Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community

Satoshi Hiraoka (), Yusuke Okazaki, Mizue Anda, Atsushi Toyoda, Shin-ichi Nakano and Wataru Iwasaki ()
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Satoshi Hiraoka: The University of Tokyo
Yusuke Okazaki: Kyoto University
Mizue Anda: The University of Tokyo
Atsushi Toyoda: National Institute of Genetics
Shin-ichi Nakano: Kyoto University
Wataru Iwasaki: The University of Tokyo

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-018-08103-y

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