RegulonDB RegulonDB 10.6.3: 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-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, 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, 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, RcsB, 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:
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 , AraC-arabinose , 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-xylose
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-cAMP activator xylAp xylB , xylA 3730878 3730900 -81.5 attccattttATTTTGCGAGCGAGCGCACACTTgtgaattatc [AIBSCS]
[GEA]
[HIBSCS]
[1]
[2]
[3]
XylR-xylose activator xylAp xylB , xylA 3730861 3730878 -62.5 agcgcacactTGTGAATTATCTCAATAGcagtgtgaaa [BPP]
[GEA]
[HIBSCS]
[1]
[2]
XylR-xylose activator xylAp xylB , xylA 3730840 3730857 -41.5 tcaatagcagTGTGAAATAACATAATTGagcaactgaa [BPP]
[GEA]
[HIBSCS]
[1]
[2]
AraC-arabinose repressor xylAp xylB , xylA 3730824 3730840 -25.0 taacataattGAGCAACTGAAAGGGAGtgcccaatat [BCE]
[GEA]
[4]
AraC-arabinose repressor xylAp xylB , xylA 3730847 3730863 -48.0 attatctcaaTAGCAGTGTGAAATAACataattgagc [BCE]
[GEA]
[HIBSCS]
[4]
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-arabinose dual araCp araC 70131 70147 -102.0 ccgctaatctTATGGATAAAAATGCTAtggcatagca [BPP]
[GEA]
[HIBSCS]
[SM]
[5]
[6]
[7]
[8]
[9]
[10]
AraC dual araCp araC 70131 70147 -102.0 ccgctaatctTATGGATAAAAATGCTAtggcatagca [BPP]
[GEA]
[HIBSCS]
[SM]
[5]
[6]
[7]
[8]
[9]
[10]
CRP-cAMP activator araCp araC 70158 70179 -72.5 tggcatagcaAAGTGTGACGCCGTGCAAATAAtcaatgtgga [BPP]
[GEA]
[HIBSCS]
[SM]
[11]
[12]
[13]
[14]
[15]
[16]
AraC repressor araCp araC 70342 70358 110.0 tctgatgcaaTATGGACAATTGGTTTCttctctgaat [BCE]
[BPP]
[HIBSCS]
[SM]
[6]
[12]
[7]
[8]
[9]
[17]
AraC-arabinose activator araCp araC 70110 70126 -123.0 ataaaaagcgTCAGGTAGGATCCGCTAatcttatgga [BPP]
[GEA]
[HIBSCS]
[SM]
[5]
[6]
[12]
[13]
[9]
[10]
AraC-arabinose repressor araCp araC 70184 70200 -49.0 aaataatcaaTGTGGACTTTTCTGCCGtgattataga [BCE]
[GEA]
[HIBSCS]
[SM]
[6]
[18]
[8]
AraC-arabinose repressor araCp araC 70205 70221 -28.0 ctgccgtgatTATAGACACTTTTGTTAcgcgtttttg [BCE]
[GEA]
[HIBSCS]
[SM]
[6]
[18]
[8]
XylR-xylose repressor araCp araC 70216 70234 -16.5 atagacacttTTGTTACGCGTTTTTGTCAtggctttggt [AIBSCS]
[BPP]
[GEA]
[19]
XylR-xylose repressor araCp araC 70195 70213 -37.5 gtggacttttCTGCCGTGATTATAGACACttttgttacg [AIBSCS]
[BPP]
[GEA]
[19]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[BCE] Binding of cellular extracts
[SM] Site mutation
Reference(s): [1] Laikova ON., et al., 2001
[2] Song S., et al., 1997
[3] Tsai MJ., et al., 2018
[4] Desai TA., et al., 2009
[5] Bustos SA., et al., 1993
[6] Gallegos MT., et al., 1997
[7] Lee DH., et al., 1989
[8] Lee NL., et al., 1981
[9] Niland P., et al., 1996
[10] Reeder T., et al., 1993
[11] Hamilton EP., et al., 1988
[12] Huo L., et al., 1988
[13] Lee N., et al., 1987
[14] Lobell RB., et al., 1991
[15] Stoltzfus L., et al., 1989
[16] Zhang X., et al., 1998
[17] Seabold RR., et al., 1998
[18] Lee DH., et al., 1992
[19] Koirala S., et al., null



Reference(s)    

 [1] Laikova ON., Mironov AA., Gelfand MS., 2001, Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria., FEMS Microbiol Lett 205(2):315-22

 [2] 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

 [3] 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

 [4] Desai TA., Rao CV., 2009, Regulation of arabinose and xylose metabolism in Escherichia coli., Appl Environ Microbiol

 [5] Bustos SA., Schleif RF., 1993, Functional domains of the AraC protein., Proc Natl Acad Sci U S A 90(12):5638-42

 [6] 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

 [7] Lee DH., Schleif RF., 1989, In vivo DNA loops in araCBAD: size limits and helical repeat., Proc Natl Acad Sci U S A 86(2):476-80

 [8] Lee NL., Gielow WO., Wallace RG., 1981, Mechanism of araC autoregulation and the domains of two overlapping promoters, Pc and PBAD, in the L-arabinose regulatory region of Escherichia coli., Proc Natl Acad Sci U S A 78(2):752-6

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

 [10] 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

 [11] Hamilton EP., Lee N., 1988, Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli., Proc Natl Acad Sci U S A 85(6):1749-53

 [12] 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

 [13] Lee N., Francklyn C., Hamilton EP., 1987, Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter., Proc Natl Acad Sci U S A 84(24):8814-8

 [14] 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

 [15] Stoltzfus L., Wilcox G., 1989, Effect of mutations in the cyclic AMP receptor protein-binding site on araBAD and araC expression., J Bacteriol 171(2):1178-84

 [16] Zhang X., Schleif R., 1998, Catabolite gene activator protein mutations affecting activity of the araBAD promoter., J Bacteriol 180(2):195-200

 [17] Seabold RR., Schleif RF., 1998, Apo-AraC actively seeks to loop., J Mol Biol 278(3):529-38

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

 [19] Koirala S., Wang X., Rao CV., null, Reciprocal Regulation of l-Arabinose and d-Xylose Metabolism in Escherichia coli., J Bacteriol 198(3):386-393


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