Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
Mol Phylogenet Evol. 2020 Nov;152:106908. doi: 10.1016/j.ympev.2020.106908. Epub 2020 Jul 21.
Mitochondrial translation often exhibits departures from the standard genetic code, but the full spectrum of these changes has certainly not yet been described and the molecular mechanisms behind the changes in codon meaning are rarely studied. Here we report a detailed analysis of the mitochondrial genetic code in the stramenopile group Labyrinthulea (Labyrinthulomycetes) and their relatives. In the genus Aplanochytrium, UAG is not a termination codon but encodes tyrosine, in contrast to the unaffected meaning of the UAA codon. This change is evolutionarily independent of the reassignment of both UAG and UAA as tyrosine codons recently reported from two uncultivated labyrinthuleans (S2 and S4), which we show are not thraustochytrids as proposed before, but represent the clade LAB14 previously recognised in environmental 18S rRNA gene surveys. We provide rigorous evidence that the UUA codon in the mitochondria of all labyrinthuleans serves as a termination codon instead of encoding leucine, and propose that a sense-to-stop reassignment has also affected the AGG and AGA codons in the LAB14 clade. The distribution of the different forms of sense-to-stop and stop-to-sense reassignments correlates with specific modifications of the mitochondrial release factor mtRF2a in different subsets of labyrinthuleans, and with the unprecedented loss of mtRF1a in Aplanochytrium and perhaps also in the LAB14 clade, pointing towards a possible mechanistic basis of the code changes observed. Curiously, we show that labyrinthulean mitochondria also exhibit a sense-to-sense codon reassignment, manifested as AUA encoding methionine instead of isoleucine. Furthermore, we show that this change evolved independently in the uncultivated stramenopile lineage MAST8b, together with the reassignment of the AGR codons from arginine to serine. Altogether, our study has uncovered novel variants of the mitochondrial genetic code and previously unknown modifications of the mitochondrial translation machinery, further enriching our understanding of the rules governing the evolution of one of the central molecular process in the cell.
线粒体翻译常常偏离标准遗传密码，但这些变化的全貌肯定尚未被描述，并且很少研究密码子含义变化背后的分子机制。在这里，我们报告了对 strepmenopile 组 Labyrinthulea（Labyrinthulomycetes）及其近亲的线粒体遗传密码的详细分析。在 Aplanochytrium 属中，UAG 不是终止密码子，而是编码酪氨酸，而 UAA 密码子的含义不受影响。这种变化与最近从两个未培养的 labyrinthulean 中报道的 UAG 和 UAA 重新分配为酪氨酸密码子的进化是独立的（S2 和 S4），我们表明它们不是以前提出的 thraustochytrids，而是代表在环境 18S rRNA 基因调查中之前已经识别出的 LAB14 分支。我们提供了严格的证据，证明所有 labyrinthulean 线粒体中的 UUA 密码子作为终止密码子，而不是编码亮氨酸，并提出 sense-to-stop 重新分配也影响了 LAB14 分支中的 AGG 和 AGA 密码子。不同形式的 sense-to-stop 和 stop-to-sense 重新分配的分布与不同 labyrinthulean 子集的线粒体释放因子 mtRF2a 的特定修饰以及 Aplanochytrium 中前所未有的 mtRF1a 缺失有关，也许也在 LAB14 分支中，指向观察到的密码子变化的可能机制基础。奇怪的是，我们表明 labyrinthulean 线粒体也表现出 sense-to-sense 密码子重新分配，表现为 AUA 编码蛋氨酸而不是异亮氨酸。此外，我们表明这种变化在未培养的 strepmenopile 谱系 MAST8b 中独立进化，同时 AGR 密码子从精氨酸重新分配为丝氨酸。总之，我们的研究揭示了线粒体遗传密码的新变体和线粒体翻译机制的以前未知的修饰，进一步丰富了我们对控制细胞中核心分子过程之一进化的规则的理解。
