Date of Award

12-2008

Degree Type

Thesis

Degree Name

Master of Science

Major

Life Sciences

Major Professor

Igor Jouline

Committee Members

Ed Uberbacher, Frank Larimer, Russell Zaretzki

Abstract

The recent completion of the sequencing of several species of the Shewanella genus provides a unique opportunity for comparative genomics studies. We chose the first 10 fully sequenced Shewanella genomes to investigate the evolution of signal transduction proteins (ST). ST is a universal and highly regulated system, and as a very well-studied system provides an excellent starting point for investigation. Furthermore, Shewanella have been shown to have a large number of two-component systems and diguanylate cyclases relative to their genome size. In this study we investigate the evolution of signal transduction across several Shewanella strains by utilizing a domainlevel approach for determining homology and orthology of the parent proteins. Proteins were broken down into their constituent domains and domain sized sequences and compared using a reciprocal best BLAST hit approach to determine homology between all of the species. Analysis of homologous domains and proteins revealed several levels of conservation and a core group of signal transduction proteins common to all members. Further analysis of domain homology provided putative annotations of previously unrecognized sequences and highlighted deficiencies in specific Pfam domain models. Analysis of paralogous domains and proteins showed agreement with 16s rRNA based estimates of evolution, although the position of S. oneidensis MR-1 was novel.

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