Difference between revisions of "Sandbox"

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* '''Description:''' DNA gyrase (subunit A) <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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|''gyrA''
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|''rrnO-16S''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA gyrase (subunit A)
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|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-16S
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
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|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=BSU00070 GyrA]
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|style="background:#ABCDEF;" align="center"| '''Gene length''' || 1553 bp
 +
|-|-
 +
 
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrA]]'', ''[[trnO-Ile]]''
 
|-
 
|-
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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=GyrA GyrA]
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnO-16S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 +
|style="background:#FAF8CC;" align="center"|''' '''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215 
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|colspan="2" | '''Genetic context''' <br/> [[Image:rrnO-16S_context.gif]]
−
|-
 
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa
 
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|-
 
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
 
−
|-
 
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00070 DNA_with_flanks]
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:GyrA_context.png]]
 
 
  <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=gyrA_6994_9459_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gyrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00070]]
 
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
−
<br/><br/><br/><br/>
+
 
−
<br/><br/><br/><br/>
+
<br/><br/><br/><br/><br/><br/>
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<br/><br/><br/><br/>
 
−
<br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[DNA condensation/ segregation]]}},
+
{{SubtiWiki category|[[translation]]}}
−
{{SubtiWiki category|[[essential genes]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00070
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
=== Database entries ===
  
−
=== Database entries ===
+
* '''DBTBS entry:''' no entry
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gyrA.html]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00005]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10071]
+
* '''Structure:'''
  
 
=== Additional information===
 
=== Additional information===
  
  
−
 
−
 
−
=The protein=
 
−
 
−
=== Basic information/ Evolution ===
 
−
 
−
* '''Catalyzed reaction/ biological activity:''' ATP-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)
 
−
 
−
* '''Protein family:''' topoisomerase gyrA/parC subunit family (according to Swiss-Prot)
 
−
 
−
* '''Paralogous protein(s):''' [[ParC]]
 
−
 
−
=== Extended information on the protein ===
 
−
 
−
* '''Kinetic information:'''
 
−
 
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* '''Domains:'''
 
−
 
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* '''Modification:'''
 
−
 
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* '''Cofactor(s):'''
 
−
 
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* '''Effectors of protein activity:'''
 
−
 
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* '''[[SubtInteract|Interactions]]:'''
 
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** [[GyrA]]-[[GyrB]]
 
−
 
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* '''[[Localization]]:'''
 
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** Nucleoid (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
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** nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 
−
 
−
=== Database entries ===
 
−
 
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* '''Structure:'''
 
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** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4DDQ 4DDQ] (DNA gyrase A-subunit lacking the C-terminal DNA-wrapping domains) {{PubMed|23602808}}
 
−
 
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* '''UniProt:''' [http://www.uniprot.org/uniprot/P05653 P05653]
 
−
 
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00070]
 
−
 
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* '''E.C. number:'''
 
−
 
−
=== Additional information===
 
−
 
−
:* subject to Clp-dependent proteolysis upon glucose starvation {{PubMed|17981983}}
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''gyrA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''rrnO'' operon (''[[rrnO-16S]] - [[trnO-Ile]] - [[trnO-Ala]] -[[rrnO-23S]] - [[rrnO-5S]]'') [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
−
 
 
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrA_6994_9459_1 gyrA] {{PubMed|22383849}}
 
  
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* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** passive transcriptional regulation by cellular GTP concentration
 +
** downregulated by stringent response upon amino acid starvation {{PubMed|21097612}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''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],  GyrA is 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]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
<pubmed>16479537,17981983 ,9539793 , 2987848  19666507 17320901 23475963 23602808 20870749</pubmed>
+
'''Additional publications:''' {{PubMed|21097612,21303765}}
−
 
+
<pubmed> 6312418, 19447912 15496987 20634236 </pubmed>  
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[[Category:Protein-coding genes]]
+
[[Category:Ribosomal RNA]]

Revision as of 14:54, 11 November 2013

Gene name rrnO-16S
Synonyms
Essential no
Product ribosomal RNA-16S
Function translation
Gene length 1553 bp
Immediate neighbours gyrA, trnO-Ile
Gene sequence (+200bp)
Genetic context
RrnO-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:
    • passive transcriptional regulation by cellular GTP concentration
    • downregulated by stringent response upon amino acid starvation PubMed
  • 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

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)

Libor Krásný, Richard L Gourse
An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation.
EMBO J: 2004, 23(22);4473-83
[PubMed:15496987] [WorldCat.org] [DOI] (P 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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