Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes.
Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes.
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DOI：
10.24272/j.issn.2095-8137.2021.348
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发表时间：
2022-01-18
影响因子：
4.9
通讯作者：
Ghiselli F
中科院分区：
文献类型：
--
作者：
Xu R;Iannello M;Havird JC;Milani L;Ghiselli F
在大多数真核生物中，氧化磷酸化（OXPHOS）是主要的能量生产过程，它涉及线粒体和核基因组。两个基因组之间的密切相互作用对于 OXPHOS 过程的协调功能至关重要。一些双壳类动物表现出线粒体的双重单亲遗传（DUI），即两个高度分化的线粒体基因组共存于同一个体中，一个通过卵子遗传（F型），另一个通过精子遗传（M型）。然而，在酒后驾车物种中，核 OXPHOS 基因如何与两个不同的线粒体基因组协调仍然是一个谜。在这项研究中，我们使用性别和组织特异性转录组比较了 DUI 物种菲律宾蛤仔线粒体和核 OXPHOS 基因的转录、多态性和同义密码子使用。线粒体和核 OXPHOS 基因显示出不同的转录谱。在线粒体（F 型和 M 型分开）和核 OXPHOS 基因内观察到强的共转录信号，但线粒体和核 OXPHOS 基因之间的信号较弱或不存在，表明线粒体和核 OXPHOS 亚基之间的协调不是通过转录实现的。 McDonald-Kreitman 和基于频谱的测试表明，M 型 OXPHOS 基因显着偏离中性，并且 F 型和 M 型 OXPHOS 基因经历不同的选择模式。密码子使用分析表明，突变偏倚和翻译选择是影响不同 OXPHOS 基因密码子使用偏倚的主要因素，然而，线粒体 OXPHOS 基因的翻译选择似乎不如核 OXPHOS 基因有效。因此，我们推测OXPHOS基因之间的协调可能涉及转录后/翻译后调控。
In most eukaryotes, oxidative phosphorylation (OXPHOS) is the main energy production process and it involves both mitochondrial and nuclear genomes. The close interaction between the two genomes is critical for the coordinated function of the OXPHOS process. Some bivalves show doubly uniparental inheritance (DUI) of mitochondria, where two highly divergent mitochondrial genomes, one inherited through eggs (F-type) and the other through sperm (M-type), coexist in the same individual. However, it remains a puzzle how nuclear OXPHOS genes coordinate with two divergent mitochondrial genomes in DUI species. In this study, we compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum using sex- and tissue-specific transcriptomes. Mitochondrial and nuclear OXPHOS genes showed different transcription profiles. Strong co-transcription signal was observed within mitochondrial (separate for F- and M-type) and within nuclear OXPHOS genes but the signal was weak or absent between mitochondrial and nuclear OXPHOS genes, suggesting that the coordination between mitochondrial and nuclear OXPHOS subunits is not achieved transcriptionally. McDonald-Kreitman and frequency-spectrum based tests indicated that M-type OXPHOS genes deviated significantly from neutrality, and that F-type and M-type OXPHOS genes undergo different selection patterns. Codon usage analysis revealed that mutation bias and translational selection were the major factors affecting the codon usage bias in different OXPHOS genes, nevertheless, translational selection in mitochondrial OXPHOS genes appears to be less efficient than nuclear OXPHOS genes. Therefore, we speculate that the coordination between OXPHOS genes may involve post-transcriptional/translational regulation.