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: • • • •

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 • • • •

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