Difference between revisions of "Sandbox"

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* '''Description:''' general stress protein, controls processing of pro-SigK by SpoIVFB <br/><br/>
+
* '''Description:''' 6S RNA<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'''
−
|''bofC''
+
|''bsrA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || forespore regulator of the sigma-K checkpoint
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|style="background:#ABCDEF;" align="center"| '''Product''' || 6S RNA
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || control of processing of pro-SigK by SpoIVFB
+
|style="background:#ABCDEF;" align="center"|'''Function''' || antagonist of [[SigA]]
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 5.753  
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  190 bp
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 510 bp, 170 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvM]]'', ''[[aspS]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ruvA]]'', ''[[csbX]]''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14735&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:BsrA_context.jpeg]]
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|-
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:bofC_context.gif]]
 
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<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
 
|-
 
|-
 
|}
 
|}
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<br/><br/>
 
<br/><br/>
  
 +
<br/><br/><br/><br/><br/>
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU27750
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
=== Database entries ===
+
reduced growth rate  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
−
 
 
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/csbX-bofC.html]
 
−
 
 
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11917]
 
−
 
 
−
=== 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:''' [[BofC]]-[[SpoIVB]],  [[BofC]]-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10931291 PubMed]
 
−
 
−
* '''Localization:'''
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2BW2 2BW2]
+
* '''DBTBS entry:''' no entry
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O05391 O05391]
+
* '''SubtiList entry:''' no entry
 +
 +
* '''Structure:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27750]
+
=== Additional information===
  
−
* '''E.C. number:'''
 
−
 
−
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''bsrA''  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
  
−
* '''Regulation:'''  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
* '''Regulation:''' expressed in vegetative cells [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:''' transcribed as 201 nt RNA, processed to mature 190 bp 6S RNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
 
−
 
−
* '''two-hybrid system:'''
 
  
−
* '''Antibody:'''
+
=Labs working on this gene/RNA=
  
−
=Labs working on this gene/protein=
+
Kouji Nakamura, Tsukuba, University, Japan
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 80:
 
=References=
 
=References=
  
−
<pubmed>11544224, </pubmed>
+
<pubmed>12177353 15811922, </pubmed>
−
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
# Suzuma S, Asari S, Bunai K, Yoshino K, Ando Y, Kakeshita H, Fujita M, Nakamura K, Yamane K (2002) Identification and characterization of novel small RNAs in the ''aspS-yrvM'' intergenic region of the ''Bacillus subtilis'' genome.. ''Microbiology'' '''148:''' 2591-2598. [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
 +
# Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR(2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.''RNA'' '''11:''' 774-784. [http://www.ncbi.nlm.nih.gov/sites/entrez/15811922 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 13:10, 8 June 2009

  • Description: 6S RNA

Gene name bsrA
Synonyms
Essential no
Product 6S RNA
Function antagonist of SigA
Gene length 190 bp
Immediate neighbours yrvM, aspS
Gene sequence (+200bp)
Genetic context
BsrA context.jpeg








The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

reduced growth rate PubMed


Database entries

  • DBTBS entry: no entry
  • SubtiList entry: no entry
  • Structure:

Additional information

Expression and regulation

  • Regulation: expressed in vegetative cells PubMed
  • Regulatory mechanism:
  • Additional information: transcribed as 201 nt RNA, processed to mature 190 bp 6S RNA PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:


Labs working on this gene/RNA

Kouji Nakamura, Tsukuba, University, Japan

Your additional remarks

References

Jeffrey E Barrick, Narasimhan Sudarsan, Zasha Weinberg, Walter L Ruzzo, Ronald R Breaker
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
RNA: 2005, 11(5);774-84
[PubMed:15811922] [WorldCat.org] [DOI] (P p)

Satoru Suzuma, Sayaka Asari, Keigo Bunai, Keiko Yoshino, Yoshinari Ando, Hiroshi Kakeshita, Masaya Fujita, Kouji Nakamura, Kunio Yamane
Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome.
Microbiology (Reading): 2002, 148(Pt 8);2591-2598
[PubMed:12177353] [WorldCat.org] [DOI] (P p)

  1. Suzuma S, Asari S, Bunai K, Yoshino K, Ando Y, Kakeshita H, Fujita M, Nakamura K, Yamane K (2002) Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome.. Microbiology 148: 2591-2598. PubMed
  2. Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR(2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.RNA 11: 774-784. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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