Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity

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Additional file 1: Table S1
Murphy, James
Klumpp, Jochen
Mahony, Jennifer
O'Connell Motherway, Mary
Nauta, Arjen
van Sinderen, Douwe
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Biomed Central Ltd.
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BACKGROUND: So-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control phage proliferation and decades of research, these phages continue to negatively impact cheese production in terms of the final product quality and consequently, monetary return. RESULTS: Whole genome sequencing and in silico analysis of three 936-type phage genomes identified several putative (orphan) methyltransferase (MTase)-encoding genes located within the packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis was performed on all three phages, allowing the identification of adenine modifications consistent with N-6 methyladenine sequence methylation, which in some cases could be attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.Phi145I/M.Phi93I and M.Phi93DAM, encoded by genes located within the packaging module, provide protection against the restriction enzymes HphI and DpnII, respectively, representing the first functional MTases identified in members of 936-type phages. CONCLUSIONS: SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage. The presence of these MTase-encoding genes on 936-type phage genomes is assumed to represent an adaptive response to circumvent host encoded restriction-modification systems thereby increasing the fitness of the phages in a dynamic dairy environment.
Lactococcus lactis , Bacteriophage , Methylome , Restriction modification , SMRT sequencing , Bacillus subtilis phages , Bacteriophage resistance , DNA methyltransferases , Functional analysis , Single molecule , Lactis phages , Genes , System , Methylation , Evolution
MURPHY, J., KLUMPP, J., MAHONY, J., O’CONNELL-MOTHERWAY, M., NAUTA, A. & VAN SINDEREN, D. 2014. Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity. BMC Genomics, 15:183, 1-11.