Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan, ROC Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan, ROC Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
Mol Biol Evol. 2016 May;33(5):1219-30. doi: 10.1093/molbev/msw006. Epub 2016 Jan 14.
The functions of proteins are usually determined by domains, and the sequential order in which domains are connected to make up a protein chain is known as the domain architecture. Here, we constructed evolutionary networks of protein domain architectures in species from three major life lineages (bacteria, fungi, and metazoans) by connecting any two architectures between which an evolutionary event could be inferred by a model that assumes maximum parsimony. We found that proteins with domain architectures with a higher level of evolvability, indicated by a greater number of connections in the evolutionary network, are present in a wider range of species. However, these proteins tend to be less essential to the organism, are duplicated more often during evolution, have more isoforms, and, intriguingly, tend to be associated with functional categories important for organismal adaptation. These results reveal the presence, in many genomes, of genes coding for a core set of nonessential proteins that have a highly evolvable domain architecture and thus a repertoire of genetic materials accessible for organismal adaptation.
蛋白质的功能通常由结构域决定，而连接结构域以构成蛋白质链的顺序被称为结构域架构。在这里，我们通过连接两个可以通过假设最大简约的模型推断出进化事件的结构域，构建了来自三个主要生命谱系（细菌、真菌和后生动物）的物种的蛋白质结构域进化网络。我们发现，在进化网络中具有更高连接性的结构域架构的蛋白质存在于更广泛的物种中。然而，这些蛋白质往往对生物体的重要性较低，在进化过程中更频繁地复制，具有更多的同工型，而且有趣的是，往往与对生物体适应很重要的功能类别相关联。这些结果表明，在许多基因组中，存在着编码一组核心非必需蛋白质的基因，这些蛋白质具有高度可进化的结构域架构，因此具有可用于生物体适应的大量遗传物质。
