Difference between revisions of "Sandbox"

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−
* '''Description:''' xylan beta-1,4-xylosidase <br/><br/>
+
* '''Description:''' transcriptional repressor of the xyl and xyn operons <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''xynB''
+
|''xylR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ynaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || xylan beta-1,4-xylosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || xylan degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of xylan and xylose utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.326  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 5.819  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1599 bp, 533 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1050 bp, 350 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynP]]'', ''[[xylR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynB]]'', ''[[xylA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xynB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xylR_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xynB_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xylR_protein.txt Protein sequence]'''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:xynB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:xylR_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 44: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xynPB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11987]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11986]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[xylA]]-[[xylB]]'' and the ''[[xynP]]-[[xynB]]'' operons
  
−
* '''Protein family:''' glycosyl hydrolase 43 family
+
* '''Protein family:''' ROK (nagC/xylR) family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 71: Line 71:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inducer: xylose
  
 
* '''Interactions:'''
 
* '''Interactions:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17580]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17590]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 91: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[xynP]]-[[xynB]]''
+
* '''Operon:''' ''xylR''
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression ([[CcpA]]), induction by xylose ([[XylR]])
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[XylR]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 116: Line 116:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 124:
  
  
−
# Lindner, C., Stülke, J. & Hecker, M. (1994) Regulation of xylanolytic enzymes in Bacillus subtilis. Microbiology 140: 753-757. [http://www.ncbi.nlm.nih.gov/sites/entrez/8012596 PubMed]
+
# Dahl, M. K., Schmiedel, D., and Hillen, W. (1995) Glucose and glucose-6-phosphate interaction with Xyl repressor proteins from Bacillus spp. may contribute to regulation of xylose utilization. J Bacteriol 177: 5467-5472. [http://www.ncbi.nlm.nih.gov/sites/entrez/7559331 PubMed]
 +
# Kauder C, Allmansberger R, Gärtner D, Schmiedel D, Hillen W. 1993. An operator binding-negative mutation of Xyl repressor from Bacillus subtilis is trans dominant in Bacillus megaterium. FEMS Microbiol. Lett. 109:81-84. [http://www.ncbi.nlm.nih.gov/sites/entrez/8319885 PubMed]
 +
# Kreuzer P, Gärtner D, Allmansberger R, Hillen W. 1989. Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator. J. Bacteriol. 171:3840-3845. [http://www.ncbi.nlm.nih.gov/sites/entrez/2544559 PubMed]
 +
# Gärtner D, Degenkolb J, Ripperger JAE, Allmansberger R, Hillen W. 1992. Regulation of the Bacillus subtilis W23 xylose utilization operon: interaction of Xyl repressor with xyl operator and the inducer xylose. Mol. Gen. Genet. 232:415-422 [http://www.ncbi.nlm.nih.gov/sites/entrez/1588910 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 04:50, 12 April 2009

  • Description: transcriptional repressor of the xyl and xyn operons

Gene name xylR
Synonyms
Essential no
Product transcriptional repressor
Function regulation of xylan and xylose utilization
MW, pI 38 kDa, 5.819
Gene length, protein length 1050 bp, 350 aa
Immediate neighbours xynB, xylA
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
XylR context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription repression of the xylA-xylB and the xynP-xynB operons
  • Protein family: ROK (nagC/xylR) family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: inducer: xylose
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon: xylR
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Wolfgang Hillen, Erlangen University, Germany Homepage

Your additional remarks

References

  1. Dahl, M. K., Schmiedel, D., and Hillen, W. (1995) Glucose and glucose-6-phosphate interaction with Xyl repressor proteins from Bacillus spp. may contribute to regulation of xylose utilization. J Bacteriol 177: 5467-5472. PubMed
  2. Kauder C, Allmansberger R, Gärtner D, Schmiedel D, Hillen W. 1993. An operator binding-negative mutation of Xyl repressor from Bacillus subtilis is trans dominant in Bacillus megaterium. FEMS Microbiol. Lett. 109:81-84. PubMed
  3. Kreuzer P, Gärtner D, Allmansberger R, Hillen W. 1989. Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator. J. Bacteriol. 171:3840-3845. PubMed
  4. Gärtner D, Degenkolb J, Ripperger JAE, Allmansberger R, Hillen W. 1992. Regulation of the Bacillus subtilis W23 xylose utilization operon: interaction of Xyl repressor with xyl operator and the inducer xylose. Mol. Gen. Genet. 232:415-422 PubMed
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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