Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan.
Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
Nat Commun. 2019 Jan 11;10(1):159. doi: 10.1038/s41467-018-08103-y.
DNA methylation plays important roles in prokaryotes, and their genomic landscapes-prokaryotic epigenomes-have recently begun to be disclosed. However, our knowledge of prokaryotic methylation systems is focused on those of culturable microbes, which are rare in nature. Here, we used single-molecule real-time and circular consensus sequencing techniques to reveal the 'metaepigenomes' of a microbial community in the largest lake in Japan, Lake Biwa. We reconstructed 19 draft genomes from diverse bacterial and archaeal groups, most of which are yet to be cultured. The analysis of DNA chemical modifications in those genomes revealed 22 methylated motifs, nine of which were novel. We identified methyltransferase genes likely responsible for methylation of the novel motifs, and confirmed the catalytic specificities of four of them via transformation experiments using synthetic genes. Our study highlights metaepigenomics as a powerful approach for identification of the vast unexplored variety of prokaryotic DNA methylation systems in nature.
DNA 甲基化在原核生物中起着重要作用，它们的基因组景观——原核表观基因组——最近开始被揭示。然而，我们对原核甲基化系统的了解主要集中在可培养微生物上，而这些微生物在自然界中却很少见。在这里，我们使用单分子实时和环形共识测序技术来揭示日本最大的湖泊琵琶湖微生物群落的“元表观基因组”。我们从各种细菌和古菌群体中重建了 19 个草案基因组，其中大多数尚未培养。对这些基因组中 DNA 化学修饰的分析揭示了 22 个甲基化模体，其中 9 个是新的。我们鉴定了可能负责新型模体甲基化的甲基转移酶基因，并通过使用合成基因的转化实验证实了其中 4 个的催化特异性。我们的研究强调了元表观基因组学作为一种强大的方法，可以识别自然界中大量尚未开发的原核 DNA 甲基化系统。
