Difference between revisions of "Main Page"

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<big>'''Paper of the month: July 2013'''</big>  
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<big>'''Paper of the month: August 2013'''</big>  
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* Ca(2+) efflux by Ca(2+) cation antiporter (CaCA) proteins is important for maintenance of Ca(2+) homeostasis across the cell membrane. Now, [http://www.ncbi.nlm.nih.gov/pubmed/23798403 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.
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* In cells, the concentration of ribonucleotides by far exceeds that of deoxyribonucleotides. This poses problems since the DNA polymerase incorporates one rNTP every 2.3 kb during [[DNA replication|chromosome replication]]. Now, [http://www.ncbi.nlm.nih.gov/pubmed/23882084 Yao et al.] investigated how these misincorporations  are repaired. The demonstrate that this repair is initiated by [[rnhB|RNase HII]] that nicks DNA at single rNMP residues to initiate replacement with dNMP.
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* '''Relevant ''Subti''Wiki pages:'''  [[ChaA]], [[membrane proteins]], [[metal ion homeostasis (K, Na, Ca, Mg)]]
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* '''Relevant ''Subti''Wiki pages:'''  [[DNA replication]], [[DNA repair/recombination|DNA repair]], ''[[rnhB]]'', ''[[rnhC]]'', ''[[mutS]]'', ''[[mutL]]''
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<pubmed> 23798403 </pubmed>
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<pubmed> 23882084 </pubmed>
  
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
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<big>'''New: Website of the month: July 2013: [http://sporeweb.molgenrug.nl/  SporeWeb]'''</big>
 
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* [http://sporeweb.molgenrug.nl/  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.
 
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* You can find:
 
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** detailed review-like descriptions of all [[sporulation]] stages,
 
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** schematic representations of regulatory events during every stage,
 
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** links to specific regulators and their [[regulons]],
 
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** access to detailed Excel sheets of all sporulation-specific [[regulons]],
 
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** Cytoscape-generated layouts of regulon interactions during a specific stage,
 
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** a tool to generate your own Cytoscape interaction figure for specific genes of interest,
 
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** heat maps showing expression values of all [[sporulation]] genes during the sporulation cycle (derived from [http://www.ncbi.nlm.nih.gov/pubmed/22383849  Nicolas ''et al''., 2012]),
 
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** direct links to other knowledge platforms, such as ''Subti''Wiki,
 
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** an extensive list of references for further detailed information.
 
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* The website is self explanatory, but you can also take a quick look at [http://youtu.be/XSTpU80o4t0 the short introduction video].
 
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* Importantly, the website is database driven: it can (and will) be updated as new exciting insights become available in literature.
 
  
 
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Revision as of 12:53, 1 August 2013

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 description of SubtiWiki, SubtiPathways, and SubtInteract in the 2012 Database issue of Nucleic Acids Research



Paper of the month: August 2013

  • In cells, the concentration of ribonucleotides by far exceeds that of deoxyribonucleotides. This poses problems since the DNA polymerase incorporates one rNTP every 2.3 kb during chromosome replication. Now, Yao et al. investigated how these misincorporations are repaired. The demonstrate that this repair is initiated by RNase HII that nicks DNA at single rNMP residues to initiate replacement with dNMP.
  • Relevant SubtiWiki pages: DNA replication, DNA repair, rnhB, rnhC, mutS, mutL

Nina Y Yao, Jeremy W Schroeder, Olga Yurieva, Lyle A Simmons, Mike E O'Donnell
Cost of rNTP/dNTP pool imbalance at the replication fork.
Proc Natl Acad Sci U S A: 2013, 110(32);12942-7
[PubMed:23882084] [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:

  • 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
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Publications describing SubtiWiki and SubtiPathways:







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