Difference between revisions of "Main Page"

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<big>'''Paper of the month: February 2015'''</big>  
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<big>'''Paper of the month: March 2015'''</big>  
* To proliferate efficiently, cells must co-ordinate [[cell division]] with [[DNA condensation/ segregation|chromosome segregation]]. In ''B. subtilis'', the nucleoid occlusion protein [[Noc]] binds to specific DNA sequences scattered around the chromosome and helps to protect genomic integrity by coupling the initiation of division to the progression of chromosome replication and segregation. However, how it inhibits division has remained unclear. Now, [http://www.ncbi.nlm.nih.gov/pubmed/25568309 Adams et al.] from the lab of [[Jeff Errington]] demonstrate that [[Noc]] associates with the cell membrane via an N-terminal amphipathic helix. Importantly, the membrane-binding affinity of this helix is weak and requires the assembly of nucleoprotein complexes, thus establishing a mechanism for DNA-dependent activation of [[Noc]]. Furthermore, division inhibition by [[Noc]] requires recruitment of [[Noc]] binding site DNA to the cell membrane and is dependent on its ability to bind DNA and membrane simultaneously. The results suggest a simple model in which the formation of large membrane-associated nucleoprotein complexes physically occludes assembly of the [[divisome|division machinery]].
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* In ''Bacillus subtilis'', [[glutamate metabolism|nitrogen acquisition]] is controlled by [[SubtInteract|protein-protein interactions]]. Regulation is brought about by [[SubtInteract|interactions]] of the [[trigger enzyme|trigger enzymes]] [[GlnA|glutamine synthetase]] with the transcription factors [[TnrA]] and [[GlnR]] to inhibit or trigger their DNA-binding activity, respectively, and by the PII protein [[NrgB]] that also interacts with [[TnrA]]. Now, [http://www.ncbi.nlm.nih.gov/pubmed/25691471 Schumacher et al.] have solved the structures of several complexes involved in nitrogen sensing. The results unravel so far unprecendented mechanisms for metabolic reprogramming of the cell in response to nitrogen availability.
* '''Relevant ''Subti''Wiki pages:''' [[Noc]], [[Jeff Errington]], [[cell division]], [[DNA condensation/ segregation|chromosome segregation]]
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* '''Relevant ''Subti''Wiki pages:''' [[GlnA]], [[trigger enzymes]], [[TnrA]], [[GlnR]], [[NrgB]]
<pubmed>25568309</pubmed>
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<pubmed>25691471</pubmed>
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 12:33, 5 March 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: March 2015

Maria A Schumacher, Naga Babu Chinnam, Bonnie Cuthbert, Nam K Tonthat, Travis Whitfill
Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Genes Dev: 2015, 29(4);451-64
[PubMed:25691471] [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)