Difference between revisions of "Main Page"

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<big>'''Paper of the month: October 2014'''</big>  
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<big>'''Paper of the month: November 2014'''</big>  
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* Drug exporters help the bacterial cell to cope with potentially toxic compounds. The expression of the transporters is usually switched on in response to the transported drugs. [http://www.ncbi.nlm.nih.gov/pubmed/25217586 Reilman et al.] have studied the regulation of the [[BmrC]]/[[BmrD]] multidrug [[ABC transporter]] in ''B. subtilis''. They report that the induction of ''[[bmrC]]-[[bmrD]]'' depends on the translation of a small leader peptide, [[BmrB]]. This is the first report on a ribosome-mediated transcriptional attenuation mechanism in the control of a multidrug [[ABC transporter]].
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* Integration of prophages into coding sequences of the host genome results in loss of function of the interrupted gene. In ''B. subtilis'' 168, the [[SP-beta prophage]] is inserted into a uncharacterized spore polysaccharide synthesis gene, ''spsM''. In vegetative cells, the lytic cycle is induced in response to DNA damage. In the process, the [[SP-beta prophage]] is excised from the genome to form phage particles. Now, [http://www.ncbi.nlm.nih.gov/pubmed/25299644 Abe et al.] demonstrate that the excision of the [[SP-beta prophage]] also occurs systematically during [[sporulation]] to reconstitute a functional ''spsM'' gene from the incomplete ''[[yodU]]'' and ''[[ypqP]]'' [[pseudogenes]]. Because phage excision is limited to the mother cell genome, and does not occur in the forespore genome, the [[SP-beta prophage]] is an integral part of the spore genome. Thus, after [[germination]], the [[SP-beta prophage]] is propagated vertically to the progeny. The authors suggest their results indicate that the two pathways of [[SP-beta prophage]] excision support both the phage life cycle and normal [[sporulation]] of the host cells.
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* '''Relevant ''Subti''Wiki pages:''' [[BmrB]], [[ABC transporter]], ''[[bmrC]]-[[bmrD]]'', [[AbrB]]
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* '''Relevant ''Subti''Wiki pages:''' [[SP-beta prophage]], [[sporulation]], ''[[yodU]], [[ypqP]]'', [[SprA]], [[SprB]]
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<pubmed> 25217586 </pubmed>
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<pubmed> 25299644 </pubmed>
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* See also:
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<pubmed> 25326298 </pubmed>
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 17:43, 14 November 2014

Welcome to SubtiWiki! - Bacillus subtilis annotation the "wiki" way!

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Contact: General Microbiology, University of Göttingen, send mail


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New: Subtiwiki is now on Facebook - please give it a +1!



Now online: A new description of SubtiWiki and its acompanying modules in the 2014 Database issue of Nucleic Acids Research

Raphael H Michna, Fabian M Commichau, Dominik Tödter, Christopher P Zschiedrich, Jörg Stülke
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information.
Nucleic Acids Res: 2014, 42(Database issue);D692-8
[PubMed:24178028] [WorldCat.org] [DOI] (I p)



Paper of the month: November 2014

  • Integration of prophages into coding sequences of the host genome results in loss of function of the interrupted gene. In B. subtilis 168, the SP-beta prophage is inserted into a uncharacterized spore polysaccharide synthesis gene, spsM. In vegetative cells, the lytic cycle is induced in response to DNA damage. In the process, the SP-beta prophage is excised from the genome to form phage particles. Now, Abe et al. demonstrate that the excision of the SP-beta prophage also occurs systematically during sporulation to reconstitute a functional spsM gene from the incomplete yodU and ypqP pseudogenes. Because phage excision is limited to the mother cell genome, and does not occur in the forespore genome, the SP-beta prophage is an integral part of the spore genome. Thus, after germination, the SP-beta prophage is propagated vertically to the progeny. The authors suggest their results indicate that the two pathways of SP-beta prophage excision support both the phage life cycle and normal sporulation of the host cells.
  • Relevant SubtiWiki pages: SP-beta prophage, sporulation, yodU, ypqP, SprA, SprB

