Context-dependent conservation of DNA methyltransferases in bacteria

Abstract

DNA methytransferases (MTs) in bacteria are best understood in the context of restriction–modification (R–M) systems, which act as bacterial immune systems against incoming DNA including phages, but have also been described as selfish elements. But several orphan MTs, which are not associated with any restriction enzyme, have also been characterized and may protect against parasitism by R–M systems. The occurrence of MTs in these two contexts, namely as part of R–M systems or as orphans, is poorly understood. Here we report the results of a comparative genomic survey of DNA MTs across ∼1000 bacterial genomes. We show that orphan MTs overwhelm R–M systems in their occurrence. In general, R–M MTs are poorly conserved, whereas orphans are nearly as conserved within a genus as any average gene. However, oligonucleotide usage and conservation patterns across genera suggest that both forms of MTs might have been horizontally acquired. We suggest that many orphan MTs might be ‘degradation’ products of R–M systems, based on the properties of orphan MTs encoded adjacent to highly diverged REs. In addition, several fully degraded R–M systems exist in which both the MT and the RE are highly divergent from their corresponding reference R–M pair. Despite their sporadic occurrence, conserved R–M systems are present in strength in two highly transformable genera, in which they may contribute to selection against integration of foreign DNA.