Main Page

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

Contact: General Microbiology, University of Göttingen, send mail

Upcoming events:

• PTS 50 - The PTS celebrates 50 years of transport and regulation, organized by Josef Deutscher, Milton Saier and Jörg Stülke will take place from September 07 to 08 in Göttingen, Germany. website, Registration form, contact
• The 1st International Conference on Post-Translational Modifications in Bacteria, organized by Ivan Mijakovic, Christophe Grangeasse, Alan Kent Nielsen and Jörg Stülke will take place from September 09 to 10 in Göttingen, Germany. website, Registration form, contact
• Past conferences

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: September 2014

• Cyclic di-AMP is the only known essential second messenger. In B. subtilis, it binds the potassium transporter KtrA and the ydaO riboswitch. This riboswitch occurs twice in the genome of B. subtilis: in the untranslated regions of the ydaO gene and the ktrA-ktrB operon. Now, two studies by Ren and Patel and Gao and Serganov report the structure of ydaO riboswitch bound to c-di-AMP. Unexpectedly, the riboswitch structure features two three-way junctions, a turn and a pseudoknot and binds two stapled c-di-AMP molecules.
• Relevant SubtiWiki pages: riboswitch, YdaO riboswitch, ktrA, metabolism of signalling nucleotides

Aiming Ren, Dinshaw J Patel
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Nat Chem Biol: 2014, 10(9);780-6
[PubMed:25086509] [WorldCat.org] [DOI] (I p)

Ang Gao, Alexander Serganov
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Nat Chem Biol: 2014, 10(9);787-92
[PubMed:25086507] [WorldCat.org] [DOI] (I p)

• Previous papers of the month

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!

https://play.google.com/store/apps/details?id=de.goettingen.uni.genmibio.subtimobile&hl=en

• 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)