Difference between revisions of "TxpA"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' toxic peptide <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqcR, yqdB''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqcR, yqdB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
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|style="background:#ABCDEF;" align="center"| '''Product''' || toxic peptide
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|style="background:#ABCDEF;" align="center"|'''Function''' || toxin
 +
|-
 +
|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=BSU26050 txpA]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 8.139   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 8.139   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 177 bp, 59 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 177 bp, 59 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqbN/2]]'', ''[[ratA]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqdB_nucleotide.txt    Gene sequence     (+200bp)  ]'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU26050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU26050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU26050 DNA_with_flanks]
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqdB_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqdB_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqdB_context.gif]]
 +
<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=yqdB_2678240_2678419_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:txpA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU26050]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
 +
{{SubtiWiki category|[[Skin element]]}},
 +
{{SubtiWiki category|[[membrane proteins]]}}
  
−
<br/><br/>
+
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[ratA regulon]]}}
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU26050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU26050&redirect=T BSU26050]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqdB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/txpA.html]
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11512]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11512]
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''  
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
 +
** cell membrane
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU26050&redirect=T BSU26050]
  
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P54373 P54373]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU26050]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''txpA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqdB_2678240_2678419_1 txpA] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** expression is prevented by the ''[[ratA]]'' antisense RNA [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
 +
** the ''[[txpA]]'' mRNA-''[[RatA]]'' RNA duplex is degraded by [[rnc|RNase III]] {{PubMed|23300471}}
  
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* '''Additional information:'''  
+
* '''Additional information:'''
 +
** next to ''[[yonT]]'', the ''[[txpA]]'' mRNA has the strongest Shine-Dalgarno region in ''B. subtilis'' {{PubMed|19210617}}
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Richard Losick]], Harvard University, Cambridge, USA [http://www.mcb.harvard.edu/Losick/ Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 23300472 </pubmed>
 +
 +
==Original publications==
 +
<pubmed>16166525, 19210617 23300471</pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 12:59, 4 February 2015

  • Description: toxic peptide

Gene name txpA
Synonyms yqcR, yqdB
Essential no
Product toxic peptide
Function toxin
Gene expression levels in SubtiExpress: txpA
MW, pI 6 kDa, 8.139
Gene length, protein length 177 bp, 59 aa
Immediate neighbours yqbN/2, ratA
Sequences Protein DNA DNA_with_flanks
Genetic context
YqdB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
TxpA expression.png















Categories containing this gene/protein

toxins, antitoxins and immunity against toxins, Skin element, membrane proteins

This gene is a member of the following regulons

ratA regulon

The gene

Basic information

  • Locus tag: BSU26050

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:

Database entries

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

Additional information

Expression and regulation

  • Regulation:
  • Additional information:
    • next to yonT, the txpA mRNA has the strongest Shine-Dalgarno region in B. subtilis PubMed

Biological materials

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

Labs working on this gene/protein

Richard Losick, Harvard University, Cambridge, USA Homepage

Your additional remarks

References

Reviews

Fabian M Commichau, Jörg Stülke
A mystery unraveled: essentiality of RNase III in Bacillus subtilis is caused by resident prophages.
PLoS Genet: 2012, 8(12);e1003199
[PubMed:23300472] [WorldCat.org] [DOI] (I p)


Original publications

Sylvain Durand, Laetitia Gilet, Ciarán Condon
The essential function of B. subtilis RNase III is to silence foreign toxin genes.
PLoS Genet: 2012, 8(12);e1003181
[PubMed:23300471] [WorldCat.org] [DOI] (I p)

Roula Daou-Chabo, Nathalie Mathy, Lionel Bénard, Ciarán Condon
Ribosomes initiating translation of the hbs mRNA protect it from 5'-to-3' exoribonucleolytic degradation by RNase J1.
Mol Microbiol: 2009, 71(6);1538-50
[PubMed:19210617] [WorldCat.org] [DOI] (I p)

Jessica M Silvaggi, John B Perkins, Richard Losick
Small untranslated RNA antitoxin in Bacillus subtilis.
J Bacteriol: 2005, 187(19);6641-50
[PubMed:16166525] [WorldCat.org] [DOI] (P p)

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