Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH 44074, USA.
Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH 44074, USA; Blue Marble Space Institute of Science, Seattle, WA 98154, USA.
Mol Phylogenet Evol. 2020 Aug;149:106837. doi: 10.1016/j.ympev.2020.106837. Epub 2020 Apr 15.
DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.
DNA 甲基转移酶是通过将甲基基团附着到核碱基上来修饰 DNA 的蛋白质，存在于细菌、古菌和真核生物的生命领域中。在这里，我们使用氨基酸序列的系统发育重建来研究大型且重要的 4mC/6mA DNA 甲基转移酶蛋白家族的复杂进化历史。我们基于对细菌和古菌超级门的分类群进行系统采样，提出了该家族的一个有充分支持的系统发育。我们将该系统发育与生命物种树的当前表示进行了比较，发现 4mC/6mA 甲基转移酶家族具有惊人复杂的进化历史，可能始于生命最后共同祖先分化为细菌和古菌谱系之后的某个时间，并可能涉及在域内和域间的多次水平基因转移。尽管其进化历史复杂，但我们推断，只有一个分子进化率的显著变化特征化了该蛋白质家族的多样化。
