Conflict and Coevolution in a Plastid- Nuclear Enzyme Complex

虽然生物体内的基因通常以互利的方式相互作用，但基因之间也存在“自私”冲突的机会，当一些基因决定自己的生存时，可能会排斥其他基因。这个项目将调查核DNA中的基因和单独质体（叶绿体）DNA中的基因之间的这种“战争”的可能性，这种“战争”是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的原因。这些研究活动将为学生和博士后研究人员提供培训机会，研究生物技术和计算基因组学的先进技术。这项研究和培训将与教育讲习班相结合，使早期本科生接触到生物信息学领域的职业机会。学生们还将在墨西哥帮助组织研讨会；这些国际服务学习经验的设计目标，将是促进美国大学在技术和定量学科中招募和留住代表性不足的少数群体。该研究项目将重点关注质体中的蛋白酶复合物（Clp），该复合物在质体和核编码亚基中都表现出加速进化和积极选择的极端特征。在烟草模型系统中，将通过修饰质体基因组来研究蛋白质序列变化的生化和表型后果。蛋白质组学技术将用于评估酶复合物的组装和蛋白酶对质体蛋白质含量的影响。最后，比较基因组学方法将用于分析蛋白质序列进化的相关率，以发现以前未被认识到的质体和核基因之间的相互作用。总的来说，这些研究路线将验证拮抗的质体-核相互作用加速了质体Clp复合物进化的假设。

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.