RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


FNR,Fur,MetR,NsrR,ppGpp 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:
MetR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator MetR
Gene name(s): metR
Functional conformation(s): MetR-L-homocysteine , MetR
Coregulator(s): FNR, Fur, MetJ, MetR, NsrR, OxyR, PurR, ppGpp
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-nitric oxide , NsrR-[2Fe-2S]2+ oxidized , 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:
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,MetR,NsrR,ppGpp Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
FNR repressor Fur repressor MetR activator NsrR repressor ppGpp activation    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Fur-Fe2+ repressor hmpAp hmp 2685793 2685811 6.0 tataagatgcATTTGAGATACATCAATTAagatgcaaaa [AS]
[GEA]
[HIBSCS]
[IMP]
[1]
[2]
[3]
MetR activator hmpAp hmp 2685710 2685724 -80.0 caggtttgtgATGCAAATTTTTCACttcatcacat [BPP]
[GEA]
[HIBSCS]
[IMP]
[SM]
[4]
[5]
[6]
[7]
[8]
NsrR repressor hmpAp hmp 2685789 2685807 2.0 tttttataagATGCATTTGAGATACATCAattaagatgc [AIBSCS]
[GEA]
[9]
FNR repressor hmpAp hmp 2685795 2685808 5.5 taagatgcatTTGAGATACATCAAttaagatgca [BPP]
[GEA]
[HIBSCS]
[SM]
[10]
[11]
[12]
NsrR repressor hmpAp hmp 2685754 2685765 -38.0 aaaacaccaaAGAACCATTTACattgcagggc [GEA]
[HIBSCS]
[13]
NsrR repressor hmpAp hmp 2685811 2685822 20.0 tacatcaattAAGATGCAAAAAaaggaagacc [GEA]
[HIBSCS]
[13]

Evidence: [AS] Author statement
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[IMP] Inferred from mutant phenotype
[BPP] Binding of purified proteins
[SM] Site mutation
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Crawford MJ., et al., 1998
[2] D'Autreaux B., et al., 2002
[3] Hernandez-Urzua E., et al., 2007
[4] Lorenz E., et al., 1995
[5] Lorenz E., et al., 1996
[6] Lorenz E., et al., 1996
[7] Lorenz E., et al., 1996
[8] Membrillo-Hernandez J., et al., 1998
[9] Bodenmiller DM., et al., 2006
[10] Cruz-Ramos H., et al., 2002
[11] Membrillo-Hernandez J., et al., 1997
[12] Poole RK., et al., 1996
[13] Partridge JD., et al., 2009



Reference(s)    

 [1] Crawford MJ., Goldberg DE., 1998, Regulation of the Salmonella typhimurium flavohemoglobin gene. A new pathway for bacterial gene expression in response to nitric oxide., J Biol Chem 273(51):34028-32

 [2] D'Autreaux B., Touati D., Bersch B., Latour JM., Michaud-Soret I., 2002, Direct inhibition by nitric oxide of the transcriptional ferric uptake regulation protein via nitrosylation of the iron., Proc Natl Acad Sci U S A 99(26):16619-24

 [3] Hernandez-Urzua E., Zamorano-Sanchez DS., Ponce-Coria J., Morett E., Grogan S., Poole RK., Membrillo-Hernandez J., 2007, Multiple regulators of the Flavohaemoglobin (hmp) gene of Salmonella enterica serovar Typhimurium include RamA, a transcriptional regulator conferring the multidrug resistance phenotype., Arch Microbiol 187(1):67-77

 [4] Lorenz E., Stauffer GV., 1995, Characterization of the MetR binding sites for the glyA gene of Escherichia coli., J Bacteriol 177(14):4113-20

 [5] Lorenz E., Stauffer GV., 1996, RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli., Microbiology 142 ( Pt 7):1819-24

 [6] Lorenz E., Stauffer GV., 1996, MetR-mediated repression of the glyA gene in Escherichia coli., FEMS Microbiol Lett 144(2-3):229-33

 [7] Lorenz E., Stauffer GV., 1996, Cooperative MetR binding in the Escherichia coli glyA control region., FEMS Microbiol Lett 137(2-3):147-52

 [8] Membrillo-Hernandez J., Coopamah MD., Channa A., Hughes MN., Poole RK., 1998, A novel mechanism for upregulation of the Escherichia coli K-12 hmp (flavohaemoglobin) gene by the 'NO releaser', S-nitrosoglutathione: nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region., Mol Microbiol 29(4):1101-12

 [9] Bodenmiller DM., Spiro S., 2006, The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator., J Bacteriol 188(3):874-81

 [10] Cruz-Ramos H., Crack J., Wu G., Hughes MN., Scott C., Thomson AJ., Green J., Poole RK., 2002, NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp., EMBO J 21(13):3235-44

 [11] Membrillo-Hernandez J., Cook GM., Poole RK., 1997, Roles of RpoS (sigmaS), IHF and ppGpp in the expression of the hmp gene encoding the flavohemoglobin (Hmp) of Escherichia coli K-12., Mol Gen Genet 254(5):599-603

 [12] Poole RK., Anjum MF., Membrillo-Hernandez J., Kim SO., Hughes MN., Stewart V., 1996, Nitric oxide, nitrite, and Fnr regulation of hmp (flavohemoglobin) gene expression in Escherichia coli K-12., J Bacteriol 178(18):5487-92

 [13] 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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