Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Beja, University of Jendouba, Jendouba, Tunisia.
Department of Evolutionary Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
BMC Ecol Evol. 2021 May 26;21(1):100. doi: 10.1186/s12862-021-01832-7.
Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection.
Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, our PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. Our statistical models indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgression, which is not uncommon in a number of hare species.
Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.
动物的线粒体通过氧化磷酸化（OXPHOS）途径在细胞中发挥着核心作用，为细胞提供能量。对不同线粒体 OXPHOS 基因的选择研究揭示了这些亚基中氨基酸变化的适应性含义。在野兔中，气候变异性和/或渐渗被认为是这种适应的起源。在这里，我们使用选择测试、蛋白质结构建模以及氨基酸取代对蛋白质功能和稳定性的影响，寻找三个线粒体 OXPHOS 基因中存在正选择的证据。我们还使用统计模型来检验气候和渐渗对正选择位点的影响。
我们的结果在 ND4 和 Cytb 中发现了七个正选择位点，但在 COX1 基因中没有发现正选择位点。三个亚基都有大量的密码子受到负选择的影响。正选择位点被映射到各自线粒体亚基的预测模型的三维结构上。在两个亚基中推断出的十个氨基酸替换中有十个是在正选择下进化的，其中六个位于跨膜结构域。另一方面，有三个密码子位于质子转移通道的边缘。此外，有四个密码子被确定为不稳定的，野生型和突变型之间的振动熵能量差异显著。此外，我们的 PROVEAN 分析表明，在所有正选择位点中，有两个固定的氨基酸替换改变了蛋白质的功能。我们的统计模型表明，气候对 ND4 和 Cytb 蛋白变异体的存在有显著影响，但跨种线粒体 DNA 渐渗没有影响，这在许多野兔物种中并不罕见。
在两个 OXPHOS 基因的几个密码子中观察到正选择。我们发现，正选择密码子的取代对编码蛋白具有结构和功能影响。我们的研究结果表明，这种适应强烈影响了野兔物种的 mtDNA 进化，可能对蛋白质功能产生影响。环境/气候变化似乎是这种适应的主要触发因素，而跨种渐渗杂交似乎对蛋白变异体的发生没有起到主要作用。
