Difference between revisions of "Main Page"

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<big>'''Paper of the month: November 2014'''</big>  
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<big>'''Paper of the month: December 2014'''</big>  
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* Integration of prophages into coding sequences of the host genome results in loss of function of the interrupted gene. In ''B. subtilis'' 168, the [[SP-beta prophage]] is inserted into a uncharacterized spore polysaccharide synthesis gene, ''spsM''. In vegetative cells, the lytic cycle is induced in response to DNA damage. In the process, the [[SP-beta prophage]] is excised from the genome to form phage particles. Now, [http://www.ncbi.nlm.nih.gov/pubmed/25299644 Abe et al.] demonstrate that the excision of the [[SP-beta prophage]] also occurs systematically during [[sporulation]] to reconstitute a functional ''spsM'' gene from the incomplete ''[[yodU]]'' and ''[[ypqP]]'' [[pseudogenes]]. Because phage excision is limited to the mother cell genome, and does not occur in the forespore genome, the [[SP-beta prophage]] is an integral part of the spore genome. Thus, after [[germination]], the [[SP-beta prophage]] is propagated vertically to the progeny. The authors suggest their results indicate that the two pathways of [[SP-beta prophage]] excision support both the phage life cycle and normal [[sporulation]] of the host cells.
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* [[Cell division]] is facilitated by a molecular machine - the [[divisome]] - that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by [[FtsZ]] is regulated by several factors, including the [[divisome]] component [[EzrA]]. [http://www.ncbi.nlm.nih.gov/pubmed/25403286 Cleverley et al.] now describe the structure of the cytoplasmic domain of [[EzrA]] which comprises five linear repeats of an unusual triple helical bundle. The [[EzrA]] structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound [[divisome]] components. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and [[EzrA]] is proposed to be the founding member of the bacterial spectrin family.  
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* '''Relevant ''Subti''Wiki pages:''' [[SP-beta prophage]], [[sporulation]], ''[[yodU]], [[ypqP]]'', [[SprA]], [[SprB]]
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* '''Relevant ''Subti''Wiki pages:''' [[EzrA]], [[FtsZ]], [[divisome]], [[cell division]], [[Rick Lewis]]
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<pubmed> 25299644 </pubmed>
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<pubmed> 25403286 </pubmed>
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* See also:
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<pubmed> 25326298 </pubmed>
 
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 13:22, 12 December 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

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: December 2014

  • Cell division is facilitated by a molecular machine - the divisome - that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by FtsZ is regulated by several factors, including the divisome component EzrA. Cleverley et al. now describe the structure of the cytoplasmic domain of EzrA which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and EzrA is proposed to be the founding member of the bacterial spectrin family.
  • Relevant SubtiWiki pages: EzrA, FtsZ, divisome, cell division, Rick Lewis

Robert M Cleverley, Jeffrey R Barrett, Arnaud Baslé, Nhat Khai Bui, Lorraine Hewitt, Alexandra Solovyova, Zhi-Qiang Xu, Richard A Daniel, Nicholas E Dixon, Elizabeth J Harry, Aaron J Oakley, Waldemar Vollmer, Richard J Lewis
Structure and function of a spectrin-like regulator of bacterial cytokinesis.
Nat Commun: 2014, 5;5421
[PubMed:25403286] [WorldCat.org] [DOI] (I e)



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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