Functional genomics of hypothetical genes in Gram-positive bacteria

Project Summary/Abstract Approximately 30% of all bacterial gene products are microbial “dark matter” and have no characterized function. Developing methods for describing gene function in commensal and pathogenic bacteria will advance the fields of fundamental bacteriology and microbial pathogenesis, driving new approaches to combat the rise of antibiotic resistance. The short-term training goal of this proposal is to provide the candidate with mentoring and training in computational biology and data science. The long-term objectives are to establish robust computational and genetic tools for functional analysis of uncharacterized bacterial genes. These will be applied to established, tractable experimental systems to make mechanistic discoveries about uncharacterized loci involved in biofilm formation and polymicrobial interactions. For career development, the candidate will undertake a comprehensive training plan with an outstanding mentor, co-mentor, and advisory committee. Aim 1 will use chemical genetics to identify hypothetical gene function in the commensal and pathogenic bacterium Enterococcus faecalis OG1RF. In Aim 2, the candidate will develop chemical genetics methodology to determine how pre-formed biofilms respond after treatment with bioactive compounds such as antibiotics. In Aim 3, these functional genomics approaches will be expanded to study interactions between OG1RF and the oral pathogen Streptococcus mutans, as the candidate determined that S. mutans kills OG1RF and a vancomycin-resistant isolate of E. faecalis through an unknown mechanism. Together, this research will generate genome-scale descriptions of gene function in medically relevant bacteria and define mechanisms by which novel factors contribute to biofilm formation and interactions between microbes. The University of Minnesota provides an ideal institutional environment for this work. This highly collaborative environment has diverse microbiology and computational biology research groups from biomedical, dental, veterinary, and basic science backgrounds. U Minnesota also offers exceptional career development opportunities, and the U Minnesota Genomics Center is a state-of-the-art facility with which the candidate has already established a productive collaboration. Together, the proposed training and research will be a platform from which the candidate will launch an independent research career combining functional genomics with in vitro model systems to study hypothetical gene function in diverse bacteria.