Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
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DOI：
10.1038/s41467-018-08103-y
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发表时间：
2019-01-11
影响因子：
16.6
通讯作者：
Iwasaki, Wataru
中科院分区：
文献类型：
--
作者：
Hiraoka, Satoshi;Okazaki, Yusuke;Iwasaki, Wataru
DNA甲基化在原核生物中发挥着重要作用，它们的基因组景观——原核表观基因组——最近开始被公开。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的甲基化系统上，这在自然界中是罕见的。在这里，我们使用单分子实时和循环一致性测序技术来揭示日本最大的湖泊琵琶湖中微生物群落的“元表观基因组”。我们重建了来自不同细菌和古菌群的 19 个基因组草图，其中大部分尚未培养。对这些基因组中 DNA 化学修饰的分析揭示了 22 个甲基化基序，其中 9 个是新的。我们鉴定了可能负责新基序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四个基因的催化特异性。我们的研究强调元表观基因组学是鉴定自然界中大量未经探索的原核 DNA 甲基化系统的强大方法。
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.