DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities

Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.

A Survey of Archaeal Restriction-Modification Systems

When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m6A and m4C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(m5C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m6A, m4C, and m5C DNA MTases, respectively, occur in approximately the ratio 4:2:1.