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XylR DNA-binding transcriptional dual regulator

Synonyms: XylR, XylR-xylose
Summary:
"Xylose regulator," XylR, is a transcription factor involved in D-xylose degradation. It coregulates with CRP, a global transcriptional regulator [3]. These regulators bind cooperatively to activate transcription of operons involved in transport and catabolism of d-xylose. Synthesis of these operons is induced when Escherichia coli is grown on D-xylose in the absence of glucose. Gene induction occurs when the physiological inducer, D-xylose, binds to XylR and when cellular cyclic AMP levels are high [3]. In the presence of D-xylose, XylR binds in tandem to four inverted repeat sequences in the xylAB/xylFGHR intergenic region to activate transcription by overlapping the -35 boxes of xylABp and xylFGHRp [3]. The binding targets for XylR consist of 18-nucleotide-long directed repeat sequences that possess conserved motifs; each monomer binds to one of these conserved sequences [3, 4].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
XylR Non-Functional   Apo [BPP] [1]
XylR-xylose Functional Allosteric Holo [APPH], [BPP], [GEA], [IEP] [1], [2], [3]
Evolutionary Family: AraC/XylS
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: xylR
  Genome position: 3734979-3736157
  Length: 1179 bp / 392 aa
Operon name: xylFGHR
TU(s) encoding the TF:
Transcription unit        Promoter
xylFGHR
xylFp
xylR
xylRp


Regulon       
Regulated gene(s) araC, xylA, xylB, xylE, xylF, xylG, xylH, xylR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (8)
Transcription related (2)
activator (2)
operon (2)
membrane (2)
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Regulated operon(s) araC, xylAB, xylE, xylFGHR
First gene in the operon(s) araC, xylA, xylF, xylE
Simple and complex regulons AraC,CRP,XylR
CRP,Fis,XylR
CRP,XylR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[XylR,-](1)
[XylR,+](3)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  XylR-xylose repressor araCp Sigma70 -37.5 -183.0 araC
gtggacttttCTGCCGTGATTATAGACACttttgttacg
70195 70213 [AIBSCS], [BPP], [GEA] [2]
  XylR-xylose repressor araCp Sigma70 -16.5 -162.0 araC
atagacacttTTGTTACGCGTTTTTGTCAtggctttggt
70216 70234 [AIBSCS], [BPP], [GEA] [2]
  XylR-xylose activator xylAp nd -62.5 -104.5 xylA, xylB
agcgcacactTGTGAATTATCTCAATAGcagtgtgaaa
3730861 3730878 [BPP], [GEA], [HIBSCS] [3], [4]
  XylR-xylose activator xylAp nd -41.5 -83.5 xylA, xylB
tcaatagcagTGTGAAATAACATAATTGagcaactgaa
3730840 3730857 [BPP], [GEA], [HIBSCS] [3], [4]
  XylR-xylose activator xylEp Sigma70 -65.0 -102.0 xylE
taagatcacaGAAAAGACATTACGTAAacgcattgta
4242348 4242364 [AIBSCS], [BPP], [GEA], [SM] [5]
  XylR-xylose activator xylEp Sigma70 -44.0 -81.0 xylE
acgtaaacgcATTGTAAAAAATGATAAttgccttaac
4242327 4242343 [AIBSCS], [BPP], [GEA], [SM] [5]
  XylR-xylose activator xylFp nd -61.5 -123.5 xylF, xylG, xylH, xylR
tcaagaaataAACCAAAAATCGTAATCGaaagataaaa
3730999 3731016 [BPP], [GEA], [HIBSCS] [3], [4]
  XylR-xylose activator xylFp nd -40.5 -102.5 xylF, xylG, xylH, xylR
gtaatcgaaaGATAAAAATCTGTAATTGttttcccctg
3731020 3731037 [BPP], [GEA], [HIBSCS] [3], [4]


Alignment and PSSM for XylR TFBSs    

Aligned TFBS of XylR   
  Sequence
  CAGTGTGAAATAACATAATTG
  CATTGTAAAAAATGATAATTG
  ATAAACCAAAAATCGTAATCG
  AAAGATAAAAATCTGTAATTG
  ACTTGTGAATTATCTCAATAG
  CATGACAAAAACGCGTAACAA
  AAGTGTCTATAATCACGGCAG
  AGAAAAGACATTACGTAAACG

Position weight matrix (PWM). XylR matrix-quality result   
A	5	5	3	2	4	1	3	7	7	6	5	5	2	0	3	0	7	7	1	3	1
C	3	1	0	0	0	2	2	0	1	0	0	1	1	6	0	2	0	0	2	2	0
G	0	1	2	2	4	0	3	0	0	0	0	0	1	1	4	0	1	1	0	0	7
T	0	1	3	4	0	5	0	1	0	2	3	2	4	1	1	6	0	0	5	3	0

Consensus   
;	consensus.strict             	aaatgtgAAaaatCgtAAtaG
;	consensus.strict.rc          	CTATTACGATTTTTCACATTT
;	consensus.IUPAC              	madkryvAAawatCryAAyhG
;	consensus.IUPAC.rc           	CDRTTRYGATWTTTBRYMHTK
;	consensus.regexp             	[ac]a[agt][gt][ag][ct][acg]AAa[at]atC[ag][ct]AA[ct][act]G
;	consensus.regexp.rc          	C[AGT][AG]TT[AG][CT]GAT[AT]TTT[CGT][AG][CT][AC][ACT]T[GT]

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [APPH] Assay of protein purified to homogeneity

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] Seeger C., Poulsen C., Dandanell G., 1995, Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli., J Bacteriol 177(19):5506-16

 [2] 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

 [3] 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

 [4] 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

 [5] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [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] Tobes R, Ramos JL, 2002, AraC-XylS database: a family of positive transcriptional regulators in bacteria., Nucleic Acids Res, 2002 Jan 1



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