Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution
Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution
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DOI：
10.1073/pnas.1007667108
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发表时间：
2011-01-25
影响因子：
11.1
通讯作者：
Small, Ian D.
中科院分区：
文献类型：
--
作者：
Fujii, Sota;Bond, Charles S.;Small, Ian D.
真核细胞在一种显然互利的共生关系中已经拥有线粒体至少15亿年了。对重要农艺性状细胞质雄性不育（CMS）的研究表明，细胞核基因组和线粒体基因组之间似乎存在寄主-寄生物关系，但缺乏分子证据。CMS系统中的关键参与者是在携带线粒体CMS基因的植物中发育功能性雄性配子体所需的育性恢复（Rf）基因。在大多数情况下，Rf基因编码五肽重复（PPR）蛋白。我们发现，大多数被子植物广泛的基因组序列数据存在含有多个PPR基因相关的Rf基因。这些类Rf基因与其他PPR基因相比，表现出许多特征，包括染色体聚类和独特的进化模式，特别是高比率的非同义到同义的取代，这表明多样化的选择。在PPR基序内的氨基酸残基1、3和6中看到多样化选择的最高概率。PPR蛋白参与RNA加工，将选择数据映射到PPR基序阵列的预测共识结构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样基因的选择模式揭示了分子之间的“军备竞赛”的核和线粒体基因组，一直坚持在被子植物的进化历史的大部分。
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.