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BsubCyc – A Model-Organism Database for Bacillus subtilis

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 )

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BsubCyc – A Model-Organism Database for Bacillus subtilis

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  1. BsubCyc – A Model-Organism Database for Bacillus subtilis Ing Ingrid M. Keseler SRI International

  2. 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)

  3. 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 re-annotated 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

  4. A Little About Biology • Endospore formation

  5. A Little More About Biology • Biofilm formation

  6. 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

  7. Metabolic Overview

  8. Further Improvements • Gene name synonyms from GenoList • Links to other databases: • SubtiWiki (U. Goettingen) • GenoList (Pasteur Institute) • SubtilisWiki (Texas A&M) • STRING (EMBL)

  9. Importing Regulatory Information • DBTBS

  10. 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

  11. Regulatory Overview Data from J Bacteriol. 2010 Feb;192(3):870-82. A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation.

  12. Riboswitches

  13. Two-Component Signal Transduction Systems • 17 signal transduction pathways

  14. 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

  15. New Pathways

  16. 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!

  17. Acknowledgements • Bioinformatics Research Group at SRI • 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

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