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 DBTB S

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