Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' general stress protein, degradation of damaged thiol-containing proteins <br/><br/>
+
* '''Description:''' Sda is a checkpoint protein that is upregulated in response to replication stress [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=11207367%5Buid%5D&log$=activity (Burkholder et al 2001, Cell)]. Sda inhibits the autokinase activity of [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinA KinA] (and likely [http://subtiwiki.uni-goettingen.de/wiki/index.php/KinB KinB] as well). This in its turn results in reduced levels of [http://subtiwiki.uni-goettingen.de/wiki/index.php/Spo0A Spo0A~P]. Thus, replication stressed cells will not iniate sporulation<br/><br/> Sda is rapidly turned over by the [http://subtiwiki.uni-goettingen.de/wiki/index.php/ClpP ClpP/X] system because of some uncharged residues at its C-terminus [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=16796683%5Buid%5D&log$=activity Ruvolo et al 2006, MolMic].
 +
 
  
 
{| 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'''
|''yraA''
+
|''sda''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 11:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cysteine proteinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || developmental checkpoint protein
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || degradation of damaged thiol-containing proteins
+
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates a developmental checkpoint coupling initiation of
 +
 
 +
sporulation (phosphorylation of Spo0A) to the function
 +
 
 +
of replication initiation proteins
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 4.729  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 507 bp, 169 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[adhA]]'', ''[[sacC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[sdaAA]]''
 
|-
 
|-
 
|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:sda_context.gif]]
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yraA_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>
 
|-
 
|-
Line 31: Line 34:
 
__TOC__
 
__TOC__
  
<br/><br/><br/><br/>
+
 
 +
<br/><br/>
 +
 
  
 
=The gene=
 
=The gene=
Line 40: Line 45:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
*sporulates at a higher frequency
 +
*will sporulate in the presence of replication stress
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yraA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13776]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 65:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
* '''Paralogous protein(s):''' [[YfkM]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 82: Line 89:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25690]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 97:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:'''  
+
* '''Operon:'''  ''sda''
  
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]
+
* '''Sigma factor:'''  [[SigA]]
  
* '''Regulation:'''  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''Regulation:'''  [[DnaA]]
  
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' Probably activated by [[DnaA]] under replication stress
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 120: Line 127:
 
=References=
 
=References=
  
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 
# Jervis et al. 2007. SigM-responsive genes of ''Bacillus subtilis'' and their promoters. J. Bacteriol. 189: 4534-4538. [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 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 15:48, 15 April 2009

  • Description: Sda is a checkpoint protein that is upregulated in response to replication stress (Burkholder et al 2001, Cell). Sda inhibits the autokinase activity of KinA (and likely KinB as well). This in its turn results in reduced levels of Spo0A~P. Thus, replication stressed cells will not iniate sporulation

    Sda is rapidly turned over by the ClpP/X system because of some uncharged residues at its C-terminus Ruvolo et al 2006, MolMic.


Gene name sda
Synonyms
Essential no
Product developmental checkpoint protein
Function mediates a developmental checkpoint coupling initiation of

sporulation (phosphorylation of Spo0A) to the function

of replication initiation proteins

MW, pI 6 kDa, 5.605
Gene length, protein length 156 bp, 52 aa
Immediate neighbours yloV, sdaAA
Hier soll was neues rein
Genetic context
Sda context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

  • sporulates at a higher frequency
  • will sporulate in the presence of replication stress

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:
  • 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

  • Operon: sda
  • Regulatory mechanism: Probably activated by DnaA under replication stress
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed