Bacterial defense systems with split methyltransferases blur Type I and Type III boundaries

A new configuration of host-dependent restriction-modification (HDRM) systems has been described in three bacterial species from different phyla, according to a study by researchers at New England Biolabs. The systems employ DNA methyltransferase (MTase) activity for host protection, NTPase activity for activation of restriction, and a GIY-YIG domain for DNA cleavage. What sets them apart is that the methylating MTase component is divided into two parts, and these parts connect with the regulatory NTPase and defensive nuclease domains in novel organizations not previously seen in restriction-modification biology.

The DrdVI system comes from Deinococcus wulumuqiensis NEB479, an organism formerly classified as Deinococcus radiodurans. DrdVI recognizes the sequence 5′-GCAGCC-3′ and modifies only one strand. The other two systems, PenI from Porphyromonas endodontalis ATCC 35406 and SmoLII from Streptobacillus moniliformis DSM12112, each recognize the shorter sequence 5′-GCAGT-3′, again modifying the A of that strand. In all three cases, the genes and proteins responsible for the MTase activity have separated catalytic motifs from DNA-binding components, but they have done so in distinct ways, giving each system its own organizational signature.

In these new systems, every one has a component subunit that connects an endonuclease to an NTP-hydrolyzing translocase domain.

The endonucleases of DrdVI and PenI require (d)ATP and divalent cations, either Mg2+ or Mn2+, as cofactors for their cutting activity. Cleavage occurs when head-to-head inverted recognition sites are present, and DNA cleavage is not at a fixed site. This combination of single-strand modification and cleavage at inverted, unfixed sites resembles the behavior of typical Type III restriction enzymes, but the connectivity of the domain components sets these systems apart from that established class.

Bioinformatic analysis reveals numerous similar putative HDRM systems. The authors suggest that these systems may represent a new subtype containing features of both Type I and Type III systems.

Subject of Research: Novel ATP-dependent restriction-modification systems with split DNA methyltransferases in bacteria

Article Title: New ATP-dependent, multi-subunit restriction-modification systems that use split DNA methyltransferases for host protection

Article References: Fomenkov, A., Potapov, V., Luyten, Y. A., Raleigh, E. A., & Roberts, R. J. (2026). New ATP-dependent, multi-subunit restriction-modification systems that use split DNA methyltransferases for host protection. Frontiers in Bacteriology, 5, Article 1753426. https://doi.org/10.3389/fbrio.2026.1753426

Image Credits: AI Generated

DOI: 10.3389/fbrio.2026.1753426

Keywords: restriction-modification, DNA methyltransferase, GIY-YIG nuclease, Type I systems, Type III systems, bacterial defense, ATPase, DrdVI, PenI, SmoLII, split domains, host protection