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

Contact: General Microbiology, University of Göttingen, send mail

Upcoming events:

• The 6th European Spores Conference will be held in London from April 9 to April 11, 2014. The meeting will be organized by Simon Cutting and Imrich Barak, website, contact
• The next European BACELL meeting will take place in Bratislava from April 29 to April 30, 2014. The meeting will be organized by Imrich Barak, contact
• Past conferences

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

Now online: A description of SubtiWiki, SubtiPathways, and SubtInteract in the 2012 Database issue of Nucleic Acids Research

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)

Paper of the month: July 2013

• Ca(2+) efflux by Ca(2+) cation antiporter (CaCA) proteins is important for maintenance of Ca(2+) homeostasis across the cell membrane. Now, Wu et al. determined the structure of the B. subtilis Ca(2+)/H(+) antiporter protein ChaA. By structural and mutational analyses, they establish structural bases for mechanisms of Ca(2+)/H(+) exchange and its pH regulation. Moreover, this work also sheds light on the evolutionary adaptation to different energy modes in the CaCA protein family.
• Relevant SubtiWiki pages: ChaA, membrane proteins, metal ion homeostasis (K, Na, Ca, Mg)

Mousheng Wu, Shuilong Tong, Sandro Waltersperger, Kay Diederichs, Meitian Wang, Lei Zheng
Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation.
Proc Natl Acad Sci U S A: 2013, 110(28);11367-72
[PubMed:23798403] [WorldCat.org] [DOI] (I p)

• Previous papers of the month

New: Website of the month: July 2013: SporeWeb

• SporeWeb is a dynamic web-based platform describing all stages of sporulation in B. subtilis from a gene regulatory point of view. The website is intended for all microbial researches interested in bacterial sporulation and/or gene regulatory networks and contains useful information for both sporulation experts and non-experts.
• You can find:
  • detailed review-like descriptions of all sporulation stages,
  • schematic representations of regulatory events during every stage,
  • links to specific regulators and their regulons,
  • access to detailed Excel sheets of all sporulation-specific regulons,
  • Cytoscape-generated layouts of regulon interactions during a specific stage,
  • a tool to generate your own Cytoscape interaction figure for specific genes of interest,
  • heat maps showing expression values of all sporulation genes during the sporulation cycle (derived from Nicolas et al., 2012),
  • direct links to other knowledge platforms, such as SubtiWiki,
  • an extensive list of references for further detailed information.
• The website is self explanatory, but you can also take a quick look at the short introduction video.
• Importantly, the website is database driven: it can (and will) be updated as new exciting insights become available in literature.

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:

• 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
• December 2010: all genes are linked to regulons, and the pages of the regulons provide an overview on all genes that are members of this specific regulon.
• December 2010: all genes/proteins are linked to categories, and the pages of the categories provide an overview on all genes/proteins that are members of this specific category.

Genes (examples)	Additional pages
spo0A	SubtiPathways
glnA	Lists of genes, proteins and RNAs
rny	Categories
psdA	Regulons
pckA	methods
dnaA	metabolism
rnpA	protein-protein interactions
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:

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)