Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages
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Published Version
Date
2016-02-19
Authors
Murphy, James
Bottacini, Francesca
Mahony, Jennifer
Kelleher, Philip
Neve, Horst
Zomer, Aldert
Nauta, Arjen
van Sinderen, Douwe
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Publishing Group
Published Version
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.
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Keywords
Phage biology , Sequence annotation , Infection mechanism , Lytic bacteriophage , Gene expression , Receptor binding protein
Citation
Murphy, J., Bottacini, F., Mahony, J., Kelleher, P., Neve, H., Zomer, A., Nauta, A. and van Sinderen, D. (2016) 'Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages', Scientific Reports, 6, pp. 21345. doi:10.1038/srep21345