A bacterial defense system targeting modified cytosine of phage genomic DNA

TL;DR

Scientists discovered a bacterial defense system that targets modified cytosine in phage DNA, which could be useful for studying epigenetics and disease.

Contribution

The study identifies and characterizes a new single-component bacterial defense system called CMoRE that specifically targets modified cytosine in phage DNA.

Findings

CMoRE is a type IV modification-dependent restriction endonuclease that degrades DNA containing 5hmC or 5ghmC modifications.

The crystal structure of CMoRE reveals a unique GIY-YIG nuclease domain and a modification-sensing domain.

CMoRE has potential applications in detecting 5hmC modifications in mammalian genomics and disease diagnostics.

Abstract

The evolutionary arms race between bacteria and phages drives the development of bacterial antiviral defense systems and phage counter-defense strategies. Restriction–modification (RM) systems protect bacteria by methylating ‘self’ DNA and cleaving unmodified phage DNA. Phages like T-even coliphages evade RM systems by substituting cytosine with 5-hydroxymethyl cytosine (5hmC) or 5-glucosylated hmC (5ghmC). Here, we characterize ‌a single-component antiviral defense system featuring a GIY-YIG endonuclease domain. Biochemical and structural analyses demonstrate that this defense system is a type IV modification-dependent restriction endonuclease that specifically degrades 5hmC- or 5ghmC-modified DNA, and we accordingly name it CMoRE (Cytosine Modification ‌R‌estriction Endonuclease). The crystal structures reveal an N-terminal GIY-YIG nuclease domain and a C-terminal modification-sensing domain. Unique features, including a ‘GIYxY-YIG’ motif and an inhibitory negatively charged loop, distinguish CMoRE as an additional member of the GIY-YIG family. This system not only highlights the evolutionary interplay between phages and bacteria but also presents CMoRE as a potential tool for precise genomic detection of 5hmC in mammals, with implications for epigenetics research and disease diagnostics.

In this study, the authors identify and structurally characterize a single-component anti-phage defense system named CMoRE (Cytosine Modification Restriction Endonuclease).

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