RegulonDB RegulonDB 10.10: Regulon Form
   
   


AraC,CRP,XylR regulon in Escherichia coli K-12 genome


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-cyclic-AMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BolA, 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, FrlR, 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, PlaR, 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, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
AraC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator AraC
Gene name(s): araC
Functional conformation(s): AraC-α-L-arabinopyranose , AraC , AraC-D-fucose
Coregulator(s): AraC, CRP, GadX, NagC, XylR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
XylR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator XylR
Gene name(s): xylR
Functional conformation(s): XylR , XylR-α-D-xylopyranose
Coregulator(s): AraC, CRP, Fis, XylR
Summary: TF Summary ...[more]

REGULATION EXERTED BY AraC,CRP,XylR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AraC repressor CRP activator XylR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cyclic-AMP activator xylAp xylB , xylA 3730878 3730900 -81.5 attccattttATTTTGCGAGCGAGCGCACACTTgtgaattatc [GEA] [1]
[2]
XylR-α-D-xylopyranose activator xylAp xylB , xylA 3730861 3730878 -62.5 agcgcacactTGTGAATTATCTCAATAGcagtgtgaaa [GEA] [1]
XylR-α-D-xylopyranose activator xylAp xylB , xylA 3730840 3730857 -41.5 tcaatagcagTGTGAAATAACATAATTGagcaactgaa [GEA] [1]
AraC-α-L-arabinopyranose repressor xylAp xylB , xylA 3730824 3730840 -25.0 taacataattGAGCAACTGAAAGGGAGtgcccaatat [GEA] [3]
AraC-α-L-arabinopyranose repressor xylAp xylB , xylA 3730847 3730863 -48.0 attatctcaaTAGCAGTGTGAAATAACataattgagc [GEA] [3]
AraC dual CRP activator XylR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
AraC-α-L-arabinopyranose activator araCp araC 70131 70147 -84.0 ccgctaatctTATGGATAAAAATGCTAtggcatagca [GEA] [4]
[5]
AraC repressor araCp araC 70131 70147 -84.0 ccgctaatctTATGGATAAAAATGCTAtggcatagca [GEA] [4]
[5]
CRP-cyclic-AMP activator araCp araC 70158 70179 -54.5 tggcatagcaAAGTGTGACGCCGTGCAAATAAtcaatgtgga [GEA] [6]
AraC repressor araCp araC 70342 70358 128.0 tctgatgcaaTATGGACAATTGGTTTCttctctgaat    
AraC-α-L-arabinopyranose activator araCp araC 70110 70126 -105.0 ataaaaagcgTCAGGTAGGATCCGCTAatcttatgga [GEA] [7]
[4]
[5]
AraC-α-L-arabinopyranose repressor araCp araC 70184 70200 -31.0 aaataatcaaTGTGGACTTTTCTGCCGtgattataga [GEA] [8]
AraC-α-L-arabinopyranose repressor araCp araC 70205 70221 -10.0 ctgccgtgatTATAGACACTTTTGTTAcgcgtttttg [GEA] [9]
[8]
XylR-α-D-xylopyranose repressor araCp araC 70216 70234 2.5 atagacacttTTGTTACGCGTTTTTGTCAtggctttggt [GEA] [10]
XylR-α-D-xylopyranose repressor araCp araC 70195 70213 -19.5 gtggacttttCTGCCGTGATTATAGACACttttgttacg [GEA] [10]

Evidence: [GEA] Gene expression analysis
Reference(s): [1] Song S., et al., 1997
[2] Tsai MJ., et al., 2018
[3] Desai TA., et al., 2010
[4] Niland P., et al., 1996
[5] Reeder T., et al., 1993
[6] Lobell RB., et al., 1991
[7] Huo L., et al., 1988
[8] Lee DH., et al., 1992
[9] Gallegos MT., et al., 1997
[10] Koirala S., et al., 2015



Reference(s)    

 [1] Song S., Park C., 1997, Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator., J Bacteriol 179(22):7025-32

 [2] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [3] Desai TA., Rao CV., 2010, Regulation of arabinose and xylose metabolism in Escherichia coli., Appl Environ Microbiol 76(5):1524-32

 [4] Niland P., Huhne R., Muller-Hill B., 1996, How AraC interacts specifically with its target DNAs., J Mol Biol 264(4):667-74

 [5] Reeder T., Schleif R., 1993, AraC protein can activate transcription from only one position and when pointed in only one direction., J Mol Biol 231(2):205-18

 [6] Lobell RB., Schleif RF., 1991, AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein., J Mol Biol 218(1):45-54

 [7] Huo L., Martin KJ., Schleif R., 1988, Alternative DNA loops regulate the arabinose operon in Escherichia coli., Proc Natl Acad Sci U S A 85(15):5444-8

 [8] Lee DH., Huo L., Schleif R., 1992, Repression of the araBAD promoter from araO1., J Mol Biol 224(2):335-41

 [9] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410

 [10] Koirala S., Wang X., Rao CV., 2015, Reciprocal Regulation of l-Arabinose and d-Xylose Metabolism in Escherichia coli., J Bacteriol 198(3):386-93


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