Conflict and Coevolution in a Plastid- Nuclear Enzyme Complex

尽管活着的有机体内的基因通常以互惠的方式相互作用，但当一些基因指导自己的生存时，也存在基因之间的“自私”冲突的机会，可能会排除其他基因。该项目将研究在许多开花植物群体中观察到的蛋白质序列的快速进化变化，是否可能是核DNA中的基因和单独的叶绿体DNA中的基因之间的“战争”。研究活动将为学生和博士后研究人员提供生物技术和计算基因组学先进技术方面的培训机会。这项研究和培训将与教育讲习班相结合，使处于早期阶段的本科生在生物信息学领域获得就业机会。学生们还将帮助在墨西哥组织研讨会；这些国际服务学习体验将旨在促进美国大学在技术和数量学科中招募和留住未被充分代表的少数群体。研究项目将专注于叶绿体中的一种蛋白酶复合体(CLP)，该复合体在叶绿体和核编码的亚基中都表现出加速进化和积极选择的极端特征。将通过修改烟草模式系统中的叶绿体基因组来研究蛋白质序列变化的生化和表型后果。蛋白质组学技术将被用来评估酶复合体的组装和蛋白酶对叶绿体蛋白质含量的影响。最后，比较基因组学方法将被用来分析蛋白质序列进化的相关速率，以发现以前未被认识到的叶绿体和核基因之间的相互作用。总而言之，这些研究将检验这样一个假设，即拮抗的叶绿体-核相互作用推动了叶绿体CLP复合体的加速进化。

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.