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

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Presentation transcript:

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 Nov 20;390(6657): One of the earliest published genome sequences – recently re-sequenced and re- annotated Microbiology Jun;155(Pt 6): ,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 AL GI: , 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 Feb;192(3): 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