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许然, MariangelaIannello, JustinC. Havird, LilianaMilani, FabrizioGhiselli. 2022: 线粒体基因与核氧化磷酸化基因之间缺乏共转录调控——当两种遗传差异极大的线粒体基因组共存时. 动物学研究, 43(1): 111-128. DOI: 10.24272/j.issn.2095-8137.2021.348
引用本文: 许然, MariangelaIannello, JustinC. Havird, LilianaMilani, FabrizioGhiselli. 2022: 线粒体基因与核氧化磷酸化基因之间缺乏共转录调控——当两种遗传差异极大的线粒体基因组共存时. 动物学研究, 43(1): 111-128. DOI: 10.24272/j.issn.2095-8137.2021.348
Ran Xu, Mariangela Iannello, Justin C. Havird, Liliana Milani, Fabrizio Ghiselli. 2022: Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes. Zoological Research, 43(1): 111-128. DOI: 10.24272/j.issn.2095-8137.2021.348
Citation: Ran Xu, Mariangela Iannello, Justin C. Havird, Liliana Milani, Fabrizio Ghiselli. 2022: Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes. Zoological Research, 43(1): 111-128. DOI: 10.24272/j.issn.2095-8137.2021.348

线粒体基因与核氧化磷酸化基因之间缺乏共转录调控——当两种遗传差异极大的线粒体基因组共存时

Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes

  • 摘要: 在大多数真核生物中,氧化磷酸化 (Oxidative phosphorylation, OXPHOS) 是主要的能量产生过程,它同时涉及线粒体基因组与核基因组。两个基因组之间密切的相互作用对于OXPHOS过程的功能协调至关重要。一些双壳类动物表现出线粒体的双单亲遗传(Doubly uniparental inheritance , DUI),其中两个遗传差异极大的线粒体基因组——一个通过卵细胞遗传(F型),另一个通过精子遗传(M型)——在同一个体中共存。然而,在DUI 物种中,核OXPHOS基因如何与两个遗传差异极大的线粒体基因组协调仍然未知。在该研究中,我们利用性别和组织特异性转录组比较了DUI 物种菲律宾蛤仔(Ruditapes philippinarum)的线粒体与核OXPHOS基因的转录、遗传多态性和密码子使用偏好。线粒体和核OXPHOS基因显示出不同的转录模式。在F型、M型线粒体基因和核 OXPHOS 基因内分别存在较强的共转录信号,但线粒体和核 OXPHOS 基因之间的信号很弱或不存在,这表明线粒体和核 OXPHOS 亚基之间的协调可能不在转录水平实现。McDonald-Kreitman检验和基于等位基因频谱的检验表明M型 OXPHOS 基因显著偏离中性,且F型和M型 OXPHOS 基因经历了不同的选择压力。对密码子的使用偏好分析表明,突变偏倚和翻译选择是影响不同OXPHOS 基因密码子使用偏好的主要因素;然而,线粒体OXPHOS基因受到的翻译选择低于核 OXPHOS 基因。综上,我们推测OXPHOS基因之间的协调可能涉及转录后/翻译调节。

     

    Abstract: 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.

     

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