Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional activator of the ''alsSD'' operon<br/><br/>
+
* '''Description:''' acetolactate decarboxylase <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'''
−
|''alsR''
+
|''alsD''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional activator(LysR family)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || acetolactate decarboxylase)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of acetoin synthesis (''alsSD'')
+
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 7.288  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.603  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 906 bp, 302 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[alsS]]'', ''[[ywrK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywrO]]'', ''[[alsS]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:alsR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:alsD_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
no acetoin production
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/alsSD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10470]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10472]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' binds the promoter region of the ''[[alsS]]-[[alsD]]'' operon in the presence of acetate, activates transcription
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' LysR family of transcription factors
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36000]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[alsS]]-[[alsD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induction by acetate ([[AlsR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], repressed as long as terminal electron acceptors are available for respiration ([[Rex]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
 +
Note: since acetate formation requires ''[[ackA]]'' activation by [[CcpA]] there is an indirect effect of [[CcpA]] on the ''alsSD'' operon: the operon is not expressed in ''[[ccpA]]'' mutants
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[AlsR]]: transcription activation in the presence of acetate [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], [[Rex]]: transcription repression if the ratio NADH2/NAD is high [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Elisabeth Härtig]], Braunschweig, Germany [http://www.tu-braunschweig.de/ifm/abt/jahn/groups/bs Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
 +
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 
# Renna, M. C., Najimudin, N., Winik, L. R., and Zahler, S. A. (1993). Regulation of the ''Bacillus subtilis alsS'', ''alsD'', and ''alsR'' genes involved in post-exponential-phase production of acetoin. J. Bacteriol. 175, 3863-3875. [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
 
# Renna, M. C., Najimudin, N., Winik, L. R., and Zahler, S. A. (1993). Regulation of the ''Bacillus subtilis alsS'', ''alsD'', and ''alsR'' genes involved in post-exponential-phase production of acetoin. J. Bacteriol. 175, 3863-3875. [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
 +
# Reents, H., R. Münch, T. Dammeyer, D. Jahn, and E. Härtig. 2006. The Fnr regulon of ''Bacillus subtilis''. J. Bacteriol. 188: 1103-1112. [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 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 17:28, 15 April 2009

  • Description: acetolactate decarboxylase

Gene name alsD
Synonyms
Essential no
Product acetolactate decarboxylase)
Function overflow metabolism
MW, pI 28 kDa, 4.603
Gene length, protein length 765 bp, 255 aa
Immediate neighbours ywrO, alsS
Hier soll was neues rein
Genetic context
AlsD 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:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated on ser/ thr/ tyr PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Regulation: induction by acetate (AlsR) PubMed, repressed as long as terminal electron acceptors are available for respiration (Rex) PubMed

Note: since acetate formation requires ackA activation by CcpA there is an indirect effect of CcpA on the alsSD operon: the operon is not expressed in ccpA mutants

  • Regulatory mechanism: AlsR: transcription activation in the presence of acetate PubMed, Rex: transcription repression if the ratio NADH2/NAD is high PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

  1. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  2. Renna, M. C., Najimudin, N., Winik, L. R., and Zahler, S. A. (1993). Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin. J. Bacteriol. 175, 3863-3875. PubMed
  3. Reents, H., R. Münch, T. Dammeyer, D. Jahn, and E. Härtig. 2006. The Fnr regulon of Bacillus subtilis. J. Bacteriol. 188: 1103-1112. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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