Although genes within living organisms generally interact in mutually beneficial ways, opportunities also exist for "selfish" conflict between genes, when some genes direct their own survival, possibly to the exclusion of other genes. This project will investigate the possibility that such "warfare" between genes in the nuclear DNA and genes in the separate plastid (chloroplast) DNA is responsible for very fast evolutionary changes in protein sequences that have been observed in many groups of flowering plants. The research activities will provide training opportunities for student and postdoctoral researchers in advanced techniques in biotechnology and computational genomics. This research and training will be integrated with educational workshops that will expose early-stage undergraduates to career opportunities in the field of bioinformatics. Students will also help organize workshops in Mexico; these international service-learning experiences will be designed with the goal of boosting recruitment and retention at the US universities of underrepresented minority groups in technical and quantitative disciplines.
The research project will focus on a protease enzyme complex (Clp) in plastids that exhibits accelerated evolution and extreme signatures of positive selection in both plastid- and nuclear-encoded subunits. Biochemical and phenotypic consequences of changes in protein sequences will be investigated by modifying the plastid genome in the Nicotiana tabacum model system. Proteomic techniques will be used to assess assembly of the enzyme complex and effects of the protease on plastid protein content. Finally, comparative genomic approaches will be used to analyze correlated rates of protein sequence evolution to discover previously unrecognized interactions between plastid and nuclear genes. Collectively, these lines of investigation will test the hypothesis that antagonistic plastid-nuclear interactions have driven accelerated evolution of the plastid Clp complex.
