RegulonDB RegulonDB 10.8: Regulon Form
   
   


Cra,Fis,Lrp,NarL 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:
Lrp Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Sensing external and internal signals
Synonym(s): AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA
Gene name(s): lrp
Functional conformation(s): Lrp-leucine , Lrp
Coregulator(s): AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, QseB, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, 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:
Cra Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator Cra, FruC, FruR, Shl
Gene name(s): cra
Functional conformation(s): Cra-;-D-fructose 1,6-bisphosphate , Cra-β-D-fructose 1,6-bisphosphate , Cra-β-D-fructofuranose 1-phosphate , Cra
Coregulator(s): AcrR, ArcA, BasR, BetI, BtsR, CRP, CpxR, Cra, CsgD, CusR, DcuR, DksA, FNR, Fis, FliZ, Fur, GadE, GlcC, GntR, H-NS, HprR, IHF, IclR, KdgR, Lrp, MarA, MarR, Mlc, MlrA, MqsA, NagC, NarL, NarP, OmpR, PdhR, PrpR, RcdA, RcsAB, Rob, RstA, SgrR, SoxS, TyrR, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY Cra,Fis,Lrp,NarL Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
Cra repressor Fis activator Lrp repressor NarL repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NarL-Phosphorylated repressor adhEp1 adhE 1298316 1298331 90.0 atcagtacccAGAAGTGAGTAATCTTgcttacgcca [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
NarL-Phosphorylated repressor adhEp1 adhE 1298325 1298340 81.0 gatcacgtaaTCAGTACCCAGAAGTGagtaatcttg [APIORCISFBSCS]
[CV(GEA/ROMA)]
[GEA]
[1]
[2]
Cra repressor adhEp1 adhE 1298370 1298386 36.5 cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa [BCE]
[CV(CHIP-SV/GEA/ROMA)]
[CV(CHIP-SV/SM)]
[CV(GEA/ROMA)]
[CV(GEA/ROMA/SM)]
[GEA]
[ICWHO]
[SM]
[3]
[4]
[5]
Fis activator adhEp1 adhE 1298554 1298568 -148.0 gccggataatGTTAGCCATAAATAAggttgaaaag [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[6]
Fis activator adhEp1 adhE 1298474 1298488 -68.0 tacttaaaatTGCTATCATTCGTTAttgttatcta [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[6]
Fis activator adhEp1 adhE 1298448 1298462 -42.0 tgttatctagTTGTGCAAAACATGCtaatgtagcc [APIORCISFBSCS]
[BPP]
[CV(CHIP-SV/GEA/ROMA)]
[CV(GEA/ROMA)]
[GEA]
[6]
Lrp repressor adhEp1 adhE 1298563 1298578 -157.0 cgaagcaaaaGCCGGATAATGTTAGCcataaataag [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[7]
Lrp repressor adhEp1 adhE 1298472 1298485 -65.0 ttaaaattgcTATCATTCGTTATTgttatctagt [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[7]
Lrp repressor adhEp1 adhE 1298412 1298427 -6.0 accaaatcatACTACAATTTATTAACtgttagctat [AIBSCS]
[CV(GEA/ROMA)]
[GEA]
[7]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(GEA/ROMA)] cross validation(GEA/ROMA)
[GEA] Gene expression analysis
[BCE] Binding of cellular extracts
[CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)
[CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)
[CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)
[ICWHO] Inferred computationally without human oversight
[SM] Site mutation
[BPP] Binding of purified proteins
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Chen YM., et al., 1991
[2] Membrillo-Hernandez J., et al., 1999
[3] Kaga N., et al., 2002
[4] Mikulskis A., et al., 1997
[5] Sarkar D., et al., 2008
[6] Membrillo-Hernandez J., et al., 1999
[7] Lintner RE., et al., 2008



Reference(s)    

 [1] Chen YM., Lin EC., 1991, Regulation of the adhE gene, which encodes ethanol dehydrogenase in Escherichia coli., J Bacteriol 173(24):8009-13

 [2] Membrillo-Hernandez J., Lin EC., 1999, Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS., J Bacteriol 181(24):7571-9

 [3] Kaga N., Umitsuki G., Clark DP., Nagai K., Wachi M., 2002, Extensive overproduction of the AdhE protein by rng mutations depends on mutations in the cra gene or in the Cra-box of the adhE promoter., Biochem Biophys Res Commun 295(1):92-7

 [4] Mikulskis A., Aristarkhov A., Lin EC., 1997, Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra., J Bacteriol 179(22):7129-34

 [5] Sarkar D., Siddiquee KA., Arauzo-Bravo MJ., Oba T., Shimizu K., 2008, Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli., Arch Microbiol 190(5):559-71

 [6] Membrillo-Hernandez J., Kwon O., De Wulf P., Finkel SE., Lin EC., 1999, Regulation of adhE (encoding ethanol oxidoreductase) by the Fis protein in Escherichia coli., J Bacteriol 181(23):7390-3

 [7] Lintner RE., Mishra PK., Srivastava P., Martinez-Vaz BM., Khodursky AB., Blumenthal RM., 2008, Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio., BMC Microbiol 8:60


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