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<big>'''Paper of the month: July 2015'''</big>  
 
<big>'''Paper of the month: July 2015'''</big>  
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* The precise functions of serine [[Protein kinases and phosphatases|protein kinases]] in ''B. subtilis'' have largely remained enigmatic until very recently. Now, two studies from the lab of [[Jonathan Dworkin]] describe functions and molecular targets for two of these kinases, [[PrkC]] and [[YabT]]. [http://www.ncbi.nlm.nih.gov/pubmed/26056311 Pereira et al.] have identified the universally conserved [[TufA|elongation factor Tu]] as a target for the protein kinase [[YabT]]. In srarving cells, YabT phosphorylates [[TufA|EF-Tu]] at a conserved threonine residue. Phosphorylation impairs the essential GTPase activity of [[TufA|EF-Tu]], thereby preventing its release from the [[ribosome]]. As a consequence, phosphorylated [[TufA|EF-Tu]] has a dominant-negative effect in [[translation]] elongation, resulting in the overall inhibition of protein synthesis. Importantly, this mechanism allows a quick and robust regulation of one of the [[most abundant proteins|most abundant cellular proteins]]. [http://www.ncbi.nlm.nih.gov/pubmed/26102633 Libby et al.] have uncovered that phosphorylation by PrkC stimulates the activity of the [[essential genes|essential]] [[Two-component systems|two-component transcription factor]] [[WalR]]. This mechanism links the presence of muropeptides that trigger [[PrkC]] activity to the expression of the genes of the [[WalR regulon]] that are involved in [[cell wall synthesis|cell wall metabolism]].
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* The cells in a biofilm experience very different conditions: While the inner cells are well protected from any harm from the environment, they have on the other hand only poor access to nutrients. For the cells on the edge of the biofilm, it is just the other way round. Now, [http://www.ncbi.nlm.nih.gov/pubmed/26200335 Liu et al.] from the lab of [[Gürol M. Süel]] have discovered oscillation in the [[biofilm formation|growth of the biofilm]]. These oscillations serve to provide the inner cells with access to nutrients. These oscillations are caused by metabolic co-dependence between cells in the biofilm periphery and interior that is driven by [[glutamate metabolism|glutamate consumption and ammonium production]], respectively.
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* '''Relevant ''Subti''Wiki pages:''' [[Jonathan Dworkin]], [[Protein kinases and phosphatases|protein kinases]], [[YabT]], [[TufA|EF-Tu]], [[PrkC]], [[WalR]], [[cell wall synthesis|cell wall metabolism]]
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* '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]]
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<pubmed>26056311 26102633</pubmed>
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* see [http://microbepost.org/2015/08/05/conflict-and-co-operation-in-bacterial-communities/ a blog presenting this paper]
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<pubmed>26200335</pubmed>
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 13:14, 10 August 2015

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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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: July 2015

Jintao Liu, Arthur Prindle, Jacqueline Humphries, Marçal Gabalda-Sagarra, Munehiro Asally, Dong-yeon D Lee, San Ly, Jordi Garcia-Ojalvo, Gürol M Süel
Metabolic co-dependence gives rise to collective oscillations within biofilms.
Nature: 2015, 523(7562);550-4
[PubMed:26200335] [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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