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Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and are composed of two enzymes: a DNA methyltransferase and a restriction endonuclease. Although RM systems are present in both archaeal and bacterial genomes, DNA methylation in archaea has not been well defined. In order to characterize the function of RM systems in archaeal species, we have made use of the model haloarchaeon  Haloferax volcanii . A genomic DNA methylation analysis of  H. volcanii  strain H26 was performed using PacBio single molecule real-time (SMRT) sequencing. This analysis was also performed on a strain of  H. volcanii  in which an annotated DNA methyltransferase gene  HVO_A0006  was deleted from the genome. Sequence analysis of H26 revealed two motifs which are modified in the genome: C m4 TAG and GCA m6 BN 6 VTGC. Analysis of the Δ HVO_A0006  strain indicated that it exhibited reduced adenine methylation compared to the parental strain and altered the detected adenine motif. However, protein domain architecture analysis and amino acid alignments revealed that HVO_A0006 is homologous only to the N-terminal endonuclease region of Type IIG RM proteins and contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK nuclease family protein. Further bioinformatic analysis of the  HVO_A0006  gene demonstrated that the gene is rare among the  Halobacteria . It is surrounded by two transposition genes suggesting that  HVO_A0006  is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s). Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene  HVO_A0006 .

frontiers in microbiology

Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006