Difference between revisions of "Main Page"

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<big>'''Paper of the month: August 2014'''</big>  
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<big>'''Paper of the month: September 2014'''</big>  
* Calcium is important for the activity of many many enzymes, and its cellular homeostasis is therefore important. Now, the previously unknown [[YetJ]] protein has been identified as a pH-sensitive calcium leak that allows reducing the inracellular calcium concentration. [http://www.ncbi.nlm.nih.gov/pubmed/24904158 Chang et al.] report the structure of [[YetJ]] and explain how two conserved Asp residues sense changes in the pH.
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* 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 [http://www.ncbi.nlm.nih.gov/pubmed/25086509 Ren and Patel] and [http://www.ncbi.nlm.nih.gov/pubmed/25086507 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 ''Subti''Wiki pages:''' [[Metal ion homeostasis (K, Na, Ca, Mg)]], [[YetJ]]
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* '''Relevant ''Subti''Wiki pages:''' [[riboswitch]], [[YdaO riboswitch]], ''[[ktrA]]'', [[metabolism of signalling nucleotides]]
<pubmed> 24904158 </pubmed>
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<pubmed> 25086507 25086509 </pubmed>
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* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 16:03, 19 September 2014

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

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Contact: General Microbiology, University of Göttingen, send mail


Upcoming events:


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



Paper of the month: September 2014

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)



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)