BsubCyc – A Model-Organism Database for Bacillus subtilis

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Ingrid M. KeselerSRI 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 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

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

•DBTBS

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