Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' general stress protein <br/><br/>
+
* '''Description:''' small regulatory RNA controlling [[AhrC]] expression<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'''
−
|''spoVC''
+
|''sr1''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pth ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzW ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || small regulatory RNA/ regulatory peptide
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || spore coat formation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of arginine metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 5.58 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4.4 kDa, 3.89
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 564 bp, 188 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 205 bp (RNA), 120 bp (ORF), 39 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ctc]]'', ''[[yabK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[slp]]'', ''[[speA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11829&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sr1_nucleotide.txt    Gene sequence        ]'''  
 +
|style="background:#FAF8CC;" align="center"|
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:spoVC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sr1_context.gif]]
−
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
 
|-
 
|-
 
|}
 
|}
Line 29: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 +
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00530
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 45: Line 44:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10116]
+
=== Additional information===
 +
Located between the ''[[slp]]'' and ''[[speA]]'' genes.
 +
 
 +
 
 +
=The RNA=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[ahrC]]'' mRNA and inhibits [[AhrC]] translation. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 +
 
 +
=== Extended information on the RNA===
 +
 
 +
* '''Kinetic information'''
 +
 
 +
* '''Interactions:''' Binds ''[[ahrC]]'' mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 +
 
 +
* '''Localization'''
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure''':
  
 
=== Additional information===
 
=== Additional information===
  
 +
Information on the structure of the RNA can be found in [http://www.ncbi.nlm.nih.gov/pubmed/17020585?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Heidrich ''et al''., 2006 ]
  
−
=The protein=
+
=The peptide=
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' N-substituted aminoacyl-tRNA + H<sub>2</sub>O = N-substituted amino acid + tRNA (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PTH family (according to Swiss-Prot)
+
* '''Protein family:''' the peptide is conserved in bacilli
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 74: Line 94:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 100:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37470 P37470]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00530]
+
* '''KEGG entry:'''
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.29 3.1.1.29]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 110:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' sr1 [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
* '''Regulation:''' Repressed in the presence of glucose by [[CcpN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' 168 sr1::cat, available in [[Brantl]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
+
=Labs working on this gene/protein=
−
 
 
−
* '''two-hybrid system:'''
 
−
 
 
−
* '''Antibody:'''
 
  
−
=Labs working on this gene/protein=
+
[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 136:
 
=References=
 
=References=
  
−
<pubmed>11544224, </pubmed>
+
<pubmed>16164558 17020585 17576690, </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]
+
# Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis. Mol. Microbiol. 58: 189-206. [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Heidrich et al. (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol. Microbiol. 62: 520-536. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 +
# Heidrich et al. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucl. Acids Res. 35: 4331-4346. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576690 PubMed]

Revision as of 13:37, 8 June 2009

  • Description: small regulatory RNA controlling AhrC expression

Gene name sr1
Synonyms ykzW
Essential no
Product small regulatory RNA/ regulatory peptide
Function control of arginine metabolism
MW, pI 4.4 kDa, 3.89
Gene length, protein length 205 bp (RNA), 120 bp (ORF), 39 aa
Immediate neighbours slp, speA
Gene sequence
Genetic context
Sr1 context.gif





The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry

Additional information

Located between the slp and speA genes.


The RNA

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: hybridizes to ahrC mRNA and inhibits AhrC translation. PubMed

Extended information on the RNA

  • Kinetic information
  • Localization

Database entries

  • Structure:

Additional information

Information on the structure of the RNA can be found in Heidrich et al., 2006

The peptide

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: the peptide is conserved in bacilli
  • 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:
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: Repressed in the presence of glucose by CcpN PubMed
  • Regulatory mechanism: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant: 168 sr1::cat, available in Brantl lab
  • Expression vector:
  • lacZ fusion:

Labs working on this gene/protein

Sabine Brantl, Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany homepage

Your additional remarks

References

Nadja Heidrich, Isabella Moll, Sabine Brantl
In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA.
Nucleic Acids Res: 2007, 35(13);4331-46
[PubMed:17576690] [WorldCat.org] [DOI] (I p)

Nadja Heidrich, Alberto Chinali, Ulf Gerth, Sabine Brantl
The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism.
Mol Microbiol: 2006, 62(2);520-36
[PubMed:17020585] [WorldCat.org] [DOI] (P p)

Andreas Licht, Sven Preis, Sabine Brantl
Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis.
Mol Microbiol: 2005, 58(1);189-206
[PubMed:16164558] [WorldCat.org] [DOI] (P p)

  1. Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis. Mol. Microbiol. 58: 189-206. PubMed
  2. Heidrich et al. (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol. Microbiol. 62: 520-536. PubMed
  3. Heidrich et al. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucl. Acids Res. 35: 4331-4346. PubMed
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=88952"