User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study

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Genomic analysis of the synthetic cost of predatory bacterial proteomes

The organisms that are the subject of my proposed project, the predatory Bdellovibrio and like organisms (BALOs), are among the most enigmatic of microorganisms. Because their life history is highly resistant to culture-dependent investigation, the molecular processes of predation and development, and their evolutionary influences have remained inscrutable {tudor2007genomic}. The application of computational comparative genomics has the potential to break the stalemate, as demonstrated in a recent paper {smith_economical_2010}. Examining a range of genomes, {smith_economical_2010}found a corrolation between protein localization and synthetic cost: they argue that selection favors more economical extracellular proteins. However, while they examined all 711 gram-negative strains in PSORTdb (a database of predicted protein localization), they reported detailed results for only 25 of them, passing over the Bdellovibrio HD 100 genome.

I propose to repeat the detailed analysis done for E. coli for the currently available predatory prokaryote genomes (Bdellovibrio HD 100, Bacteriovorax marinus SJ and Bdellovibrio strain W). I will be operating under the working hypothesis that because of the BALOs’ unique life history: (1) predicted extracellular proteins would be under much weaker selection for economy (cf. endosymbionts), and (2) the majority of the 34% of proteins classified as ``unknown" in PSORTdb for HD 100 are expressed in the bdelloplast and would thus trend towards less economy.

Notes

Weeks 1–4: Automated annotation of genomes.

Weeks 5–6: Protein localization data collection and prediction.

Weeks 7–11: Data analysis.

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