Difference between revisions of "Sandbox"

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* '''Description:''' inhibition of the pro-sigma-K processing machinery <br/><br/>
+
* '''Description:''' [[16S rRNA]]<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'''
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|''bofA''
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|''rrnA-16S''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || inhibitor of pro-[[SigK]] processing
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|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-16S
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigK]] activation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00230 bofA]
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 1553 bp
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=BofA BofA]
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bofA]]'', ''[[trnA-Ile]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 9.32 
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnA-16S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 261 bp, 87 aa
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rrnA-16S_context.gif]]
−
|-
 
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaL]]'', ''[[rrnA-16S]]''
 
−
|-
 
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00230 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00230 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00230 DNA_with_flanks]
 
−
|-
 
−
|-
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:bofA_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>
−
|-
 
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=bofA_29772_30035_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:bofA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00230]]
 
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
−
<br/><br/><br/><br/>
+
 
−
<br/><br/><br/><br/>
 
−
<br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[sigma factors and their control]]}},
+
{{SubtiWiki category|[[translation]]}}
−
{{SubtiWiki category|[[sporulation proteins]]}},
 
−
{{SubtiWiki category|[[membrane proteins]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[SigE regulon]]}},
+
 
−
{{SubtiWiki regulon|[[SpoIIID regulon]]}}
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00230
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bofA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10087]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00011]
−
 
 
−
=== 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:'''
 
−
 
 
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* '''Cofactor(s):'''
 
−
 
 
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* '''Effectors of protein activity:'''
 
−
 
 
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* '''[[SubtInteract|Interactions]]:'''
 
−
** [[BofA]]-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
 
−
** [[SpoIVFB]]-[[BofA]], to inhibit proteolytic activity of [[SpoIVFB]] {{PubMed|15087499}}
 
−
** [[SpoIVFA]]-[[BofA]], recruitment of [[BofA]] to [[SpoIVFB]] {{PubMed|11959848}}
 
−
 
 
−
* '''[[Localization]]:'''
 
−
** forespore outer membrane (according to Swiss-Prot)
 
−
** integral membrane protein {{PubMed|11959848}}
 
−
 
 
−
=== Database entries ===
 
  
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P24282 P24282]
+
=== Additional information===
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00230]
 
  
−
* '''E.C. number:'''
 
  
−
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''bofA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Operon:''' ''[[rrnA-16S]]-[[trnA-Ile]]-[[trnA-Ala]]-[[rrnA-23S]]-[[rrnA-5S]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
−
 
 
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=bofA_29772_30035_1 bofA] {{PubMed|22383849}}
 
  
−
* '''Sigma factor:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
−
* '''Regulation:''' expressed during sporulation  [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[SpoIIID]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
 
* '''Mutant:'''
 
* '''Mutant:'''
−
** 1S100 ( ''bofA''::''cat''), {{PubMed|1577688}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S100&Search=1S100 BGSC]
 
−
** 1S96 ( ''bofA''::''erm''), {{PubMed|1315731}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S96&Search=1S96 BGSC]
 
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
−
 
−
* '''GFP fusion:'''
 
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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* '''Antibody:'''
 
* '''Antibody:'''
  
−
=Labs working on this gene/protein=
+
=Labs working on this gene/RNA=
−
 
 
−
Simon Cutting, London, UK [http://personal.rhul.ac.uk/uhba/009/bacillus/simon_cutting.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
'''Additional publications:''' {{PubMed|21303765}}
 +
<pubmed> 6312418, 19447912 20634236 </pubmed>
  
−
<pubmed>11959848, 9501233, 1577688, 15292188, 2115401, 12940997, 12884008,, 15292188 1315731, 15752199 16818230 15087499</pubmed>
+
[[Category:Ribosomal RNA]]
−
 
 
−
[[Category:Protein-coding genes]]
 

Revision as of 14:54, 11 November 2013

Gene name rrnA-16S
Synonyms
Essential
Product ribosomal RNA-16S
Function translation
Gene length 1553 bp
Immediate neighbours bofA, trnA-Ile
Gene sequence (+200bp)
Genetic context
RrnA-16S context.gif
This image was kindly provided by SubtiList






Categories containing this gene/protein

translation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

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

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/RNA

Your additional remarks

References

Additional publications: PubMed

Hideaki Nanamiya, Makiko Sato, Kenta Masuda, Mikiko Sato, Tetsuya Wada, Shota Suzuki, Yousuke Natori, Masato Katano, Genki Akanuma, Fujio Kawamura
Bacillus subtilis mutants harbouring a single copy of the rRNA operon exhibit severe defects in growth and sporulation.
Microbiology (Reading): 2010, 156(Pt 10);2944-2952
[PubMed:20634236] [WorldCat.org] [DOI] (I p)

Yousuke Natori, Kazumi Tagami, Kana Murakami, Sawako Yoshida, Osamu Tanigawa, Yoonsuh Moh, Kenta Masuda, Tetsuya Wada, Shota Suzuki, Hideaki Nanamiya, Yuzuru Tozawa, Fujio Kawamura
Transcription activity of individual rrn operons in Bacillus subtilis mutants deficient in (p)ppGpp synthetase genes, relA, yjbM, and ywaC.
J Bacteriol: 2009, 191(14);4555-61
[PubMed:19447912] [WorldCat.org] [DOI] (I p)

N Ogasawara, S Moriya, H Yoshikawa
Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome.
Nucleic Acids Res: 1983, 11(18);6301-18
[PubMed:6312418] [WorldCat.org] [DOI] (P p)

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