Abstract
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: Cm4TAG and GCAm6BN6VTGC. Analysis of the ΔHVO_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.
Highlights
Restriction-modification (RM) systems in bacteria and archaea provide individuals the ability to recognize self from non-self DNA and function as host defense mechanisms, protecting their genomes from foreign DNA invasion (Arber and Dussoix, 1962; Meselson et al, 1972; Vasu and Nagaraja, 2013)
A study on DNA extracted from H. volcanii demonstrated that it is resistant to digestion from restriction endonucleases, such as XbaI, which recognize motifs containing CTAG (Charlebois et al, 1987). These results indicated that H. volcanii DNA was methylated at CTAG tetranucleotide regions; it has since been hypothesized that a putative Type II CTAG methyltransferase HVO_0794 is responsible for this methylation (Hartman et al, 2010)
Analysis of the methylated bases and motifs in each strain was performed using the Characterization of DNA Methylation in Haloferax volcanii H26 In order to characterize the methylome of H. volcanii, the genome of laboratory strain H26 (Table 1) was sequenced via single molecule real-time (SMRT) sequencing
Summary
Restriction-modification (RM) systems in bacteria and archaea provide individuals the ability to recognize self from non-self DNA and function as host defense mechanisms, protecting their genomes from foreign DNA invasion (Arber and Dussoix, 1962; Meselson et al, 1972; Vasu and Nagaraja, 2013). These systems are composed of a pair of enzymes: a restriction endonuclease and its cognate methyltransferase, which recognize identical short DNA sequences known as the recognition sequence. RM systems play roles in recombination, where they mediate integration of horizontally transferred DNA into the host genome (Alm et al, 1999; Nobusato et al, 2000) and have been implicated in genetic isolation and subsequent speciation (Jeltsch, 2003)
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