Difference between revisions of "Sandbox"

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−
* '''Description:''' RNase R<br/><br/>
+
* '''Description:''' general stress protein, similar to L25 <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'''
−
|''rnr''
+
|''ctc''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvaJ ''
+
|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''' || exoribonuclease R (EC 3.1.-.-)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || nonspecific degradation of rRNA
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 88 kDa, 5.703  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 4.216  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2337 bp, 779 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 612 bp, 204 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[smpB]]'', ''[[yvaK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[prs]]'', ''[[spoVC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rnr_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ctc_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rnr_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ctc_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rnr_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ctc_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 42: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gcaD-prs-ctc.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14065]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10115]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 3'-5'-exoribonuclease
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 71: Line 71:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' binds 5S rRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' in the ribosome (large subunit) [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 81: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33610]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00520]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 87: Line 87:
 
=== Additional information===
 
=== Additional information===
  
 +
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[gcaD]]-[[prs]]-[[ctc]]'', ''[[ctc]]''
  
−
* '''Sigma factor:''' ''[[SigB]]'' [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]  
+
* '''Sigma factor:''' ''[[gcaD]]'': [[SigA]], ''[[ctc]]'': [[SigB]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced under stress conditions
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' alternative sigma factor, [[SigB]]
  
−
* '''Additional information:'''  
+
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 111: Line 112:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:'''
+
* '''Antibody:''' available in [[Stülke]] lab
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
Line 119: Line 120:
 
=References=
 
=References=
  
−
# H�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]
+
# H\U+00F6per 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]
−
# 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]
+
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
# Schmalisch, M., Langbein, I. & Stülke, J. (2002) The general stress protein Ctc of ''Bacillus subtilis'' is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4: 495-501.  [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
 +
# Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the ''Bacillus subtilis'' chromosome. J. Bacteriol. 147: 432-442. [http://www.ncbi.nlm.nih.gov/sites/entrez/6790515 PubMed]
 +
# Truitt, C. L., Weaver, E. A. and Haldenwang, W. G. 1988. Effects on growth and sporulation of inactivation of a ''Bacillus subtilis'' gene (''ctc'') transcribed in vitro by minor vegetative cell RNA polymerases (E-sigma(37), E-sigma(32)). Mol. Gen. Genet. 212: 166-171. [http://www.ncbi.nlm.nih.gov/sites/entrez/2836704 PubMed]
 +
# Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in ''Bacillus subtilis''. Nature 282, 256-260 [http://www.ncbi.nlm.nih.gov/pubmed/116131 PubMed]
 +
# Gongadze GM, Korepanov AP, Korobeinikova AV, Garber MB (2008) Bacterial 5S rRNA-binding proteins of the CTC family. ''Biochemistry (Moscow)'' '''73:''' 1405-1417. [http://www.ncbi.nlm.nih.gov/sites/entrez/19216708 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 15:29, 27 March 2009

  • Description: general stress protein, similar to L25

Gene name ctc
Synonyms
Essential no
Product ribosomal protein
Function unknown
MW, pI 21 kDa, 4.216
Gene length, protein length 612 bp, 204 aa
Immediate neighbours prs, spoVC
Gene sequence (+200bp) Protein sequence
Genetic context
Ctc 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:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: binds 5S rRNA PubMed
  • Localization: in the ribosome (large subunit) PubMed

Database entries

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

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation: induced under stress conditions
  • Regulatory mechanism: alternative sigma factor, SigB
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody: available in Stülke lab

Labs working on this gene/protein

Your additional remarks

References

  1. H\U+00F6per 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 PubMed
  2. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. Schmalisch, M., Langbein, I. & Stülke, J. (2002) The general stress protein Ctc of Bacillus subtilis is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4: 495-501. PubMed
  4. Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J. Bacteriol. 147: 432-442. PubMed
  5. Truitt, C. L., Weaver, E. A. and Haldenwang, W. G. 1988. Effects on growth and sporulation of inactivation of a Bacillus subtilis gene (ctc) transcribed in vitro by minor vegetative cell RNA polymerases (E-sigma(37), E-sigma(32)). Mol. Gen. Genet. 212: 166-171. PubMed
  6. Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis. Nature 282, 256-260 PubMed
  7. Gongadze GM, Korepanov AP, Korobeinikova AV, Garber MB (2008) Bacterial 5S rRNA-binding proteins of the CTC family. Biochemistry (Moscow) 73: 1405-1417. PubMed
  8. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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