and anaerobic induction of fdn (formate dehydrogenase-N) operon expression in Escherichia coli K-12., J Bacteriol 174(15):4935-42

 [6] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [7] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4

 [8] Partridge JD., Browning DF., Xu M., Newnham LJ., Scott C., Roberts RE., Poole RK., Green J., 2008, Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP., Microbiology 154(Pt 2):608-18

 [9] Kang Y., Weber KD., Qiu Y., Kiley PJ., Blattner FR., 2005, Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function., J Bacteriol 187(3):1135-60


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