Difference between revisions of "Main Page"

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<big>'''Paper of the month: April 2015'''</big>  
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<big>'''Paper of the month: May 2015'''</big>  
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* In a [http://www.ncbi.nlm.nih.gov/pubmed/15096624 groundbreaking study from 2004], several candidate [[riboswitch]]es have been discovered in ''Bacillus subtilis''. While the [[ydaO riboswitch]] has recently been discovered to be a target of the second messenger c-di-AMP, two new studies identify manganese ions as the ligand of the [[yybP-ykoY motif]] that controls the expression of the ''[[yybP]]'' and ''[[ykoY]]'' genes. Both genes are induced in the presence of Mn<sup>2+</sup>, due to the interaction of the ion with the [[riboswitch]]. This finding implies that [[YybP]] and [[YkoY]], which have not yet been functionally studied, are implicated in the control of manganese homeostasis.
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* In ''B. subtilis'', ribosomal stalling is used to regulate the expression of the membrane protein biogenesis factor [[YidC2]]. This is achieved by stalling during [[translation]] of the [[MifM]] leader peptide. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. [http://www.ncbi.nlm.nih.gov/pubmed/25903689 Sohmen et al.] have determined the structure of the [[MifM]]-stalled 70S [[ribosome]] and have unraveled a network of interactions between [[MifM]] and the ribosomal tunnel, which induces translational arrest. Complementary genetic analyses identify a single amino acid within [[ribosomal protein]] [[rplV|L22]] that dictates the species specificity of the stalling event.  
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* '''Relevant ''Subti''Wiki pages:''' [[yybP-ykoY motif]], [[riboswitch]], ''[[yybP]]'', ''[[ykoY]]'', [[John Helmann]]
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** '''Relevant ''Subti''Wiki pages:''' [[translation]], [[ribosome]], ''[[yidC2]]'', [[MifM]], [[rplV|L22]]
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<pubmed>25794618 25794619</pubmed>
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<pubmed> 25903689</pubmed>
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  

Revision as of 08:43, 13 May 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: May 2015

  • In B. subtilis, ribosomal stalling is used to regulate the expression of the membrane protein biogenesis factor YidC2. This is achieved by stalling during translation of the MifM leader peptide. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Sohmen et al. have determined the structure of the MifM-stalled 70S ribosome and have unraveled a network of interactions between MifM and the ribosomal tunnel, which induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event.

Daniel Sohmen, Shinobu Chiba, Naomi Shimokawa-Chiba, C Axel Innis, Otto Berninghausen, Roland Beckmann, Koreaki Ito, Daniel N Wilson
Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Nat Commun: 2015, 6;6941
[PubMed:25903689] [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:







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