Diverse DNA modification in marine prokaryotic and viral communities

2022 Fiscal Year Final Research Report

• Project/Area Number: 20K15444
• Research Category: Grant-in-Aid for Early-Career Scientists
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 38020:Applied microbiology-related
• Research Institution: Japan Agency for Marine-Earth Science and Technology
• Principal Investigator: Hiraoka Satoshi 国立研究開発法人海洋研究開発機構, 海洋機能利用部門(生命理工学センター), 研究員 (70824423)
• Project Period (FY): 2020-04-01 – 2023-03-31
• Keywords: メタエピゲノム解析 / メタゲノム解析 / ロングリード / バイオインフォマティクス / 海洋微生物 / 原核生物 / ウイルス / エピゲノム

Outline of Final Research Achievements

DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time (SMRT) sequencing, we conducted culture-independent ‘metaepigenomic’ analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. We reconstructed >400 metagenomic-assembled genomes (MAGs) from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.

Free Research Field

環境微生物学

Academic Significance and Societal Importance of the Research Achievements

本研究課題では、海洋微生物叢を対象に「メタエピゲノム解析」を実施し、ゲノム上のDNA化学修飾（エピゲノム）を大規模に解明した。本研究は、塩基配列のみを解析対象とする狭義のゲノム解析を越えて、エピゲノムをも含む広義のゲノム解析を行うことで、微生物の生理生態や進化により深くアプローチできることを示した成果である。今後、海洋のみならず土壌や腸内といった幅広い環境に生息する微生物叢を対象に解析を実施することで、従来のゲノム解析を越えた、より深い微生物生態系や進化の理解が進むことが期待される。