The 380-kb chlorella virus NY-2A genome is highly methylated; 45% of the cytosines are 5-methylcytosine (5mC) and 37% of the adenines are N6- methyladenine (6mA). Based on the sensitivity/resistance of NY-2A DNA to 80 methylation-sensitive DNA restriction endonucleases, the virus is predicted to encode at least 10 DNA methyltransferases: 7 6mA-specific methyltransferases, M.CviQI (GT(m)AC), M.CvQII (R(m)AR), M.CviQIII (TCG(m)A), M.CviQIV (G(m)ATC), M.CviQV (TGC(m)A), M.CviQVI (G(m)ANTC), and M.CviQVII (C(m)ATG); and 3 5mC-specific methyltransferases, M.CviQVIII [RG(m)C(T/C/G)], M.CviQIX ((m)CC), and M.CviQX ((m)CGR). Five of the 6mA methyltransferase genes, M.CviQI, M. CviQIII, M. CviQV, M.CviQVI, and M.CviQVII, were cloned and sequenced. In addition, 2 site-specific endonuclease activities, R.CviQI (G/TAC) and NY2A-nickase (R/AG), were detected in cell-free extracts from NY- 2A virus-infected chlorella. Therefore, the NY-2A genome contains at least 12 DNA methyltransferase and endonuclease genes which, altogether, compose about 3-4% of the virus genome.
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