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Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases

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Item Type:Article
Title:Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases
Creators Name:Sun, C., Chen, J., Jin, M., Zhao, X., Li, Y., Dong, Y., Gao, N., Liu, Z., Bork, P., Zhao, X.M. and Chen, W.H.
Abstract:DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. In this study, DNA methylation patterns are analyzed in 8848 metagenome-assembled high-quality phages from 104 fecal samples using single-molecule real-time sequencing. The results demonstrate that 97.60% of gut phages exhibit methylation, with certain factors correlating with methylation densities. Phages with higher methylation densities appear to have potential viability advantages. Strikingly, more than one-third of the phages possess their own DNA methyltransferases (MTases). Increased MTase copies are associated with higher genome methylation densities, specific methylation motifs, and elevated prevalence of certain phage groups. Notably, the majority of these MTases share close homology with those encoded by gut bacteria, suggesting their exchange during phage-bacterium interactions. Furthermore, these MTases can be employed to accurately predict phage-host relationships. Overall, the findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems, with a substantial contribution from phage-encoded MTases.
Keywords:DNA Methylome, DNA Methyltransferase, Double-Stranded DNA Phage, Pacbio Sequencing, Phage–Bacterium Interaction, Phage–Host Prediction, Viral-Like Particles
Source:Advanced Science
ISSN:2198-3844
Publisher:Wiley
Volume:10
Number:25
Page Range:2302159
Date:5 September 2023
Official Publication:https://doi.org/10.1002/advs.202302159
PubMed:View item in PubMed

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