Sequencing and analysis of bacterial genomes has become routine in the development of diagnostics, drug targets and improved production strains. Problems with this approach include: (1) unassignable, hypothetical ORFs, comprising 25-50 percent of an average genome; (2) lack of hierarchical organization of information; and (3) insufficient connections to experimental biology, both in verification of predictions and in high throughput methods. IG (Integrated Genomics) has already produced gapped genomes of Enterococcus faecium and Fusobacterium nucleatum. The grant applicants propose to address the problems identified above using those bacteria as model organisms. In addition, the bacteria themselves have obvious importance as human pathogens. In Phase I, the investigators will use primer-walking to complete these gapped genomes, leaving 0 to 10 gaps. They will assign new and corrected ORFs, and make improvements in functional assignments using proprietary WIT-Pro(TM) genomic analysis software suite. The investigators go on to outline their goals for Phase II and Phase III of the project, which are (1) to correlate hypothetical ORFs with """"""""orphan functions"""""""" missing from metabolic pathways, (2) to clone and over express selected ORFs and determine their enzymatic function(s), and (3) in collaboration with a second company Sigma-Genosis, to design proprietary gene expression arrays for commercialization.
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