Difference between revisions of "Sandbox"

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−
* '''Description:''' polynucleotide phosphorylase <br/><br/>
+
* '''Description:''' ribosomal protein  <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'''
−
|''pnpA''
+
|''rpsO''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''comR ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || polynucleotide phosphorylase (PNPase) (EC 2.7.7.8)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal protein S15 (BS18)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || necessary for competence development
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 77 kDa, 4.89  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 10.975  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2115 bp, 705 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 267 bp, 89 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpsO]]'', ''[[ylxY]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ribC]]'', ''[[pnpA]]''
 
|-
 
|-
 
|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:pnpA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rpsO_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11491]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19010]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PnpA]]-[[RnjA]], [[PnpA]]-[[PfkA]], [[PnpA]]-[[Rny]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CDI 3CDI] (protein from ''E. coli'')
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16690]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16680]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
required for the expression of late competence genes [[comG]] and [[comK]], requirement bypassed by a [[mecA]] disruption; may be necessary for modification of the [[srfA]] transcript (stabilization or translation activation)
 
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' [[RelA]] dependent downregulation (Class I) during stringent response [http://www.ncbi.nlm.nih.gov/sites/entrez/11948165 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 110: Line 110:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 120:
 
=References=
 
=References=
  
−
# Bechhofer, D. H. & Wang, W. (1998). Decay of ''ermC'' mRNA in a polynucleotide phosphorylase mutant of ''Bacillus subtilis''. J Bacteriol 180:5968-5977. [http://www.ncbi.nlm.nih.gov/sites/entrez/9811656 PubMed]
 
−
# Campos-Guillen, J., Bralley, P., Jones, G. H., Bechhofer, D. H. & Olmedo-Alvarez, G. (2005). Addition of poly(A) and heteropolymeric 3´ ends in ''Bacillus subtilis'' wild-type and polynucleotide phosphorylase-deficient strains. J Bacteriol 187:4698-4706.  [http://www.ncbi.nlm.nih.gov/sites/entrez/15995184 PubMed]
 
−
# Deutscher, M. P. & Reuven, N. B. (1991). Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in ''Escherichia coli'' and Bacillus subtilis. Proc Natl Acad Sci U S A 88:3277-3280. [http://www.ncbi.nlm.nih.gov/sites/entrez/xxx PubMed]
 
−
# Mitra, S., Hue, K. & Bechhofer, D. H. (1996). ''In vitro'' processing activity of ''Bacillus subtilis'' polynucleotide phosphorylase. Mol Microbiol 19:329-342. [http://www.ncbi.nlm.nih.gov/sites/entrez/8825778 PubMed]
 
−
# Wang, W. & Bechhofer, D. H. (1996). Properties of a ''Bacillus subtilis'' polynucleotide phosphorylase deletion strain. J Bacteriol 178:2375-2382. [http://www.ncbi.nlm.nih.gov/sites/entrez/8636041 PubMed]
 
−
# Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of ''Bacillus subtilis'' mRNA. J Bacteriol 187:2758-2767. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805522 PubMed]
 
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 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 19:46, 15 April 2009

  • Description: ribosomal protein

Gene name rpsO
Synonyms
Essential yes PubMed
Product ribosomal protein S15 (BS18)
Function translation
MW, pI 10 kDa, 10.975
Gene length, protein length 267 bp, 89 aa
Immediate neighbours ribC, pnpA
Hier soll was neues rein
Genetic context
RpsO context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • 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
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