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

Satoshi Hiraoka,Shin-Ichi Nakano,Wataru Iwasaki,Yusuke Okazaki,Atsushi Toyoda,Mizue Anda

doi:10.1038/s41467-018-08103-y

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.

Highlights

DNA methylation plays important roles in prokaryotes, and their genomic landscapes— prokaryotic epigenomes—have recently begun to be disclosed
In an approach referred to as circular consensus sequencing (CCS), a circular DNA library is prepared as a sequence template to allow the generation of a single ultralong raw read containing multiple sequences (‘subreads’) that correspond to the same stretch on the template[19,20]; a cultivated clonal population is not required[21]
CCS has far been applied in only a few shotgun metagenomics studies[22] and, to the best of our knowledge, has not yet been applied to ‘metaepigenomics’ or direct methylome analysis of environmental microbial communities, which are usually constituted by uncultured prokaryotes

Summary

Introduction

DNA methylation plays important roles in prokaryotes, and their genomic landscapes— prokaryotic epigenomes—have recently begun to be disclosed. The Thaumarchaeota BD3 genome contained two MTases that showed the best sequence similarities to those that recognize AGCT and GATC motif sequences, which were perfectly congruent with the two motifs detected in our metaepigenomic analysis.

Results

Conclusion