DNA methylation is a biological process through which methyl groups are added to the DNA (genetic material). It is used as an epigenetic, i.e., a non-genetic strategy by prokaryotes to perform an array of functions such as gene regulation, repair, and protection against viral invasion using restriction-modification (RM) systems, which function as prokaryotic immune systems. Until recently, studies related to DNA methylation have been restricted to microorganisms that can be cultured in laboratory settings. This has led to a poor understanding of its role in microbial ecology. It is, therefore, essential to conduct genome-wide epigenetic studies of environmental microbes, particularly those which cannot be cultured in the laboratory, but only thrive under natural conditions.
To this end, a team of researchers led by Professor Woo Jun Sul from Chung-Ang University and Dr. Hoon Je Seong (currently from Macrogen Inc.), South Korea has explored the differences in DNA methylation patterns across different members of the ocean microbial communities in the northwest Pacific Ocean. Their study was published online on September 28, 2022, in Volume 10 of Microbiome. “In-depth DNA methylation project began only in 2014, with the release of long-read sequencers. This sparked our curiosity and we wanted to apply it to microbial ecology. Hence, we used a metagenomics approach to explore DNA methylation in a community rather than at an organism level,” says Prof. Sul while discussing the motivation behind their study.
The hustle began back in 2015, when the large-scale Shipborne Pole-to-Pole Observations (SHIPPO) project was initiated by the Korea Polar Research Institute. It involved filtering out microorganisms from ocean surface samples across 10 different stations from the Pacific Northwest to the Bering Sea.
The team extracted DNA from these captured specimens and used short- and long-read sequencers to perform metagenomic sequencing. These sequences were then aligned using computational analysis to generate massive 15,056 viral (v), 252 prokaryotic (pro), 56 giant viral (gv), and 6 eukaryotic (eu) metagenome-assembled genomes (MAGs). Upon further analyses, the team was surprised to find that nearly 95% of the sequenced proMAGs belonged to new taxa that could not be classified using existing genomic databases. “This finding clearly demonstrates the amount of potential this technique has, and how it could provide new insights into the genomes of unculturable ocean microbes,” Prof. Sul explains.
Next, the team used this approach to explore the diversity of DNA methyltransferase (MTase) enzyme classes expressed by the genomes identified in the SHIPPO database. They found that MTase II was the most common class of MTase expressed in these organisms. Interestingly, most of the proMAGs lacked complete RM systems due to the absence of restriction enzymes. Furthermore, the identification of methylated motifs across the ocean microbiome revealed unique DNA methylation patterns, which eventually led to the discovery of a distinct methylation profile in Alphaproteobacteria.
Next, the team used single molecule real-time (SMRT) sequencing to observe methylation patterns in Pelagibacter. They discovered heterogeneity in the methylation profile of the bacteria even at the “strain-level”. This implies that dynamic cellular events occur within Pelagibacter in the surface waters of the northwest Pacific Ocean.
A comparative analysis of the bacterial and viral genomes also provided clues to their evolutionary patterns and interactions. The team found the presence of uneven methylation patterns in the Cand. P. Giovannoni NP1 genome, suggesting potential defense mechanisms used by this bacterium.
These findings have already paved the way for a new era of meta-epigenomics, which directly measures methylation in environmental microbes. The potential of studying the epigenome of various organisms at once is far-reaching, as Prof. Sul illustrates, by surmising, “Along with studies to identify methylation patterns of strains showing actual pathogenicity, our study also helps discover candidate targets to prevent pathogenicity in the environment. This can be of immense importance to the global public health systems by detecting pathogenic signals that threaten human health”.
Authors: Hoon Je Seong1, Simon Roux2, Chung Yeon Hwang3 and Woo Jun Sul1
1 Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea.
2DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
3School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea.
About Professor Woo Jun Sul from Chung-Ang University
Dr. Woo Jun Sul is a Professor at the Department of Systems Biotechnology, and the Center Director of Skin and Biotechnology Research Center, Chung-Ang University, South Korea. He obtained his Ph.D. in microbial ecology from the Michigan State University, USA in 2010. At present, his research is focused on microbial ecology, ecological theory, and the use of genomics and metagenomics to understand speciation, community structure and functions, as well as on the human skin microbiome.
About Dr. Hoon Je Seong from Macrogen Inc.
Dr. Hoon Je Seong is currently working as a microbiome analysis manager for a sequencing company known as Macrogen, Inc. He is responsible for the study of children's gut microbiome affected by various environmental exosomes. Prior to working at this company, he received his Ph.D. in microbial ecology under Professor Woo Jun Sul at Chung-Ang University in 2022.
Method of Research
Subject of Research
Marine DNA methylation patterns are associated with microbial community composition and inform virus‑host dynamics
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The authors declare that they have no competing interests.