RegulonDB RegulonDB 10.8: Regulon Form
   
   


CRP,FNR,GcvA,Lrp,PurR 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:
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:
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:
GcvA Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator GcvA, positive regulator of gcv operon
Gene name(s): gcvA
Functional conformation(s): GcvA-Purine , GcvA , GcvA-gly
Coregulator(s): CRP, FNR, GcvA, Lrp, PurR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PurR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional repressor PurR
Gene name(s): purR
Functional conformation(s): PurR , PurR-Guanine , PurR-hypoxanthine
Coregulator(s): CRP, DnaA, FNR, Fis, Fur, GadE, GcvA, IHF, Lrp, MarA, MetR, Nac, PepA, PhoP, PurR, RbsR, RutR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,FNR,GcvA,Lrp,PurR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator FNR activator GcvA dual Lrp activator PurR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
GcvA activator gcvTp gcvP , gcvH , gcvT 3051023 3051037 -258.0 ttttcctcatTTGAAATAAACTAATttcacctccg [APIORCISFBSCS]
[BCE]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
GcvA activator gcvTp gcvP , gcvH , gcvT 3050991 3051005 -226.0 ccgttttcgcATTATATTTTCTAATgccattattt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
Lrp activator gcvTp gcvP , gcvH , gcvT 3050926 3050940 -161.0 gctcttaataTTGTCTTATTCAAATtgactttctc [GEA]
[SM]
[9]
[8]
GcvA repressor gcvTp gcvP , gcvH , gcvT 3050809 3050823 -44.0 aatgtgatgaTCAATTTTACCTTATggttaacagt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[IC]
[SM]
[1]
[10]
[3]
[6]
[8]
[11]
PurR-hypoxanthine repressor gcvTp gcvP , gcvH , gcvT 3050758 3050773 7.5 gttcaggcaaAAGAGAACGATTGCGTtggggaccgg [AIBSCS]
[APIORCISFBSCS]
[CV(GEA)]
[GEA]
[12]
[8]
GcvA repressor gcvTp gcvP , gcvH , gcvT 3050831 3050845 -66.0 ttgcatttttTAACCATAAGCTAATgtgatgatca [APIORCISFBSCS]
[BCE]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[10]
[3]
[6]
[8]
[11]
CRP-cAMP activator gcvTp gcvP , gcvH , gcvT 3051075 3051097 -313.5 tcctctgttgTTTATTTGATACCCATCACACTTtcatctcccg [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[13]
CRP-cAMP activator gcvTp gcvP , gcvH , gcvT 3050907 3050929 -145.5 tgtcttattcAAATTGACTTTCTCATCACATCAtctttgtata [APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[13]
GcvA repressor gcvTp gcvP , gcvH , gcvT 3050991 3051005 -226.0 ccgttttcgcATTATATTTTCTAATgccattattt [APIORCISFBSCS]
[BCE]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
GcvA repressor gcvTp gcvP , gcvH , gcvT 3051023 3051037 -258.0 ttttcctcatTTGAAATAAACTAATttcacctccg [APIORCISFBSCS]
[BCE]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
FNR activator gcvTp gcvP , gcvH , gcvT         [AIBSCS]
[CV(GEA)]
[GEA]
[14]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BCE] Binding of cellular extracts
[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
[IC] Inferred by curator
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Jourdan AD., et al., 1999
[2] Jourdan AD., et al., 1998
[3] Stauffer LT., et al., 2005
[4] Stauffer LT., et al., 1998
[5] Stauffer LT., et al., 1998
[6] Wilson RL., et al., 1994
[7] Wilson RL., et al., 1993
[8] Wilson RL., et al., 1995
[9] Stauffer LT., et al., 1999
[10] McArthur SD., et al., 2006
[11] Wonderling LD., et al., 2000
[12] Cho BK., et al., 2011
[13] Wonderling LD., et al., 1999
[14] Salmon K., et al., 2003



Reference(s)    

 [1] Jourdan AD., Stauffer GV., 1999, Genetic analysis of the GcvA binding site in the gcvA control region., Microbiology 145 ( Pt 8):2153-62

 [2] Jourdan AD., Stauffer GV., 1998, Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding., J Bacteriol 180(18):4865-71

 [3] Stauffer LT., Stauffer GV., 2005, GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon., FEMS Microbiol Lett 242(2):333-8

 [4] Stauffer LT., Stauffer GV., 1998, Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli., Microbiology 144 ( Pt 5):1417-22

 [5] Stauffer LT., Stauffer GV., 1998, Roles for GcvA-binding sites 3 and 2 and the Lrp-binding region in gcvT::lacZ expression in Escherichia coli., Microbiology 144 ( Pt 10):2865-72

 [6] Wilson RL., Stauffer GV., 1994, DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system., J Bacteriol 176(10):2862-8

 [7] Wilson RL., Steiert PS., Stauffer GV., 1993, Positive regulation of the Escherichia coli glycine cleavage enzyme system., J Bacteriol 175(3):902-4

 [8] Wilson RL., Urbanowski ML., Stauffer GV., 1995, DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli., J Bacteriol 177(17):4940-6

 [9] Stauffer LT., Stauffer GV., 1999, Role for the leucine-responsive regulatory protein (Lrp) as a structural protein in regulating the Escherichia coli gcvTHP operon., Microbiology 145 ( Pt 3):569-76

 [10] McArthur SD., Pulvermacher SC., Stauffer GV., 2006, The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules., BMC Microbiol 6:52

 [11] Wonderling LD., Urbanowski ML., Stauffer GV., 2000, GcvA binding site 1 in the gcvTHP promoter of Escherichia coli is required for GcvA-mediated repression but not for GcvA-mediated activation., Microbiology 146 ( Pt 11):2909-18

 [12] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

 [13] Wonderling LD., Stauffer GV., 1999, The cyclic AMP receptor protein is dependent on GcvA for regulation of the gcv operon., J Bacteriol 181(6):1912-9

 [14] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55


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