Australian Research Council Centre of Excellence in Plant Energy Biology and School of Biomedical, Biomolecular, and Chemical Sciences, University of Western Australia, Crawley, WA 6009, Australia.
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1723-8. doi: 10.1073/pnas.1007667108. Epub 2011 Jan 10.
Eukaryotic cells have harbored mitochondria for at least 1.5 billion years in an apparently mutually beneficial symbiosis. Studies on the agronomically important crop trait cytoplasmic male sterility (CMS) have suggested the semblance of a host-parasite relationship between the nuclear and mitochondrial genomes, but molecular evidence for this is lacking. Key players in CMS systems are the fertility restorer (Rf) genes required for the development of a functional male gametophyte in plants carrying a mitochondrial CMS gene. In the majority of cases, Rf genes encode pentatricopeptide repeat (PPR) proteins. We show that most angiosperms for which extensive genomic sequence data exist contain multiple PPR genes related to Rf genes. These Rf-like genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering and unique patterns of evolution, notably high rates of nonsynonymous to synonymous substitutions, suggesting diversifying selection. The highest probabilities of diversifying selection were seen for amino acid residues 1, 3, and 6 within the PPR motif. PPR proteins are involved in RNA processing, and mapping the selection data to a predicted consensus structure of an array of PPR motifs suggests that these residues are likely to form base-specific contacts to the RNA ligand. We suggest that the selection patterns on Rf-like genes reveal a molecular "arms-race" between the nuclear and mitochondrial genomes that has persisted throughout most of the evolutionary history of angiosperms.
真核细胞已经在明显互利共生的关系中拥有线粒体至少 15 亿年。对农业上重要的作物性状细胞质雄性不育（CMS）的研究表明，核基因组和线粒体基因组之间存在宿主-寄生虫关系的表象，但缺乏这方面的分子证据。CMS 系统的关键因素是育性恢复（Rf）基因，对于携带线粒体 CMS 基因的植物中功能性雄性配子体的发育是必需的。在大多数情况下，Rf 基因编码五肽重复（PPR）蛋白。我们表明，对于绝大多数拥有广泛基因组序列数据的被子植物来说，含有多个与 Rf 基因相关的 PPR 基因。与其他 PPR 基因相比，这些 Rf 样基因具有许多特征，包括染色体聚类和独特的进化模式，特别是非同义替换与同义替换的高比率，表明了多样化选择。在 PPR 基序内的第 1、3 和 6 位氨基酸残基处观察到最高的多样化选择概率。PPR 蛋白参与 RNA 处理，并且将选择数据映射到 PPR 基序的预测共识结构上表明，这些残基可能与 RNA 配体形成碱基特异性接触。我们认为，Rf 样基因上的选择模式揭示了核基因组和线粒体基因组之间持续存在的分子“军备竞赛”，这在被子植物的大部分进化历史中都存在。
