Transcript BsubCyc - Bioinformatics Research Group at SRI International

BsubCyc – A Model-Organism
Database for Bacillus subtilis
Ing
Ingrid M. Keseler
SRI International
Why Bacillus subtilis?
• Gram-positive bacterium
• Long history of basic research
• Interesting life cycle (sporulation, competence, biofilm)
• Model organism for a variety of important pathogens
(e.g. Staphylococcus aureus) and bioterrorism agents
(e.g. Bacillus anthracis)
• Important industrial microorganism: production of
enzymes (e.g. Novozymes, Genencor)
Bacillus subtilis Vital Stats
• One of the earliest published genome
sequences
Nature. 1997 Nov 20;390(6657):249-56.
• One of the earliest published genome
sequences – recently re-sequenced and reannotated
Microbiology. 2009 Jun;155(Pt 6):1758-75.
• 4,215,606 bp, 4,400+ genes
• PubMed keyword search “subtilis” – 25,753
publications on 10/22/2010
A Little About Biology
• Endospore formation
A Little More About Biology
• Biofilm formation
Building BsubCyc
• Based on GenBank AL009126.3 GI:225184640,
deposited by the Genoscope group October 1,
2009
• Resulting in
• 1222 metabolic reactions
• 214 metabolic pathways
BsubCyc.org
Metabolic Overview
Further Improvements
• Gene name synonyms from GenoList
• Links to other databases:
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SubtiWiki (U. Goettingen)
GenoList (Pasteur Institute)
SubtilisWiki (Texas A&M)
STRING (EMBL)
Importing Regulatory Information
•DBTB
S
Transcriptional Regulation
• Imported from DBTBS (Database of
Transcriptional regulation in Bacillus subtilis):
• 1076 transcription start sites
• 1226 transcription units
• 703 transcription factor binding sites
• Import is incomplete due to a variety of
complications
Regulatory Overview
Data from J Bacteriol. 2010 Feb;192(3):870-82. A comprehensive proteomics and
transcriptomics analysis of Bacillus subtilis salt stress adaptation.
Riboswitches
Two-Component Signal Transduction
Systems
• 17 signal transduction pathways
New Literature
• New publications from 2009 and 2010 added
to genes/proteins:
• Publication year 2009: 87
• Publication year 2010: 169
• Approximate number of new gene functions
since the beginning of this project: ~70? (gene
name changed)
• 2 new pathways
New Pathways
Future Directions
• Work on metabolic pathways – recruit
scientists with expertise
• Improve transcriptional regulatory network
• Post-transcriptional regulation
• Import data from the co-PIs of the project
• Funding!
Acknowledgements
• Bioinformatics Research Group at SRI
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Tomer Altman
Pallavi Kaipa
Markus Krummenacker
Ron Caspi
• David Rudner, Anna-Barbara Hachmann (Harvard)
• Jim Hu (Texas A&M)
• Funding: NIH Grand Opportunity grant
RC2 GM092616