Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence

Abstract

Type II DNA methyltransferases (MTases) are enzymes found ubiquitously in the prokaryotic world, where they play important roles in several cellular processes, such as host protection and epigenetic regulation. Three classes of type II MTases have been identified thus far in bacteria which function in transferring a methyl group from S-adenosyl-l-methionine (SAM) to a target nucleotide base, forming N-6-methyladenine (class I), N-4-methylcytosine (class II), or C-5-methylcytosine (class III). Often, these MTases are associated with a cognate restriction endonuclease (REase) to form a restriction-modification (R-M) system protecting bacterial cells from invasion by foreign DNA. When MTases exist alone, which are then termed orphan MTases, they are believed to be mainly involved in regulatory activities in the bacterial cell. Genomes of various lytic and lysogenic phages have been shown to encode multi- and mono-specific orphan MTases that have the ability to confer protection from restriction endonucleases of their bacterial host(s). The ability of a phage to overcome R-M and other phage-targeting resistance systems can be detrimental to particular biotechnological processes such as dairy fermentations. Conversely, as phages may also be beneficial in certain areas such as phage therapy, phages with additional resistance to host defenses may prolong the effectiveness of the therapy. This minireview will focus on bacteriophage-encoded MTases, their prevalence and diversity, as well as their potential origin and function.

Fig 1

Potential advantageous effects of phage-encoded orphan MTases (see text for further details). (A) Methylation of the GATC sites within the pac region of the phage P1 genome by a self-encoded DAM MTase facilitates the efficient release of progeny phage. Generation of both dam mutant hosts and dmt⁻ phage (phage DAM knockout) prevents methylation of the phage DNA during packaging, leading to a decreased level of phage progeny released. (B) Protection of phage genomes from host-encoded restriction endonucleases through the protection afforded by the phage-encoded orphan MTase. (C) DAM methylation is essential for lysogeny of the Shiga toxin-encoding phage 933W and release of Shiga toxin by EHEC. Loss of GATC methylation results in release of integrated phage and loss of Shiga toxin production by EHEC. Me, methyl group.

Fig 2

Genomic organization of lactococcal phage Tuc2009, Brucella phage Tb, and Pseudomonas phage B3 highlighting examples of orphan MTases and flanking genes to show that orphan MTases can be found in different locations in a given phage genome (regions encoding predicted structural and replication proteins).