Prediction of protein functions and metabolic pathways.

My research includes predicting functions for gene products encoded by the genome of Shewanella oneidensis MR-1 and of about 20 additional members of the Shewanella genus. Our manual curation efforts emphasize the use of published experimental work on homologous sequences as well as experimental data obtained by Shewanella researchers (e.g. gene and protein expression data, mutant analysis, promoter predictions etc.). We also make use of protein domains, protein families, and genome context to infer functions. A database of Shewanella orthologs is being generated to infer functions across genomes and to facilitate cross genome comparisons.

Our work also includes prediction of metabolic pathways or cellular roles for gene products encoded in the S. oneidensis MR-1 genome. We have built an S. oneidensis MR-1 specific Pathway Genome Database (PGDB) using the Pathway Tools software system. The database will be made publicly available in the near future. The SEED annotation environment is in the process of being implemented for annotation of functional subsystems and for comparison of Shewanella species.

Ecophysiological adatipations and speciation of Shewanella.

Members of the Shewanella genus occupy a variety of ecological niches including lakes, rivers, oceans, sediments, and terrestrial sub-surfaces. This suggests a high degree of physiological variety and the existence of several ecotypes. Diversity among Shewanella strains has been detected in some metabolic processes including the use of metals and radionuclides for respiration. Genes involved in environmental sensing and signaling also vary among the strains. Further the Shewanella are believed to play an important role driving biogeochemical cycles of C, N and S in redox interfaces of marine environments. We are interested in whether the genomic content and functions therein can be linked to the various ecological niches.

The Shewanella genomes sequenced were selected based on their phylogenetic relatedness. They represent a gradient of closely to more distantly related species. We are currently analyzing members of this genus to better understand how speciation and ecology relate to observed genotypes and phenotypes.

Protein families: a means to study functional diversity and metabolic capabilities.

My research interests also involve studying protein families both as a means to understand functional diversity and to link this diversity to metabolic capabilities and environmental adaptations. We are using protein groups for cross genome comparisons with the goal of relating family differences to functional capacity.