Kimihiro Abe, Yuta Kawano, Keito Iwamoto, Kenji Arai, Yuki Maruyama, Patrick Eichenberger, Tsutomu Sato
Developmentally-regulated excision of the SPβ prophage reconstitutes a gene required for spore envelope maturation in Bacillus subtilis.
PLoS Genet: 2014, 10(10);e1004636
[PubMed:25299644] [WorldCat.org] [DOI] (I e)

  • See also:

Pilar Sanchez-Vizuete, Dominique Le Coq, Arnaud Bridier, Jean-Marie Herry, Stéphane Aymerich, Romain Briandet
Identification of ypqP as a New Bacillus subtilis biofilm determinant that mediates the protection of Staphylococcus aureus against antimicrobial agents in mixed-species communities.
Appl Environ Microbiol: 2015, 81(1);109-18
[PubMed:25326298] [WorldCat.org] [DOI] (I p)


New procedure for account creation:

  • Due to massive spam attacks, we had to change our policy for the creation of accounts. If you want to create an account, just send me a mail. We will create the account for you as quickly as possible, then you can change your password. This does not affect existing accounts, which remain active.
  • Please remember that all members of the Bacillus community are invited to create accounts and to contribute to SubtiWiki!



News in SubtiWiki:

  • August 2014: The first mobile application for SubtiWiki is now available for users of Android phones: Go for SubtiWiki in Google Play! IPhone users, please be patient! You will be served next! Click here to install!
  • April 2013: SubtiWiki uses a new, faster Mediawiki platform! The times for page access are significantly reduced. Enjoy!
  • March 2013: updated Excel files that map all genes to categories and regulons as well as the general updated identity mapping of all genes were uploaded.
  • October 2012: the essential genes have been categorized
  • September 2012: 300 mutant strains available at the BGSC were added to the corresponding gene pages
  • August 2012: SubtiExpress, the new compagnon of SubtiWiki devoted to gene expression is online! Try it out!
  • April 2012: Links for expression data under 104 different conditions (based on Nicolas et al., 2012) have been added to the expression section of the individual gene pages
  • April 2011: SubtInteract, a presentation of protein-protein interactions in B. subtilis, is online!
  • December 2010: SubtiCellPublisher allows the conversion of CellDesigner diagrams to navigatable presentations in the style of SubtiPathways



Genes (examples) Additional pages
spo0A SubtiPathways
glnA SubtInteract
rny SubtiExpress
psdA Regulons
pckA methods
dnaA metabolism
rnpA categories
sigB genome-wide analyses
ptkA list of plasmids
mreC labs working on Bacillus
ccpA the people behind SubtiWiki
sr1 template


Publications describing SubtiWiki and SubtiPathways:

Raphael H Michna, Fabian M Commichau, Dominik Tödter, Christopher P Zschiedrich, Jörg Stülke
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information.
Nucleic Acids Res: 2014, 42(Database issue);D692-8
[PubMed:24178028] [WorldCat.org] [DOI] (I p)

Ulrike Mäder, Arne G Schmeisky, Lope A Flórez, Jörg Stülke
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Nucleic Acids Res: 2012, 40(Database issue);D1278-87
[PubMed:22096228] [WorldCat.org] [DOI] (I p)

Lope A Flórez, Sebastian F Roppel, Arne G Schmeisky, Christoph R Lammers, Jörg Stülke
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.
Database (Oxford): 2009, 2009;bap012
[PubMed:20157485] [WorldCat.org] [DOI] (I p)

Christoph R Lammers, Lope A Flórez, Arne G Schmeisky, Sebastian F Roppel, Ulrike Mäder, Leendert Hamoen, Jörg Stülke
Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
Microbiology (Reading): 2010, 156(Pt 3);849-859
[PubMed:19959575] [WorldCat.org] [DOI] (I p)







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