Extreme variation in rates of evolution in the plastid Clp protease complex
Extreme variation in rates of evolution in the plastid Clp protease complex
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DOI：
10.1111/tpj.14208
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发表时间：
2018-08
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影响因子：
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通讯作者：
Alissa M. Williams;G. Friso;K. V. van Wijk;Daniel B. Sloan
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作者：
Alissa M. Williams;G. Friso;K. V. van Wijk;Daniel B. Sloan
真核细胞代表了多个基因组之间的复杂协作，甚至下降到线粒体和质体中的多亚基复合物的水平。植物中的一种这样的复合物是酪蛋白分解蛋白酶（Clp），其在质体蛋白质周转中起重要作用。Clp的蛋白水解核心包括来自一个质体编码基因（clpP1）和多个核基因的亚基。clpP1基因在大多数绿色植物中是高度保守的，但它是迄今为止在一些被子植物中进化最快的质体编码基因。为了更好地理解这些极端而神秘的分歧模式，我们通过从988个已发表的质体基因组中提取序列，研究了clpP1分子在绿色植物中的进化历史。我们发现clpP1经历了非常频繁的加速序列进化和结构变化（例如，内含子和RNA编辑位点的丢失）。虽然clpP1通常被认为是一个假基因在这种情况下，多线的证据表明，这是很少的情况。我们应用比较天然凝胶电泳的叶绿体蛋白质复合物，然后在两个物种内的被子植物属蝇子草，这具有高度升高和异构率clpP1进化的蛋白质质谱。我们证实，clpP1表达为一个稳定的蛋白质，并形成寡聚体复合物与核编码的Clp亚基，即使在一个最不同的Silene物种。此外，在广泛的被子植物样本中，clpP1和核编码的Clp亚基的氨基酸取代率之间存在紧密的相关性，这表明正在进行的选择在这个复杂的相互作用。
Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multisubunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g., loss of introns and RNA-editing sites) within seed plants. Although clpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely the case. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus Silene, which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino-acid substitution rates in clpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting ongoing selection on interactions within this complex.