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Nat Commun. 2019 Jan 11;10(1):159. doi: 10.1038/s41467-018-08103-y.

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

Author information

1
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan. hiraokas@jamstec.go.jp.
2
Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan. hiraokas@jamstec.go.jp.
3
Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.
4
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
5
National Institute of Genetics, Mishima, 411-8540, Japan.
6
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan. iwasaki@bs.s.u-tokyo.ac.jp.
7
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan. iwasaki@bs.s.u-tokyo.ac.jp.
8
Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan. iwasaki@bs.s.u-tokyo.ac.jp.

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.

PMID:
30635580
PMCID:
PMC6329791
DOI:
10.1038/s41467-018-08103-y
[Indexed for MEDLINE]
Free PMC Article

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