Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages.

James Murphy,Philip Kelleher,Jennifer Mahony,Horst Neve,Francesca Bottacini,Arjen Nauta,Douwe Van Sinderen,Aldert Zomer

doi:10.1038/srep21345

Abstract

Genome sequencing and comparative analysis of bacteriophage collections has greatly enhanced our understanding regarding their prevalence, phage-host interactions as well as the overall biodiversity of their genomes. This knowledge is very relevant to phages infecting Lactococcus lactis, since they constitute a significant risk factor for dairy fermentations. Of the eighty four lactococcal phage genomes currently available, fifty five belong to the so-called 936 group, the most prevalent of the ten currently recognized lactococcal phage groups. Here, we report the genetic characteristics of a new collection of 936 group phages. By combining these genomes to those sequenced previously we determined the core and variable elements of the 936 genome. Genomic variation occurs across the 936 phage genome, such as genetic elements that (i) lead to a +1 translational frameshift resulting in the formation of additional structures on the phage tail, (ii) specify a double neck passage structure, and (iii) encode packaging module-associated methylases. Hierarchical clustering of the gene complement of the 936 group phages and nucleotide alignments allowed grouping of the ninety 936 group phages into distinct clusters, which in general appear to correspond with their geographical origin.

Highlights

V3 V3 V3 V2 V3 V3 V3 V3 V3 V2 V3 V2 V3 V2 V2 V3 V3 V3 V2 V3 V3 V3 V2 V2 V1 V3 V3 V2 V5 V2 V3 V3 V4 V2 V4 V3 V2 V2
To determine the core genome of the 936 group phages, thirty five phage genome sequences derived from a recently assembled collection, members of which had originated from four dairy factories, designated F1–F4, in The Netherlands, were added to those sequenced previously, giving a total collection of ninety phages
A set of twenty nine protein families were identified to be commonly encoded by all examined phage genomes and believed to correspond to the core genome of the 936 group of lactococcal phages[16]

Summary

Introduction

Comparative analysis of the analysed phage genomes revealed various regions of diversity, which are likely to have arisen due to host-mediated phage resistance systems and/or man-made, processing-imposed hurdles to reduce their number and infectivity

Methods

Results

Conclusion