Abstract
BackgroundSo-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.ResultsWhole 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.ConclusionsSMRT 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-831) contains supplementary material, which is available to authorized users.
Highlights
-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures
Identification of 936-type phages encoding putative methyltransferases Initial genome sequencing was performed on a 454 device on phage DNA isolated from three lactococcal 936-type phages (Phi93, Phi145 and Phi15), previously isolated from whey samples obtained from Goudaproducing cheese factories (Table 1) [23]
The three genomes each encompass 55 Open reading frames (ORFs) (Additional file 1: Table S1), apparently organised into three transcriptional modules, a gene arrangement that is typical for 936-type phages (Figure 1) [26,28]
Summary
-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. The bacterio(phage) – host arms race represents a dynamic interplay of survival among a population of bacteria and their infecting viral parasites [1]. Phage genomes have been shown to acquire methyltransferase (MTase)encoding genes, which are termed orphan MTases if they occur in the absence of their cognate restriction enzyme-encoding gene [11]. Their function is to actively methylate phage DNA to negate the activity of host encoded restriction endonucleases which recognize the same sequence. MTase-encoding genes are found on the genomes of, among others, T-even phages of E. coli, several Bacillus subtilis phages, and the lactococcal phi-50 (P335-type phage) [12,13,14]. In some cases phages have been shown to specify complete R-M systems as observed in the Staphylococcus aureus quadruple converting (causes lysogenized bacteria to acquire or lose the ability to express phenotypic traits) phage π42, which harbours a BcgI-like R-M system [15]
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